diff --git a/Custom_Hooks/eb_hooks.py b/Custom_Hooks/eb_hooks.py
new file mode 100644
index 0000000000000000000000000000000000000000..456645f44032314930fb704bbafe5de2b63a544b
--- /dev/null
+++ b/Custom_Hooks/eb_hooks.py
@@ -0,0 +1,238 @@
+import grp
+import os
+
+from easybuild.tools.run import run_cmd
+from easybuild.tools.config import build_option
+from easybuild.tools.config import install_path
+from easybuild.tools.build_log import EasyBuildError, print_warning
+from easybuild.tools.toolchain.toolchain import SYSTEM_TOOLCHAIN_NAME
+from easybuild.toolchains.compiler.systemcompiler import TC_CONSTANT_SYSTEM
+
+SUPPORTED_COMPILERS = ["GCC", "iccifort", "PGI", "GCCcore"]
+SUPPORTED_MPIS = ["impi", "psmpi", "OpenMPI", "MVAPICH2"]
+# Maintain toplevel list for easy use of --try-toolchain
+SUPPORTED_TOPLEVEL_TOOLCHAIN_FAMILIES = [
+ "intel",
+ "intel-para",
+ "iomkl",
+ "gpsmkl",
+ "gomkl",
+ "pmvmklc",
+ "gmvmklc",
+]
+# Could potentially make a dictionary of names and supported versions here but that is
+# probably overkill
+SUPPORTED_TOOLCHAIN_FAMILIES = (
+ SUPPORTED_COMPILERS
+ + ["gcccoremkl", "gpsmpi", "ipsmpi", "iimpi", "iompi", "gmvapich2c", "pmvapich2c"]
+ + SUPPORTED_TOPLEVEL_TOOLCHAIN_FAMILIES
+)
+# Also maintain a list of CUDA enabled compilers
+CUDA_ENABLED_TOOLCHAINS = ["pmvmklc", "gmvmklc", "gmvapich2c", "pmvapich2c"]
+# Use this for a heuristic to see if the easyconfig comes from the Golden Repo
+GOLDEN_REPO = "Golden_Repo"
+
+# Some modules should use modaltsoftname by default
+REQUIRE_MODALTSOFTNAME = {
+ "impi": "IntelMPI",
+ "psmpi": "ParaStationMPI",
+ "iccifort": "Intel",
+}
+
+
+def parse_hook(ec, *args, **kwargs):
+ """Custom parse hook to manage installations intended for JSC systems."""
+
+ ec_dict = ec.asdict()
+ # Compilers are are a family (in the Lmod sense)
+ if ec.name in SUPPORTED_COMPILERS:
+ key = "modluafooter"
+ value = 'family("compiler")'
+ if key in ec_dict:
+ if not value in ec_dict[key]:
+ ec[key] = "\n".join([ec[key], value])
+ else:
+ ec[key] = value
+ ec.log.info("[parse hook] Injecting Lmod compiler family")
+ # Supported compilers should also be recursively unloaded
+ key = "recursive_module_unload"
+ if not key in ec_dict or ec_dict[key] is None:
+ ec[key] = True
+ ec.log.info(
+ "[parse hook] Injecting recursive module unloading for supported compiler"
+ )
+ # MPI are are a family (in the Lmod sense)
+ if ec.name in SUPPORTED_MPIS:
+ key = "modluafooter"
+ value = 'family("mpi")'
+ if key in ec_dict:
+ if not value in ec_dict[key]:
+ ec[key] = "\n".join([ec[key], value])
+ else:
+ ec[key] = value
+ ec.log.info("[parse hook] Injecting Lmod mpi family")
+
+ # Check if we need to use 'modaltsoftname'
+ if ec.name in REQUIRE_MODALTSOFTNAME:
+ key = "modaltsoftname"
+ if not key in ec_dict or ec_dict[key] is None:
+ ec[key] = REQUIRE_MODALTSOFTNAME[ec.name]
+ ec.log.info(
+ "[parse hook] Injecting modaltsoftname '%s' for '%s'",
+ key,
+ REQUIRE_MODALTSOFTNAME[ec.name],
+ )
+
+ # Check if CUDA is in the dependencies, if so add the GPU Lmod tag
+ if (
+ "CUDA" in [dep[0] for dep in iter(ec_dict["dependencies"])]
+ or ec_dict["toolchain"]["name"] in CUDA_ENABLED_TOOLCHAINS
+ ):
+ key = "modluafooter"
+ value = 'add_property("arch","gpu")'
+ if key in ec_dict:
+ if not value in ec_dict[key]:
+ ec[key] = "\n".join([ec_dict[key], value])
+ else:
+ ec[key] = value
+ ec.log.info("[parse hook] Injecting gpu as Lmod arch property")
+
+ # Check where installations are going to go and add appropriate site contact
+ # not sure of a fool-proof way to do this, let's just try a heuristic
+ site_contacts = None
+ if "stages" in install_path().lower():
+ users_groups = [grp.getgrgid(g).gr_name for g in os.getgroups()]
+ if any(group in user_groups for group in ["swmanage", "software"]):
+ site_contacts = "sc@fz-juelich.de"
+ if site_contacts is None:
+ # Inject the user
+ site_contacts = os.getenv("USER")
+ # Tag the build as a user build
+ key = "modluafooter"
+ value = 'add_property("build","user")'
+ if key in ec_dict:
+ if not value in ec_dict[key]:
+ ec[key] = "\n".join([ec_dict[key], value])
+ else:
+ ec[key] = value
+ ec.log.info("[parse hook] Injecting user as Lmod build property")
+ if site_contacts:
+ key = "site_contacts"
+ value = site_contacts
+ if key in ec_dict:
+ if ec_dict[key] is not None and value not in ec_dict[key]:
+ value = ",".join([ec_dict[key], value])
+ ec[key] = value
+ ec.log.info("[parse hook] Injecting contact %s", value)
+
+ # If we are parsing we are not searching, in this case if the easyconfig is
+ # located in the search path, warn that it's dependencies will (most probably)
+ # not be resolved
+ if build_option("robot"):
+ search_paths = build_option("search_paths") or []
+ robot_paths = list(set(build_option("robot_path") + build_option("robot")))
+ if ec.path:
+ ec_dir_path = os.path.dirname(os.path.abspath(ec.path))
+ else:
+ ec_dir_path = ''
+ if any(search_path in ec_dir_path for search_path in search_paths) and not any(
+ robot_path in ec_dir_path for robot_path in robot_paths
+ ):
+ raise EasyBuildError(
+ "\nYou are attempting to install an easyconfig distributed with "
+ "EasyBuild but are not properly configured to resolve dependencies "
+ "for this case. Please add additonal options:\n"
+ " eb --robot=$EASYBUILD_ROBOT:$EBROOTEASYBUILD/easybuild/easyconfigs --try-update-deps ...."
+ )
+
+
+def pre_ready_hook(self, *args, **kwargs):
+ "When we are building something, do some checks for bad behaviour"
+ ec = self.cfg
+ # Grab name, path, toolchain, install path and check if we are installing
+ # GCCcore/MPI
+ name = ec["name"]
+ path_to_ec = os.path.abspath(ec.path)
+ toolchain = ec["toolchain"]
+ is_gcccore = ec["name"] == "GCCcore"
+ is_mpi = ec["moduleclass"] == "mpi" or name in SUPPORTED_MPIS
+
+ # Don't let people use unsupported toolchains (by default)
+ override_toolchain_check = os.getenv("JSC_OVERRIDE_TOOLCHAIN_CHECK")
+ if not override_toolchain_check:
+ toolchain_name = toolchain["name"]
+ if not toolchain_name in SUPPORTED_TOOLCHAIN_FAMILIES:
+ stage = os.getenv("STAGE", default=None)
+ if stage:
+ # Clean things up if it is a Devel stage
+ stage = stage.replace("Devel-", "")
+ else:
+ stage = "<TOOLCHAIN_VERSION>"
+ print_warning(
+ "\nYou are attempting to install software with an unsupported "
+ "toolchain (%s), please use additional arguments to map this to a supported"
+ " toolchain:\n"
+ " eb --try-toolchain=<SUPPORTED_TOOLCHAIN>,%s --try-update-deps ...\n"
+ "where <SUPPORTED_TOOLCHAIN> comes from the list %s\n"
+ "(if you really know what you are doing, you can override this "
+ "behaviour by setting the %s environment variable)\n\n"
+ "...exiting",
+ toolchain_name,
+ stage,
+ SUPPORTED_TOPLEVEL_TOOLCHAIN_FAMILIES,
+ "JSC_OVERRIDE_TOOLCHAIN_CHECK",
+ )
+ exit(1)
+
+ # Don't let people install GCCcore since this probably won't work and will lead them
+ # to reinstall most of our stack. Don't advertise that this can be overridden, only
+ # experts should know that.
+ override_gcccore_check = os.getenv("JSC_OVERRIDE_GCCCORE_CHECK")
+ if not override_gcccore_check:
+ if is_gcccore and not "stages" in install_path().lower():
+ print_warning(
+ "\nYou are attempting to install GCCcore (%s) into a non-system "
+ "location (%s), this won't work as expected without additional effort "
+ "and is likely to lead to building a whole stack of dependencies even "
+ "for simple software. Please contact sc@fz-juelich.de if you wish to "
+ "discuss this further.\n\n"
+ "...exiting",
+ path_to_ec,
+ install_path(),
+ )
+ exit(1)
+
+ # Don't let people install a non-JSC MPI (and don't advertise that this can be
+ # overridden, only experts should know that)
+ override_mpi_check = os.getenv("JSC_OVERRIDE_MPI_CHECK")
+ if not override_mpi_check:
+ if is_mpi and GOLDEN_REPO not in path_to_ec:
+ print_warning(
+ "\nYou are attempting to install a non-system MPI implementation (%s), "
+ "this is very likely to lead to severe performance degradation. Please "
+ "contact sc@fz-juelich.de if you wish to discuss this further.\n\n"
+ "...exiting",
+ path_to_ec,
+ )
+ exit(1)
+
+
+def end_hook(*args, **kwargs):
+ # If the user is part of the development group and the installation is systemwide,
+ # rebuild the system cache
+ "Refresh Lmod's cache"
+
+ if "stages" in install_path().lower():
+ user = os.getenv("USER")
+ if user == "swmanage":
+ cmd = (
+ "/gpfs/software/juwels/configs/update_system_module_cache.sh"
+ ) # Need to make this generic
+ if os.path.isfile(cmd):
+ print("== Refreshing Lmod's cache...")
+ run_cmd(cmd, log_all=True)
+ else:
+ # Otherwise do nothing, no need to build a user cache, it's very unlikely they
+ # will have loads of modules
+ pass
+
diff --git a/Golden_Repo/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Python-3.8.5.eb b/Golden_Repo/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Python-3.8.5.eb
index 213c01ad8ff911f480f2ecc0e510968d77524b93..ee3ab68467797446a6bae0c3278ff2f2c11bbc0a 100644
--- a/Golden_Repo/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Python-3.8.5.eb
+++ b/Golden_Repo/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Python-3.8.5.eb
@@ -25,7 +25,7 @@ builddependencies = [
]
dependencies = [
- ('Java', '1.8', '', True),
+ ('Java', '1.8', '', SYSTEM),
('Python', '3.8.5'),
]
diff --git a/Golden_Repo/a/ARPACK-NG/ARPACK-NG-3.7.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb b/Golden_Repo/a/ARPACK-NG/ARPACK-NG-3.7.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb
new file mode 100644
index 0000000000000000000000000000000000000000..e917f93387fa7c3738b0b532a9f7e2b4d700ce70
--- /dev/null
+++ b/Golden_Repo/a/ARPACK-NG/ARPACK-NG-3.7.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb
@@ -0,0 +1,56 @@
+easyblock = 'ConfigureMake'
+
+name = 'ARPACK-NG'
+version = '3.7.0'
+versionsuffix = '-nompi'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
+
+libarpack.a and libparpack.a have been installed in $EBROOTARPACKMINNG.
+
+In addition the variables ARPACK_ROOT, ARPACK_LIB, PARPACK_ROOT, and PARPACK_LIB are set.
+"""
+
+examples = 'Examples can be found in $ARPACK_ROOT/EXAMPLES'
+
+site_contacts = 'I. Gutheil (i.gutheil@fz-juelich.de)'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ["%(version)s.tar.gz"]
+checksums = ['972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6']
+
+patches = [
+ 'ARPACK-NG-%(version)s-install-arpack-examples_gpsmkl.patch'
+]
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('Autotools', '20200321'),
+ ('pkg-config', '0.29.2')
+]
+
+# We hide it since this should be used just for Jupyter and the MPI version should be preferred for normal cases
+hidden = True
+
+preconfigopts = 'sh bootstrap &&'
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+postinstallcmds = [
+ "cp -r EXAMPLES %(installdir)s/EXAMPLES",
+]
+
+sanity_check_paths = {
+ 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, ],
+ 'dirs': []
+}
+
+modextravars = {
+ 'ARPACK_ROOT': '%(installdir)s',
+ 'ARPACK_LIB': '%(installdir)s/lib',
+}
+
+moduleclass = 'numlib'
diff --git a/Golden_Repo/a/ant/ant-1.10.9-Java-15.eb b/Golden_Repo/a/ant/ant-1.10.9-Java-15.eb
new file mode 100644
index 0000000000000000000000000000000000000000..299ccd4b4fc08db690844212a670ba2a73e422e1
--- /dev/null
+++ b/Golden_Repo/a/ant/ant-1.10.9-Java-15.eb
@@ -0,0 +1,29 @@
+easyblock = 'PackedBinary'
+
+name = 'ant'
+version = '1.10.9'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in
+ build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of
+ Java applications."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = SYSTEM
+
+source_urls = ['https://archive.apache.org/dist/ant/binaries/']
+sources = ['apache-%(name)s-%(version)s-bin.tar.gz']
+checksums = ['5f8a85ddee6effe79163aa54c7bef6b60305e37200dedc1986437fb5c072a9f3']
+
+dependencies = [('Java', '15')]
+
+sanity_check_paths = {
+ 'files': ['bin/ant', 'lib/ant.jar'],
+ 'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'
diff --git a/Golden_Repo/b/basemap/basemap-1.2.2-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb b/Golden_Repo/b/basemap/basemap-1.2.2-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..6892be2a0c371d4eb9e0ac43ac9ab14a297a97f5
--- /dev/null
+++ b/Golden_Repo/b/basemap/basemap-1.2.2-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
@@ -0,0 +1,50 @@
+easyblock = 'Bundle'
+
+name = 'basemap'
+version = '1.2.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://matplotlib.org/basemap/'
+description = """Basemap is a Python matplotlib toolkit for plotting data on maps.
+
+This is the last version of Basemap. Please move development efforts over to Cartopy!
+"""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('SciPy-Stack', '2020', versionsuffix),
+ ('GEOS', '3.8.1', versionsuffix),
+ ('PROJ', '7.1.0'),
+]
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+exts_filter = ('python -c "import %(ext_name)s"', '')
+exts_download_dep_fail = True
+
+exts_list = [
+ ('pyshp', '2.1.2', {
+ 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'],
+ 'modulename': 'shapefile',
+ }),
+ ('pyproj', '2.6.1.post1', { # PyProj 3 needs PROJ 7.2.0, which was released after PROJ went into production
+ 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj'],
+ 'prebuildopts': 'PROJ_DIR="$EBROOTPROJ" ',
+ 'preinstallopts': 'PROJ_DIR="$EBROOTPROJ" ',
+ }),
+ ('basemap', '1.2.2', {
+ 'source_urls': ['https://github.com/matplotlib/basemap/archive/'],
+ 'source_tmpl': 'v%(version)srel.tar.gz',
+ 'prebuildopts': 'GEOS_DIR="$EBROOTGEOS" ',
+ 'preinstallopts': 'GEOS_DIR="$EBROOTGEOS" ',
+ 'modulename': 'mpl_toolkits.basemap',
+ }),
+]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/c/Cartopy/Cartopy-0.18.0-gpsmpi-2020-Python-3.8.5.eb b/Golden_Repo/c/Cartopy/Cartopy-0.18.0-gpsmpi-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..aeeee5746469ce1e28ac97d2d2d0a4536d986254
--- /dev/null
+++ b/Golden_Repo/c/Cartopy/Cartopy-0.18.0-gpsmpi-2020-Python-3.8.5.eb
@@ -0,0 +1,49 @@
+easyblock = 'PythonBundle'
+
+name = 'Cartopy'
+version = '0.18.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://scitools.org.uk/cartopy/docs/latest/'
+description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Fiona', '1.8.16', versionsuffix),
+ ('GDAL', '3.1.2', versionsuffix),
+ ('GEOS', '3.8.1', versionsuffix),
+ ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
+ ('pyproj', '2.6.1.post1', versionsuffix),
+ ('Shapely', '1.7.1', versionsuffix),
+ ('PROJ', '7.1.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+ ('OWSLib', '0.20.0', {
+ 'checksums': ['334988857b260c8cdf1f6698d07eab61839c51acb52ee10eed1275439200a40e'],
+ }),
+ ('pyepsg', '0.4.0', {
+ 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'],
+ }),
+ ('pykdtree', '1.3.1', {
+ 'checksums': ['0d49d3bbfa0366dbe29176754ec86df75114a25525b530dcbbb75d3ac4c263e9'],
+ }),
+ ('pyshp', '2.1.0', {
+ 'modulename': 'shapefile',
+ 'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'],
+ }),
+ (name, version, {
+ 'checksums': ['7ffa317e8f8011e0d965a3ef1179e57a049f77019867ed677d49dcc5c0744434'],
+ }),
+]
+
+moduleclass = 'geo'
diff --git a/Golden_Repo/c/cppcheck/cppcheck-2.2-GCCcore-9.3.0.eb b/Golden_Repo/c/cppcheck/cppcheck-2.2-GCCcore-9.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..a9c8a8dc2a70edc8681c36946c8e69e436baedb4
--- /dev/null
+++ b/Golden_Repo/c/cppcheck/cppcheck-2.2-GCCcore-9.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'CMakeMake'
+name = 'cppcheck'
+version = '2.2'
+
+homepage = 'http://cppcheck.sourceforge.net/'
+description = """Cppcheck is a static analysis tool for C/C++ code"""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s-%(version)s.tar.bz2']
+
+dependencies = [
+ ('binutils', '2.34'),
+ ('Qt5', '5.14.2'),
+ ('PCRE', '8.44'),
+ ('CMake', '3.18.0'),
+]
+
+configopts = '-DUSE_Z3:BOOL=OFF'
+
+sanity_check_paths = {
+ 'files': ['bin/cppcheck'],
+ 'dirs': [],
+}
+
+moduleclass = 'lang'
diff --git a/Golden_Repo/d/distributed/distributed-2.30.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb b/Golden_Repo/d/distributed/distributed-2.30.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..8fcf4a476aaa2078f73c1e5450461c9a9757b67b
--- /dev/null
+++ b/Golden_Repo/d/distributed/distributed-2.30.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
@@ -0,0 +1,64 @@
+easyblock = 'Bundle'
+
+name = 'distributed'
+version = '2.30.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://distributed.readthedocs.io/'
+description = """Dask.distributed is a lightweight library for distributed computing in Python.
+ It extends both the concurrent.futures and dask APIs to moderate sized clusters."""
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('dask', '2.22.0', versionsuffix),
+ ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
+]
+
+
+exts_default_options = {
+ 'source_urls': [PYPI_SOURCE],
+ 'sanity_pip_check': True,
+}
+
+exts_list = [
+ ('zict', '2.0.0', {
+ 'source_urls': ['https://pypi.python.org/packages/source/z/zict'],
+ 'source_tmpl': 'zict-%(version)s.tar.gz',
+ }),
+ ('HeapDict', '1.0.1', {
+ 'modulename': 'heapdict',
+ 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'],
+ }),
+ ('tornado', '5.0.2', {
+ 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'],
+ }),
+ ('tblib', '1.7.0', {
+ 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'],
+ }),
+ ('msgpack', '1.0.0', {
+ 'modulename': 'msgpack',
+ 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'],
+ }),
+ ('sortedcontainers', '2.3.0', {
+ 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'],
+ }),
+ (name, version, {
+ 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'],
+ }),
+]
+
+sanity_check_paths = {
+ 'files': ['bin/dask-scheduler', 'bin/dask-ssh', 'bin/dask-worker'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/f/FFTW/FFTW-3.3.8-GCCcore-9.3.0-nompi.eb b/Golden_Repo/f/FFTW/FFTW-3.3.8-GCCcore-9.3.0-nompi.eb
new file mode 100644
index 0000000000000000000000000000000000000000..62f5c8bd660de89ea0d6ccb047c13a5cb0bb6fa8
--- /dev/null
+++ b/Golden_Repo/f/FFTW/FFTW-3.3.8-GCCcore-9.3.0-nompi.eb
@@ -0,0 +1,44 @@
+name = 'FFTW'
+version = '3.3.8'
+versionsuffix = '-nompi'
+
+homepage = 'http://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete
+Fourier transform (DFT) in one or more dimensions, of arbitrary input size,
+and of both real and complex data."""
+
+site_contacts = 'i.gutheil@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303']
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+# We hide it since this should be used just for Jupyter and the MPI version should be preferred for normal cases
+hidden = True
+
+# no quad precision, requires GCC v4.6 or higher
+# see also
+# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html
+with_quad_prec = True
+
+# compilation fails on AMD systems when configuring with --enable-avx-128-fma,
+# because Intel compilers do not support FMA4 instructions
+use_fma4 = True
+
+# can't find mpirun/mpiexec and fails
+# runtest = 'check'
+
+modextravars = {
+ 'FFTW_ROOT': '%(installdir)s',
+ 'FFTW_INCLUDE': '%(installdir)s/include',
+ 'FFTW_LIB': '%(installdir)s/lib',
+}
+
+moduleclass = 'numlib'
diff --git a/Golden_Repo/f/FFTW/FFTW-3.3.8-ipsmpi-2020-mt.eb b/Golden_Repo/f/FFTW/FFTW-3.3.8-ipsmpi-2020-mt.eb
new file mode 100644
index 0000000000000000000000000000000000000000..ec54be2c15a4b1e054dc17e1d5c53fc2b79d4150
--- /dev/null
+++ b/Golden_Repo/f/FFTW/FFTW-3.3.8-ipsmpi-2020-mt.eb
@@ -0,0 +1,42 @@
+name = 'FFTW'
+version = '3.3.8'
+
+homepage = 'http://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete
+Fourier transform (DFT) in one or more dimensions, of arbitrary input size,
+and of both real and complex data."""
+
+site_contacts = 'i.gutheil@fz-juelich.de'
+
+toolchain = {'name': 'ipsmpi', 'version': '2020-mt'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+
+# See https://github.com/FFTW/fftw3/commit/10e2040af822a08ed49d2f6a1db45a7a3ad50582
+patches = ['fftw_no-gcc-intel_2020.patch']
+
+checksums = [
+ '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303',
+ 'f226cc6dbdc9d11d4340567ef3227d78284c4dc44b8e63c3901a079aa9527da6'
+]
+
+# no quad precision, requires GCC v4.6 or higher
+# see also
+# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html
+with_quad_prec = False
+
+# Intel compilers do not support FMA4 instructions
+use_fma4 = False
+
+# can't find mpirun/mpiexec and fails
+# runtest = 'check'
+
+modextravars = {
+ 'FFTW_ROOT': '%(installdir)s',
+ 'FFTW_INCLUDE': '%(installdir)s/include',
+ 'FFTW_LIB': '%(installdir)s/lib',
+}
+
+moduleclass = 'numlib'
diff --git a/Golden_Repo/f/Fiona/Fiona-1.8.16-gpsmpi-2020-Python-3.8.5.eb b/Golden_Repo/f/Fiona/Fiona-1.8.16-gpsmpi-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..ada1c48ea2f5913390314432c8e10b2c825a3db4
--- /dev/null
+++ b/Golden_Repo/f/Fiona/Fiona-1.8.16-gpsmpi-2020-Python-3.8.5.eb
@@ -0,0 +1,50 @@
+easyblock = 'PythonBundle'
+
+name = 'Fiona'
+version = '1.8.16'
+versionsuffix = "-Python-%(pyver)s"
+
+homepage = 'https://github.com/Toblerity/Fiona'
+description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data
+in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries,
+mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using
+multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS
+packages such as pyproj, Rtree, and Shapely."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('GDAL', '3.1.2', versionsuffix),
+ ('Shapely', '1.7.1', versionsuffix), # optional
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+ ('cligj', '0.5.0', {
+ 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'],
+ }),
+ ('click-plugins', '1.1.1', {
+ 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'],
+ }),
+ ('munch', '2.5.0', {
+ 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'],
+ }),
+ (name, version, {
+ 'checksums': ['fd6dfb65959becc916e9f6928618bfd59c16cdbc413ece0fbac61489cd11255f'],
+ }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+ 'files': ['bin/fio'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'data'
diff --git a/Golden_Repo/g/GPAW/GPAW-20.1.0-gpsmkl-2020-Python-3.8.5.eb b/Golden_Repo/g/GPAW/GPAW-20.1.0-gpsmkl-2020-Python-3.8.5.eb
index 30786b3f7a2f1341cfef22b6241b3a0b55fb2c6c..0801b3b3e9789ea0f80f72f017509934c18b24fb 100644
--- a/Golden_Repo/g/GPAW/GPAW-20.1.0-gpsmkl-2020-Python-3.8.5.eb
+++ b/Golden_Repo/g/GPAW/GPAW-20.1.0-gpsmkl-2020-Python-3.8.5.eb
@@ -35,7 +35,7 @@ dependencies = [
('HDF5', '1.10.6'),
('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
('libvdwxc', '0.4.0'),
- ('GPAW-setups', '0.9.20000', '', True),
+ ('GPAW-setups', '0.9.20000', '', SYSTEM),
]
preconfigopts = 'export MKL_ROOT=$MKLROOT && '
diff --git a/Golden_Repo/g/GROMACS/GROMACS-2020.4-gpsmkl-2020.eb b/Golden_Repo/g/GROMACS/GROMACS-2020.4-gpsmkl-2020.eb
index 78e0e5ebffd41e5d70075fe1d944895f0dade8eb..3e66180645f0ffc436de682571f484d7f0f54e7b 100644
--- a/Golden_Repo/g/GROMACS/GROMACS-2020.4-gpsmkl-2020.eb
+++ b/Golden_Repo/g/GROMACS/GROMACS-2020.4-gpsmkl-2020.eb
@@ -48,7 +48,7 @@ builddependencies = [
# Removed ('hwloc', '2.0.3') from dependencies due to runtime failures.
dependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
]
configopts = '-DCMAKE_PREFIX_PATH=$EBROOTHWLOC -DMPIEXEC_MAX_NUMPROCS="24" '
diff --git a/Golden_Repo/g/GROMACS/GROMACS-2020.4-intel-para-2020.eb b/Golden_Repo/g/GROMACS/GROMACS-2020.4-intel-para-2020.eb
index 60a7ecd70b79c667cc4ed992596c8104c8486a74..f8f204c652c3acc104ad549907e3fc8ce50f8abd 100644
--- a/Golden_Repo/g/GROMACS/GROMACS-2020.4-intel-para-2020.eb
+++ b/Golden_Repo/g/GROMACS/GROMACS-2020.4-intel-para-2020.eb
@@ -47,7 +47,7 @@ builddependencies = [
# Removed ('hwloc', '2.0.3') from dependencies due to runtime failures.
dependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
]
configopts = '-DCMAKE_PREFIX_PATH=$EBROOTHWLOC -DMPIEXEC_MAX_NUMPROCS="24"'
diff --git a/Golden_Repo/g/GSL/GSL-2.6-GCCcore-9.3.0.eb b/Golden_Repo/g/GSL/GSL-2.6-GCCcore-9.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..fd66530a9250d41f6b71b93581b355da88ee294c
--- /dev/null
+++ b/Golden_Repo/g/GSL/GSL-2.6-GCCcore-9.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'GSL'
+version = '2.6'
+
+homepage = 'http://www.gnu.org/software/gsl/'
+description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
+ The library provides a wide range of mathematical routines such as random number generators, special functions
+ and least-squares fitting.
+"""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True}
+
+builddependencies = [('binutils', '2.34')]
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = "--with-pic"
+
+moduleclass = 'numlib'
diff --git a/Golden_Repo/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0.eb b/Golden_Repo/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0.eb
index 10741d030f3611b43505166f1910ed4083a6f54b..973ed942e553d3b8bcc8366b05b7a1e938921277 100644
--- a/Golden_Repo/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0.eb
+++ b/Golden_Repo/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0.eb
@@ -37,7 +37,7 @@ dependencies = [
('Ghostscript', '9.52'),
('GLib', '2.64.4'),
('GTS', '0.7.6'),
- ('Java', '1.8', '', True),
+ ('Java', '1.8', '', SYSTEM),
('libpng', '1.6.37'),
('librsvg', '2.48.8'),
('Pango', '1.44.7'),
diff --git a/Golden_Repo/g/gcccoremkl/gcccoremkl-9.3.0-2020.2.254.eb b/Golden_Repo/g/gcccoremkl/gcccoremkl-9.3.0-2020.2.254.eb
index 4901086ff29cb198c3dedc7b9c47fc410b8bb1bd..8a73818e9690d6b87797922e0cd3fba7d7d3708c 100644
--- a/Golden_Repo/g/gcccoremkl/gcccoremkl-9.3.0-2020.2.254.eb
+++ b/Golden_Repo/g/gcccoremkl/gcccoremkl-9.3.0-2020.2.254.eb
@@ -19,9 +19,9 @@ local_comp = (local_comp_name, local_comp_version)
dependencies = [
local_comp,
('binutils', '2.34', '', local_comp),
- ('imkl', local_mklver, '', True),
+ ('imkl', local_mklver, '', SYSTEM),
]
-hiddendependencies = [('imkl', local_mklver, '', True)]
+hiddendependencies = [('imkl', local_mklver, '', SYSTEM)]
moduleclass = 'toolchain'
diff --git a/Golden_Repo/h/HDF/HDF-4.2.15-GCC-9.3.0.eb b/Golden_Repo/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
index 347165359d20775aa70bc8e1f71f75f8b88edf01..6d7aa30ea9f519149816b1dddc4a2b38df2dabe4 100644
--- a/Golden_Repo/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
+++ b/Golden_Repo/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
builddependencies = [
('flex', '2.6.4'),
('Bison', '3.6.4'),
+ ('Java', '15', '', SYSTEM),
]
dependencies = [
@@ -30,7 +31,8 @@ source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.s
preconfigopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
preconfigopts += 'export LIBS="-ltirpc $LIBS" && '
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
prebuildopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
diff --git a/Golden_Repo/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb b/Golden_Repo/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
index b63df713c01a118cea327c4cdce40ca1edab824d..437dc04eaf54f04616c25eda39085499a44fe6ed 100644
--- a/Golden_Repo/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
+++ b/Golden_Repo/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
builddependencies = [
('flex', '2.6.4'),
('Bison', '3.6.4'),
+ ('Java', '15', '', SYSTEM),
]
dependencies = [
@@ -30,7 +31,8 @@ source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.s
preconfigopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
preconfigopts += 'export LIBS="-ltirpc $LIBS" && '
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
prebuildopts = 'export CPATH="/usr/include/tirpc:$CPATH" && '
diff --git a/Golden_Repo/h/HDF5/HDF5-1.10.6-GCCcore-9.3.0-serial.eb b/Golden_Repo/h/HDF5/HDF5-1.10.6-GCCcore-9.3.0-serial.eb
index bb2213c8207dc83822f5eed5345b76a32ee37546..4e9795c14cfea61c371e6345370c9b51db261870 100644
--- a/Golden_Repo/h/HDF5/HDF5-1.10.6-GCCcore-9.3.0-serial.eb
+++ b/Golden_Repo/h/HDF5/HDF5-1.10.6-GCCcore-9.3.0-serial.eb
@@ -20,6 +20,7 @@ checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa']
builddependencies = [
('binutils', '2.34'),
+ ('Java', '15', '', SYSTEM)
]
dependencies = [
@@ -27,4 +28,6 @@ dependencies = [
('Szip', '2.1.1'),
]
+configopts = '--enable-java'
+
moduleclass = 'data'
diff --git a/Golden_Repo/h/HDFView/HDFView-2.14-GCC-9.3.0.eb b/Golden_Repo/h/HDFView/HDFView-2.14-GCC-9.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..1b24781cf8f543eff5bafa69cde65b7c5a7e8d58
--- /dev/null
+++ b/Golden_Repo/h/HDFView/HDFView-2.14-GCC-9.3.0.eb
@@ -0,0 +1,46 @@
+easyblock = 'PackedBinary'
+
+name = 'HDFView'
+version = '3.1.1'
+
+homepage = 'https://www.hdfgroup.org/products/java/'
+description = """The HDF Java Products consist of HDFView (a Java browser for HDF4 and HDF5 files) and the HDF-Java wrappers.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'GCC', 'version': '9.3.0'}
+
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfview-%(version)s/src/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+
+builddependencies = [
+ ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM),
+]
+
+dependencies = [
+ ('Java', '15', '', SYSTEM),
+ ('HDF', '4.2.15'),
+ ('HDF5', '1.10.6', '-serial'),
+]
+
+install_cmd = (
+ # build HDFView
+ 'export HDFLIBS=$EBROOTHDF && '
+ 'export HDF5LIBS=$EBROOTHDF5 && '
+ 'cd %(builddir)s/hdfview-%(version)s && '
+ 'ant run && '
+ 'ant package && '
+ 'tar -xzf build/dist/HDFView-%(version)s-Linux-x86_64.tar.gz && '
+ # install HDFView
+ 'cd %(installdir)s && '
+ '%(builddir)s/hdfview-%(version)s/build/dist/HDFView-%(version)s-Linux.sh --skip-license && '
+ 'mv %(installdir)s/HDFView/%(version)s/* %(installdir)s && '
+ 'mkdir %(installdir)s/bin && '
+ 'mv %(installdir)s/hdfview.sh %(installdir)s/bin/ && '
+ 'ln -s %(installdir)s/bin/hdfview.sh %(installdir)s/bin/hdfview && '
+ "sed -i 's#JAVABIN=.*#JAVABIN=$JAVA_HOME/bin#g' %(installdir)s/bin/hdfview.sh && "
+ 'sed -i "s#INSTALLDIR=.*#INSTALLDIR=%(installdir)s#g" %(installdir)s/bin/hdfview.sh '
+)
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/h/Horovod/Horovod-0.20.3-gomkl-2020-Python-3.8.5.eb b/Golden_Repo/h/Horovod/Horovod-0.20.3-gomkl-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..5f3d9fc6fdf60bf759e5bb4aa7c3a98eb7d8bed6
--- /dev/null
+++ b/Golden_Repo/h/Horovod/Horovod-0.20.3-gomkl-2020-Python-3.8.5.eb
@@ -0,0 +1,101 @@
+# on juwels booster, one needs to call "export UCX_LOG_LEVEL=FATAL ebw ...
+
+easyblock = 'PythonBundle'
+
+name = 'Horovod'
+version = '0.20.3'
+local_tf_version = '2.3.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/uber/horovod'
+description = "Horovod is a distributed training framework for TensorFlow and PyTorch."
+
+toolchain = {'name': 'gomkl', 'version': '2020'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+builddependencies = [
+ ('CMake', '3.18.0'),
+]
+dependencies = [
+ ('Python', '3.8.5'),
+ ('TensorFlow', local_tf_version, '-Python-%(pyver)s', ('gcccoremkl', '9.3.0-2020.2.254')),
+ ('UCX', '1.9.0', '', SYSTEM), # Forced because default was 1.8.1. If the default is 1.9.0, this can go away
+ ('PyTorch', '1.7.0', '-Python-%(pyver)s', ('gcccoremkl', '9.3.0-2020.2.254')),
+ ('NCCL', '2.8.3-1', '-CUDA-11.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# possible vars:
+# HOROVOD_BUILD_ARCH_FLAGS - additional C++ compilation flags to pass in for your build architecture.
+# HOROVOD_CUDA_HOME - path where CUDA include and lib directories can be found.
+# HOROVOD_BUILD_CUDA_CC_LIST - List of compute capabilities to build Horovod CUDA
+# kernels for (example: HOROVOD_BUILD_CUDA_CC_LIST=60,70,75)
+# HOROVOD_ROCM_HOME - path where ROCm include and lib directories can be found.
+# HOROVOD_NCCL_HOME - path where NCCL include and lib directories can be found.
+# HOROVOD_NCCL_INCLUDE - path to NCCL include directory.
+# HOROVOD_NCCL_LIB - path to NCCL lib directory.
+# HOROVOD_NCCL_LINK - {SHARED, STATIC}. Mode to link NCCL library. Defaults to STATIC for CUDA, SHARED for ROCm.
+# HOROVOD_WITH_GLOO - {1}. Require that Horovod is built with Gloo support enabled.
+# HOROVOD_WITHOUT_GLOO - {1}. Skip building with Gloo support.
+# HOROVOD_WITH_MPI - {1}. Require that Horovod is built with MPI support enabled.
+# HOROVOD_WITHOUT_MPI - {1}. Skip building with MPI support.
+# HOROVOD_GPU - {CUDA, ROCM}. Framework to use for GPU operations.
+# HOROVOD_GPU_OPERATIONS - {NCCL, MPI}. Framework to use for GPU tensor allreduce, allgather, and broadcast.
+# HOROVOD_GPU_ALLREDUCE - {NCCL, MPI}. Framework to use for GPU tensor allreduce.
+# HOROVOD_GPU_ALLGATHER - {NCCL, MPI}. Framework to use for GPU tensor allgather.
+# HOROVOD_GPU_BROADCAST - {NCCL, MPI}. Framework to use for GPU tensor broadcast.
+# HOROVOD_ALLOW_MIXED_GPU_IMPL - {1}. Allow Horovod to install with NCCL allreduce and MPI GPU allgather /
+# broadcast. Not recommended due to a possible deadlock.
+# HOROVOD_CPU_OPERATIONS - {MPI, GLOO, CCL}. Framework to use for CPU tensor allreduce, allgather, and broadcast.
+# HOROVOD_CMAKE - path to the CMake binary used to build Gloo (not required when using MPI).
+# HOROVOD_WITH_TENSORFLOW - {1}. Require Horovod to install with TensorFlow support enabled.
+# HOROVOD_WITHOUT_TENSORFLOW - {1}. Skip installing TensorFlow support.
+# HOROVOD_WITH_PYTORCH - {1}. Require Horovod to install with PyTorch support enabled.
+# HOROVOD_WITHOUT_PYTORCH - {1}. Skip installing PyTorch support.
+# HOROVOD_WITH_MXNET - {1}. Require Horovod to install with MXNet support enabled.
+# HOROVOD_WITHOUT_MXNET - {1}. Skip installing MXNet support.
+
+# prebuildopts = 'export LDSHARED="$CC -shared" && '
+# prebuildopts += ' HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 '
+# prebuildopts += ' HOROVOD_NCCL_LINK=SHARED HOROVOD_NCCL_HOME=$EBROOTNCCL '
+# prebuildopts += ' HOROVOD_GPU_OPERATIONS=NCCL '
+# prebuildopts += ' HOROVOD_CPU_OPERATIONS=MPI '
+# prebuildopts += ' HOROVOD_GPU_ALLREDUCE=NCCL '
+# prebuildopts += ' HOROVOD_GPU_BROADCAST=NCCL '
+# prebuildopts += ' HOROVOD_WITH_MPI=1 '
+
+
+prebuildopts = 'export LDSHARED="$CC -shared" && '
+prebuildopts += ' HOROVOD_NCCL_LINK=SHARED HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_NCCL_HOME=$EBROOTNCCL '
+prebuildopts += ' HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1'
+prebuildopts += ' NVCC_GENCODE="-gencode=arch=compute_70,code=sm_70 \
+ -gencode=arch=compute_75,code=sm_75 \
+ -gencode=arch=compute_80,code=sm_80"'
+
+preinstallopts = prebuildopts
+
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+exts_list = [
+ ('horovod', version, {
+ 'checksums': ['6ebc90d627af486d44335ed48489e1e8dc190607574758867c52e4e17d75a247'],
+ 'cuda_compute_capabilities': ['7.0', '7.5', '8.0'],
+ }),
+]
+
+sanity_check_paths = {
+ 'files': ['bin/horovodrun'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# This makes openmpi work. It's up to the sysadmins to correct me here.
+modextravars = {'HOROVOD_MPI_THREADS_DISABLE': '1'}
+
+modloadmsg = 'Setting HOROVOD_MPI_THREADS_DISABLE=1. '
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb b/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
index ec81e25c4bd30963b3e6ee6fd0cb7cc0de28cc3f..6178b0c12adac5ef08a67a76dd1afc8cb3e585d7 100644
--- a/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
+++ b/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
builddependencies = [
('flex', '2.6.4'),
('Bison', '3.6.4'),
+ ('Java', '15', '', SYSTEM),
]
dependencies = [
@@ -28,7 +29,8 @@ dependencies = [
sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]]
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
sanity_check_paths = {
'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'],
diff --git a/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb b/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
index 1f25d07deebddfb7ec4eb214c9b708458c516c8b..b3d0a06f6ac30a4a58270b00cf6ea4150dc7eec3 100644
--- a/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
+++ b/Golden_Repo/hdfml_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
builddependencies = [
('flex', '2.6.4'),
('Bison', '3.6.4'),
+ ('Java', '15', '', SYSTEM),
]
dependencies = [
@@ -28,7 +29,8 @@ dependencies = [
sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]]
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
sanity_check_paths = {
'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'],
diff --git a/Golden_Repo/hidden_deps.txt b/Golden_Repo/hidden_deps.txt
index 3a45b6bcafcf5486d586b98afa8db444c934be51..74c6b3e597f0de59005ed1b80327342ce36c69c5 100644
--- a/Golden_Repo/hidden_deps.txt
+++ b/Golden_Repo/hidden_deps.txt
@@ -85,6 +85,15 @@ JSON-C
JSON-GLib
JsonCpp
JUnit
+JupyterKernel-Bash
+JupyterKernel-Cling
+JupyterKernel-JavaScript
+JupyterKernel-Julia
+JupyterKernel-Octave
+JupyterKernel-PyParaView
+JupyterKernel-R
+JupyterKernel-Ruby
+JupyterProxy-XpraHTML5
kbproto
LAME
LevelDB
diff --git a/Golden_Repo/i/ITK/ITK-5.1.2-GCCcore-9.3.0-nompi-Python-3.8.5.eb b/Golden_Repo/i/ITK/ITK-5.1.2-GCCcore-9.3.0-nompi-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..87c9cb20686820c9147a754183dd376a839732e3
--- /dev/null
+++ b/Golden_Repo/i/ITK/ITK-5.1.2-GCCcore-9.3.0-nompi-Python-3.8.5.eb
@@ -0,0 +1,93 @@
+easyblock = 'CMakeMake'
+
+name = 'ITK'
+version = '5.1.2'
+versionsuffix = '-nompi-Python-%(pyver)s'
+
+homepage = 'https://itk.org'
+description = """Insight Segmentation and Registration Toolkit (ITK) provides
+ an extensive suite of software tools for registering and segmenting
+ multidimensional imaging data."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60']
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('CMake', '3.18.0'),
+ ('Bison', '3.6.4'),
+ ('pkg-config', '0.29.2'),
+ ('Perl', '5.32.0'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('HDF5', '1.10.6', '-serial'),
+ ('SWIG', '3.0.12', '-Python-%(pyver)s'),
+ ('libpng', '1.6.37'),
+ ('LibTIFF', '4.1.0'),
+ ('expat', '2.2.9'),
+ ('Eigen', '3.3.7'),
+ # ('ParaView', '5.8.1', '-Python-%(pyver)s'),
+ ('tbb', '2020.3'),
+ ('Qt5', '5.14.2'),
+ ('OpenGL', '2020'),
+ ('X11', '20200222'),
+]
+
+separate_build_dir = True
+
+configopts = "-DCMAKE_BUILD_TYPE=Release "
+configopts += "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON "
+
+configopts += "-DBUILD_SHARED_LIBS=ON "
+configopts += "-DBUILD_TESTING=OFF "
+# configopts += "-DITK_FORBID_DOWNLOADS=ON "
+
+configopts += "-DITKV4_COMPATIBILITY=ON "
+configopts += "-DITK_LEGACY_SILENT=ON "
+
+configopts += "-DITK_USE_SYSTEM_SWIG=ON "
+configopts += "-DSWIG_EXECUTABLE=${EBROOTSWIG}/bin/swig "
+configopts += "-DSWIG_DIR=${EBROOTSWIG} "
+
+configopts += "-DITK_USE_SYSTEM_EIGEN=ON "
+configopts += "-DEigen3_DIR=$EBROOTEIGEN/share/eigen3/cmake "
+
+configopts += "-DITK_USE_SYSTEM_HDF5=ON "
+configopts += "-DHDF5_DIR=$EBROOTHDF5 "
+
+configopts += "-DITK_WRAP_PYTHON=ON "
+configopts += "-DModule_ITKReview=ON "
+
+# fails with ITK_WRAP_PYTON=ON, error, because vtkImage*.h cannot be found
+# read: https://discourse.itk.org/t/problem-with-building-itk-with-module-itkvtkglue-on/2315
+# code: https://github.com/InsightSoftwareConsortium/ITKVtkGlue/blob/itk-5.0.1/CMakeLists.txt#L81
+# configopts="-DModule_ITKVtkGlue=ON ${configopts} "
+# configopts="-DVTK_DIR=$EBROOTPARAVIEW/lib64/cmake/paraview-5.8/vtk ${configopts} "
+# configopts="-DVTK_INCLUDE_DIRS=$EBROOTPARAVIEW/include/paraview-5.8 ${configopts} "
+# configopts="-DVTK_LIBRARIES=$EBROOTPARAVIEW/lib64 ${configopts} "
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+sanity_check_paths = {
+ 'files': ['bin/itkTestDriver',
+ 'lib/libITKVTK-%(version_major_minor)s.so',
+ 'lib/libITKIOJPEG-%(version_major_minor)s.so',
+ 'lib/libITKCommon-%(version_major_minor)s.so'],
+ 'dirs': ['include/ITK-%(version_major_minor)s',
+ 'lib/python%(pyshortver)s/site-packages',
+ 'share'],
+}
+
+sanity_check_commands = [('python', "-c 'import %(namelower)s'")]
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/i/ITK/ITK-5.1.2-gompi-2020-Python-3.8.5.eb b/Golden_Repo/i/ITK/ITK-5.1.2-gompi-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..2bfa842e22d52eab5f9d404bcf933bb82fff1011
--- /dev/null
+++ b/Golden_Repo/i/ITK/ITK-5.1.2-gompi-2020-Python-3.8.5.eb
@@ -0,0 +1,93 @@
+easyblock = 'CMakeMake'
+
+name = 'ITK'
+version = '5.1.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://itk.org'
+description = """Insight Segmentation and Registration Toolkit (ITK) provides
+ an extensive suite of software tools for registering and segmenting
+ multidimensional imaging data."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gompi', 'version': '2020'}
+toolchainopts = {'pic': True, 'usempi': False}
+
+source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60']
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('CMake', '3.18.0'),
+ ('Bison', '3.6.4'),
+ ('pkg-config', '0.29.2'),
+ ('Perl', '5.32.0'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('HDF5', '1.10.6', '-serial'),
+ ('SWIG', '3.0.12', '-Python-%(pyver)s'),
+ ('libpng', '1.6.37'),
+ ('LibTIFF', '4.1.0'),
+ ('expat', '2.2.9'),
+ ('Eigen', '3.3.7'),
+ # ('ParaView', '5.8.1', '-Python-%(pyver)s'),
+ ('tbb', '2020.3'),
+ ('Qt5', '5.14.2'),
+ ('OpenGL', '2020'),
+ ('X11', '20200222'),
+]
+
+separate_build_dir = True
+
+configopts = "-DCMAKE_BUILD_TYPE=Release "
+configopts += "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON "
+
+configopts += "-DBUILD_SHARED_LIBS=ON "
+configopts += "-DBUILD_TESTING=OFF "
+# configopts += "-DITK_FORBID_DOWNLOADS=ON "
+
+configopts += "-DITKV4_COMPATIBILITY=ON "
+configopts += "-DITK_LEGACY_SILENT=ON "
+
+configopts += "-DITK_USE_SYSTEM_SWIG=ON "
+configopts += "-DSWIG_EXECUTABLE=${EBROOTSWIG}/bin/swig "
+configopts += "-DSWIG_DIR=${EBROOTSWIG} "
+
+configopts += "-DITK_USE_SYSTEM_EIGEN=ON "
+configopts += "-DEigen3_DIR=$EBROOTEIGEN/share/eigen3/cmake "
+
+configopts += "-DITK_USE_SYSTEM_HDF5=ON "
+configopts += "-DHDF5_DIR=$EBROOTHDF5 "
+
+configopts += "-DITK_WRAP_PYTHON=ON "
+configopts += "-DModule_ITKReview=ON "
+
+# fails with ITK_WRAP_PYTON=ON, error, because vtkImage*.h cannot be found
+# read: https://discourse.itk.org/t/problem-with-building-itk-with-module-itkvtkglue-on/2315
+# code: https://github.com/InsightSoftwareConsortium/ITKVtkGlue/blob/itk-5.0.1/CMakeLists.txt#L81
+# configopts="-DModule_ITKVtkGlue=ON ${configopts} "
+# configopts="-DVTK_DIR=$EBROOTPARAVIEW/lib64/cmake/paraview-5.8/vtk ${configopts} "
+# configopts="-DVTK_INCLUDE_DIRS=$EBROOTPARAVIEW/include/paraview-5.8 ${configopts} "
+# configopts="-DVTK_LIBRARIES=$EBROOTPARAVIEW/lib64 ${configopts} "
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+sanity_check_paths = {
+ 'files': ['bin/itkTestDriver',
+ 'lib/libITKVTK-%(version_major_minor)s.so',
+ 'lib/libITKIOJPEG-%(version_major_minor)s.so',
+ 'lib/libITKCommon-%(version_major_minor)s.so'],
+ 'dirs': ['include/ITK-%(version_major_minor)s',
+ 'lib/python%(pyshortver)s/site-packages',
+ 'share'],
+}
+
+sanity_check_commands = [('python', "-c 'import %(namelower)s'")]
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/i/ITK/ITK-5.1.2-gpsmpi-2020-Python-3.8.5.eb b/Golden_Repo/i/ITK/ITK-5.1.2-gpsmpi-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..75f56451296a006c4f4390b526d77e7e187d2f31
--- /dev/null
+++ b/Golden_Repo/i/ITK/ITK-5.1.2-gpsmpi-2020-Python-3.8.5.eb
@@ -0,0 +1,93 @@
+easyblock = 'CMakeMake'
+
+name = 'ITK'
+version = '5.1.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://itk.org'
+description = """Insight Segmentation and Registration Toolkit (ITK) provides
+ an extensive suite of software tools for registering and segmenting
+ multidimensional imaging data."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+toolchainopts = {'pic': True, 'usempi': False}
+
+source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60']
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('CMake', '3.18.0'),
+ ('Bison', '3.6.4'),
+ ('pkg-config', '0.29.2'),
+ ('Perl', '5.32.0'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('HDF5', '1.10.6', '-serial'),
+ ('SWIG', '3.0.12', '-Python-%(pyver)s'),
+ ('libpng', '1.6.37'),
+ ('LibTIFF', '4.1.0'),
+ ('expat', '2.2.9'),
+ ('Eigen', '3.3.7'),
+ # ('ParaView', '5.8.1', '-Python-%(pyver)s'),
+ ('tbb', '2020.3'),
+ ('Qt5', '5.14.2'),
+ ('OpenGL', '2020'),
+ ('X11', '20200222'),
+]
+
+separate_build_dir = True
+
+configopts = "-DCMAKE_BUILD_TYPE=Release "
+configopts += "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON "
+
+configopts += "-DBUILD_SHARED_LIBS=ON "
+configopts += "-DBUILD_TESTING=OFF "
+# configopts += "-DITK_FORBID_DOWNLOADS=ON "
+
+configopts += "-DITKV4_COMPATIBILITY=ON "
+configopts += "-DITK_LEGACY_SILENT=ON "
+
+configopts += "-DITK_USE_SYSTEM_SWIG=ON "
+configopts += "-DSWIG_EXECUTABLE=${EBROOTSWIG}/bin/swig "
+configopts += "-DSWIG_DIR=${EBROOTSWIG} "
+
+configopts += "-DITK_USE_SYSTEM_EIGEN=ON "
+configopts += "-DEigen3_DIR=$EBROOTEIGEN/share/eigen3/cmake "
+
+configopts += "-DITK_USE_SYSTEM_HDF5=ON "
+configopts += "-DHDF5_DIR=$EBROOTHDF5 "
+
+configopts += "-DITK_WRAP_PYTHON=ON "
+configopts += "-DModule_ITKReview=ON "
+
+# fails with ITK_WRAP_PYTON=ON, error, because vtkImage*.h cannot be found
+# read: https://discourse.itk.org/t/problem-with-building-itk-with-module-itkvtkglue-on/2315
+# code: https://github.com/InsightSoftwareConsortium/ITKVtkGlue/blob/itk-5.0.1/CMakeLists.txt#L81
+# configopts="-DModule_ITKVtkGlue=ON ${configopts} "
+# configopts="-DVTK_DIR=$EBROOTPARAVIEW/lib64/cmake/paraview-5.8/vtk ${configopts} "
+# configopts="-DVTK_INCLUDE_DIRS=$EBROOTPARAVIEW/include/paraview-5.8 ${configopts} "
+# configopts="-DVTK_LIBRARIES=$EBROOTPARAVIEW/lib64 ${configopts} "
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+sanity_check_paths = {
+ 'files': ['bin/itkTestDriver',
+ 'lib/libITKVTK-%(version_major_minor)s.so',
+ 'lib/libITKIOJPEG-%(version_major_minor)s.so',
+ 'lib/libITKCommon-%(version_major_minor)s.so'],
+ 'dirs': ['include/ITK-%(version_major_minor)s',
+ 'lib/python%(pyshortver)s/site-packages',
+ 'share'],
+}
+
+sanity_check_commands = [('python', "-c 'import %(namelower)s'")]
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/j/Java/Java-15.0.1.eb b/Golden_Repo/j/Java/Java-15.0.1.eb
new file mode 100644
index 0000000000000000000000000000000000000000..8a385d353f128ab7b2d8d8bdff34c987fe6570ff
--- /dev/null
+++ b/Golden_Repo/j/Java/Java-15.0.1.eb
@@ -0,0 +1,16 @@
+name = 'Java'
+version = '15.0.1'
+
+homepage = 'http://openjdk.java.net'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+ Java applications on desktops and servers."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = SYSTEM
+
+source_urls = ['https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/']
+sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz']
+checksums = ['83ec3a7b1649a6b31e021cde1e58ab447b07fb8173489f27f427e731c89ed84a']
+
+moduleclass = 'lang'
diff --git a/Golden_Repo/j/Java/Java-15.eb b/Golden_Repo/j/Java/Java-15.eb
new file mode 100644
index 0000000000000000000000000000000000000000..78c52a44db6d95cbedb8977958761b2c9773a3a6
--- /dev/null
+++ b/Golden_Repo/j/Java/Java-15.eb
@@ -0,0 +1,14 @@
+easyblock = 'ModuleRC'
+
+name = 'Java'
+version = '15'
+
+homepage = 'https://java.com/'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+ Java applications on desktops and servers."""
+
+toolchain = SYSTEM
+
+dependencies = [('Java', '%(version)s.0.1')]
+
+moduleclass = 'lang'
diff --git a/Golden_Repo/j/Jupyter/401html.patch b/Golden_Repo/j/Jupyter/401html.patch
new file mode 100644
index 0000000000000000000000000000000000000000..c3e71a800541a396377737132022c67a077d7564
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/401html.patch
@@ -0,0 +1,135 @@
+diff -Naur jupyterlab-2.2.9.orig/401.html jupyterlab-2.2.9/401.html
+--- jupyterlab-2.2.9.orig/401.html 1970-01-01 01:00:00.000000000 +0100
++++ jupyterlab-2.2.9/401.html 2020-12-11 23:24:45.301738818 +0100
+@@ -0,0 +1,131 @@
++<!DOCTYPE html>
++<html><head>
++ <meta http-equiv="Refresh" content="0; url=https://jupyter-jsc.fz-juelich.de/hub/logout?stopall=false&alldevices=false" />
++
++ <meta http-equiv="content-type" content="text/html; charset=UTF-8">
++ <meta charset="utf-8">
++
++ <title>jupyter-jsc</title>
++ <meta http-equiv="X-UA-Compatible" content="chrome=1">
++ <meta property="og:image" content="/hub/static/images/mini_website.jpg">
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diff --git a/Golden_Repo/j/Jupyter/Jupyter-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb b/Golden_Repo/j/Jupyter/Jupyter-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..b5b826ec34b3b8385af35bf77c3ea82903fc14c2
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/Jupyter-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
@@ -0,0 +1,1317 @@
+easyblock = 'Bundle'
+
+name = 'Jupyter'
+version = '2020.2.5'
+versionsuffix = '-Python-%(pyver)s'
+
+local_jlab_version = '2.2.9'
+
+homepage = 'http://www.jupyter.org'
+description = """
+Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across
+dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('unzip', '6.0'),
+ ('Autotools', '20200321'),
+ ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('libyaml', '0.2.5'),
+ ('Pandoc', '2.11.0.4', '', SYSTEM), # For doc-generation
+ ('texlive', '20200406'),
+ ('ITK', '5.1.2', '-nompi' + versionsuffix),
+ ('HDF5', '1.10.6', '-serial'),
+ ('netcdf4-python', '1.5.4', '-serial' + versionsuffix),
+ ('FFmpeg', '4.3.1'), # for pydub
+ ('LLVM', '10.0.1'), # llvmlite
+ ('git', '2.28.0'), # for jupyterlab-git (req. >=2.0)
+ ('SciPy-Stack', '2020', versionsuffix),
+]
+
+osdependencies = [('openssl'), ('git')]
+
+local_common_opts = {
+ 'req_py_majver': '3',
+ 'req_py_minver': '0'
+}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+ 'filter': ('python -c "import %(ext_name)s"', ''),
+ 'download_dep_fail': True,
+ 'source_urls': [PYPI_SOURCE],
+ 'use_pip': True,
+ 'sanity_pip_check': True,
+ 'use_pip_for_deps': False,
+}
+
+components = [
+ ('nodejs', '14.15.3', {
+ 'easyblock': 'ConfigureMake',
+ 'source_urls': ['http://nodejs.org/dist/v%(version)s/'],
+ 'sources': ['node-v%(version)s.tar.gz'],
+ 'start_dir': 'node-v%(version)s',
+ }),
+]
+
+exts_list = [
+ ('distro', '1.5.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92')]),
+ ])),
+ ('scikit-build', '0.11.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c')]),
+ ('modulename', 'skbuild'),
+ ])),
+ ('ptvsd', '4.3.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'ptvsd-4.3.2.zip'),
+ ('checksums', [('sha256', '3b05c06018fdbce5943c50fb0baac695b5c11326f9e21a5266c854306bda28ab')]),
+ ])),
+ # ('cryptography', '2.8', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651')]),
+ # ])), # part of Python module
+ ('pyOpenSSL', '19.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9a24494b2602aaf402be5c9e30a0b82d4a5c67528fe8fb475e3f3bc00dd69507')]),
+ ('modulename', 'OpenSSL'),
+ ])),
+ ('entrypoints', '0.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451')]),
+ ('use_pip', False),
+ ])),
+ ('async_generator', '1.10', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144')]),
+ ])),
+ ('nest_asyncio', '1.4.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'eaa09ef1353ebefae19162ad423eef7a12166bcc63866f8bff8f3635353cd9fa')]),
+ ])),
+ ('absl-py', '0.8.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd9129186431e150d7fe455f1cb1ecbb92bb5dba9da9bc3ef7b012d98c4db2526')]),
+ ('modulename', 'absl'),
+ ])),
+ ('websockify', '0.9.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c35b5b79ebc517d3b784dacfb993be413a93cda5222c6f382443ce29c1a6cada')]),
+ ])),
+ ('typing_extensions', '3.7.4.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '79ee589a3caca649a9bfd2a8de4709837400dfa00b6cc81962a1e6a1815969ae')]),
+ ])),
+ # General Python packages
+ ('tornado', '6.0.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c845db36ba616912074c5b1ee897f8e0124df269468f25e4fe21fe72f6edd7a9')]),
+ ])),
+ ('bokeh', '2.0.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd9248bdb0156797abf6d04b5eac581dcb121f5d1db7acbc13282b0609314893a')]),
+ ])),
+ ('seaborn', '0.9.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f')]),
+ ])),
+ ('nbformat', '5.0.8', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f545b22138865bfbcc6b1ffe89ed5a2b8e2dc5d4fe876f2ca60d8e6f702a30f8')]),
+ ])),
+ ('param', '1.9.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '8370d41616e257b8ed2e242ec531e0340b8c954bea414b791fa0ef6235959981')]),
+ ])),
+ # Jupyter-core and dependencies
+ ('alabaster', '0.7.12', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02')]),
+ ])),
+ ('Babel', '2.7.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e86135ae101e31e2c8ec20a4e0c5220f4eed12487d5cf3f78be7e98d3a57fc28')]),
+ ('modulename', 'babel'),
+ ])),
+ ('snowballstemmer', '2.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52')]),
+ ])),
+ ('docutils', '0.15.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99')]),
+ ])),
+ ('imagesize', '1.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5')]),
+ ])),
+ ('sphinxcontrib-websupport', '1.1.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc')]),
+ ('modulename', 'sphinxcontrib'),
+ ])),
+ ('Sphinx', '1.8.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08')]),
+ ('modulename', 'sphinx'),
+ ])),
+ # ('pexpect', '4.7.0', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '9e2c1fd0e6ee3a49b28f95d4b33bc389c89b20af6a1255906e90ff1262ce62eb')]),
+ # ])), # part of Python module, but in version 4.6.0 (sanity check fails if package used from Python dependency)
+ ('ipython', '7.9.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'dfd303b270b7b5232b3d08bd30ec6fd685d8a58cabd54055e3d69d8f029f7280')]),
+ ('modulename', 'IPython'),
+ ])), # part of Python module, but in version 7.4.0 (sanity check fails if package used from Python dependency)
+ ('ipynb', '0.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '8d834c777ca3885289938728cc382f081c86a58e92961e86f0aba60c96938ce5')]),
+ ])),
+ ('jupyter_core', '4.7.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'aa1f9496ab3abe72da4efe0daab0cb2233997914581f9a071e07498c6add8ed3')]),
+ ])),
+ ('retrying', '1.3.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b')]),
+ ])),
+ ('plotly', '4.12.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9ec2c9f4cceac7c595ebb77c98cbeb6566a97bef777508584d9bb7d9bcb8854c')]),
+ ])),
+ ('tikzplotlib', '0.8.4', dict(list(local_common_opts.items()) + [ # renamed to matplotlib2tikz with version 0.8.0
+ ('checksums', [('sha256', '284e70915fc6994472abd2fa47af947e7606085e9957898fc645f0dd9b44da8c')]),
+ ])),
+ # Jupyter client
+ ('jupyter_client', '6.1.7', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1')]),
+ ])),
+ ('pynvml', '8.0.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c8d4eadc648c7e12a3c9182a9750afd8481b76412f83747bcc01e2aa829cde5d')]),
+ ])),
+ # Jupyter notebook and dependencies
+ # ('traitlets', '4.3.3', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', 'd023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7')]),
+ # ])), # part of Python module (sanity check fails if package used from Python dependency)
+ ('pyzmq', '18.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '93f44739db69234c013a16990e43db1aa0af3cf5a4b8b377d028ff24515fbeb3')]),
+ ('modulename', 'zmq'),
+ ])),
+ ('singledispatch', '3.4.0.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c')]),
+ ])),
+ ('ipyparallel', '6.2.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '76c7b028962b0ba762e4e45b450ee3a4353e7221526a8af812e817d7ef6ac065')]),
+ ])),
+ ('ipykernel', '5.1.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b368ad13edb71fa2db367a01e755a925d7f75ed5e09fbd3f06c85e7a8ef108a8')]),
+ ])),
+ ('terminado', '0.8.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2')]),
+ ('use_pip', False),
+ ])),
+ ('bleach', '3.1.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'aa8b870d0f46965bac2c073a93444636b0e1ca74e9777e34f03dd494b8a59d48')]),
+ ])),
+ ('mistune', '0.8.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e')]),
+ ])),
+ ('pandocfilters', '1.4.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9')]),
+ ])),
+ ('testpath', '0.4.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e')]),
+ ('use_pip', False),
+ ])),
+ ('nbconvert', '6.0.7', dict(list(local_common_opts.items()) + [ # convert Jupyter notebooks to: HTML, Latex, etc.
+ # !!! nbconvert will try to read from all paths in <jupyter-config-path> the file nbconvert/templates/conf.json
+ # ensure it has permissions (https://github.com/jupyter/nbconvert/issues/1430)
+ ('checksums', [('sha256', 'cbbc13a86dfbd4d1b5dee106539de0795b4db156c894c2c5dc382062bbc29002')]),
+ # 6.0.7 - patch for jupyter_contrib_nbextensions needed:
+ # https://github.com/ipython-contrib/jupyter_contrib_nbextensions/pull/1532
+ ])),
+ # ('ipython_genutils', '0.2.0', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', 'eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8')]),
+ # ])), # part of Python module (sanity check fails if package used from Python dependency)
+ ('Send2Trash', '1.5.0', dict(list(local_common_opts.items()) + [ # req. by widgetsnbextension
+ ('checksums', [('sha256', '60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2')]),
+ ('modulename', 'send2trash'),
+ ])),
+ ('argon2-cffi', '20.1.0', dict(list(local_common_opts.items()) + [ # req. for notebook >= 6.1
+ ('checksums', [('sha256', 'd8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d')]),
+ ('modulename', 'argon2'),
+ ])),
+ ('notebook', '6.1.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3db37ae834c5f3b6378381229d0e5dfcbfb558d08c8ce646b1ad355147f5e91d')]),
+ ('patches', ['notebook-6.0.3_jsc.patch']), # allow others to read/write in .ipynb_checkpoints
+ ])),
+ ('version_information', '1.0.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '811b9cea4b376aa62a77dc729a937ce8e2844573b8686b5c1840147054fb938d')]),
+ ])),
+ ('lesscpy', '0.13.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f3c6d0b544c5bcdadcd3d8319feccb4128d06676d4117c6c9396ab39c25372ad')]),
+ ])),
+ ('prometheus_client', '0.7.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da')]),
+ ])),
+ ('jupyterthemes', '0.20.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '2a8ebc0c84b212ab99b9f1757fc0582a3f53930d3a75b2492d91a7c8b36ab41e')]),
+ ])),
+ # Jupyter Lab and dependencies
+ ('zipp', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e')]),
+ ])),
+ ('jupyter-packaging', '0.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd89134d2df88c30098bce0f8d8fb07b988ef0f616775dbd4b82dac9562b5cae6')]),
+ ])),
+ ('importlib_metadata', '0.23', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26')]),
+ ])),
+ ('jsonschema', '3.1.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '2fa0684276b6333ff3c0b1b27081f4b2305f0a36cf702a23db50edb141893c3f')]),
+ ])), # part of Python module in version 3.0.1 (sanity check fails if package used from Python dependency)
+ ('jupyterlab_launcher', '0.13.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f880eada0b8b1f524d5951dc6fcae0d13b169897fc8a247d75fb5beadd69c5f0')]),
+ ])),
+ ('sphinx_rtd_theme', '0.4.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '728607e34d60456d736cc7991fd236afb828b21b82f956c5ea75f94c8414040a')]),
+ ])),
+ ('future', '0.18.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '858e38522e8fd0d3ce8f0c1feaf0603358e366d5403209674c7b617fa0c24093')]),
+ ])),
+ ('commonmark', '0.9.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60')]),
+ ])),
+ ('recommonmark', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '29cd4faeb6c5268c633634f2d69aef9431e0f4d347f90659fd0aab20e541efeb')]),
+ ])),
+ ('jupyterlab', local_jlab_version, dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3be8f8edea173753dd838c1b6d3bbcb6f5c801121f824a477025c1b6a1d33dc6')]),
+ ('patches', [('401html.patch', 1)])
+ ])),
+ ('json5', '0.8.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '124b0f0da1ed2ff3bfe3a3e9b8630abd3c650852465cb52c15ef60b8e82a73b0')]),
+ ])),
+ ('jupyterlab_server', '1.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c')]),
+ ])),
+ ('jupyter_kernel_gateway', '2.4.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '6424a9f118e757ef18e9bed7784ca05ad9e633945df328ac4d8810eadc6f6ccd')]),
+ ('modulename', 'kernel_gateway'),
+ ])),
+ ('nbclient', '0.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '01e2d726d16eaf2cde6db74a87e2451453547e8832d142f73f72fddcd4fe0250')]),
+ ])),
+ # Jupyter Kernel and dependencies
+ ('ptyprocess', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0')]),
+ ('use_pip', False),
+ ])),
+ # Jupyter Widgets and dependencies
+ ('defusedxml', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5')]),
+ ])),
+ ('widgetsnbextension', '3.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7')]),
+ ])),
+ ('ipywidgets', '7.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97')]),
+ ])),
+ # ('ipyscales', '0.5.0', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '')]),
+ # ])),
+ ('ipydatawidgets', '4.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd9f94828c11e3b40350fb14a02e027f42670a7c372bcb30db18d552dcfab7c01')]),
+ ])),
+ ('traittypes', '0.2.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'be6fa26294733e7489822ded4ae25da5b4824a8a7a0e0c2dccfde596e3489bd6')]),
+ ])),
+ ('bqplot', '0.12.17', dict(list(local_common_opts.items()) + [ # 2-D plotting with d3.js
+ ('checksums', [('sha256', 'f103d82e7c05ec29e2c4c2357cb207acb99cf5fedbad55f26e04d8bbdb3248ad')]),
+ ])),
+ ('jupyter_bokeh', '2.0.2', dict(list(local_common_opts.items()) + [ # ipywidget for bokeh
+ ('checksums', [('sha256', '8dc63198833e478c3231ba5a1c5492bac859f875b1dc4e8190ce308276aa01fc')]),
+ ])),
+ ('pythreejs', '2.2.0', dict(list(local_common_opts.items()) + [ # 3-D scene visualization with three.js
+ ('checksums', [('sha256', 'c05f52932efd58ff18beb333a6b2bb80341e980718a313b74821c4a5c8640721')]),
+ ])),
+ ('PyWavelets', '1.1.1', dict(list(local_common_opts.items()) + [ # for a nice threejs example notebook
+ ('checksums', [('sha256', '1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9')]),
+ ('modulename', 'pywt'),
+ ])),
+ ('imageio', '2.6.1', dict(list(local_common_opts.items()) + [ # for a nice threejs example notebook
+ ('checksums', [('sha256', 'f44eb231b9df485874f2ffd22dfd0c3c711e7de076516b9374edea5c65bc67ae')]),
+ ])),
+ ('networkx', '2.3', dict(list(local_common_opts.items()) + [ # for a nice threejs example notebook
+ ('source_tmpl', 'networkx-2.3.zip'),
+ ('checksums', [('sha256', '8311ddef63cf5c5c5e7c1d0212dd141d9a1fe3f474915281b73597ed5f1d4e3d')]),
+ ])),
+ ('scikit-image', '0.16.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'dd7fbd32da74d4e9967dc15845f731f16e7966cee61f5dc0e12e2abb1305068c')]),
+ ('modulename', 'skimage'),
+ ])),
+ ('ipywebrtc', '0.5.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '4db2be7d0bfcbd142b2f9f9e8303b926832a632ed4a3bc5681b319a5f226285a')]),
+ ])),
+ ('ipyvolume', '0.6.0a6', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1a71c681dd39b514db966c4812bbbd1347ce082ee7a7bcc53f494e0546bf37ff')]),
+ ])),
+ ('branca', '0.3.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3e762c9bdf40725f3d05ea1fda8fae9b470bfada6474e43a1242c8204a7bb15e')]),
+ ])),
+ ('ipyleaflet', '0.13.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c05f138327926bc81f29a629588bd656be5ff76dd8785c1e7eac5445b1d5a432')]),
+ ])),
+ ('ipympl', '0.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c33243047166fbedf3729af116186ae1894ee45db71cbc6632bf057a913ae010')]),
+ ])),
+ # ('PyYAML', '5.1.2', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4')]),
+ # ('modulename', 'yaml'),
+ # ])), # part of Python module (sanity check fails if package used from Python dependency)
+ # Jupyter Notebook Extensions
+ ('jupyter_nbextensions_configurator', '0.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83')]),
+ ])),
+ ('jupyter_latex_envs', '1.4.6', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '070a31eb2dc488bba983915879a7c2939247bf5c3b669b398bdb36a9b5343872')]),
+ ('patches', ['jupyter_latex_envs-template_paths.patch']),
+ # support for nbconvert>=6.x -> https://github.com/jfbercher/jupyter_latex_envs/pull/58
+ ('modulename', 'latex_envs'),
+ ])),
+ ('jupyter_highlight_selected_word', '0.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b')]),
+ ])),
+ ('prompt_toolkit', '2.0.10', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f15af68f66e664eaa559d4ac8a928111eebd5feda0c11738b5998045224829db')]),
+ ])),
+ ('jupyter_contrib_core', '0.3.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794')]),
+ ])),
+ ('jupyter_contrib_nbextensions', '0.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'eecd28ecc2fc410226c0a3d4932ed2fac4860ccf8d9e9b1b29548835a35b22ab')]),
+ ('patches', ['jupyter_contrib_nbextensions-template_paths.patch']),
+ # support for nbconvert>=6.x -> https://github.com/ipython-contrib/jupyter_contrib_nbextensions/pull/1532
+ ])),
+ ('rise', '5.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '2be45c3dbe27e63aae047c6a90be19798b6e17e9b6b0e25408b3c4f645658e26')]),
+ ])),
+ ('idna-ssl', '1.1.0', dict(list(local_common_opts.items()) + [ # indirect dep of jupyter-server-proxy
+ ('checksums', [('sha256', 'a933e3bb13da54383f9e8f35dc4f9cb9eb9b3b78c6b36f311254d6d0d92c6c7c')]),
+ ])),
+ ('multidict', '4.7.5', dict(list(local_common_opts.items()) + [ # indirect dep of jupyter-server-proxy
+ ('checksums', [('sha256', 'aee283c49601fa4c13adc64c09c978838a7e812f85377ae130a24d7198c0331e')]),
+ ])),
+ ('yarl', '1.4.2', dict(list(local_common_opts.items()) + [ # indirect dep of jupyter-server-proxy
+ ('checksums', [('sha256', '58cd9c469eced558cd81aa3f484b2924e8897049e06889e8ff2510435b7ef74b')]),
+ ])),
+ ('async-timeout', '3.0.1', dict(list(local_common_opts.items()) + [ # indirect dep of jupyter-server-proxy
+ ('checksums', [('sha256', '0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f')]),
+ ])),
+ ('aiohttp', '3.6.2', dict(list(local_common_opts.items()) + [ # indirect dep of jupyter-server-proxy
+ ('checksums', [('sha256', '259ab809ff0727d0e834ac5e8a283dc5e3e0ecc30c4d80b3cd17a4139ce1f326')]),
+ ])),
+ ('simpervisor', '0.3', dict(list(local_common_opts.items()) + [ # indirect dep of jupyter-server-proxy
+ ('checksums', [('sha256', 'd82e4527ae326747551e4bdfa632ff4ebef275ce721f80886c747adfdbf41c2e')]),
+ ])),
+ ('jupyter_server', '1.0.7', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b0b3185975b32a03520aa577d90145bc288a3a12124e0e80306ec6216c9b8634')]),
+ ])),
+ ('jupyter-server-proxy', '1.5.2', dict(list(local_common_opts.items()) + [
+ ('source_urls', ['https://github.com/jupyterhub/jupyter-server-proxy/archive/']),
+ ('source_tmpl', 'v%(version)s.tar.gz'),
+ ('checksums', [('sha256', '140bd642c511519ddd2acc5f70e0b46a40bbc673c888dcb3b19981005286853b')]),
+ ('patches', ['jupyterserverproxy-urlfile.patch']),
+ ])),
+ # Jupyter Lab Extensions
+ ('jupyterlab_github', '2.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1f560a91711b779d08118161af044caff44159e315cb80ae830d3dfbded7bac9')]),
+ # do not use pypi for download -> we need to patch drive.json
+ ('source_urls', ['https://github.com/jupyterlab/jupyterlab-github/archive']),
+ ('source_tmpl', 'v%(version)s.tar.gz'),
+ ('patches', ['jupyterlab_github-%(version)s_jsc.patch']),
+ ])),
+ ('jupyterlab-gitlab', '2.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '31d3fbd9b139aca7704dd13967ac22c81e372b50c4db730f342ab7800db7a5c6')]),
+ # do not use pypi for download -> we need to patch drive.json
+ ('source_urls', ['https://gitlab.com/beenje/jupyterlab-gitlab/-/archive/%(version)s']),
+ ('source_tmpl', 'jupyterlab-gitlab-%(version)s.tar.gz'),
+ ('patches', ['jupyterlab-gitlab-%(version)s_jsc.patch']),
+ ])),
+ ('jupyterlab-quickopen', '0.5.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('90cba3a7e6ff8d2b3eaf2594079c25f82e2c158d2ec63ebd951e4042a7445f8e')]),
+ ])),
+ ('zstandard', '0.12.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a110fb3ad1db344fbb563942d314ec5f0f3bdfd6753ec6331dded03ad6c2affb')]),
+ ])),
+
+ # https://blog.kitware.com/itk-is-on-pypi-pip-install-itk-is-here/
+ ('itk_core', '5.1.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_core-5.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', '1f0254f0f134b709e6df3601dc38ccc45c2d5d5576fc10e1a0313d1fe8aefa84')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('itk_filtering', '5.1.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_filtering-5.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', 'f4a1256c8c684329780b9f4326fb571023af1d96fbda7cb7b513b4a395a9cd42')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('itk_segmentation', '5.1.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_segmentation-5.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', 'f81ba4881f7802eb5b911c4e1eac4706220647196ebda68477318630542db226')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('itk_numerics', '5.1.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_numerics-5.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', '6ac84a6386cd51692ed9605b6daefcc6230ec976f93161c9c5d89cfdfe042eba')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('itk_registration', '5.1.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_registration-5.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', 'd25b578ffb859f07cbad6987d1adb507e357d91f82863faeae337d8645b9d29d')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('itk_io', '5.1.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_io-5.1.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', '6ecc528ce4ae42b6d14c972d51055856f130a13474463ba4bf187ed2afdb04b1')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('itk_meshtopolydata', '0.6.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'itk_meshtopolydata-0.6.2-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', '486e418808c27ccc76619737219fa57fcd1de2da5fcd0325ee8c4395965deb39')]),
+ ('unpack_sources', False),
+ ('modulename', 'itk'),
+ ])),
+ ('pyct', '0.4.6', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'df7b2d29f874cabdbc22e4f8cba2ceb895c48aa33da4e0fe679e89873e0a4c6e')]),
+ ])),
+ ('colorcet', '2.0.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '514813790a74b578c3eaff76b2102274c2ba8b0239c9504586df685223007dee')]),
+ ])),
+ ('itkwidgets', '0.32.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '11ee93007cf354405e01bf9a28fb1eb2fb0a5d139e1cdded1a07b47f7ee76972')]),
+ ])),
+ ('ujson', '3.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'abb1996ba1c1d2faf5b1e38efa97da7f64e5373a31f705b96fe0587f5f778db4')]),
+ ])),
+ # ('jupyterlab_iframe', '0.2.2', dict(list(local_common_opts.items()) + [ # open HTML URLs in Jupyter-Tabs
+ # ('checksums', [('sha256', '7c26cddc5f29f0b5ac6ba4707ce811f9787282549d22098b691bcdcc6692238c')]),
+ # ('use_pip', False),
+ # ])),
+ ('python-dotenv', '0.10.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f157d71d5fec9d4bd5f51c82746b6344dffa680ee85217c123f4a0c8117c4544')]),
+ ('modulename', 'dotenv'),
+ ])),
+ # ('ipyauth', '0.2.5', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '189db0e9fd48cf52f333ef8ac1a71b9e3a9eec6561f5085e3d7239ca2588ba87')]),
+ # ])),
+ ('jupyterlab_latex', '2.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '722558144e6ce71abe4fba0fb01c13c37271fa2497881bfebe9b6422d1fc795b')]),
+ ])),
+ # ('jupyterlab_slurm', '1.0.5', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', 'f7c6a54efe529cc47194cb4a7cbf1225fc0b0668d4dfe118405b68bde805c061')]),
+ # ])),
+ ('jupyterlmod', '2.0.2', dict(list(local_common_opts.items()) + [
+ ('source_urls', ['https://github.com/cmd-ntrf/jupyter-lmod/archive/']),
+ ('source_tmpl', '%(version)s.tar.gz'),
+ ('checksums', [('sha256', 'f547432afb30cb87c8dabf78fd4cc4c35ff4b6d2aafbae19c249b7d596015c6a')]),
+ ('patches', [
+ 'jupyterlmod-urlfile.patch',
+ 'jupyterlmod-packagejson.patch',
+ ]),
+ ])),
+ ('nbresuse', '0.3.6', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '5ba19dd0b08ff19470aeb34cda2f07276a3fb1cd750bc53f3a3e06322664e98e')]),
+ ])),
+ ('colorama', '0.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d')]),
+ ])),
+ ('nbdime', '2.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '4e3efdcfda31c3074cb565cd8e76e2e5421b1c4560c3a00c56f8679dd15590e5')]),
+ ])),
+ ('smmap2', '2.0.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '29a9ffa0497e7f2be94ca0ed1ca1aa3cd4cf25a1f6b4f5f87f74b46ed91d609a')]),
+ ('modulename', 'smmap'),
+ ])),
+ ('gitdb2', '2.0.6', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1b6df1433567a51a4a9c1a5a0de977aa351a405cc56d7d35f3388bad1f630350')]),
+ ('modulename', 'gitdb'),
+ ])),
+ ('GitPython', '3.0.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3237caca1139d0a7aa072f6735f5fd2520de52195e0fa1d8b83a9b212a2498b2')]),
+ ('modulename', 'git'),
+ ])),
+ ('jupyterlab_git', '0.23.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3c709c33df0b838e50f76fa2e7e0302bd3c32ec24e161ee0e8f436a3844e8b16')]),
+ ])),
+ ('sidecar', '0.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3e79de269ddd2c0eff1cb26025cb9f434cf9914b777cf03eeab8347f6de7160e')]),
+ ])),
+ ('pycodestyle', '2.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c58a7d2815e0e8d7972bf1803331fb0152f867bd89adf8a01dfd55085434192e')]),
+ ])),
+ ('autopep8', '1.4.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '4d8eec30cc81bc5617dbf1218201d770dc35629363547f17577c61683ccfb3ee')]),
+ ])),
+ ('yapf', '0.28.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '6f94b6a176a7c114cfa6bad86d40f259bbe0f10cf2fa7f2f4b3596fc5802a41b')]),
+ ])),
+ ('isort', '4.3.21', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '54da7e92468955c4fceacd0c86bd0ec997b0e1ee80d97f67c35a78b719dccab1')]),
+ ])),
+ ('toml', '0.10.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c')]),
+ ])),
+ ('pathspec', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e285ccc8b0785beadd4c18e5708b12bb8fcf529a1e61215b3feff1d1e559ea5c')]),
+ ])),
+ ('typed_ast', '1.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '66480f95b8167c9c5c5c87f32cf437d585937970f3fc24386f313a4c97b44e34')]),
+ ])),
+ ('regex', '2019.11.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '720e34a539a76a1fedcebe4397290604cc2bdf6f81eca44adb9fb2ea071c0c69')]),
+ ])),
+ ('black', '19.3b0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '68950ffd4d9169716bcb8719a56c07a2f4485354fec061cdd5910aa07369731c')]),
+ ])),
+ ('jupyterlab_code_formatter', '1.3.8', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '7c415caff528e55027e82c96b60dcab0537aa5cda168997f03a4964c51e2b7b5')]),
+ ])),
+ ###############
+ # extras
+ ('mccabe', '0.6.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f')]),
+ ])),
+ ('pyflakes', '2.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '35b2d75ee967ea93b55750aa9edbbf72813e06a66ba54438df2cfac9e3c27fc8')]),
+ ])),
+ ('flake8', '3.8.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f04b9fcbac03b0a3e58c0ab3a0ecc462e023a9faf046d57794184028123aa208')]),
+ ])),
+ ('pydocstyle', '5.0.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f4f5d210610c2d153fae39093d44224c17429e2ad7da12a8b419aba5c2f614b5')]),
+ ])),
+ ('rope', '0.16.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd2830142c2e046f5fc26a022fe680675b6f48f81c7fc1f03a950706e746e9dfe')]),
+ ])),
+ # base for python language server
+ ('parso', '0.7.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c')]),
+ ])),
+ ('jedi', '0.17.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20')]),
+ ])),
+ ('python-jsonrpc-server', '0.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '62c543e541f101ec5b57dc654efc212d2c2e3ea47ff6f54b2e7dcb36ecf20595')]),
+ ('modulename', 'pyls_jsonrpc'),
+ ])),
+ ('pluggy', '0.13.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0')]),
+ ])),
+ # test
+ ('versioneer', '0.18', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'ead1f78168150011189521b479d3a0dd2f55c94f5b07747b484fd693c3fbf335')]),
+ ])),
+ ('lazy-object-proxy', '1.4.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0')]),
+ ])),
+ ('wrapt', '1.11.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1')]),
+ ])),
+ ('astroid', '2.3.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '71ea07f44df9568a75d0f354c49143a4575d90645e9fead6dfb52c26a85ed13a')]),
+ ])),
+ ('wrapt', '1.11.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1')]),
+ ])),
+ ('lazy-object-proxy', '1.4.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0')]),
+ ])),
+ ('typed_ast', '1.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '66480f95b8167c9c5c5c87f32cf437d585937970f3fc24386f313a4c97b44e34')]),
+ ])),
+ ('six', '1.12.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73')]),
+ ])),
+ ('pylint', '2.4.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '3db5468ad013380e987410a8d6956226963aed94ecb5f9d3a28acca6d9ac36cd')]),
+ ])),
+ ('pytest', '5.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970')]),
+ ])),
+ ('mock', '4.0.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'dd33eb70232b6118298d516bbcecd26704689c386594f0f3c4f13867b2c56f72')]),
+ ])),
+ ('pytest-cov', '2.8.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'cc6742d8bac45070217169f5f72ceee1e0e55b0221f54bcf24845972d3a47f2b')]),
+ ])),
+ ('pytest-xprocess', '0.13.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '779aeca517cd9c996d1544bdc510cb3cff40c48136d94bbce6148e27f30a93ff')]),
+ ])),
+ ('coverage', '5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f90bfc4ad18450c80b024036eaf91e4a246ae287701aaa88eaebebf150868052')]),
+ ])),
+ # python language server
+ ('python-language-server', '0.36.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9984c84a67ee2c5102c8e703215f407fcfa5e62b0ae86c9572d0ada8c4b417b0')]),
+ ('modulename', 'pyls'),
+ ])),
+ ('jupyter-lsp', '0.9.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '73b5cb47fbe672bee6c02ddc4f2fbe728dc3bff589b5741835ebb80a862163af')]),
+ ])),
+
+ ####################
+ # Jupyter Hub
+ # ('SQLAlchemy', '1.3.10', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '0f0768b5db594517e1f5e1572c73d14cf295140756431270d89496dc13d5e46c')]),
+ # ])), # part of Python module in version 1.3.1
+ # ('python-oauth2', '1.1.1', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', 'd7a8544927ac18215ba5317edd8f640a5f1f0593921bcf3ce862178312c8c9a4')]),
+ # ('modulename', 'oauth2'),
+ # ])), # part of Python module
+ ('pamela', '1.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c')]),
+ ])),
+ # ('alembic', '1.2.1', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '9f907d7e8b286a1cfb22db9084f9ce4fde7ad7956bb496dc7c952e10ac90e36a')]),
+ # ])), # part of Python module in version 1.0.8
+ ('certipy', '0.1.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859')]),
+ ])),
+ ('oauthlib', '3.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889')]),
+ ])),
+ ('ruamel.yaml', '0.16.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '412a6f5cfdc0525dee6a27c08f5415c7fd832a7afcb7a0ed7319628aed23d408')]),
+ ])),
+ ('ruamel.yaml.clib', '0.1.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'cee86ecc893a6a8ecaa7c6a9c2d06f75f614176210d78a5f155f8e78d6989509')]),
+ ('modulename', 'ruamel.yaml'),
+ ])),
+ ('python-json-logger', '0.1.11', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b7a31162f2a01965a5efb94453ce69230ed208468b0bbc7fdfc56e6d8df2e281')]),
+ ('modulename', 'pythonjsonlogger'),
+ ])),
+ ('Jinja2', '2.11.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '93187ffbc7808079673ef52771baa950426fd664d3aad1d0fa3e95644360e250')]),
+ ])),
+ ('jupyter_telemetry', '0.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314')]),
+ ])),
+ ('jupyterhub', '1.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '852a70225a03abd631b36a207f3ffdf69326a0db4cef539825fde39ec1b713d7')]),
+ ('patches', ['jupyterhub-1.1.0_logoutcookie-2.0.patch']),
+ # copy 401.html -> <jupyter-install-dir>/share/jupyter/lab/static/
+ ])),
+ ('appmode', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'deac99adaa95e28fa8a56c072be653603cffa49dc06469701ac9c014b690e7c4')]),
+ ])),
+ ('HeapDict', '1.0.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6')]),
+ ])),
+ ('zict', '1.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e34dd25ea97def518fb4c77f2c27078f3a7d6c965b0a3ac8fe5bdb0a8011a310')]),
+ ])),
+ ('tblib', '1.5.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1735ff8fd6217446384b5afabead3b142cf1a52d242cfe6cab4240029d6d131a')]),
+ ])),
+ ('sortedcontainers', '2.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a')]),
+ ])),
+ ('msgpack', '0.6.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'ea3c2f859346fcd55fc46e96885301d9c2f7a36d453f5d8f2967840efa1e1830')]),
+ ])),
+ ('dask', '2.30.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a1669022e25de99b227c3d83da4801f032415962dac431099bf0534648e41a54')]),
+ ])),
+ ('cloudpickle', '1.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0b6258a20a143603d53b037a20983016d4e978f554ec4f36b3d0895b947099ae')]),
+ ])),
+ ('distributed', '2.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '30b0ca195ace1e39bdd278bf1ad257f7674b3e2b8e7a2a37ce7e2ade4aecccf3')]),
+ ])),
+ ('dask-jobqueue', '0.7.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd32ddf3e3c7db29ace102037fa5f61c8db2d945176454dc316a6ffdb8bbfe88b')]),
+ ])),
+ ('dask_labextension', '3.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c613f5c76b8fce4fae167eeab3377e0706e5045a27da1200b3b173025a94d94b')]),
+ ])),
+ ('Automat', '0.8.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '269a09dfb063a3b078983f4976d83f0a0d3e6e7aaf8e27d8df1095e09dc4a484')]),
+ ])),
+ ('PyHamcrest', '1.9.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '8ffaa0a53da57e89de14ced7185ac746227a8894dbd5a3c718bf05ddbd1d56cd')]),
+ ('modulename', 'hamcrest'),
+ ])),
+ ('pyasn1', '0.4.8', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba')]),
+ ])),
+ ('pyasn1-modules', '0.2.8', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e')]),
+ ])),
+ ('service_identity', '18.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0858a54aabc5b459d1aafa8a518ed2081a285087f349fe3e55197989232e2e2d')]),
+ ])),
+ ('Twisted', '19.7.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd5db93026568f60cacdc0615fcd21d46f694a6bfad0ef3ff53cde2b4bb85a39d')]),
+ ('source_tmpl', '%(name)s-%(version)s.tar.bz2'),
+ ])),
+ ('autobahn', '19.10.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '734385b00547448b3f30a752cbfd2900d15924d77dc4a1699b8bce1ea8899f39')]),
+ ])),
+ ('constantly', '15.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '586372eb92059873e29eba4f9dec8381541b4d3834660707faf8ba59146dfc35')]),
+ ])),
+ ('hyperlink', '19.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '4288e34705da077fada1111a24a0aa08bb1e76699c9ce49876af722441845654')]),
+ ])),
+ ('incremental', '17.5.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '7b751696aaf36eebfab537e458929e194460051ccad279c72b755a167eebd4b3')]),
+ ])),
+ ('txaio', '18.8.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '67e360ac73b12c52058219bb5f8b3ed4105d2636707a36a7cdafb56fe06db7fe')]),
+ ])),
+ ('zope.interface', '4.7.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'fd1101bd3fcb4f4cf3485bb20d6cb0b56909b94d3bd2a53a6cb9d381c3da3365')]),
+ ])),
+ # ('backcall', '0.1.0', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4')]),
+ # ])), # part of Python module (sanity check fails if package used from Python dependency)
+ ('wslink', '0.1.13', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '6983114e978717a2681815b1ef4b8a0fa2c80c89c6ed09b9554a36c5869cf935')]),
+ ])),
+ ('jupyterlab_pygments', '0.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '31deda75bd11b014190764c79f6199aa04ef2d4cf35c1c94270fc2e19c23a5c5')]),
+ ])),
+ # ('jupyterlab-nvdashboard', '0.2.1', dict(list(local_common_opts.items()) + [
+ # # throughs too many errors if nvtools or driver are not installed
+ # ('checksums', [('sha256', '2f69a1c3b35250cda252fe6bc684c0e99c3eac87e012843d7fc52f204ab3d0c6')]),
+ # ])),
+ ('ipyvue', '1.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '5b59cf92a1eb7fbef4f2d02be49ac562a721a6cf34f991ac963222cf4c8885a1')]),
+ ])),
+ ('ipyvuetify', '1.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '593f5d6761e304cbb78bca967030485d8835e8d310ef7d83ac1b0e6a13e4911c')]),
+ ])),
+ ('voila', '0.2.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '332725b88fb026ad421db90fdad53d7e8de2ffd03a8584a55d9940465932ede8')]),
+ ])),
+ ('voila-material', '0.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0827a27f0f23ca87bd8f565c4c227c754516d2a120ffce0f7ab1ee12fdec959f')]),
+ ('modulename', 'voila'), # fake module name to trick the sanity check
+ ])),
+ ('voila-gridstack', '0.0.11', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '851dafe1912199ba36ad5544fb0f624bcb1421d2d31c0f1d03fcdcbf6d626dee')]),
+ ('modulename', 'voila'),
+ ])),
+ ('voila-vuetify', '0.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '522f4ec91eb3912a21215b6b04ad58070d1675809d7d4289ca8e42b577fde100')]),
+ ('modulename', 'voila'),
+ ])),
+ ('pydicom', '1.4.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9488495a9f3e202d1219f7cb165aee0de31efd512d938c0226d34147ce860391')]),
+ ])),
+ ('dicom_upload', '0.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'd03f309bbae2094d3db75ffaa9753cca5982d2096ec55720a1f54343cc4a6877')]),
+ ])),
+ ('jsfileupload', '0.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '245cd74a3c2ed4356df9a33d0072d8ab295b60b6fdfd69c6795396d455fc8a77')]),
+ ])),
+ ('pvlink', '0.3.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a2d5f2c204e0e779a5b865742019b4646b8592d76de87cac724dc84f64eaf80f')]),
+ ])),
+
+ ('textwrap3', '0.9.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'textwrap3-0.9.2.zip'),
+ ('checksums', [('sha256', '5008eeebdb236f6303dcd68f18b856d355f6197511d952ba74bc75e40e0c3414')]),
+ ('use_pip', True),
+ ])),
+ ('ansiwrap', '0.8.4', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'ansiwrap-0.8.4.zip'),
+ ('checksums', [('sha256', 'ca0c740734cde59bf919f8ff2c386f74f9a369818cdc60efe94893d01ea8d9b7')]),
+ ])),
+ ('backports.weakref', '1.0.post1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2')]),
+ ])),
+ ('backports.tempfile', '1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1c648c452e8770d759bdc5a5e2431209be70d25484e1be24876cf2168722c762')]),
+ ])),
+ ('tqdm', '4.41.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '166a82cdea964ae45528e0cc89436255ff2be73dc848bdf239f13c501cae5dc7')]),
+ ])),
+ ('tenacity', '6.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '72f397c2bb1887e048726603f3f629ea16f88cb3e61e4ed3c57e98582b8e3571')]),
+ ])),
+ ('papermill', '2.2.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1c452b1c5a9ab52b94c99d8b7705ae7173f6aa88a3d28a5d30cffba48a46f5b6')]),
+ ])),
+ ('pyviz_comms', '0.7.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '712df4cca33dda351de754742b24361eee8e4b7c1cfb0e24f50dcb802fa25624')]),
+ ])),
+ ('Markdown', '3.2.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17')]),
+ ('modulename', 'markdown'),
+ ])),
+ ('panel', '0.9.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '53340615f30f67f3182793695ebe52bf25e7bbb0751aba6f29763244350d0f42')]),
+ ])),
+ ('holoviews', '1.13.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'cf2dd426cdc08bf2ca669268ca0432634574429e5b143314ee06ad88c5382802')]),
+ ])),
+
+ # PythonPackages for Tutorials
+ ('xarray', '0.16.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4')]),
+ ])),
+ ('patsy', '0.5.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991')]),
+ ])),
+ ('statsmodels', '0.10.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9cd2194c6642a8754e85f9a6e6912cdf996bebf6ff715d3cc67f65dadfd37cc9')]),
+ ])),
+ ('cftime', '1.0.4.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1ac64f8f9066ea756ea27d67cedaf064e7c866275218fa7c84684066a5890f70')]),
+ ])),
+ ('vega_datasets', '0.8.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'db8883dab72b6f414e1fafdbf1e8db7543bba6ed77912a4e0c197d74fcfa1c20')]),
+ ])),
+ ('Theano', '1.0.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913')]),
+ ('modulename', 'theano'),
+ ])),
+ ('altair', '3.3.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '9f7c521239ac5a207c3cffc29c5bdde0854fff0dec0b5f91f086ba8e5f1de8a9')]),
+ ])),
+ ('cssselect', '1.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'f95f8dedd925fd8f54edb3d2dfb44c190d9d18512377d3c1e2388d16126879bc')]),
+ ])),
+ ('smopy', '0.0.7', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '578b5bc2502176d210f176ab94e77974f43b32c95cd0768fb817ea2499199592')]),
+ ])),
+ ('joblib', '0.14.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8')]),
+ ])),
+ ('scikit-learn', '0.22', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '314abf60c073c48a1e95feaae9f3ca47a2139bd77cebb5b877c23a45c9e03012')]),
+ ('modulename', 'sklearn'),
+ ])),
+ ('memory_profiler', '0.55.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '5fa47b274c929dd2cbcd9190afb62fec110701251d2ac2d301caaf545c81afc1')]),
+ ])),
+ ('h5py', '2.10.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d')]),
+ ])),
+ ('line_profiler', '3.1.0', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '7218ad6bd81f8649b211974bf108933910f016d66b49651effe7bbf63667d141')]),
+ # ('use_pip', False), # no pip ! uses PEP 517
+ ('source_tmpl', 'line_profiler-3.1.0-cp38-cp38-manylinux1_x86_64.whl'),
+ ('checksums', [('sha256', 'a66e089e6d98ab8a70b5f89c0367c6780abad0f0b1d624dbe5edd8f0083986c7')]),
+ ('unpack_sources', False), # whl package instead of tar.gz because building with skbuild->cmake fails
+ ])),
+ ('llvmlite', '0.35.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc')]),
+ ])),
+ ('numba', '0.52.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933')]),
+ ])),
+ ('arviz', '0.10.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'dc1f08ce02459989dd4f41fa6012e736cf2ba00ee44b29bebe0a451c58a68e42')]),
+ ])),
+ ('pymc3', '3.8', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1bb2915e4a29877c681ead13932b0b7d276f7f496e9c3f09ba96b977c99caf00')]),
+ ])),
+ ('numexpr', '2.7.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1')]),
+ ])),
+ ('ipythonblocks', '1.9.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'ba923cb7a003bddee755b5a7ac9e046ffc093a04b0bdede8a0a51ef900aed0ba')]),
+ ])),
+ ('pydub', '0.23.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'c362fa02da1eebd1d08bd47aa9b0102582dff7ca2269dbe9e043d228a0c1ea93')]),
+ ])),
+ ('multipledispatch', '0.6.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea')]),
+ ])),
+ ('partd', '1.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0')]),
+ ])),
+ ('locket', '0.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1fee63c1153db602b50154684f5725564e63a0f6d09366a1cb13dffcec179fb4')]),
+ ])),
+ ('fsspec', '0.6.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'ffd7cd5ac32f36698097c3d78c2c433d4c12f7e4bce3a3a4036fd3491188046d')]),
+ ])),
+ ('datashape', '0.5.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '2356ea690c3cf003c1468a243a9063144235de45b080b3652de4f3d44e57d783')]),
+ ])),
+ ('datashader', '0.11.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b1f80415f72f92ccb660aaea7b2881ddd35d07254f7c44101709d42e819d6be6')]),
+ ])),
+ ('selenium', '3.141.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'deaf32b60ad91a4611b98d8002757f29e6f2c2d5fcaf202e1c9ad06d6772300d')]),
+ ])),
+ ('graphviz', '0.13.2', dict(list(local_common_opts.items()) + [
+ ('source_tmpl', 'graphviz-0.13.2.zip'),
+ ('checksums', [('sha256', '60acbeee346e8c14555821eab57dbf68a169e6c10bce40e83c1bf44f63a62a01')]),
+ ])),
+ ('vincent', '0.4.4', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '5765bcd360140d2304e52728ad1d4382f3f919ea259a13932828680f2d84fcd3')]),
+ ])),
+ ('tailer', '0.4.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '78d60f23a1b8a2d32f400b3c8c06b01142ac7841b75d8a1efcb33515877ba531')]),
+ ])),
+ # Dash
+ ('Flask', '1.1.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52')]),
+ ])),
+ ('Flask-Compress', '1.4.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '468693f4ddd11ac6a41bca4eb5f94b071b763256d54136f77957cfee635badb3')]),
+ ])),
+ ('Werkzeug', '1.0.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c')]),
+ ])),
+ ('hiredis', '1.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '996021ef33e0f50b97ff2d6b5f422a0fe5577de21a8873b58a779a5ddd1c3132')]),
+ ])),
+ ('redis', '3.5.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0e7e0cfca8660dea8b7d5cd8c4f6c5e29e11f31158c0b0ae91a397f00e5a05a2')]),
+ ])),
+ ('Flask-Caching', '1.9.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a0356ad868b1d8ec2d0e675a6fe891c41303128f8904d5d79e180d8b3f952aff')]),
+ ])),
+ ('dash', '1.16.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'fdfe2a16c4041c7769e06e4e0eaaeb65cfd8351797ed4b37efe001384637b6c7')]),
+ ])),
+ ('dash_renderer', '1.8.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '736f8e0dcce244699457b54a2ee262a04baf389db1a8f54e98c949bb3e7e487f')]),
+ ])),
+ ('dash_core_components', '1.12.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '803b54d01ca48b90f3fc1652f7be9f818ed2882da8975a51b99fc2d77dd2727e')]),
+ ])),
+ ('dash_html_components', '1.1.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '2c662e640528c890aaa0fa23d48e51c4d13ce69a97841d856ddcaaf2c6a47be3')]),
+ ])),
+ ('dash_table', '4.10.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '1aa02180faef13434364286b60404d26164d1ce2779c765c9c52e6935991a4e9')]),
+ ])),
+ ('dash-bootstrap-components', '0.10.5', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '40500e692f59648dbc024b9e921a1e1410ee0bc97cfa963990e54e42523679b4')]),
+ ])),
+ ('dash_daq', '0.5.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a1d85b6799f7b885652fbc44aebdb58c41254616a8d350b943beeb42ade4256a')]),
+ ])),
+ ('dash_player', '0.0.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '46114910b497f35f1aa496ed8b9ff1457d07c96171227961b671ba4164c537a0')]),
+ ])),
+ ('dash_canvas', '0.1.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '72fcfb37e1c0f68c08f6fa6cf0b5be67ecc66fcfb5253231ffc450957b640b31')]),
+ ])),
+ ('dash_bio', '0.4.8', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'a6f480b060488ab9be26129562a7bcb491ef40ae0ffae46f499fb7d5997de06c')]),
+ ])),
+ ('dash_cytoscape', '0.2.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '0669c79c197e4b150a5db7a278d1c7acebc947f3f5cbad5274835ebb44f712cd')]),
+ ])),
+ ('ansi2html', '1.5.2', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '96ae85ae7b26b7da674d87de2870ba4d1964bca733ae4614587080b6358c3ba9')]),
+ ])),
+ ('jupyter-dash', '0.3.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'e41d68aa85a7dd53480cc33feae04f4cfd7ac2ace8089c1e1630a2342e8bd8aa')]),
+ ])),
+ # more
+ ('fastcore', '1.3.6', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '550c201f6a0f7001994898260588e3df310968165c43ecc4fa3062dd6eee5956')]),
+ ])),
+ ('fastscript', '1.0.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '67d2315a508ffd0499af590fffaa63d276ce6eaff73ffbd60eb3315ba38d08fa')]),
+ ])),
+ # ('nbdev', '1.1.5', dict(list(local_common_opts.items()) + [
+ # # nbdev < 2 needs nbconvert < 6, will change with nbdev >= 2
+ # ('checksums', [('sha256', '0ce349625514e2865bbc023db597d791c45b572a7bbc8a49b320a327b9e7b721')]),
+ # ])),
+ ('PyJWT', '1.7.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96')]),
+ ('modulename', 'jwt'),
+ ])),
+ ('pyunicore', '0.9.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '09cd91562feb7677c8bd9cbbe02e1b0d27d1b5817e12ef5bf4701619cac77d9b')]),
+ ])),
+
+ # misc
+ # ('rpy2', '3.2.4', dict(list(local_common_opts.items()) + [
+ # ('checksums', [('sha256', '3daf1a4b28c4e354ef989093f03b066908bf6e5082a6f4af72cc3fd928a28dc6')]),
+ # ])),
+]
+
+local_jupyter_config_path = 'etc/jupyter'
+local_jupyter_path = 'share/jupyter'
+local_jupyterlab_dir = 'share/jupyter/lab'
+
+modextrapaths = {
+ 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+ # search path to find installable data files, such as kernelspecs and notebook extensions
+ 'JUPYTER_PATH': [local_jupyter_path],
+ 'JUPYTERLAB_DIR': [local_jupyterlab_dir],
+ # do NOT set JUPYTER_CONFIG_DIR: if not set, if will be ${HOME}/.jupyter, which is just right
+ 'JUPYTER_CONFIG_PATH': [local_jupyter_config_path] # config dir at install time.
+ # ATTENTION: not config dir at runtime, because this is fixed to {sys.prefix}/etc/jupyter/
+}
+
+modextravars = {
+ 'JUPYTER': '%(installdir)s/bin/jupyter',
+ 'MKL_THREADING_LAYER': 'GNU', # https://github.com/Theano/Theano/issues/6568
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is fist entry in JUPYTHER_PATH and JUPYTER_DATA_DIR
+# https://jupyter.readthedocs.io/en/latest/projects/jupyter-directories.html#envvar-JUPYTER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+prepend_path("JUPYTER_DATA_DIR", pathJoin(os.getenv("HOME"),".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ # ensure we install in the correct directory !!!
+ 'python3 -m venv %(installdir)s --system-site-packages',
+
+ 'echo "#!/bin/bash" > %(builddir)s/env.sh',
+ 'echo "source %(installdir)s/bin/activate" >> %(builddir)s/env.sh',
+ (
+ 'echo "export PYTHONPATH='
+ '%(installdir)s/lib/python3.8/site-packages:${EBROOTPYTHON}/lib/python3.8/site-packages:${PYTHONPATH}"'
+ ' >> %(builddir)s/env.sh'
+ ),
+ # Jupyter Paths - http://jupyter.readthedocs.io/en/latest/projects/jupyter-directories.html
+ 'echo "export JUPYTER=%(installdir)s/bin/jupyter" >> %(builddir)s/env.sh',
+ 'echo "export JUPYTER_PATH=%%(installdir)s/%s" >> %%(builddir)s/env.sh' % local_jupyter_path,
+ 'echo "export JUPYTERLAB_DIR=%%(installdir)s/%s" >> %%(builddir)s/env.sh' % local_jupyterlab_dir,
+ # Config dir at install time. ATTENTION: not config dir at runtime. This is picked up by JUPYTER_CONFIG_PATH
+ 'echo "export JUPYTER_CONFIG_DIR=%%(installdir)s/%s" >> %%(builddir)s/env.sh' % local_jupyter_config_path,
+ # jupyter will use $JUPYTER_CONFIG_DIR with "--user"
+ 'echo "export JUPYTER_DATA_DIR=%%(installdir)s/%s" >> %%(builddir)s/env.sh' % local_jupyter_path,
+ 'echo "export PATH=%(installdir)s/bin:${PATH}" >> %(builddir)s/env.sh',
+
+ # NodeJS packages
+ 'source %(builddir)s/env.sh && npm install -g phantomjs-prebuilt@2.1.16', # req. export_png/export_svg of bokeh
+
+ # Jupyter Notebook Extensions
+ 'source %(builddir)s/env.sh && jupyter contrib nbextension install --user',
+ 'source %(builddir)s/env.sh && jupyter nbextensions_configurator enable --user',
+ 'source %(builddir)s/env.sh && jupyter nbextension enable codefolding/main --user',
+
+ ('source %(builddir)s/env.sh && '
+ ' jupyter nbextension install widgetsnbextension --py --nbextensions=${JUPYTER_PATH}/nbextensions'),
+ 'source %(builddir)s/env.sh && jupyter nbextension enable widgetsnbextension --py --user',
+
+ 'source %(builddir)s/env.sh && jupyter nbextension enable ipyvuetify --py --user',
+
+ 'source %(builddir)s/env.sh && jupyter nbextension install rise --py --nbextensions=${JUPYTER_PATH}/nbextensions',
+ 'source %(builddir)s/env.sh && jupyter nbextension enable rise --py --user',
+
+ 'source %(builddir)s/env.sh && jupyter nbextension enable appmode --py --user',
+ 'source %(builddir)s/env.sh && jupyter serverextension enable appmode --py',
+
+ # Jupyter Notebook Extensions
+ 'source %(builddir)s/env.sh && jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @jupyter-widgets/jupyterlab-sidecar@0.5.0 --no-build',
+
+ # 'source %(builddir)s/env.sh && jupyter labextension install @jupyterlab/server-proxy@2.1.1 --no-build',
+ ('source %(builddir)s/env.sh && '
+ ' cd %(builddir)s/jupyterserverproxy/jupyter-server-proxy-1.5.2/jupyterlab-server-proxy/ && '
+ ' npm install && ' # install npm package dependencies incurrent directory
+ ' npm run build && ' # optional build step if using TypeScript, babel, etc.
+ ' jupyter labextension install --no-build'), # install the current directory as an extension'
+ # 'source %(builddir)s/env.sh && jupyter labextension install @jupyterlab/github@2.0.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @jupyterlab/latex@2.0.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @jupyterlab/git@0.23.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @jupyterlab/toc@4.0.0 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-datawidgets@6.3.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-plotly@4.8.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-gitlab@2.0.0 --no-build',
+ # 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab_iframe@0.2.2 --no-build',
+
+ # this might interfer with Xpra-icon: https://github.com/cmd-ntrf/jupyter-lmod/issues/30
+ ('source %(builddir)s/env.sh && '
+ ' cd %(builddir)s/jupyterlmod/jupyter-lmod-2.0.2/jupyterlab/ && '
+ ' npm install && ' # install npm package dependencies incurrent directory
+ ' npm run build && ' # optional build step if using TypeScript, babel, etc.
+ ' jupyter labextension install --no-build'), # install the current directory as an extension
+ # 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-nvdashboard@0.3.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-dash@0.3.0 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-topbar-extension@0.5.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-system-monitor@0.6.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-theme-toggle@0.5.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-control@1.1.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-favorites@2.0.0 --no-build',
+ # store default in ../share/jupyter/lab/schemas/jupyterlab-favorites/favorites.json
+ # 'source %(builddir)s/env.sh && jupyter labextension install jupyterlab-tour@2.1.1 --no-build',
+ # tour-state on/off is saved in workspace-file in ~/.jupyter/lab/workspaces/
+
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyter-matplotlib@0.7.4 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyter-leaflet@0.13.2 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyter-threejs@2.2.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jupyter-vuetify@1.5.1 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install nbdime-jupyterlab@2.0.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install dask-labextension@3.0.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install ipyvolume@0.6.0-alpha.5 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install plotlywidget@4.12.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install bqplot@0.5.17 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install dicom-upload@0.2.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install jsfileupload@0.2.0 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install @pyviz/jupyterlab_pyviz@1.0.4 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @bokeh/jupyter_bokeh@2.0.2 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @jupyter-voila/jupyterlab-preview@1.1.0 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install @parente/jupyterlab-quickopen@0.5.0 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install @ryantam626/jupyterlab_code_formatter@1.3.8 --no-build',
+ ('source %(builddir)s/env.sh && '
+ ' jupyter labextension install @krassowski/jupyterlab_go_to_definition@1.0.0 --no-build'),
+ 'source %(builddir)s/env.sh && jupyter labextension install @krassowski/jupyterlab-lsp@2.1.2 --no-build',
+
+ 'source %(builddir)s/env.sh && jupyter labextension install pvlink@0.3.1 --no-build',
+ 'source %(builddir)s/env.sh && jupyter labextension install itkwidgets@0.32.0 --no-build',
+
+ # build JupyterLab app directory for all previous installed extensions in one go
+ 'source %(builddir)s/env.sh && jupyter lab build --dev-build=False', # --minimize=False
+
+ # jupyterlab server extensions
+ 'source %(builddir)s/env.sh && jupyter serverextension enable jupyter_server_proxy --py',
+ 'source %(builddir)s/env.sh && jupyter serverextension enable jupyterlab_code_formatter --py',
+ # 'source %(builddir)s/env.sh && jupyter serverextension enable jupyterlab_sql --py',
+ # 'source %(builddir)s/env.sh && jupyter serverextension enable jupyterlab_iframe --py',
+ 'source %(builddir)s/env.sh && jupyter serverextension enable jupyterlab_git --py',
+ 'source %(builddir)s/env.sh && jupyter serverextension enable jupyter_lsp --py',
+ 'source %(builddir)s/env.sh && jupyter serverextension enable dask_labextension --py',
+
+ # configure jupyterlab extensions
+
+ # Send2Trash
+ # disable
+ (
+ '{ cat >> %(installdir)s/etc/jupyter/jupyter_notebook_config.py; } << \'EOF\'\n'
+ 'c.FileContentsManager.delete_to_trash = False\n'
+ 'EOF'
+ ),
+
+ # GitLab-extension
+ # for security reasons access-token must be set in the server extension:
+ (
+ '{ cat >> %(installdir)s/etc/jupyter/jupyter_notebook_config.py; } << \'EOF\'\n'
+ '# no username+password needed, if repo is public or we have the token for a specific URL\n'
+ '# c.GitLabConfig.access_token = "<API-TOKEN>" # give api-access of user "jupyter.jsc@fz-juelich.de"\n'
+ 'c.GitLabConfig.allow_client_side_access_token = False\n'
+ 'c.GitLabConfig.url = "https://gitlab.version.fz-juelich.de"\n'
+ 'c.GitLabConfig.validate_cert = False\n'
+ 'EOF'
+ ),
+
+ # GitHub-extension
+ # for security reasons access-token must be set in the server extension:
+ (
+ '{ cat >> %(installdir)s/etc/jupyter/jupyter_notebook_config.py; } << \'EOF\'\n'
+ '# no username+password needed, if repo is public or we have the token for a specific URL\n'
+ '# c.GitHubConfig.access_token = "<API-TOKEN>"\n'
+ 'c.GitHubConfig.allow_client_side_access_token = False\n'
+ 'c.GitHubConfig.url = "https://github.com"\n'
+ 'c.GitHubConfig.validate_cert = False\n'
+ 'EOF'
+ ),
+
+ # iframe-extension
+ (
+ '{ cat >> %(installdir)s/etc/jupyter/jupyter_notebook_config.py; } << \'EOF\'\n'
+ '# c.JupyterLabIFrame.iframes = [\'list\', \'of\', \'sites\']\n'
+ 'c.JupyterLabIFrame.welcome = "http://www.fz-juelich.de/jsc"\n'
+ 'EOF'
+ ),
+
+ # define .ipynb_checkpoints permissions
+ (
+ '{ cat >> %(installdir)s/etc/jupyter/jupyter_notebook_config.py; } << \'EOF\'\n'
+ 'c.FileCheckpoints.checkpoint_permissions = 0o664\n'
+ 'c.FileCheckpoints.restore_permissions = 0o644\n'
+ 'c.FileCheckpoints.checkpoint_dir_umask = 0o002\n'
+ 'EOF'
+ ),
+
+ # modify the installation files, which would be overwritten if done before (must be last commands to run)
+ (
+ 'cp %(builddir)s/jupyterlabgitlab/jupyterlab-gitlab-2.0.0/schema/drive.json'
+ ' %(installdir)s/share/jupyter/lab/schemas/jupyterlab-gitlab/drive.json'
+ ),
+
+ # Add the overrides file
+ (
+ '{ cat > %(builddir)s/file_jupyter-overrides_jsc.patch; } << \'EOF\'\n'
+ 'diff -Naur share.orig/jupyter/lab/settings/overrides.json share/jupyter/lab/settings/overrides.json\n'
+ '--- share.orig/jupyter/lab/settings/overrides.json 1970-01-01 01:00:00.000000000 +0100\n'
+ '+++ share/jupyter/lab/settings/overrides.json 2019-11-26 13:40:46.560731000 +0100\n'
+ '@@ -0,0 +1,8 @@\n'
+ '+{\n'
+ '+ "jupyterlab-gitlab:drive": {\n'
+ '+ "baseUrl": "https://gitlab.version.fz-juelich.de"\n'
+ '+ },\n'
+ '+ "@parente/jupyterlab-quickopen:plugin": {\n'
+ '+ "relativeSearch": true\n'
+ '+ }\n'
+ '+}\n'
+ 'EOF'
+ ),
+ 'patch -p0 -d %(installdir)s < %(builddir)s/file_jupyter-overrides_jsc.patch',
+
+ # add webpage, which leads back to https://jupyter-jsc.fz-juelich.de
+ 'cp %%(builddir)s/jupyterlab/jupyterlab-%s/401.html %%(installdir)s/share/jupyter/lab/static/' % local_jlab_version,
+
+ # ###################################################
+ # IMPORTANT:
+ # start JupyterLab once (for 60 seconds) to allow some cleanup at first start
+ # ###################################################
+ (
+ 'source %(builddir)s/env.sh && '
+ '{(jupyter lab --no-browser) & } && JLAB_PID=$! && '
+ 'sleep 60 && '
+ 'jupyter notebook list --json | grep $JLAB_PID | '
+ 'awk \'{for(i=1;i<=NF;i++)if($i=="\\"port\\":")print $(i+1)}\' | sed \'s/,*$//g\' | '
+ 'xargs -i jupyter notebook stop {}'
+ ),
+
+ # Ensure Jupyter does not want to build anything on startup
+ # The build_config.json file is used to track the local directories that have been installed
+ # using jupyter labextension install <directory>, as well as core extensions that have been explicitly uninstalled.
+ # 'if [ -e %(installdir)s/share/jupyter/lab/settings/build_config.json ]; then exit 1; fi ',
+ (
+ '{ cat > %(installdir)s/share/jupyter/lab/settings/build_config.json; } << \'EOF\'\n'
+ '{\n'
+ ' "local_extensions": {}\n'
+ '}\n'
+ 'EOF'
+ ),
+
+ # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+ 'rm %(installdir)s/pyvenv.cfg',
+ 'rm %(installdir)s/bin/python',
+ 'rm %(installdir)s/bin/python3',
+ 'rm %(installdir)s/bin/activate',
+ 'rm %(installdir)s/bin/activate*',
+ 'rm %(installdir)s/bin/easy_install*',
+ 'rm %(installdir)s/bin/pip*',
+
+ # Compile Python files to byte-code to speedup execution
+ # ERROR: returns with exit code 1, because some files cannot be compiled for different reasons
+ # ###################################################
+ # Disable possible, because sanity check will #
+ # force the compile of all python packages anyway#
+ # ###################################################
+ # 'source %(builddir)s/env.sh && python -m compileall %(installdir)s',
+
+ # ###################################################
+ # IMPORTANT: must be done manual after eb-install: #
+ # ###################################################
+ # 'chmod -R g-w %(installdir)s ', # software-group must not modify the installation on accident
+ # 'chmod -R ugo-w %(installdir)s/share ', # Noone should add files/configs to the global share after install
+ # 'chmod -R ug-w ...../2020/software/Python/3.8.5-GCCcore-9.3.0/share ', # Python module, too
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True # would result in sanity-errors about yaml,ipython_genutils,IPython,traitlets
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/Jupyter/jupyter_contrib_nbextensions-template_paths.patch b/Golden_Repo/j/Jupyter/jupyter_contrib_nbextensions-template_paths.patch
new file mode 100644
index 0000000000000000000000000000000000000000..c51dfd38ddbf859c8282aa48875224addaf60f38
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyter_contrib_nbextensions-template_paths.patch
@@ -0,0 +1,121 @@
+diff -Naur jupyter_contrib_nbextensions.orig/CHANGELOG.md jupyter_contrib_nbextensions/CHANGELOG.md
+--- jupyter_contrib_nbextensions.orig/CHANGELOG.md 2020-11-22 12:43:10.086824740 +0100
++++ jupyter_contrib_nbextensions/CHANGELOG.md 2020-11-22 12:47:11.839564000 +0100
+@@ -21,6 +21,9 @@
+ This is where each new PR to the project should add a summary of its changes,
+ which makes it much easier to fill in each release's changelog :)
+
++- Replace `template_path` with `template_paths` [#1532](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/pull/1532). Nbconvert 6.0 replaced `template_path` with `template_paths` (see https://nbconvert.readthedocs.io/en/latest/changelog.html#significant-changes). This change in Nbconvert 6.0 causes errors in jupyter_latex_envs and in jupyter_contrib_nbextensions (see [#1529](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1529).
++- Update `install_requires` list in `setup.py` with 'nbconvert >=6.0'
++
+ 0.5.1
+ -----
+
+diff -Naur jupyter_contrib_nbextensions.orig/setup.py jupyter_contrib_nbextensions/setup.py
+--- jupyter_contrib_nbextensions.orig/setup.py 2020-11-22 12:43:10.325780000 +0100
++++ jupyter_contrib_nbextensions/setup.py 2020-11-22 12:47:11.842264000 +0100
+@@ -67,7 +67,7 @@
+ 'jupyter_highlight_selected_word >=0.1.1',
+ 'jupyter_latex_envs >=1.3.8',
+ 'jupyter_nbextensions_configurator >=0.4.0',
+- 'nbconvert >=4.2',
++ 'nbconvert >=6.0',
+ 'notebook >=4.0',
+ 'pyyaml',
+ 'tornado',
+@@ -81,7 +81,7 @@
+ 'pip',
+ 'requests',
+ ],
+- 'test:python_version == "2.7"': [
++ 'test:python_version == "3.8"': [
+ 'mock',
+ ],
+ },
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/config_scripts/highlight_html_cfg.py jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/config_scripts/highlight_html_cfg.py
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/config_scripts/highlight_html_cfg.py 2020-11-22 12:43:10.330209000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/config_scripts/highlight_html_cfg.py 2020-11-22 12:47:11.799365000 +0100
+@@ -7,7 +7,7 @@
+
+ c = get_config() # noqa
+ c.NbConvertApp.export_format = "html"
+-c.Exporter.template_path = [
++c.Exporter.template_paths = [
+ '.',
+ jupyter_contrib_nbextensions.nbconvert_support.templates_directory(),
+ os.path.join(jcnbe_dir, 'nbextensions', 'highlighter')
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/config_scripts/highlight_latex_cfg.py jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/config_scripts/highlight_latex_cfg.py
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/config_scripts/highlight_latex_cfg.py 2020-11-22 12:43:10.331124000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/config_scripts/highlight_latex_cfg.py 2020-11-22 12:47:11.801863000 +0100
+@@ -7,7 +7,7 @@
+
+ c = get_config() # noqa
+ c.NbConvertApp.export_format = "latex"
+-c.Exporter.template_path = [
++c.Exporter.template_paths = [
+ '.',
+ jupyter_contrib_nbextensions.nbconvert_support.templates_directory(),
+ os.path.join(jcnbe_dir, 'nbextensions', 'highlighter')
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/install.py jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/install.py
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/install.py 2020-11-22 12:43:10.332127000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/install.py 2020-11-22 12:47:11.804683000 +0100
+@@ -124,7 +124,7 @@
+ if logger:
+ logger.info('-- Configuring nbconvert template path')
+ # our templates directory
+- _update_config_list(config, 'Exporter.template_path', [
++ _update_config_list(config, 'Exporter.template_paths', [
+ '.',
+ jupyter_contrib_nbextensions.nbconvert_support.templates_directory(),
+ ], install)
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/migrate.py jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/migrate.py
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/migrate.py 2020-11-22 12:43:10.333126000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/migrate.py 2020-11-22 12:47:11.807881000 +0100
+@@ -128,7 +128,7 @@
+ config = Config(cm.get(config_basename))
+ if config and logger:
+ logger.info('- Removing old config values from {}'.format(config_path))
+- _update_config_list(config, 'Exporter.template_path', [
++ _update_config_list(config, 'Exporter.template_paths', [
+ '.', os.path.join(jupyter_data_dir(), 'templates'),
+ ], False)
+ _update_config_list(config, 'Exporter.preprocessors', [
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/nbconvert_support/exporter_inliner.py jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/nbconvert_support/exporter_inliner.py
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/nbconvert_support/exporter_inliner.py 2020-11-22 12:43:10.337543000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/nbconvert_support/exporter_inliner.py 2020-11-22 12:47:11.811491000 +0100
+@@ -39,8 +39,8 @@
+ templates_directory)
+ contrib_templates_dir = templates_directory()
+
+- template_path = c.TemplateExporter.setdefault('template_path', [])
+- if contrib_templates_dir not in template_path:
+- template_path.append(contrib_templates_dir)
++ template_paths = c.TemplateExporter.setdefault('template_paths', [])
++ if contrib_templates_dir not in template_paths:
++ template_paths.append(contrib_templates_dir)
+
+ return c
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/nbconvert_support/toc2.py jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/nbconvert_support/toc2.py
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/nbconvert_support/toc2.py 2020-11-22 12:45:58.854592000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/nbconvert_support/toc2.py 2020-11-22 12:47:11.814530000 +0100
+@@ -52,7 +52,7 @@
+ templates_directory)
+ c.merge(super(TocExporter, self).default_config)
+
+- c.TemplateExporter.template_path = [
++ c.TemplateExporter.template_paths = [
+ '.',
+ templates_directory(),
+ ]
+diff -Naur jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/nbextensions/runtools/readme.md jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/nbextensions/runtools/readme.md
+--- jupyter_contrib_nbextensions.orig/src/jupyter_contrib_nbextensions/nbextensions/runtools/readme.md 2020-11-22 12:43:10.871469000 +0100
++++ jupyter_contrib_nbextensions/src/jupyter_contrib_nbextensions/nbextensions/runtools/readme.md 2020-11-22 12:47:11.816660000 +0100
+@@ -78,7 +78,7 @@
+ ```
+
+ The template needs to be in a path where nbconvert can find it. This can be your local path or specified in
+-`jupyter_nbconvert_config` or `jupyter_notebook_config` as `c.Exporter.template_path`, see [Jupyter docs](https://jupyter-notebook.readthedocs.io/en/latest/config.html).
++`jupyter_nbconvert_config` or `jupyter_notebook_config` as `c.Exporter.template_paths`, see [Jupyter docs](https://jupyter-notebook.readthedocs.io/en/latest/config.html).
+
+ For HTML export a template is provided as `nbextensions.tpl` in the `jupyter_contrib_nbextensions` templates directory. Alternatively you can create your own template:
+ ```
diff --git a/Golden_Repo/j/Jupyter/jupyter_latex_envs-template_paths.patch b/Golden_Repo/j/Jupyter/jupyter_latex_envs-template_paths.patch
new file mode 100644
index 0000000000000000000000000000000000000000..451f439ae2cb32668895a3c8b77a58896b8e8040
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyter_latex_envs-template_paths.patch
@@ -0,0 +1,48 @@
+diff -Naur jupyter_latex_envs.orig/src/latex_envs/latex_envs.py jupyter_latex_envs/src/latex_envs/latex_envs.py
+--- jupyter_latex_envs.orig/src/latex_envs/latex_envs.py 2020-11-22 17:04:43.617982112 +0100
++++ jupyter_latex_envs/src/latex_envs/latex_envs.py 2020-11-22 17:05:35.063217000 +0100
+@@ -301,12 +301,12 @@
+ )
+ c.merge(super(LenvsHTMLExporter, self).default_config)
+ if os.path.isdir(os.path.join(os.path.dirname(__file__), 'templates')):
+- c.TemplateExporter.template_path = ['.',
++ c.TemplateExporter.template_paths = ['.',
+ os.path.join(os.path.dirname(__file__), 'templates')]
+ else:
+ from jupyter_contrib_nbextensions.nbconvert_support import (
+ templates_directory)
+- c.TemplateExporter.template_path = ['.', templates_directory()]
++ c.TemplateExporter.template_paths = ['.', templates_directory()]
+
+ return c
+
+@@ -364,12 +364,12 @@
+ )
+ c.merge(super(LenvsSlidesExporter, self).default_config)
+ if os.path.isdir(os.path.join(os.path.dirname(__file__), 'templates')):
+- c.TemplateExporter.template_path = ['.',
++ c.TemplateExporter.template_paths = ['.',
+ os.path.join(os.path.dirname(__file__), 'templates')]
+ else:
+ from jupyter_contrib_nbextensions.nbconvert_support import (
+ templates_directory)
+- c.TemplateExporter.template_path = ['.', templates_directory()]
++ c.TemplateExporter.template_paths = ['.', templates_directory()]
+
+ return c
+
+@@ -483,12 +483,12 @@
+ c.merge(super(LenvsLatexExporter, self).default_config)
+
+ if os.path.isdir(os.path.join(os.path.dirname(__file__), 'templates')):
+- c.TemplateExporter.template_path = ['.',
++ c.TemplateExporter.template_paths = ['.',
+ os.path.join(os.path.dirname(__file__), 'templates')]
+ else:
+ from jupyter_contrib_nbextensions.nbconvert_support import (
+ templates_directory)
+- c.TemplateExporter.template_path = ['.', templates_directory()]
++ c.TemplateExporter.template_paths = ['.', templates_directory()]
+ return c
+
+ def tocrefrm(self, text):
diff --git a/Golden_Repo/j/Jupyter/jupyterhub-1.1.0_logoutcookie-2.0.patch b/Golden_Repo/j/Jupyter/jupyterhub-1.1.0_logoutcookie-2.0.patch
new file mode 100644
index 0000000000000000000000000000000000000000..dc420a9b2607b58f666925f4cb608a94298e7c15
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyterhub-1.1.0_logoutcookie-2.0.patch
@@ -0,0 +1,123 @@
+diff -Naur jupyterhub-1.1.0.orig/jupyterhub/services/auth.py jupyterhub-1.1.0/jupyterhub/services/auth.py
+--- jupyterhub-1.1.0.orig/jupyterhub/services/auth.py 2019-12-03 10:13:48.000000000 +0100
++++ jupyterhub-1.1.0/jupyterhub/services/auth.py 2020-12-23 08:24:38.868452725 +0100
+@@ -28,6 +28,7 @@
+ from tornado.log import app_log
+ from tornado.web import HTTPError
+ from tornado.web import RequestHandler
++from traitlets import Bool
+ from traitlets import default
+ from traitlets import Dict
+ from traitlets import Instance
+@@ -191,6 +192,29 @@
+ """,
+ ).tag(config=True)
+
++ session_id_required = Bool(
++ os.getenv('JUPYTERHUB_SESSION_ID_REQUIRED', 'false').lower()=="true",
++ help="""
++ Blocks any requests, if there's no jupyterhub-session-id cookie.
++ """,
++ ).tag(config=True)
++
++ session_id_required_user = Bool(
++ os.getenv('JUPYTERHUB_SESSION_ID_REQUIRED_USER', 'false').lower()=="true",
++ help="""
++ Blocks any requests to /user, if there's no jupyterhub-session-id cookie.
++ """,
++ ).tag(config=True)
++
++ last_session_id_validation = 0
++ last_session_id_validation_result = None
++
++ last_session_id_validation_cache_time = Integer(
++ int(os.getenv('JUPYTERHUB_SESSION_ID_CACHE_TIME', "10")),
++ help="""The maximum time (in seconds) to cache the Hub's responses for session_id verification. Default is 10.
++ """,
++ ).tag(config=True)
++
+ hub_prefix = Unicode(
+ '/hub/',
+ help="""The URL prefix for the Hub itself.
+@@ -461,6 +485,18 @@
+ """
+ return handler.get_cookie('jupyterhub-session-id', '')
+
++ def validate_session_id(self, username, session_id):
++ if time.time() - self.last_session_id_validation > self.last_session_id_validation_cache_time:
++ self.last_session_id_validation = int(time.time())
++ url = url_path_join(
++ self.api_url, "authorizations/sessionid", quote(username, safe=''),
++ )
++ headers = {"sessionid": session_id}
++ self.last_session_id_validation_result = self._api_request(
++ 'GET', url, allow_404=True, headers=headers
++ )
++ return self.last_session_id_validation_result
++
+ def get_user(self, handler):
+ """Get the Hub user for a given tornado handler.
+
+@@ -484,16 +520,33 @@
+ handler._cached_hub_user = user_model = None
+ session_id = self.get_session_id(handler)
+
+- # check token first
+- token = self.get_token(handler)
+- if token:
+- user_model = self.user_for_token(token, session_id=session_id)
++ if self.session_id_required and not session_id:
++ app_log.info("Unauthorized access. Only users with a session id are allowed.")
++ return {'name': '<session_id_required>', 'kind': 'User'}
++ elif self.session_id_required_user and not session_id and handler.request.uri.startswith('/user'):
++ app_log.info("Unauthorized access. Only users with a session id are allowed to access /user.")
++ return {'name': '<session_id_required>', 'kind': 'User'}
++ elif self.session_id_required or ( self.session_id_required_user and handler.request.uri.startswith('/user')):
++ token = self.get_token(handler)
++ if token:
++ user_model = self.user_for_token(token)
++ if user_model:
++ handler._token_authenticated = True
++ if user_model is None:
++ user_model = self._get_user_cookie(handler)
+ if user_model:
+- handler._token_authenticated = True
++ user_model = self.validate_session_id(user_model.get('name', ''), session_id)
++ else:
++ # check token first
++ token = self.get_token(handler)
++ if token:
++ user_model = self.user_for_token(token, session_id=session_id)
++ if user_model:
++ handler._token_authenticated = True
+
+- # no token, check cookie
+- if user_model is None:
+- user_model = self._get_user_cookie(handler)
++ # no token, check cookie
++ if user_model is None:
++ user_model = self._get_user_cookie(handler)
+
+ # cache result
+ handler._cached_hub_user = user_model
+@@ -904,10 +957,16 @@
+ # tries to redirect to login URL, 403 will be raised instead.
+ # This is not the best, but avoids problems that can be caused
+ # when get_current_user is allowed to raise.
+- def raise_on_redirect(*args, **kwargs):
+- raise HTTPError(
+- 403, "{kind} {name} is not allowed.".format(**user_model)
+- )
++ if user_model.get('name', '') == '<session_id_required>':
++ def raise_on_redirect(*args, **kwargs):
++ raise HTTPError(
++ 401, "Please login to proceed."
++ )
++ else:
++ def raise_on_redirect(*args, **kwargs):
++ raise HTTPError(
++ 403, "{kind} {name} is not allowed.".format(**user_model)
++ )
+
+ self.redirect = raise_on_redirect
+ return
diff --git a/Golden_Repo/j/Jupyter/jupyterlab-gitlab-2.0.0_jsc.patch b/Golden_Repo/j/Jupyter/jupyterlab-gitlab-2.0.0_jsc.patch
new file mode 100644
index 0000000000000000000000000000000000000000..a382b73c04e2bd356a7a1ce4813ab80d7cf9591d
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyterlab-gitlab-2.0.0_jsc.patch
@@ -0,0 +1,23 @@
+diff
+--- jupyterlab-gitlab-2.0.0.orig/schema/drive.json 2019-05-02 08:22:45.219143000 +0200
++++ jupyterlab-gitlab-2.0.0/schema/drive.json 2019-05-02 08:25:15.392631000 +0200
+@@ -6,8 +6,8 @@
+ "properties": {
+ "baseUrl": {
+ "type": "string",
+- "title": "The GitLab Base URL",
+- "default": "https://gitlab.com"
++ "title": "JSC GitLab Base URL",
++ "default": "https://gitlab.version.fz-juelich.de"
+ },
+ "accessToken": {
+ "type": "string",
+@@ -18,7 +18,7 @@
+ "defaultRepo": {
+ "type": "string",
+ "title": "Default Repository",
+- "default": ""
++ "default": "jupyter4jsc/j4j_notebooks"
+ }
+ },
+ "type": "object"
diff --git a/Golden_Repo/j/Jupyter/jupyterlab_github-2.0.0_jsc.patch b/Golden_Repo/j/Jupyter/jupyterlab_github-2.0.0_jsc.patch
new file mode 100644
index 0000000000000000000000000000000000000000..ebee87027b2ee62abbf2c08f58506edd7b898f35
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyterlab_github-2.0.0_jsc.patch
@@ -0,0 +1,13 @@
+diff
+--- jupyterlab-github-2.0.0.orig/schema/drive.json 2018-10-10 21:14:53.986184891 +0200
++++ jupyterlab_github-2.0.0/schema/drive.json 2018-10-11 00:28:34.846777384 +0200
+@@ -18,7 +18,7 @@
+ "defaultRepo": {
+ "type": "string",
+ "title": "Default Repository",
+- "default": ""
++ "default": "FZJ-JSC/jupyter-jsc-notebooks"
+ }
+ },
+ "type": "object"
+
diff --git a/Golden_Repo/j/Jupyter/jupyterlmod-packagejson.patch b/Golden_Repo/j/Jupyter/jupyterlmod-packagejson.patch
new file mode 100644
index 0000000000000000000000000000000000000000..0d166fec22bceb14c1f704b3ee57d04831efe8c8
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyterlmod-packagejson.patch
@@ -0,0 +1,17 @@
+diff -Naur jupyter-lmod-2.0.2.orig/jupyterlab/package.json jupyter-lmod-2.0.2/jupyterlab/package.json
+--- jupyter-lmod-2.0.2.orig/jupyterlab/package.json 2020-11-25 16:19:57.000000000 +0100
++++ jupyter-lmod-2.0.2/jupyterlab/package.json 2020-12-29 16:50:58.803504000 +0100
+@@ -31,10 +31,12 @@
+ "prepare": "npm run clean && npm run build"
+ },
+ "dependencies": {
+- "@jupyterlab/application": ">=2.0.0",
++ "@jupyterlab/application": "^2.0.0",
++ "@jupyterlab/apputils": "^2.1.0",
+ "@jupyterlab/launcher": "^2.1.0"
+ },
+ "devDependencies": {
++ "@types/react": "^16.9.16",
+ "rimraf": "~2.6.2",
+ "typescript": "~3.7.3"
+ },
diff --git a/Golden_Repo/j/Jupyter/jupyterlmod-urlfile.patch b/Golden_Repo/j/Jupyter/jupyterlmod-urlfile.patch
new file mode 100644
index 0000000000000000000000000000000000000000..0b56aa3e3705f48801d287a08eaad4505016c81f
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyterlmod-urlfile.patch
@@ -0,0 +1,37 @@
+diff -Naur jupyter-lmod-2.0.1/jupyterlab/src/index.ts jupyter-lmod-2.0.1_devel/jupyterlab/src/index.ts
+--- jupyter-lmod-2.0.1/jupyterlab/src/index.ts 2020-10-05 17:08:01.000000000 +0200
++++ jupyter-lmod-2.0.1_devel/jupyterlab/src/index.ts 2020-11-25 11:55:24.000000000 +0100
+@@ -244,7 +244,13 @@
+ const namespace = 'server-proxy';
+ const command = namespace + ':' + 'open';
+ for (let server_process of data.server_processes) {
+- const url = PageConfig.getBaseUrl() + server_process.name + '/';
++
++ let urlfile = '';
++ if (server_process.launcher_entry.urlfile) {
++ urlfile = server_process.launcher_entry.urlfile;
++ }
++ const url = PageConfig.getBaseUrl() + server_process.name + '/' + urlfile;
++
+ const title = server_process.launcher_entry.title;
+ const newBrowserTab = server_process.new_browser_tab;
+ const id = namespace + ':' + server_process.name;
+diff -Naur jupyter-lmod-2.0.1/jupyterlmod/static/main.js jupyter-lmod-2.0.1_devel/jupyterlmod/static/main.js
+--- jupyter-lmod-2.0.1/jupyterlmod/static/main.js 2020-10-05 17:08:01.000000000 +0200
++++ jupyter-lmod-2.0.1_devel/jupyterlmod/static/main.js 2020-11-25 11:55:24.000000000 +0100
+@@ -316,10 +316,14 @@
+ .addClass('new-' + server_process.name);
+
+ /* create our list item's link */
++ let urlfile = '';
++ if (server_process.launcher_entry.urlfile) {
++ urlfile = server_process.launcher_entry.urlfile;
++ }
+ let entry_link = $('<a>')
+ .attr('role', 'menuitem')
+ .attr('tabindex', '-1')
+- .attr('href', base_url + server_process.name + '/')
++ .attr('href', base_url + server_process.name + '/' + urlfile)
+ .attr('target', '_blank')
+ .text(server_process.launcher_entry.title);
+
diff --git a/Golden_Repo/j/Jupyter/jupyterserverproxy-urlfile.patch b/Golden_Repo/j/Jupyter/jupyterserverproxy-urlfile.patch
new file mode 100644
index 0000000000000000000000000000000000000000..de883561447a477f8ad6286b61d0b93c07d0265a
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/jupyterserverproxy-urlfile.patch
@@ -0,0 +1,82 @@
+diff -Naur jupyter-server-proxy.orig/jupyterlab-server-proxy/src/index.ts jupyter-server-proxy/jupyterlab-server-proxy/src/index.ts
+--- jupyter-server-proxy.orig/jupyterlab-server-proxy/src/index.ts 2020-11-19 06:40:34.521630000 +0100
++++ jupyter-server-proxy/jupyterlab-server-proxy/src/index.ts 2020-11-19 06:41:35.023864000 +0100
+@@ -79,8 +79,11 @@
+ if (!server_process.launcher_entry.enabled) {
+ continue;
+ }
+-
+- const url = PageConfig.getBaseUrl() + server_process.name + '/';
++ var urlfile = '';
++ if (server_process.launcher_entry.urlfile) {
++ urlfile = server_process.launcher_entry.urlfile;
++ }
++ const url = PageConfig.getBaseUrl() + server_process.name + '/' + urlfile;
+ const title = server_process.launcher_entry.title;
+ const newBrowserTab = server_process.new_browser_tab;
+ const id = namespace + ':' + server_process.name;
+diff -Naur jupyter-server-proxy.orig/jupyter_server_proxy/api.py jupyter-server-proxy/jupyter_server_proxy/api.py
+--- jupyter-server-proxy.orig/jupyter_server_proxy/api.py 2020-11-19 06:40:34.516286000 +0100
++++ jupyter-server-proxy/jupyter_server_proxy/api.py 2020-11-19 06:41:35.015090000 +0100
+@@ -19,7 +19,8 @@
+ 'name': sp.name,
+ 'launcher_entry': {
+ 'enabled': sp.launcher_entry.enabled,
+- 'title': sp.launcher_entry.title
++ 'title': sp.launcher_entry.title,
++ 'urlfile': sp.launcher_entry.urlfile,
+ },
+ 'new_browser_tab' : sp.new_browser_tab
+ }
+diff -Naur jupyter-server-proxy.orig/jupyter_server_proxy/config.py jupyter-server-proxy/jupyter_server_proxy/config.py
+--- jupyter-server-proxy.orig/jupyter_server_proxy/config.py 2020-11-19 06:40:34.516753000 +0100
++++ jupyter-server-proxy/jupyter_server_proxy/config.py 2020-11-19 06:41:35.016181000 +0100
+@@ -99,7 +99,7 @@
+ ))
+ return handlers
+
+-LauncherEntry = namedtuple('LauncherEntry', ['enabled', 'icon_path', 'title'])
++LauncherEntry = namedtuple('LauncherEntry', ['enabled', 'icon_path', 'title', 'urlfile'])
+ ServerProcess = namedtuple('ServerProcess', [
+ 'name', 'command', 'environment', 'timeout', 'absolute_url', 'port', 'mappath', 'launcher_entry', 'new_browser_tab'])
+
+@@ -116,7 +116,8 @@
+ launcher_entry=LauncherEntry(
+ enabled=le.get('enabled', True),
+ icon_path=le.get('icon_path'),
+- title=le.get('title', name)
++ title=le.get('title', name),
++ urlfile=le.get('urlfile', ''),
+ ),
+ new_browser_tab=server_process_config.get('new_browser_tab', True)
+ )
+@@ -175,6 +176,10 @@
+ title
+ Title to be used for the launcher entry. Defaults to the name of the server if missing.
+
++ urlfile
++ URL file name and URL parameters to be added to the base URL of the launcher entry.
++ Default is none.
++
+ new_browser_tab
+ Set to True (default) to make the proxied server interface opened as a new browser tab. Set to False
+ to have it open a new JupyterLab tab. This has no effect in classic notebook.
+diff -Naur jupyter-server-proxy.orig/jupyter_server_proxy/static/tree.js jupyter-server-proxy/jupyter_server_proxy/static/tree.js
+--- jupyter-server-proxy.orig/jupyter_server_proxy/static/tree.js 2020-11-19 06:40:34.519694000 +0100
++++ jupyter-server-proxy/jupyter_server_proxy/static/tree.js 2020-11-19 06:41:35.020051000 +0100
+@@ -33,10 +33,14 @@
+ .addClass('new-' + server_process.name);
+
+ /* create our list item's link */
++ var urlfile = '';
++ if (server_process.launcher_entry.urlfile) {
++ urlfile = server_process.launcher_entry.urlfile;
++ }
+ var $entry_link = $('<a>')
+ .attr('role', 'menuitem')
+ .attr('tabindex', '-1')
+- .attr('href', base_url + server_process.name + '/')
++ .attr('href', base_url + server_process.name + '/' + urlfile)
+ .attr('target', '_blank')
+ .text(server_process.launcher_entry.title);
+
diff --git a/Golden_Repo/j/Jupyter/notebook-6.0.3_jsc.patch b/Golden_Repo/j/Jupyter/notebook-6.0.3_jsc.patch
new file mode 100644
index 0000000000000000000000000000000000000000..d7a9bb20d7d6eea484462bd8bf68c8e018546b4e
--- /dev/null
+++ b/Golden_Repo/j/Jupyter/notebook-6.0.3_jsc.patch
@@ -0,0 +1,143 @@
+diff
+--- notebook-6.0.3.orig/notebook/services/contents/filecheckpoints.py 2020-04-28 06:26:51.384296390 +0200
++++ notebook-6.0.3/notebook/services/contents/filecheckpoints.py 2020-04-28 06:30:55.139342947 +0200
+@@ -14,7 +14,7 @@
+
+ from jupyter_core.utils import ensure_dir_exists
+ from ipython_genutils.py3compat import getcwd
+-from traitlets import Unicode
++from traitlets import Unicode, Integer
+
+ from notebook import _tz as tz
+
+@@ -28,6 +28,35 @@
+ you want file-based checkpoints with another ContentsManager.
+ """
+
++ checkpoint_permissions = Integer(
++ 0o644,
++ config=True,
++ help="""The permission of your checkpoint files.
++
++ By default, it is 0o644
++ """,
++ )
++
++ restore_permissions = Integer(
++ 0o644,
++ config=True,
++ help="""The permission of a restored checkpoint.
++
++ By default, it is 0o644
++ """,
++ )
++
++ checkpoint_dir_umask = Integer(
++ 0o022,
++ config=True,
++ help="""The umask for the checkpoint directory.
++
++ Keep in mind that it depends on your system umask, too.
++
++ By default, it is 0o022
++ """,
++ )
++
+ checkpoint_dir = Unicode(
+ '.ipynb_checkpoints',
+ config=True,
+@@ -50,21 +79,29 @@
+ # ContentsManager-dependent checkpoint API
+ def create_checkpoint(self, contents_mgr, path):
+ """Create a checkpoint."""
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ checkpoint_id = u'checkpoint'
+ src_path = contents_mgr._get_os_path(path)
+ dest_path = self.checkpoint_path(checkpoint_id, path)
+ self._copy(src_path, dest_path)
+- return self.checkpoint_model(checkpoint_id, dest_path)
++ os.chmod(dest_path, self.checkpoint_permissions)
++ ret = self.checkpoint_model(checkpoint_id, dest_path)
++ os.umask(original_umask)
++ return ret
+
+ def restore_checkpoint(self, contents_mgr, checkpoint_id, path):
+ """Restore a checkpoint."""
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ src_path = self.checkpoint_path(checkpoint_id, path)
+ dest_path = contents_mgr._get_os_path(path)
+ self._copy(src_path, dest_path)
++ os.chmod(dest_path, self.restore_permissions)
++ os.umask(original_umask)
+
+ # ContentsManager-independent checkpoint API
+ def rename_checkpoint(self, checkpoint_id, old_path, new_path):
+ """Rename a checkpoint from old_path to new_path."""
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ old_cp_path = self.checkpoint_path(checkpoint_id, old_path)
+ new_cp_path = self.checkpoint_path(checkpoint_id, new_path)
+ if os.path.isfile(old_cp_path):
+@@ -75,9 +112,11 @@
+ )
+ with self.perm_to_403():
+ shutil.move(old_cp_path, new_cp_path)
++ os.umask(original_umask)
+
+ def delete_checkpoint(self, checkpoint_id, path):
+ """delete a file's checkpoint"""
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ path = path.strip('/')
+ cp_path = self.checkpoint_path(checkpoint_id, path)
+ if not os.path.isfile(cp_path):
+@@ -86,23 +125,29 @@
+ self.log.debug("unlinking %s", cp_path)
+ with self.perm_to_403():
+ os.unlink(cp_path)
++ os.umask(original_umask)
+
+ def list_checkpoints(self, path):
+ """list the checkpoints for a given file
+
+ This contents manager currently only supports one checkpoint per file.
+ """
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ path = path.strip('/')
+ checkpoint_id = "checkpoint"
+ os_path = self.checkpoint_path(checkpoint_id, path)
+ if not os.path.isfile(os_path):
++ os.umask(original_umask)
+ return []
+ else:
+- return [self.checkpoint_model(checkpoint_id, os_path)]
++ ret = self.checkpoint_model(checkpoint_id, os_path)
++ os.umask(original_umask)
++ return [ret]
+
+ # Checkpoint-related utilities
+ def checkpoint_path(self, checkpoint_id, path):
+ """find the path to a checkpoint"""
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ path = path.strip('/')
+ parent, name = ('/' + path).rsplit('/', 1)
+ parent = parent.strip('/')
+@@ -117,16 +162,19 @@
+ with self.perm_to_403():
+ ensure_dir_exists(cp_dir)
+ cp_path = os.path.join(cp_dir, filename)
++ os.umask(original_umask)
+ return cp_path
+
+ def checkpoint_model(self, checkpoint_id, os_path):
+ """construct the info dict for a given checkpoint"""
++ original_umask = os.umask(self.checkpoint_dir_umask)
+ stats = os.stat(os_path)
+ last_modified = tz.utcfromtimestamp(stats.st_mtime)
+ info = dict(
+ id=checkpoint_id,
+ last_modified=last_modified,
+ )
++ os.umask(original_umask)
+ return info
+
+ # Error Handling
+
diff --git a/Golden_Repo/j/JupyterCollection/JupyterCollection-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb b/Golden_Repo/j/JupyterCollection/JupyterCollection-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..3c95d6f138d593c2b7672401e04b22170c4fc4d9
--- /dev/null
+++ b/Golden_Repo/j/JupyterCollection/JupyterCollection-2020.2.5-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
@@ -0,0 +1,33 @@
+easyblock = 'Bundle'
+
+name = 'JupyterCollection'
+version = '2020.2.5'
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'http://www.jupyter.org'
+description = """
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+dependencies = [
+ ('JupyterKernel-Bash', '0.7.1', '-' + version),
+ ('JupyterKernel-Cling', '0.7', '-' + version),
+ ('JupyterKernel-JavaScript', '5.2.0', '-' + version),
+ ('JupyterKernel-Julia', '1.5.2', '-' + version),
+ ('JupyterKernel-Octave', '6.1.0', '-' + version),
+ ('JupyterKernel-PyParaView', '5.8.1', '-' + version),
+ # ('JupyterKernel-PyQuantum', '1.1', '-' + version),
+ ('JupyterKernel-R', '4.0.2', '-' + version),
+ ('JupyterKernel-Ruby', '2.7.1', '-' + version),
+ ('JupyterProxy-XpraHTML5', '0.3.0', '-' + version),
+ ('Jupyter', version, local_pysuffix),
+]
+
+skipsteps = ['configure', 'build', 'install', 'sanity_check']
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-Bash/JupyterKernel-Bash-0.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-Bash/JupyterKernel-Bash-0.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..65d3c8c014f31e4058e31c0235782028857441e8
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-Bash/JupyterKernel-Bash-0.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,98 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Bash'
+version = '0.7.1'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/takluyver/bash_kernel'
+description = """
+Native Bash kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, local_pysuffix),
+]
+
+local_common_opts = {
+ 'req_py_majver': '3',
+ 'req_py_minver': '0'
+}
+
+exts_defaultclass = 'PythonPackage'
+exts_filter = ('python -c "import %(ext_name)s"', '')
+exts_default_options = {
+ 'download_dep_fail': True,
+ 'source_urls': [PYPI_SOURCE],
+ 'use_pip': True,
+}
+
+exts_list = [
+ # 0.7.2 fails with BackendUnavailable. Might be fixable --no-use-pep517
+ ('bash_kernel', '0.7.1', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', '29f895819e076e3f225e37034b70b5265a559e2964e020c942024f51ea6153e8')]),
+ ('use_pip', True),
+ ])),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+ 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ # Create virtual environment to ensure we install in the correct directory !!!
+ 'python3 -m venv %(installdir)s --system-site-packages',
+ (
+ '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+ '#!/bin/bash\n'
+ 'source %%(installdir)s/bin/activate\n'
+ 'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+ 'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+ 'EOF'
+ ) % (local_jupyter_path),
+
+ # Jupyter Kernel: Bash - https://github.com/takluyver/bash_kernel
+ # installs bash_kernel in $JUPYTER_DATA_DIR/kernels
+ 'source %(builddir)s/env.sh && ${EBROOTPYTHON}/bin/python3 -m bash_kernel.install --user',
+ 'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+
+ # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+ 'rm %(installdir)s/pyvenv.cfg',
+ 'rm -r %(installdir)s/bin',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/bash/kernel.json',
+ ],
+ 'dirs': [
+ 'lib/python%(pyshortver)s/site-packages',
+ 'share/jupyter/kernels/bash/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-Cling/JupyterKernel-Cling-0.7-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-Cling/JupyterKernel-Cling-0.7-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..8de48fc00e6eafc78dd98cda09d2bc72fde8d6cb
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-Cling/JupyterKernel-Cling-0.7-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,93 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Cling'
+version = '0.7'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/root-project/cling'
+description = """
+Native C kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, local_pysuffix),
+ ('Cling', version),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+ 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ # Create virtual environment to ensure we install in the correct directory !!!
+ 'python3 -m venv %(installdir)s --system-site-packages',
+ (
+ '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+ '#!/bin/bash\n'
+ 'source %%(installdir)s/bin/activate\n'
+ 'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+ 'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+ 'EOF'
+ ) % (local_jupyter_path),
+
+ # Jupyter Kernel: Cling (C++)
+ 'source %(builddir)s/env.sh && pip3 install ${EBROOTCLING}/share/cling/Jupyter/kernel',
+ (
+ 'source %(builddir)s/env.sh && '
+ ' jupyter-kernelspec install --prefix=%(installdir)s ${EBROOTCLING}/share/cling/Jupyter/kernel/cling-cpp17'
+ ),
+
+ # correct shebang to correct python binary
+ (
+ 'source %(builddir)s/env.sh && '
+ ' abs2python="#! ${EBROOTPYTHON}/bin/python" && '
+ ' sed "1s@^.*@$abs2python@g" -i %(installdir)s/bin/jupyter-cling-kernel'
+ ),
+ 'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+
+ # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+ 'rm %(installdir)s/pyvenv.cfg',
+ 'rm %(installdir)s/bin/python',
+ 'rm %(installdir)s/bin/python3',
+ 'rm %(installdir)s/bin/activate',
+ 'rm %(installdir)s/bin/activate*',
+ 'rm %(installdir)s/bin/easy_install*',
+ 'rm %(installdir)s/bin/pip*',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/cling-cpp17/kernel.json',
+ ],
+ 'dirs': [
+ # 'lib/python%(pyshortver)s/site-packages',
+ 'share/jupyter/kernels/cling-cpp17/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-JavaScript/JupyterKernel-JavaScript-5.2.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-JavaScript/JupyterKernel-JavaScript-5.2.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..63f3f746f56cbc0dc82f569bf0ad6eff20181df8
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-JavaScript/JupyterKernel-JavaScript-5.2.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,71 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-JavaScript'
+version = '5.2.0'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'https://www.npmjs.com/package/ijavascript'
+description = """
+Native JavaScript kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Jupyter', local_jupyterver, local_pysuffix),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+ 'PATH': ['bin'],
+ 'NODE_PATH': ['lib/node_modules'], # npm´s search path to extra modules
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ (
+ '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+ '#!/bin/bash\n'
+ 'export PATH=%%(installdir)s/bin:${PATH}\n'
+ 'export NODE_PATH=%%(installdir)s/lib/node_modules\n'
+ 'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+ 'EOF'
+ ) % (local_jupyter_path),
+
+ 'source %(builddir)s/env.sh && npm install ijavascript@5.2.0 -g --prefix %(installdir)s',
+ # installs ijavascript in $JUPYTER_DATA_DIR/kernels
+ 'source %(builddir)s/env.sh && ijsinstall --install=local',
+ 'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/javascript/kernel.json',
+ ],
+ 'dirs': [
+ 'lib/node_modules/',
+ 'share/jupyter/kernels/javascript/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-Julia/JupyterKernel-Julia-1.5.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-Julia/JupyterKernel-Julia-1.5.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..735b3cd4ce2e2a3e87d92493c03d91c7d5347ef9
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-Julia/JupyterKernel-Julia-1.5.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,117 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Julia'
+version = '1.5.2'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/IRkernel/IRkernel'
+description = """
+Native R kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, local_pysuffix),
+ ('Julia', version),
+]
+
+local_common_opts = {
+ 'req_py_majver': '3',
+ 'req_py_minver': '0'
+}
+
+exts_defaultclass = 'PythonPackage'
+exts_filter = ('python -c "import %(ext_name)s"', '')
+exts_default_options = {
+ 'download_dep_fail': True,
+ 'source_urls': [PYPI_SOURCE],
+ 'use_pip': True,
+}
+
+exts_list = [
+ ('julia', '0.5.3', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'b13207125709fdba069a25c4e54ff366f0bc308807b2aa0f3b66924101799c58')]),
+ ('use_pip', True),
+ ])),
+]
+
+local_jupyter_path = 'share/jupyter'
+local_julia_depot_path = "%(installdir)s/share/julia/site/" # for Julia packages needed for Jupyter
+
+modextrapaths = {
+ 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+modextravars = {
+ 'JULIA_DEPOT_PATH': local_julia_depot_path,
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ # Create virtual environment to ensure we install in the correct directory !!!
+ 'python3 -m venv %(installdir)s --system-site-packages',
+ (
+ '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+ '#!/bin/bash\n'
+ 'source %%(installdir)s/bin/activate\n'
+ 'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+ ''
+ 'export JULIA_DEPOT_PATH=%s\n'
+ 'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+ 'EOF'
+ ) % (local_julia_depot_path, local_jupyter_path),
+
+ # installs ijulia in JULIA_DEPOT_PATH and kernel in $JUPYTER_DATA_DIR/kernels
+ 'source %(builddir)s/env.sh && julia -e \'using Pkg; Pkg.add("IJulia"); Pkg.build("IJulia")\'',
+
+ # to trigger the precompilation
+ 'source %(builddir)s/env.sh && julia -e \'using IJulia\'',
+
+ # adjust permissions of precompiled files
+ 'for i in $(find %s); do chmod +r $i; done' % local_julia_depot_path,
+
+ # configure Python<->Julia bridge (of python package julia)
+ 'source %(builddir)s/env.sh && python -c "import julia; julia.install()"',
+
+ # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+ 'rm %(installdir)s/pyvenv.cfg',
+ 'rm %(installdir)s/bin/python',
+ 'rm %(installdir)s/bin/python3',
+ 'rm %(installdir)s/bin/activate',
+ 'rm %(installdir)s/bin/activate*',
+ 'rm %(installdir)s/bin/easy_install*',
+ 'rm %(installdir)s/bin/pip*',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/julia-%(version_major_minor)s/kernel.json',
+ ],
+ 'dirs': [
+ 'lib/python%(pyshortver)s/site-packages',
+ 'share/jupyter/kernels/julia-%(version_major_minor)s/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-Octave/JupyterKernel-Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-Octave/JupyterKernel-Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..c712e30c7783628b321266ffa1c3e9b35d38f66e
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-Octave/JupyterKernel-Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,137 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Octave'
+version = '6.1.0'
+local_octavever = '6.1.0'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/Calysto/octave_kernel'
+description = """
+Native Octave kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('Octave', local_octavever, '-nompi'), # ensure it is available
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, local_pysuffix),
+ # no dependency to Octave as it is loaded in kernel.sh
+]
+
+local_jupyter_path = 'share/jupyter'
+local_kernel_dir = 'octave'
+local_kernel_name = 'Octave-%s' % local_octavever
+
+modextrapaths = {
+ 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ # Create virtual environment to ensure we install in the correct directory !!!
+ 'python3 -m venv %(installdir)s --system-site-packages',
+ (
+ '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+ '#!/bin/bash\n'
+ 'source %%(installdir)s/bin/activate\n'
+ 'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH}\n'
+ 'export JUPYTER_DATA_DIR=%%(installdir)s/%s\n'
+ 'EOF'
+ ) % (local_jupyter_path),
+
+ # enable use of Octave from production stage Stages/2020
+ 'source %(builddir)s/env.sh && pip3 install ipykernel ',
+ 'rm -rf %(installdir)s/share/jupyter/kernels/', # remove any kernel installed by ipykernel
+ 'source %(builddir)s/env.sh && pip3 install ipyparallel ',
+
+ # install Python package octave_kernel
+ 'source %(builddir)s/env.sh && pip3 install octave_kernel==0.32.0 ',
+
+ # write kernel.sh
+ (
+ '{ cat >> %%(builddir)s/env.sh; } << \'EOF\'\n'
+ 'export KERNEL_DIR=%s\n'
+ 'export KERNEL_NAME=%s\n'
+ 'EOF'
+ ) % (local_kernel_dir, local_kernel_name),
+ (
+ '{ source %%(builddir)s/env.sh && '
+ ' cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.sh; } << \'EOF\'\n'
+ '#!/bin/bash \n'
+ '\n'
+ '# Load required modules \n'
+ 'module purge \n'
+ 'module load Stages/2020 \n'
+ 'module load GCC/9.3.0 \n'
+ '\n' \
+ 'module load Python/%%(pyver)s \n'
+ 'module load Jupyter/%s%s \n'
+ 'module load Octave/%s-nompi \n'
+ '\n'
+ 'export PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:${PYTHONPATH} \n'
+ '\n'
+ 'exec python $@\n'
+ 'EOF'
+ ) % (local_kernel_dir, local_jupyterver, local_pysuffix, local_octavever),
+ 'source %(builddir)s/env.sh && chmod +x %(installdir)s/share/jupyter/kernels/${KERNEL_DIR}/kernel.sh',
+
+ # write kernel.json
+ (
+ '{ source %%(builddir)s/env.sh && '
+ ' cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.json; } << \'EOF\'\n'
+ '{ \n'
+ ' "argv": [ \n'
+ ' "%%(installdir)s/share/jupyter/kernels/%s/kernel.sh", \n'
+ ' "-m", \n'
+ ' "octave_kernel", \n'
+ ' "-f", \n'
+ ' "{connection_file}" \n'
+ ' ], \n'
+ ' "display_name": "%s", \n'
+ ' "mimetype": "text/x-octave", \n'
+ ' "language": "python", \n'
+ ' "name": "%s" \n'
+ '}\n'
+ 'EOF'
+ ) % (local_kernel_dir, local_kernel_dir, local_kernel_name, local_kernel_name),
+
+ # ensure correct permissions
+ 'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+
+ # Ensure we remove the virtuel environment to avoid wrong search path for python packages
+ 'rm %(installdir)s/pyvenv.cfg',
+ 'rm -r %(installdir)s/bin',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/%s/kernel.sh' % local_kernel_dir,
+ 'share/jupyter/kernels/%s/kernel.json' % local_kernel_dir,
+ ],
+ 'dirs': [
+ 'lib/python%(pyshortver)s/site-packages',
+ 'share/jupyter/kernels/octave/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-PyParaView/JupyterKernel-PyParaView-5.8.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-PyParaView/JupyterKernel-PyParaView-5.8.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..02ad2914a3351aa6ab1ef393d1bc817069fdb2e4
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-PyParaView/JupyterKernel-PyParaView-5.8.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,130 @@
+easyblock = 'Binary'
+
+name = 'JupyterKernel-PyParaView'
+version = '5.8.1'
+local_paraviewver = '5.8.1'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.paraview.org'
+description = """
+Special ParaView kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+sources = [
+ ('logo-128x128.png'),
+ ('logo-32x32.png'),
+ ('logo-64x64.png'),
+]
+
+builddependencies = [
+ ('binutils', '2.34'),
+ # ('ParaView', local_paraviewver, '-EGL' + local_pysuffix, ('gpsmkl', '2020')), # ensure it is available
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, local_pysuffix),
+]
+
+local_kernel_dir = 'pyparaview'
+local_kernel_name = 'PyParaView-%s' % local_paraviewver
+
+modextrapaths = {
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ (
+ '{ cat >> %%(builddir)s/env.sh; } << \'EOF\'\n'
+ 'export KERNEL_DIR=%s\n'
+ 'export KERNEL_NAME=%s\n'
+ 'EOF'
+ ) % (local_kernel_dir, local_kernel_name),
+ 'source %%(builddir)s/env.sh && python -m ipykernel install --name=%s --prefix=%%(installdir)s' % local_kernel_dir,
+
+ # write logo image
+ (
+ 'source %%(builddir)s/env.sh && '
+ ' cp %%(builddir)s/logo-32x32.png %%(installdir)s/share/jupyter/kernels/%s/logo-32x32.png'
+ ) % (local_kernel_dir),
+ (
+ 'source %%(builddir)s/env.sh && '
+ ' cp %%(builddir)s/logo-64x64.png %%(installdir)s/share/jupyter/kernels/%s/logo-64x64.png'
+ ) % (local_kernel_dir),
+ (
+ 'source %%(builddir)s/env.sh && '
+ ' cp %%(builddir)s/logo-128x128.png %%(installdir)s/share/jupyter/kernels/%s/logo-128x128.png'
+ ) % (local_kernel_dir),
+
+ # write kernel.sh
+ (
+ '{ source %%(builddir)s/env.sh && '
+ ' cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.sh; } << \'EOF\'\n'
+ '#!/bin/bash \n'
+ '\n'
+ '# Load required modules \n'
+ 'module purge \n'
+ 'module use $OTHERSTAGES \n'
+ 'module load Stages/2020 \n'
+ 'module load GCC/9.3.0 \n'
+ 'module load ParaStationMPI \n'
+ 'module load Python/%%(pyver)s \n'
+ 'module load Jupyter/%s%s \n'
+ '\n'
+ 'module load ParaView/%s-EGL%s \n'
+ 'module unload VTK \n'
+ '\n'
+ 'exec python -m ipykernel $@\n'
+ 'EOF'
+ ) % (local_kernel_dir,
+ local_jupyterver, local_pysuffix,
+ local_paraviewver, local_pysuffix),
+ 'source %(builddir)s/env.sh && chmod +x %(installdir)s/share/jupyter/kernels/${KERNEL_DIR}/kernel.sh',
+
+ # write kernel.json
+ (
+ '{ source %%(builddir)s/env.sh && '
+ ' cat > %%(installdir)s/share/jupyter/kernels/%s/kernel.json; } << \'EOF\'\n'
+ '{ \n'
+ ' "argv": [ \n'
+ ' "%%(installdir)s/share/jupyter/kernels/%s/kernel.sh", \n'
+ ' "-m", \n'
+ ' "ipykernel_launcher", \n'
+ ' "-f", \n'
+ ' "{connection_file}" \n'
+ ' ], \n'
+ ' "display_name": "%s", \n'
+ ' "language": "python", \n'
+ ' "name": "%s" \n'
+ '}\n'
+ 'EOF'
+ ) % (local_kernel_dir, local_kernel_dir, local_kernel_name, local_kernel_name),
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/%s/kernel.sh' % local_kernel_dir,
+ 'share/jupyter/kernels/%s/kernel.json' % local_kernel_dir,
+ ],
+ 'dirs': [
+ 'share/jupyter/kernels/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-R/JupyterKernel-R-4.0.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-R/JupyterKernel-R-4.0.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..ee02c803106fcea641d1bd70912d2ad3052aa32e
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-R/JupyterKernel-R-4.0.2-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,61 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-R'
+version = '4.0.2'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'https://github.com/IRkernel/IRkernel'
+description = """
+Native R kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Jupyter', local_jupyterver, local_pysuffix),
+ ('R', '4.0.2', '-nompi'),
+]
+
+modextrapaths = {
+ 'JUPYTER_PATH': 'share/jupyter', # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ # Jupyter Kernel: R - https://github.com/IRkernel/IRkernel
+ # installs R kernel in $EBROOTJUPYTER/share/jupyter/kernels
+ 'R -e \'IRkernel::installspec(name="ir40", displayname="R 4.0", prefix="%(installdir)s")\'',
+
+ # force options(bitmapType='cairo') -> https://github.com/IRkernel/IRkernel/issues/388
+ (
+ 'sed -i "s#IRkernel::main()#options(bitmapType=\'cairo\') ; IRkernel::main()#g" '
+ ' %(installdir)s/share/jupyter/kernels/ir40/kernel.json'
+ ),
+]
+
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/ir40/kernel.json',
+ ],
+ 'dirs': [
+ 'share/jupyter/kernels/ir40/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterKernel-Ruby/JupyterKernel-Ruby-2.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterKernel-Ruby/JupyterKernel-Ruby-2.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..a88416c91842db501138d1430faf784f9e915615
--- /dev/null
+++ b/Golden_Repo/j/JupyterKernel-Ruby/JupyterKernel-Ruby-2.7.1-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,65 @@
+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Ruby'
+version = '2.7.1'
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-3.8.5'
+
+homepage = 'https://github.com/SciRuby/iruby'
+description = """
+Native Ruby kernel for Jupyter.
+Project Jupyter exists to develop open-source software, open-standards, and services
+for interactive computing across dozens of programming languages.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, local_pysuffix),
+ ('Ruby', '2.7.1'),
+]
+
+local_jupyter_path = 'share/jupyter'
+
+modextrapaths = {
+ 'JUPYTER_PATH': ['share/jupyter'], # add search path for kernelspecs
+}
+
+# Ensure that the user-specific $HOME/.local/share/jupyter is always first entry in JUPYTHER_PATH
+modluafooter = """
+prepend_path("JUPYTER_PATH", pathJoin(os.getenv("HOME"), ".local/share/jupyter"))
+"""
+
+postinstallcmds = [
+ 'echo "#!/bin/bash" > %(builddir)s/env.sh',
+ 'echo "export JUPYTER_DATA_DIR=%%(installdir)s/%s" >> %%(builddir)s/env.sh' % local_jupyter_path,
+
+ # install Ruby kernel in $JUPYTHER_PATH
+ 'source %(builddir)s/env.sh && iruby register --force ',
+
+ # ensure correct permissions
+ 'source %(builddir)s/env.sh && chmod -R o+x %(installdir)s/share',
+]
+
+# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module
+# full_sanity_check = True
+sanity_check_paths = {
+ 'files': [
+ 'share/jupyter/kernels/ruby/kernel.json',
+ ],
+ 'dirs': [
+ 'share/jupyter/kernels/ruby/',
+ ],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterProxy-XpraHTML5/JupyterProxy-XpraHTML5-0.3.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb b/Golden_Repo/j/JupyterProxy-XpraHTML5/JupyterProxy-XpraHTML5-0.3.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..8fde03a92d49c001e80d348d9bd7c8bc68a240b3
--- /dev/null
+++ b/Golden_Repo/j/JupyterProxy-XpraHTML5/JupyterProxy-XpraHTML5-0.3.0-gcccoremkl-9.3.0-2020.2.254-2020.2.5.eb
@@ -0,0 +1,57 @@
+easyblock = 'PythonBundle'
+
+name = 'JupyterProxy-XpraHTML5'
+version = '0.3.0'
+
+local_jupyterver = '2020.2.5'
+versionsuffix = '-' + local_jupyterver
+
+homepage = 'https://xpra.org'
+description = """
+Jupyter proxy for Xpra HTML5 sessions.
+Xpra is an open-source multi-platform persistent remote display server and client
+for forwarding applications and desktop screens.
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('Jupyter', local_jupyterver, '-Python-%(pyver)s'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+ 'download_dep_fail': True,
+ 'source_urls': [PYPI_SOURCE],
+ 'use_pip': True,
+}
+
+local_common_opts = {
+ 'req_py_majver': '3',
+ 'req_py_minver': '0'
+}
+
+exts_list = [
+ ('jupyter-xprahtml5-proxy', '0.3.0', dict(list(local_common_opts.items()) + [
+ ('checksums', [('sha256', 'db852682e8e366091e6a3984b60ac3d2e6b3197be2ef074440c11cb09e23b80b')]),
+ ('source_urls', ['https://github.com/FZJ-JSC/jupyter-xprahtml5-proxy/archive/']),
+ ('source_tmpl', 'v0.3.0_devel.tar.gz'),
+ ('patches', ['jupyter_xprahtml5_proxy-launch_xpra.patch']),
+ ('modulename', 'jupyter_xprahtml5_proxy'),
+ ])),
+]
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/j/JupyterProxy-XpraHTML5/jupyter_xprahtml5_proxy-launch_xpra.patch b/Golden_Repo/j/JupyterProxy-XpraHTML5/jupyter_xprahtml5_proxy-launch_xpra.patch
new file mode 100644
index 0000000000000000000000000000000000000000..329d2ac2728fc42991d54a2f7a74e9c081fc50b0
--- /dev/null
+++ b/Golden_Repo/j/JupyterProxy-XpraHTML5/jupyter_xprahtml5_proxy-launch_xpra.patch
@@ -0,0 +1,27 @@
+diff -Naur jupyter-xprahtml5-proxy.orig/jupyter_xprahtml5_proxy/share/launch_xpra.sh jupyter-xprahtml5-proxy/jupyter_xprahtml5_proxy/share/launch_xpra.sh
+--- jupyter-xprahtml5-proxy.orig/jupyter_xprahtml5_proxy/share/launch_xpra.sh 2020-11-19 00:13:39.000000000 +0100
++++ jupyter-xprahtml5-proxy/jupyter_xprahtml5_proxy/share/launch_xpra.sh 2020-11-20 18:49:09.557792000 +0100
+@@ -5,10 +5,17 @@
+ # Do it here.
+
+ # example
+-# module purge > /dev/null
+-# module use $OTHERSTAGES > /dev/null
+-# module load Stages/2020 > /dev/null
+-# module load GCCcore/.9.3.0 > /dev/null
+-# module load xpra/4.0.4-Python-3.8.5 > /dev/null
++module purge
++module use $OTHERSTAGES
++module load Stages/2020
++module load GCCcore/.9.3.0
++module load xpra/4.0.4-Python-3.8.5
++module load jsc-xdg-menu/.2020.3
++
++if ! command -v xterm &> /dev/null
++then
++ echo "xterm not found - trying to load the xterm-module"
++ module load xterm
++fi
+
+ xpra "$@"
+
diff --git a/Golden_Repo/jurecadc_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb b/Golden_Repo/jurecadc_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
index ddee966f3e5b79e371d41631ff7432683350fd79..7210f37bc48a792d042c384051407ef0e62e7057 100644
--- a/Golden_Repo/jurecadc_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
+++ b/Golden_Repo/jurecadc_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
@@ -36,7 +36,7 @@ builddependencies = [
('archspec', '0.1.0', '-Python-%(pyver)s'),
]
dependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('Python', '3.8.5'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.0.5'),
diff --git a/Golden_Repo/jurecadc_overlay/v/Vampir/Vampir-9.9.0.eb b/Golden_Repo/jurecadc_overlay/v/Vampir/Vampir-9.9.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..bd7449cc1fe09bb86fd46f2d4a6c7f77bdd1d167
--- /dev/null
+++ b/Golden_Repo/jurecadc_overlay/v/Vampir/Vampir-9.9.0.eb
@@ -0,0 +1,40 @@
+# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild
+# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany
+# Authors:: Bernd Mohr <b.mohr@fz-juelich.de>
+# License:: New BSD
+#
+# This work is based from experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+##
+easyblock = 'Binary'
+
+name = "Vampir"
+version = "9.9.0"
+local_archsuffix = "-linux-x86_64"
+
+homepage = 'http://www.vampir.eu'
+description = """The VAMPIR software tool provides an easy-to-use framework that enables
+developers to quickly display and analyze arbitrary program behavior at any level of detail.
+The tool suite implements optimized event analysis algorithms and customizable displays that
+enable fast and interactive rendering of very complex performance monitoring data.
+
+"""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = SYSTEM
+
+sources = ['vampir-%s%s-setup.sh' % (version, local_archsuffix)]
+
+install_cmd = './vampir-%(version)s-linux-x86_64-setup.sh --silent --instdir=%(installdir)s'
+
+sanity_check_paths = {
+ 'files': ["bin/vampir", "doc/vampir-manual.pdf"],
+ 'dirs': []
+}
+
+modextravars = {
+ 'VAMPIR_LICENSE': '/p/software/jurecadc/licenses/vampir/vampir.license',
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/jurecadc_overlay/v/VampirServer/VampirServer-9.9.0-gpsmpi-2020.eb b/Golden_Repo/jurecadc_overlay/v/VampirServer/VampirServer-9.9.0-gpsmpi-2020.eb
new file mode 100644
index 0000000000000000000000000000000000000000..fb750f42d8eaa5a0f75070b125e0a4ee43d1f821
--- /dev/null
+++ b/Golden_Repo/jurecadc_overlay/v/VampirServer/VampirServer-9.9.0-gpsmpi-2020.eb
@@ -0,0 +1,61 @@
+# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild
+# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany
+# Authors:: Bernd Mohr <b.mohr@fz-juelich.de>
+# License:: New BSD
+#
+# This work is based from experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+##
+easyblock = 'Binary'
+
+name = "VampirServer"
+version = "9.9.0"
+
+homepage = 'http://www.vampir.eu'
+description = """The VAMPIR software tool provides an easy-to-use framework that enables
+developers to quickly display and analyze arbitrary program behavior at any level of detail.
+The tool suite implements optimized event analysis algorithms and customizable displays that
+enable fast and interactive rendering of very complex performance monitoring data.
+"""
+
+usage = """
+To start VampirServer
+module load Vampir VampirServer
+vampir &
+BATCH_OPT="--account=<budget> --partition=<partition>" vampirserver start -n 4 mpi
+(note server + port + server_id)
+- Use it
+Vampir GUI-> open other -> remote file -> server + port
+- To stop VampirServer
+vampirserver stop <server_id>
+"""
+
+site_contacts = 'sc@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+
+toolchainopts = {"usempi": True}
+
+sources = ['vampirserver-%s-linux-x86_64-setup.sh' % (version)]
+
+install_cmd = ('./vampirserver-%(version)s-linux-x86_64-setup.sh --silent --instdir=%(installdir)s '
+ '&& %(installdir)s/bin/vampirserver config --silent')
+
+sanity_check_paths = {
+ 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"],
+ 'dirs': []
+}
+
+# Remove Cray-specific 'ap' launcher,
+# use SLURM launcher as MPI launcher and default
+postinstallcmds = [
+ 'rm %(installdir)s/etc/server/launcher/ap',
+ '''sed -i s/'BATCH_OPT=""'/'#BATCH_OPT=""'/g %(installdir)s/etc/server/launcher/custom/slurm''',
+ 'cp %(installdir)s/etc/server/launcher/custom/slurm %(installdir)s/etc/server/launcher/mpi',
+]
+
+modextravars = {
+ 'VAMPIR_LICENSE': '/p/software/jurecadc/licenses/vampir/vampir.license',
+}
+
+moduleclass = 'perf'
diff --git a/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb b/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
index ec81e25c4bd30963b3e6ee6fd0cb7cc0de28cc3f..6178b0c12adac5ef08a67a76dd1afc8cb3e585d7 100644
--- a/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
+++ b/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-GCC-9.3.0.eb
@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
builddependencies = [
('flex', '2.6.4'),
('Bison', '3.6.4'),
+ ('Java', '15', '', SYSTEM),
]
dependencies = [
@@ -28,7 +29,8 @@ dependencies = [
sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]]
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
sanity_check_paths = {
'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'],
diff --git a/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb b/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
index 1f25d07deebddfb7ec4eb214c9b708458c516c8b..b3d0a06f6ac30a4a58270b00cf6ea4150dc7eec3 100644
--- a/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
+++ b/Golden_Repo/jusuf_overlay/h/HDF/HDF-4.2.15-iccifort-2020.2.254-GCC-9.3.0.eb
@@ -16,6 +16,7 @@ toolchainopts = {'opt': True, 'pic': True}
builddependencies = [
('flex', '2.6.4'),
('Bison', '3.6.4'),
+ ('Java', '15', '', SYSTEM),
]
dependencies = [
@@ -28,7 +29,8 @@ dependencies = [
sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]]
-configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --includedir=%(installdir)s/include/%(namelower)s'
+configopts = '--with-szlib=$EBROOTSZIP --with-zlib=$EBROOTZLIB --enable-java '
+configopts += '--includedir=%(installdir)s/include/%(namelower)s '
sanity_check_paths = {
'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'],
diff --git a/Golden_Repo/juwelsbooster_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb b/Golden_Repo/juwelsbooster_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
index ddee966f3e5b79e371d41631ff7432683350fd79..7210f37bc48a792d042c384051407ef0e62e7057 100644
--- a/Golden_Repo/juwelsbooster_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
+++ b/Golden_Repo/juwelsbooster_overlay/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
@@ -36,7 +36,7 @@ builddependencies = [
('archspec', '0.1.0', '-Python-%(pyver)s'),
]
dependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('Python', '3.8.5'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.0.5'),
diff --git a/Golden_Repo/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb b/Golden_Repo/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
index b7411d242a805cb6bf5f3f11ae0e693ba31e223b..3a53f84ceb7dd4b9f45a5bdd24bf46daaac26f6c 100644
--- a/Golden_Repo/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
+++ b/Golden_Repo/l/LAMMPS/LAMMPS-29Oct2020-gpsmkl-2020-CUDA.eb
@@ -36,7 +36,7 @@ builddependencies = [
('archspec', '0.1.0', '-Python-%(pyver)s'),
]
dependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('Python', '3.8.5'),
('libpng', '1.6.37'),
('libjpeg-turbo', '2.0.5'),
diff --git a/Golden_Repo/l/libxc/README.md b/Golden_Repo/l/libxc/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..8b554daccd9029e27a209691fdab65caa674ff1d
--- /dev/null
+++ b/Golden_Repo/l/libxc/README.md
@@ -0,0 +1,25 @@
+# libxc
+
+The default version of `libxc` in the stage `2020` is `4.3.4`. We decided against the newer version `libxc/5.0.0`, as some applications would need to be patched. However, also not every application is working with version `4.3.4`, as the API changed between version 3 and 4. This lead to the fact that we need two different version:
+
+- `libxc/3.0.1`
+- `libxc/4.3.4`
+
+Both versions are installed for the following toolchains:
+
+- `GCC/9.3.0`
+- `iccifort-2020.2.254-GCC-9.3.0`
+
+## ABINIT
+
+`ABINIT/8.X` is only working with `libxc/3.0.1` due to changes in the API. Starting with `ABINIT/9.X` version 4.3.0 or later is supported.
+
+## Quantum ESPRESSO
+
+While Quantum ESPRESSO 6.6 would work with `libxc/5.0.0`, QE would require a patch. From the Quantum ESPRESSO User Guide (https://www.quantum-espresso.org/Doc/user_guide.pdf):
+
+**Note for version 5.0.0:** the `f03` interfaces are no longer available in `libxc` 5.0.0. They have been reintroduced in the current develop version. Version 5.0.0 is still usable, but, before compiling Quantum ESPRESSO, a string replacement is necessary, namely `‘xcf03’` must berepalced with `‘xcf90’` everywhere in the following files: `funct.f90, xcldalsdadrivers.f90, xcggadrivers.f90, xcmggadrivers.f90, dmxcdrivers.f90` and `dgcxcdrivers.f90` in `Modules` folder and `xctestqelibxc.f90` in `PP/src` folder.
+
+## Note for future Stage 2021
+
+Check if all application can work with the newest version of `libxc`, e.g. 5.0.0. One common version would be desirable.
diff --git a/Golden_Repo/l/libxc/libxc-3.0.1-GCC-9.3.0.eb b/Golden_Repo/l/libxc/libxc-3.0.1-GCC-9.3.0.eb
index 3041617f624344f7a24b7a980c25d692339abb56..c50654fe0634458014e8daea9605e157abf00352 100644
--- a/Golden_Repo/l/libxc/libxc-3.0.1-GCC-9.3.0.eb
+++ b/Golden_Repo/l/libxc/libxc-3.0.1-GCC-9.3.0.eb
@@ -9,7 +9,7 @@ Libxc is a library of exchange-correlation functionals for density-functional th
The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
"""
-site_contacts = 'Sebastian Achilles (s.achilles@fz-juelich.de)'
+site_contacts = 'Sebastian Achilles <s.achilles@fz-juelich.de>'
toolchain = {'name': 'GCC', 'version': '9.3.0'}
# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings.
diff --git a/Golden_Repo/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb b/Golden_Repo/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb
index fa00a133155d8ad92ca38b7c9140c67c8f9e6db0..89152e411f290f6a40395301a61b0b8e813ecd14 100644
--- a/Golden_Repo/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb
+++ b/Golden_Repo/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb
@@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz']
source_urls = ['https://github.com/hfp/libxsmm/archive/']
dependencies = [
- ('imkl', '2020.2.254', '', True),
+ ('imkl', '2020.2.254', '', SYSTEM),
]
# install both static and dynamic version
diff --git a/Golden_Repo/l/libxsmm/libxsmm-1.16.1-iccifort-2020.2.254-GCC-9.3.0.eb b/Golden_Repo/l/libxsmm/libxsmm-1.16.1-iccifort-2020.2.254-GCC-9.3.0.eb
index c46b09870e6687143d89f2af3f793fa669214f83..e424c8064e7b6844838cacdf2ad6b43828fb3615 100644
--- a/Golden_Repo/l/libxsmm/libxsmm-1.16.1-iccifort-2020.2.254-GCC-9.3.0.eb
+++ b/Golden_Repo/l/libxsmm/libxsmm-1.16.1-iccifort-2020.2.254-GCC-9.3.0.eb
@@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz']
source_urls = ['https://github.com/hfp/libxsmm/archive/']
dependencies = [
- ('imkl', '2020.2.254', '', True),
+ ('imkl', '2020.2.254', '', SYSTEM),
]
# install both static and dynamic version
diff --git a/Golden_Repo/m/magma/magma-2.5.4-gcccoremkl-9.3.0-2020.2.254.eb b/Golden_Repo/m/magma/magma-2.5.4-gcccoremkl-9.3.0-2020.2.254.eb
index 53c0ff98cae3078e56396775c7795f3713bafc30..f4def944cc3a11eb0bd00343ed7a9211df35b8b0 100644
--- a/Golden_Repo/m/magma/magma-2.5.4-gcccoremkl-9.3.0-2020.2.254.eb
+++ b/Golden_Repo/m/magma/magma-2.5.4-gcccoremkl-9.3.0-2020.2.254.eb
@@ -22,7 +22,7 @@ builddependencies = [
]
dependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
]
# make sure both static and shared libs are built
diff --git a/Golden_Repo/m/mpi4py/mpi4py-3.0.3-iimpi-2020-Python-3.8.5.eb b/Golden_Repo/m/mpi4py/mpi4py-3.0.3-iimpi-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..403d9b55a92573b407c346d59092cbc5d3d4ff38
--- /dev/null
+++ b/Golden_Repo/m/mpi4py/mpi4py-3.0.3-iimpi-2020-Python-3.8.5.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'mpi4py'
+version = '3.0.3'
+
+homepage = 'https://bitbucket.org/mpi4py/mpi4py'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors.
+"""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'iimpi', 'version': '2020'}
+
+source_urls = [BITBUCKET_DOWNLOADS]
+sources = [SOURCE_TAR_GZ]
+
+versionsuffix = '-Python-%(pyver)s'
+
+dependencies = [('Python', '3.8.5')]
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'],
+}
+
+moduleclass = 'mpi'
diff --git a/Golden_Repo/m/mpi4py/mpi4py-3.0.3-iompi-2020-Python-3.8.5.eb b/Golden_Repo/m/mpi4py/mpi4py-3.0.3-iompi-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..a047689c7a499148c6dfdb36da3811e0e47867c1
--- /dev/null
+++ b/Golden_Repo/m/mpi4py/mpi4py-3.0.3-iompi-2020-Python-3.8.5.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'mpi4py'
+version = '3.0.3'
+
+homepage = 'https://bitbucket.org/mpi4py/mpi4py'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors.
+"""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'iompi', 'version': '2020'}
+
+source_urls = [BITBUCKET_DOWNLOADS]
+sources = [SOURCE_TAR_GZ]
+
+versionsuffix = '-Python-%(pyver)s'
+
+dependencies = [('Python', '3.8.5')]
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'],
+}
+
+moduleclass = 'mpi'
diff --git a/Golden_Repo/m/mpi4py/mpi4py-3.0.3-ipsmpi-2020-mt-Python-3.8.5.eb b/Golden_Repo/m/mpi4py/mpi4py-3.0.3-ipsmpi-2020-mt-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..9aa9df5da18424443a1c83f9f11fc808e73686c6
--- /dev/null
+++ b/Golden_Repo/m/mpi4py/mpi4py-3.0.3-ipsmpi-2020-mt-Python-3.8.5.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'mpi4py'
+version = '3.0.3'
+
+homepage = 'https://bitbucket.org/mpi4py/mpi4py'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors.
+"""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'ipsmpi', 'version': '2020-mt'}
+
+source_urls = [BITBUCKET_DOWNLOADS]
+sources = [SOURCE_TAR_GZ]
+
+versionsuffix = '-Python-%(pyver)s'
+
+dependencies = [('Python', '3.8.5')]
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'],
+}
+
+moduleclass = 'mpi'
diff --git a/Golden_Repo/n/Nsight-Compute/Nsight-Compute-2020.3.0-GCCcore-9.3.0.eb b/Golden_Repo/n/Nsight-Compute/Nsight-Compute-2020.3.0-GCCcore-9.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..c6029d714fce57ffe2b3fdaa402cf00a1a29a11f
--- /dev/null
+++ b/Golden_Repo/n/Nsight-Compute/Nsight-Compute-2020.3.0-GCCcore-9.3.0.eb
@@ -0,0 +1,49 @@
+# jg (CSCS)
+# AH (JSC)
+easyblock = 'Binary'
+
+name = 'Nsight-Compute'
+version = '2020.3.0'
+homepage = 'https://developer.nvidia.com/nsight-compute'
+description = 'NVIDIA Nsight Compute is an interactive kernel profiler for CUDA applications'
+
+site_contacts = 'Andreas Herten <a.herten@fz-juelich.de>'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+# Download source binary package manually, requires Nvidia Developer Account
+# source_urls = 'https://developer.nvidia.com/nsight-compute'
+sources = [{
+ 'filename': 'nsight-compute-linux-%(version)s.18-29307467.run',
+ 'extract_cmd': '/bin/sh %s'
+}]
+checksums = ['af838473286e180904ec972892faf13ef4546b0e0fb539b87c06382daadfe2c1']
+
+# Not really necessary, but useful if we use this as a template for another package
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ # ('nvidia-driver', 'default', '', SYSTEM),
+ ('X11', '20200222')
+]
+
+extract_sources = True
+unpack_options = '--nochown --noexec --nox11 --target %(builddir)s'
+
+install_cmd = 'cp -r %(builddir)s/pkg/* %(installdir)s/'
+
+# Workaround due to wrong permissions once the files are extracted from the .run file
+postinstallcmds = ['find %(installdir)s -type f -and -executable -and ! -name "lib*" -exec chmod go+x {} \;']
+
+sanity_check_paths = {
+ 'files': ['ncu-ui', 'ncu'],
+ 'dirs': ['docs', 'extras', 'host', 'sections', 'target']
+}
+
+modluafooter = """
+add_property("arch","gpu")
+"""
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/o/Octave/Octave-5.2.0-gpsmkl-2020.eb b/Golden_Repo/o/Octave/Octave-5.2.0-gpsmkl-2020.eb
index f269520d75a34746df74ba1b52393662c994f6e6..7ba5b3411e29ac03d42f3a0faa7d8a941d06661a 100644
--- a/Golden_Repo/o/Octave/Octave-5.2.0-gpsmkl-2020.eb
+++ b/Golden_Repo/o/Octave/Octave-5.2.0-gpsmkl-2020.eb
@@ -35,8 +35,9 @@ dependencies = [
('GLPK', '4.65'),
('GL2PS', '1.4.2'),
('gnuplot', '5.2.8'),
- ('Java', '1.8', '', True),
+ ('Java', '1.8', '', SYSTEM),
('OpenGL', '2020'),
+ ('freeglut', '3.2.1'),
('zlib', '1.2.11'),
('Qhull', '2020.1'),
('Qt5', '5.14.2'),
@@ -61,6 +62,6 @@ sanity_check_paths = {
'dirs': []
}
-sanity_check_commands = [('octave', '--eval "1+2"')]
+sanity_check_commands = [('octave-cli', '--eval "1+2"')]
moduleclass = 'math'
diff --git a/Golden_Repo/o/Octave/Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb b/Golden_Repo/o/Octave/Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb
new file mode 100644
index 0000000000000000000000000000000000000000..dff7022148519d11b831f92623c453785bc3ee76
--- /dev/null
+++ b/Golden_Repo/o/Octave/Octave-6.1.0-gcccoremkl-9.3.0-2020.2.254-nompi.eb
@@ -0,0 +1,70 @@
+easyblock = 'ConfigureMake'
+
+name = 'Octave'
+version = '6.1.0'
+versionsuffix = '-nompi'
+
+homepage = 'http://www.gnu.org/software/octave/'
+description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations."""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+ ('binutils', '2.34'),
+ ('Bison', '3.6.4'),
+ ('flex', '2.6.4'),
+ ('pkg-config', '0.29.2'),
+ ('texinfo', '6.7'),
+ ('gperf', '3.1'),
+ ('Autotools', '20200321'),
+]
+
+dependencies = [
+ ('X11', '20200222'),
+ ('PCRE', '8.44'),
+ ('ncurses', '6.2'),
+ ('libreadline', '8.0'),
+ ('ARPACK-NG', '3.7.0', '-nompi'),
+ ('cURL', '7.71.1'),
+ ('FLTK', '1.3.5'),
+ ('fontconfig', '2.13.92'),
+ ('freetype', '2.10.1'),
+ ('GLPK', '4.65'),
+ ('GL2PS', '1.4.2'),
+ ('gnuplot', '5.2.8'),
+ ('Java', '15', '', SYSTEM),
+ ('OpenGL', '2020'),
+ ('freeglut', '3.2.1'),
+ ('zlib', '1.2.11'),
+ ('Qhull', '2020.1'),
+ ('Qt5', '5.14.2'),
+ ('HDF5', '1.10.6', '-serial'),
+ ('qrupdate', '1.1.2'),
+ ('GraphicsMagick', '1.3.35'),
+ ('FFTW', '3.3.8', '-nompi'),
+ ('texlive', '20200406'),
+]
+
+maxparallel = 12
+
+configopts = 'MOC=$EBROOTQT5/bin/moc '
+configopts += 'UIC=$EBROOTQT5/bin/uic '
+configopts += 'RCC=$EBROOTQT5/bin/rcc '
+configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease '
+configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs '
+# correct for both GCC and Intel compilers
+configopts += '--enable-fortran-calling-convention=gfortran '
+
+sanity_check_paths = {
+ 'files': ['bin/octave'],
+ 'dirs': []
+}
+
+sanity_check_commands = [('octave-cli', '--eval "1+2"')]
+
+moduleclass = 'math'
diff --git a/Golden_Repo/o/Octave/Octave-6.1.0-gpsmkl-2020.eb b/Golden_Repo/o/Octave/Octave-6.1.0-gpsmkl-2020.eb
new file mode 100644
index 0000000000000000000000000000000000000000..c18bec08905494c893b7a97af80a1976f818a7ed
--- /dev/null
+++ b/Golden_Repo/o/Octave/Octave-6.1.0-gpsmkl-2020.eb
@@ -0,0 +1,67 @@
+easyblock = 'ConfigureMake'
+
+name = 'Octave'
+version = '6.1.0'
+
+homepage = 'http://www.gnu.org/software/octave/'
+description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations."""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'gpsmkl', 'version': '2020'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+ ('Bison', '3.6.4'),
+ ('flex', '2.6.4'),
+ ('pkg-config', '0.29.2'),
+ ('texinfo', '6.7'),
+ ('gperf', '3.1'),
+ ('Autotools', '20200321'),
+]
+
+dependencies = [
+ ('X11', '20200222'),
+ ('PCRE', '8.44'),
+ ('ncurses', '6.2'),
+ ('libreadline', '8.0'),
+ ('ARPACK-NG', '3.7.0'),
+ ('cURL', '7.71.1'),
+ ('FLTK', '1.3.5'),
+ ('fontconfig', '2.13.92'),
+ ('freetype', '2.10.1'),
+ ('GLPK', '4.65'),
+ ('GL2PS', '1.4.2'),
+ ('gnuplot', '5.2.8'),
+ ('Java', '15', '', SYSTEM),
+ ('OpenGL', '2020'),
+ ('freeglut', '3.2.1'),
+ ('zlib', '1.2.11'),
+ ('Qhull', '2020.1'),
+ ('Qt5', '5.14.2'),
+ ('HDF5', '1.10.6'),
+ ('qrupdate', '1.1.2'),
+ ('SuiteSparse', '5.7.1', '-CUDA'),
+ ('GraphicsMagick', '1.3.35'),
+ ('FFTW', '3.3.8'),
+ ('texlive', '20200406'),
+]
+
+configopts = 'MOC=$EBROOTQT5/bin/moc '
+configopts += 'UIC=$EBROOTQT5/bin/uic '
+configopts += 'RCC=$EBROOTQT5/bin/rcc '
+configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease '
+configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs '
+# correct for both GCC and Intel compilers
+configopts += '--enable-fortran-calling-convention=gfortran '
+
+sanity_check_paths = {
+ 'files': ['bin/octave'],
+ 'dirs': []
+}
+
+sanity_check_commands = [('octave-cli', '--eval "1+2"')]
+
+moduleclass = 'math'
diff --git a/Golden_Repo/p/Pillow-SIMD/Pillow-SIMD-7.0.0.post3-GCCcore-9.3.0-Python-3.8.5.eb b/Golden_Repo/p/Pillow-SIMD/Pillow-SIMD-7.0.0.post3-GCCcore-9.3.0-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..c2110159fe17783ec386b8ca4e083c49df3e6ee2
--- /dev/null
+++ b/Golden_Repo/p/Pillow-SIMD/Pillow-SIMD-7.0.0.post3-GCCcore-9.3.0-Python-3.8.5.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonPackage'
+
+name = 'Pillow-SIMD'
+version = '7.0.0.post3'
+versionsuffix = '-Python-%(pyver)s'
+
+
+homepage = 'https://github.com/uploadcare/pillow-simd'
+description = """Pillow-SIMD is a drop-in replacement for Pillow with AVX support
+Pillow is the 'friendly PIL fork' by Alex Clark and Contributors.
+ PIL is the Python Imaging Library by Fredrik Lundh and Contributors."""
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+source_urls = ['https://github.com/uploadcare/pillow-simd/archive/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [('binutils', '2.34')]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('libjpeg-turbo', '2.0.5'),
+ ('libpng', '1.6.37'),
+ ('zlib', '1.2.11'),
+ ('LibTIFF', '4.1.0'),
+ ('freetype', '2.10.1')
+]
+
+use_pip = True
+download_dep_fail = True
+
+options = {'modulename': 'PIL'}
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'],
+}
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/p/PostgreSQL/PostgreSQL-12.3-GCCcore-9.3.0.eb b/Golden_Repo/p/PostgreSQL/PostgreSQL-12.3-GCCcore-9.3.0.eb
index e18f87f8d34dd5f804eeca69be97bacf47e6a11c..a869d62bf93773a4b99e88d4f7efd384b7c0bad5 100644
--- a/Golden_Repo/p/PostgreSQL/PostgreSQL-12.3-GCCcore-9.3.0.eb
+++ b/Golden_Repo/p/PostgreSQL/PostgreSQL-12.3-GCCcore-9.3.0.eb
@@ -25,7 +25,7 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
osdependencies = [('openssl-devel', 'libssl-dev')]
dependencies = [
- ('Java', '1.8', '', True),
+ ('Java', '1.8', '', SYSTEM),
('libreadline', '8.0'),
('zlib', '1.2.11'),
]
diff --git a/Golden_Repo/p/PyFerret/Faddpath b/Golden_Repo/p/PyFerret/Faddpath
new file mode 100755
index 0000000000000000000000000000000000000000..e97792348b685397f6c75bcffc2aa697be7749ea
--- /dev/null
+++ b/Golden_Repo/p/PyFerret/Faddpath
@@ -0,0 +1,11 @@
+# Wrapper to compensate for the lack of function definition (defined when sourcing a PyFerret script)
+#!/bin/sh
+if [ -n "$*" ]
+then
+ export FER_GO="$FER_GO $*"
+ export FER_DATA="$FER_DATA $*"
+ export FER_DESCR="$FER_DESCR $*"
+ export FER_GRIDS="$FER_GRIDS $*"
+else
+ echo " Usage: Faddpath new_directory_1 ..."
+fi
diff --git a/Golden_Repo/p/PyFerret/PyFerret-7.6.3-gpsmkl-2020-Python-3.8.5.eb b/Golden_Repo/p/PyFerret/PyFerret-7.6.3-gpsmkl-2020-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..c3fc983f42e8f61935e007745a9616463676a521
--- /dev/null
+++ b/Golden_Repo/p/PyFerret/PyFerret-7.6.3-gpsmkl-2020-Python-3.8.5.eb
@@ -0,0 +1,96 @@
+easyblock = 'ConfigureMake'
+
+name = 'PyFerret'
+version = '7.6.3'
+local_dataset_ver = '7.6'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://ferret.pmel.noaa.gov/'
+description = '''PyFerret is an interactive computer visualization and analysis environment
+designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.'''
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gpsmkl', 'version': '2020'}
+toolchainopts = {'usempi': False}
+
+source_urls = [
+ 'https://github.com/NOAA-PMEL/PyFerret/archive/',
+ 'https://github.com/NOAA-PMEL/FerretDatasets/archive/'
+]
+sources = [
+ 'v%(version)s.tar.gz',
+ 'v7.6.tar.gz'
+]
+
+checksums = [
+ ('sha256', 'f062c20bedf64713f57c3d45aaeb63eb9b4d3ba622e5c5e4a99e61fdf08d2224'),
+ ('sha256', 'b2fef758ec1817c1c19e6225857ca3a82c727d209ed7fd4697d45c5533bb2c72'),
+]
+
+patches = [
+ ('pyferret', 'bin'),
+ ('Faddpath', 'bin'),
+ ('configure_pyferret-7.6.3_stage2020.patch')
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
+ ('netCDF', '4.7.4'),
+ ('netCDF-Fortran', '4.5.3'),
+ ('HDF5', '1.10.6'),
+ ('zlib', '1.2.11'),
+ ('cURL', '7.71.1'),
+ ('Pango', '1.44.7'),
+ ('libpng', '1.6.37'),
+ ('cairo', '1.17.2'),
+ ('freetype', '2.10.1'),
+ ('fontconfig', '2.13.92'),
+ ('pixman', '0.40.0'),
+ ('GLib', '2.64.4'),
+ ('PyQt5', '5.15.1', versionsuffix),
+]
+
+maxparallel = 1 # yes!
+
+skipsteps = ['configure']
+start_dir = '%(builddir)s/%(name)s-%(version)s'
+
+prebuildopts = ['export FER_SRC_PREFIX=%(builddir)s/%(name)s-%(version)s && ']
+
+preinstallopts = ['export FER_DIR=%(installdir)s && ']
+
+modextrapaths = {
+ 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+ 'LD_LIBRARY_PATH': 'lib/python%(pyshortver)s/site-packages/pyferret',
+}
+
+modextravars = {
+ 'FER_DIR': '%(installdir)s',
+ 'FER_DSETS': '%(installdir)s/datasets',
+ # 'FER_WEB_BROWSER': 'firefox', # Probably nobody should use this
+ 'FER_DATA_THREDDS': 'http://ferret.pmel.noaa.gov/geoide/geoIDECleanCatalog.xml %(installdir)s/datasets',
+ 'FER_DATA': '. %(installdir)s/datasets/data %(installdir)s/go %(installdir)s/examples',
+ 'FER_DESCR': '. %(installdir)s/datasets/descr',
+ 'FER_GRIDS': '. %(installdir)s/datasets/grids',
+ 'FER_GO': '. %(installdir)s/go %(installdir)s/examples %(installdir)s/contrib',
+ 'FER_EXTERNAL_FUNCTIONS': '%(installdir)s/ext_func/libs',
+ 'PYFER_EXTERNAL_FUNCTIONS': '%(installdir)s/ext_func/pylibs',
+ 'FER_PALETTE': '. %(installdir)s/ppl',
+ 'SPECTRA': '%(installdir)s/ppl',
+ 'FER_FONTS': '%(installdir)s/ppl/fonts',
+ 'PLOTFONTS': '%(installdir)s/ppl/fonts',
+ 'FER_LIBS': '%(installdir)s/lib',
+ 'FER_DAT': '%(installdir)s',
+}
+
+postinstallcmds = [
+ 'chmod +x %(installdir)s/bin/pyferret',
+ 'mkdir %(installdir)s/datasets',
+ 'mv %%(builddir)s/FerretDatasets-%s/data %%(installdir)s/datasets' % local_dataset_ver,
+ 'mv %%(builddir)s/FerretDatasets-%s/descr %%(installdir)s/datasets' % local_dataset_ver,
+ 'mv %%(builddir)s/FerretDatasets-%s/grids %%(installdir)s/datasets' % local_dataset_ver,
+]
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/p/PyFerret/configure_pyferret-7.6.3_stage2020.patch b/Golden_Repo/p/PyFerret/configure_pyferret-7.6.3_stage2020.patch
new file mode 100644
index 0000000000000000000000000000000000000000..39846aaef0874e38f911531151609f56ef3b72e4
--- /dev/null
+++ b/Golden_Repo/p/PyFerret/configure_pyferret-7.6.3_stage2020.patch
@@ -0,0 +1,438 @@
+diff -Naur PyFerret-7.6.3.orig/external_functions/ef_utility/site_specific.mk PyFerret-7.6.3/external_functions/ef_utility/site_specific.mk
+--- PyFerret-7.6.3.orig/external_functions/ef_utility/site_specific.mk 1970-01-01 01:00:00.000000000 +0100
++++ PyFerret-7.6.3/external_functions/ef_utility/site_specific.mk 2020-12-17 15:22:43.154040000 +0100
+@@ -0,0 +1,75 @@
++## Site-dependent definitions included in external function Makefiles
++## of an installed PyFerret directory.
++
++## =========================
++## Machine type for which to build Ferret/PyFerret
++## x86_64-linux for 64-bit RHEL
++## x86_64-linux-gnu for 64-bit Ubuntu and many "free" Linux systems
++## i386-linux for 32-bit RHEL
++## i386-linux-gnu for 32-bit Ubuntu and many "free" Linux systems
++## intel-mac for Max OSX
++## This value is used to determine which platform_specific.mk
++## file to include in the Makefiles.
++## =========================
++# BUILDTYPE = $(HOSTTYPE)
++BUILDTYPE = x86_64-linux
++# BUILDTYPE = x86_64-linux-gnu
++# BUILDTYPE = i386-linux
++# BUILDTYPE = i386-linux-gnu
++# BUILDTYPE = intel-mac
++
++## =========================
++## INSTALL_FER_DIR and PYTHON_EXE are only used to construct
++## the location of pyferret library. The library should be
++## (for either 32-bit or 64-bit Linux)
++## $(INSTALL_FER_DIR)/lib/$(PYTHON_EXE)/site-package/pyferret/libpyferret.so
++## or possibly (for 64-bit Linux only)
++## $(INSTALL_FER_DIR)/lib64/$(PYTHON_EXE)/site-package/pyferret/libpyferret.so
++##
++## PyFerret installation directory, usually just $(FER_DIR)
++## Must be $(FER_DIR) when building pyferret from source.
++## (This file is also found in PyFerret installations, thus the option.)
++## =========================
++# INSTALL_FER_DIR = $(HOME)/PyFerret
++INSTALL_FER_DIR = $(FER_DIR)
++
++## =========================
++## C and Fortran compilers to use. The construct "$(shell which gcc)" assigns
++## the response to "which gcc" run from a Bourne shell (such as bash).
++## When compiling for Mac OS X, one may wish to use clang instead of gcc.
++## If you wish to use values already defined in you shell environment when
++## you run make, comment out all definitions of CC and FC (do NOT leave blank).
++## =========================
++# CC = $(shell which clang)
++CC = $(shell which gcc)
++FC = $(shell which gfortran)
++
++## =========================
++## Linker used to generate executables and shared-object libraries.
++## Normally the Fortran compiler is used which then calls the actual
++## linker with appropriate flags and system-level Fortran libraries.
++## The construct "$(shell which gfortran)" assigns the response to
++## "which gfortran" run from a Bourne shell (such as bash).
++## If you wish to use a value already defined in you shell environment when
++## you run make, comment out all definitions of LD (do NOT leave blank).
++## =========================
++LD = $(shell which gfortran)
++
++## =========================
++## Python version used by PyFerret
++## =========================
++# PYTHON_EXE = python2.6
++# PYTHON_EXE = python2.7
++# PYTHON_EXE = python3.6
++# PYTHON_EXE = python3.7
++PYTHON_EXE = python3.8
++
++## =========================
++## FER_LOCAL_EXTFCNS is the directory in which to install
++## the Ferret Fortran external functions. The example
++## functions that come with the PyFerret installation are
++## installed in $(INSTALL_FER_DIR)/ext_func/pylibs
++## =========================
++FER_LOCAL_EXTFCNS = $(INSTALL_FER_DIR)/ext_func/pylibs
++
++##
+diff -Naur PyFerret-7.6.3.orig/Makefile PyFerret-7.6.3/Makefile
+--- PyFerret-7.6.3.orig/Makefile 2020-09-28 21:10:48.000000000 +0200
++++ PyFerret-7.6.3/Makefile 2020-12-17 14:37:08.501952000 +0100
+@@ -74,10 +74,12 @@
+ export CFLAGS="$(CFLAGS) -DNDEBUG -O" ; \
+ export BUILDTYPE=$(BUILDTYPE) ; \
+ export NETCDF_LIBDIR=$(NETCDF_LIBDIR) ; \
++ export NETCDFFORTRAN_LIBDIR=$(NETCDFFORTRAN_LIBDIR) ; \
+ export HDF5_LIBDIR=$(HDF5_LIBDIR) ; \
+ export SZ_LIBDIR=$(SZ_LIBDIR) ; \
+ export CAIRO_LIBDIR=$(CAIRO_LIBDIR) ; \
+ export PIXMAN_LIBDIR=$(PIXMAN_LIBDIR) ; \
++ export HARFBUZZ_LIBDIR=$(HARFBUZZ_LIBDIR) ; \
+ export PANGO_LIBDIR=$(PANGO_LIBDIR) ; \
+ export GLIB2_LIBDIR=$(GLIB2_LIBDIR) ; \
+ export GFORTRAN_LIB=$(GFORTRAN_LIB) ; \
+@@ -94,10 +96,12 @@
+ export CFLAGS="$(CFLAGS) -DNDEBUG -O" ; \
+ export BUILDTYPE=$(BUILDTYPE) ; \
+ export NETCDF_LIBDIR=$(NETCDF_LIBDIR) ; \
++ export NETCDFFORTRAN_LIBDIR=$(NETCDFFORTRAN_LIBDIR) ; \
+ export HDF5_LIBDIR=$(HDF5_LIBDIR) ; \
+ export SZ_LIBDIR=$(SZ_LIBDIR) ; \
+ export CAIRO_LIBDIR=$(CAIRO_LIBDIR) ; \
+ export PIXMAN_LIBDIR=$(PIXMAN_LIBDIR) ; \
++ export HARFBUZZ_LIBDIR=$(HARFBUZZ_LIBDIR) ; \
+ export PANGO_LIBDIR=$(PANGO_LIBDIR) ; \
+ export GLIB2_LIBDIR=$(GLIB2_LIBDIR) ; \
+ export GFORTRAN_LIB=$(GFORTRAN_LIB) ; \
+@@ -117,10 +121,12 @@
+ export CFLAGS="$(CFLAGS) -UNDEBUG -O0 -g" ; \
+ export BUILDTYPE=$(BUILDTYPE) ; \
+ export NETCDF_LIBDIR=$(NETCDF_LIBDIR) ; \
++ export NETCDFFORTRAN_LIBDIR=$(NETCDFFORTRAN_LIBDIR) ; \
+ export HDF5_LIBDIR=$(HDF5_LIBDIR) ; \
+ export SZ_LIBDIR=$(SZ_LIBDIR) ; \
+ export CAIRO_LIBDIR=$(CAIRO_LIBDIR) ; \
+ export PIXMAN_LIBDIR=$(PIXMAN_LIBDIR) ; \
++ export HARFBUZZ_LIBDIR=$(HARFBUZZ_LIBDIR) ; \
+ export PANGO_LIBDIR=$(PANGO_LIBDIR) ; \
+ export GLIB2_LIBDIR=$(GLIB2_LIBDIR) ; \
+ export GFORTRAN_LIB=$(GFORTRAN_LIB) ; \
+@@ -137,10 +143,12 @@
+ export CFLAGS="$(CFLAGS) -UNDEBUG -O0 -g" ; \
+ export BUILDTYPE=$(BUILDTYPE) ; \
+ export NETCDF_LIBDIR=$(NETCDF_LIBDIR) ; \
++ export NETCDFFORTRAN_LIBDIR=$(NETCDFFORTRAN_LIBDIR) ; \
+ export HDF5_LIBDIR=$(HDF5_LIBDIR) ; \
+ export SZ_LIBDIR=$(SZ_LIBDIR) ; \
+ export CAIRO_LIBDIR=$(CAIRO_LIBDIR) ; \
+ export PIXMAN_LIBDIR=$(PIXMAN_LIBDIR) ; \
++ export HARFBUZZ_LIBDIR=$(HARFBUZZ_LIBDIR) ; \
+ export PANGO_LIBDIR=$(PANGO_LIBDIR) ; \
+ export GLIB2_LIBDIR=$(GLIB2_LIBDIR) ; \
+ export GFORTRAN_LIB=$(GFORTRAN_LIB) ; \
+@@ -185,10 +193,12 @@
+ export CFLAGS="$(CFLAGS) -O" ; \
+ export BUILDTYPE=$(BUILDTYPE) ; \
+ export NETCDF_LIBDIR=$(NETCDF_LIBDIR) ; \
++ export NETCDFFORTRAN_LIBDIR=$(NETCDFFORTRAN_LIBDIR) ; \
+ export HDF5_LIBDIR=$(HDF5_LIBDIR) ; \
+ export SZ_LIBDIR=$(SZ_LIBDIR) ; \
+ export CAIRO_LIBDIR=$(CAIRO_LIBDIR) ; \
+ export PIXMAN_LIBDIR=$(PIXMAN_LIBDIR) ; \
++ export HARFBUZZ_LIBDIR=$(HARFBUZZ_LIBDIR) ; \
+ export PANGO_LIBDIR=$(PANGO_LIBDIR) ; \
+ export GLIB2_LIBDIR=$(GLIB2_LIBDIR) ; \
+ export GFORTRAN_LIB=$(GFORTRAN_LIB) ; \
+diff -Naur PyFerret-7.6.3.orig/platform_specific.mk.x86_64-linux PyFerret-7.6.3/platform_specific.mk.x86_64-linux
+--- PyFerret-7.6.3.orig/platform_specific.mk.x86_64-linux 2020-09-28 21:10:48.000000000 +0200
++++ PyFerret-7.6.3/platform_specific.mk.x86_64-linux 2020-12-17 14:36:27.694118000 +0100
+@@ -17,6 +17,7 @@
+ # Include directories
+ #
+ NETCDF_INCLUDE = -I$(NETCDF_LIBDIR)/../include
++ NETCDFFORTRAN_INCLUDE = -I$(NETCDFFORTRAN_LIBDIR)/../include
+
+ ifeq ($(strip $(HDF5_LIBDIR)),)
+ HDF5_INCLUDE =
+@@ -36,6 +37,12 @@
+ PIXMAN_INCLUDE = -I$(PIXMAN_LIBDIR)/../include
+ endif
+
++ifeq ($(strip $(HARFBUZZ_LIBDIR)),)
++ HARFBUZZ_INCLUDE = -I/usr/include/harfbuzz
++else
++ HARFBUZZ_INCLUDE = -I$(HARFBUZZ_LIBDIR)/../include/harfbuzz
++endif
++
+ ifeq ($(strip $(PANGO_LIBDIR)),)
+ PANGO_INCLUDE = -I/usr/include/pango-1.0
+ else
+@@ -64,9 +71,11 @@
+ -I$(DIR_PREFIX)/pyfermod \
+ -I$(DIR_PREFIX)/external_functions/ef_utility \
+ $(NETCDF_INCLUDE) \
++ $(NETCDFFORTRAN_INCLUDE) \
+ $(HDF5_INCLUDE) \
+ $(CAIRO_INCLUDE) \
+ $(PIXMAN_INCLUDE) \
++ $(HARFBUZZ_INCLUDE) \
+ $(PANGO_INCLUDE) \
+ $(GLIB2_INCLUDE)
+
+diff -Naur PyFerret-7.6.3.orig/setup.py PyFerret-7.6.3/setup.py
+--- PyFerret-7.6.3.orig/setup.py 2020-09-28 21:10:48.000000000 +0200
++++ PyFerret-7.6.3/setup.py 2020-12-17 14:36:06.465376000 +0100
+@@ -30,6 +30,13 @@
+ if not netcdf_libdir:
+ raise ValueError("Environment variable NETCDF_LIBDIR is not defined")
+
++# NETCDFFORTAN_LIBDIR must be given, either for the static library or the shared-object library
++netcdffortran_libdir = os.getenv("NETCDFFORTRAN_LIBDIR")
++if netcdffortran_libdir:
++ netcdffortran_libdir = netcdffortran_libdir.strip()
++else:
++ netcdffortran_libdir = netcdf_libdir
++
+ # HDF5_LIBDIR is only given if the HDF5 and NetCDF libraries are to be statically linked
+ hdf5_libdir = os.getenv("HDF5_LIBDIR")
+ if hdf5_libdir:
+@@ -50,6 +57,11 @@
+ if pixman_libdir:
+ pixman_libdir = pixman_libdir.strip()
+
++# HARFBUZZ gives a non-standard location of the harfbuzz libraries
++harfbuzz_libdir = os.getenv("HARFBUZZ_LIBDIR")
++if harfbuzz_libdir:
++ harfbuzz_libdir = harfbuzz_libdir.strip()
++
+ # PANGO_LIBDIR gives a non-standard location of the pango libraries
+ pango_libdir = os.getenv("PANGO_LIBDIR")
+ if pango_libdir:
+@@ -66,6 +78,8 @@
+
+ # The list of additional directories to examine for libraries
+ libdir_list = [ "lib", netcdf_libdir, ]
++if netcdffortran_libdir:
++ libdir_list.append(netcdffortran_libdir)
+ if hdf5_libdir:
+ libdir_list.append(hdf5_libdir)
+ if sz_libdir:
+@@ -74,6 +88,8 @@
+ libdir_list.append(cairo_libdir)
+ if pixman_libdir:
+ libdir_list.append(pixman_libdir)
++if harfbuzz_libdir:
++ libdir_list.append(harfbuzz_libdir)
+ if pango_libdir:
+ libdir_list.append(pango_libdir)
+ libdir_list.append(python_libdir)
+@@ -103,7 +119,7 @@
+ # The hdf5 libraries are only used to resolve netcdf library function
+ # calls when statically linking in the netcdf libraries.
+ if hdf5_libdir:
+- netcdff_lib = os.path.join(netcdf_libdir, "libnetcdff.a")
++ netcdff_lib = os.path.join(netcdffortran_libdir, "libnetcdff.a")
+ addn_link_args.append(netcdff_lib)
+ netcdf_lib = os.path.join(netcdf_libdir, "libnetcdf.a")
+ addn_link_args.append(netcdf_lib)
+diff -Naur PyFerret-7.6.3.orig/site_specific.mk PyFerret-7.6.3/site_specific.mk
+--- PyFerret-7.6.3.orig/site_specific.mk 1970-01-01 01:00:00.000000000 +0100
++++ PyFerret-7.6.3/site_specific.mk 2020-12-17 14:41:42.140897914 +0100
+@@ -0,0 +1,195 @@
++## Site-dependent definitions included in Makefiles
++
++## !!! Also verify the values in external_functions/ef_utility/site_specific.mk !!!
++
++## =========================
++## Full path name of the directory containing this file (the ferret root directory).
++## Do not use $(shell pwd) since this is included in Makefiles in other directories.
++## =========================
++# DIR_PREFIX = $(HOME)/build/pyferret_dev
++# DIR_PREFIX = $(HOME)/svn/pyferret
++DIR_PREFIX = $(FER_SRC_PREFIX)
++
++## =========================
++## Installation directory for built PyFerret.
++## Using the "install" Makefile target creates a generic pyferret-*.tar.gz file
++## and then extracts it to create a PyFerret installation at this location.
++## =========================
++# INSTALL_FER_DIR = $(HOME)/ferret_distributions/rhel6_64
++INSTALL_FER_DIR = $(FER_DIR)
++
++## =========================
++## Machine type for which to build Ferret/PyFerret
++## x86_64-linux for 64-bit RHEL
++## x86_64-linux-gnu for 64-bit Ubuntu and many "free" Linux systems
++## i386-linux for 32-bit RHEL
++## i386-linux-gnu for 32-bit Ubuntu and many "free" Linux systems
++## intel-mac for Mac OSX
++## =========================
++# BUILDTYPE = $(HOSTTYPE)
++BUILDTYPE = x86_64-linux
++# BUILDTYPE = x86_64-linux-gnu
++# BUILDTYPE = i386-linux
++# BUILDTYPE = i386-linux-gnu
++# BUILDTYPE = intel-mac
++
++## =========================
++## C and Fortran compilers to use. The construct "$(shell which gcc)" assigns
++## the response to "which gcc" run from a Bourne shell (such as bash).
++## When compiling for Mac OS X, one may wish to use clang instead of gcc.
++## If you wish to use values already defined in you shell environment when
++## you run make, comment out all definitions of CC and FC (do NOT leave blank).
++## =========================
++# CC = $(shell which clang)
++CC = $(shell which gcc)
++FC = $(shell which gfortran)
++
++## =========================
++## Python executable to invoke for build and install.
++## =========================
++# PYTHON_EXE = python2.6
++# PYTHON_EXE = python2.7
++# PYTHON_EXE = python3.6
++# PYTHON_EXE = python3.7
++PYTHON_EXE = python3.8
++
++## =========================
++## Full path to the python include files directory.
++## Should not need any modifications.
++## =========================
++PYTHONINCDIR := $(shell $(PYTHON_EXE) -c "from __future__ import print_function ; import distutils.sysconfig; print(distutils.sysconfig.get_python_inc())")
++
++## =========================
++## If given and not empty, the full path name to the gfortran library to use.
++## This is primarily used for the intel-mac build.
++## The given scripts (commented out) should provide the correct value for the gfortran libraries.
++## If empty or not given, the gfortran library is linked in using the "-lgfortran" flag.
++## =========================
++# GFORTRAN_LIB = $(shell $(FC) --print-file-name=libgfortran.dylib)
++# GFORTRAN_LIB = $(shell $(FC) --print-file-name=libgfortran.a)
++GFORTRAN_LIB =
++
++## =========================
++## Directory containing the Cairo static libraries (v1.12 or later).
++## Include files are assumed to be located in an "include" sibling directory.
++## If given and not empty, the Cairo static libraries found under this directory will be used.
++## If empty or not given, the system's Cairo shared libraries will be used.
++## =========================
++# CAIRO_LIBDIR = /usr/local/cairo/lib
++# CAIRO_LIBDIR = $(HOME)/.local/lib
++# CAIRO_LIBDIR = /usr/local/lib
++# CAIRO_LIBDIR = /p/software/juwels/stages/Devel-2020/software/cairo/1.17.2-GCCcore-9.3.0/lib64
++CAIRO_LIBDIR = $(EBROOTCAIRO)/lib
++
++## =========================
++## Directory containing the Pixman static libraries used by the above Cairo static libraries.
++## Include files are assumed to be located in an "include" sibling directory.
++## If given and not empty, the Pixman-1 static libraries found in this directory will be used.
++## If empty or not given, the system's Pixman-1 shared library will be used.
++## This value should be empty or not given if CAIRO_LIBDIR is empty or not given.
++## =========================
++# PIXMAN_LIBDIR = /usr/local/pixman/lib
++# PIXMAN_LIBDIR = $(HOME)/.local/lib
++# PIXMAN_LIBDIR = /usr/local/lib
++# PIXMAN_LIBDIR = /gpfs/software/juwels/stages/Devel-2020/software/pixman/0.40.0-GCCcore-9.3.0/lib
++PIXMAN_LIBDIR = $(EBROOTPIXMAN)/lib
++
++## =========================
++## Directory containing the HarfBuzz shared libraries.
++## Include files are assumed to be located in an "include" sibling directory.
++## If given and not empty, the HarfBuzz shared libraries under this directory are used.
++## If empty or not given, the system's HarfBuzz shared libraries are used.
++## This value should be empty or not given if CAIRO_LIBDIR is empty or not given.
++## =========================
++#HARFBUZZ_LIBDIR = /p/software/juwels/stages/Devel-2020/software/HarfBuzz/2.6.7-GCCcore-9.3.0/lib64
++HARFBUZZ_LIBDIR = $(EBROOTHARFBUZZ)/lib
++
++## =========================
++## Directory containing the Pango shared libraries.
++## Include files are assumed to be located in an "include" sibling directory.
++## If given and not empty, the Pango shared libraries under this directory are used.
++## If empty or not given, the system's Pango shared libraries are used.
++## This value should be empty or not given if CAIRO_LIBDIR is empty or not given.
++## =========================
++# PANGO_LIBDIR = $(HOME)/.local/lib
++# PANGO_LIBDIR = /usr/local/lib
++# PANGO_LIBDIR = /gpfs/software/juwels/stages/Devel-2020/software/Pango/1.44.7-GCCcore-9.3.0/lib
++PANGO_LIBDIR = $(EBROOTPANGO)/lib
++
++## =========================
++## Library directory containing a "glib-2.0" subdirectory with GLib-2.0 include file(s)
++## (yes, a little unusual) used by the above Pango shared libraries.
++## An "include" sibling directory containing a "glib-2.0" subdirectory with more
++## GLib-2.0 include files is assumed to exist.
++## If given and not empty, GLib-2.0 include files under this directory are used.
++## If empty or not given, the system's GLib-2.0 shared libraries are used.
++## This value should be empty or not given if PANGO_LIBDIR is empty or not given.
++## =========================
++# GLIB2_LIBDIR = $(HOME)/.local/lib
++# GLIB2_LIBDIR = /usr/local/lib
++# GLIB2_LIBDIR = /gpfs/software/juwels/stages/Devel-2020/software/GLib/2.64.4-GCCcore-9.3.0/lib
++GLIB2_LIBDIR = $(EBROOTGLIB)/lib
++
++## =========================
++## Directory containing the HDF5 static libraries.
++## Include files are assumed to be located in an "include" sibling directory.
++## If given and not empty, HDF5 and NetCDF static libraries will be used.
++## If empty or not given, NetCDF shared libraries (which specify the HDF5 and
++## compression libraries required) will be used.
++## =========================
++# HDF5_LIBDIR = /usr/local/hdf5/lib
++# HDF5_LIBDIR = $(HOME)/.local/lib
++# HDF5_LIBDIR = /usr/local/lib
++# HDF5_LIBDIR = /usr/lib64
++# HDF5_LIBDIR = /usr/lib
++# HDF5_LIBDIR = /p/software/juwels/stages/Devel-2020/software/HDF5/1.10.6-gompi-2020/lib64
++# HDF5_LIBDIR = $(EBROOTHDF5)/lib
++
++## =========================
++## Location of the SZ compression static library.
++## This value should be given only if the SZ compression library was used in
++## building the HDF5 library, and the NetCDF and HDF5 static libraries are being
++## used (HDF5_LIBDIR is given and not empty).
++## If given and not empty, the SZ compression static library is used.
++## If empty or not given, the SZ compression library will not be used
++## (which is what you want if the HDF5 libraries were built using the Z compression library).
++## =========================
++# SZ_LIBDIR = $(HOME)/.local/lib
++# SZ_LIBDIR = /usr/local/lib
++# SZ_LIBDIR = /usr/lib64
++# SZ_LIBDIR = /usr/lib
++# SZ_LIBDIR = /gpfs/software/juwels/stages/Devel-2020/software/Szip/2.1.1-GCCcore-9.3.0/lib
++SZ_LIBDIR = $(EBROOTSZIP)/lib
++
++## =========================
++## Location of the NetCDF libraries.
++## Include files are assumed to be located in an "include" sibling directory.
++## If HDF5_LIBDIR is given and not empty, the static libraries will be used
++## (along with the HDF5 static libraries).
++## If HDF5_LIBDIR is empty or not given, NetCDF shared libraries will be used.
++## =========================
++# NETCDF_LIBDIR = /usr/local/netcdf/lib
++# NETCDF_LIBDIR = $(HOME)/.local/lib
++# NETCDF_LIBDIR = /usr/local/lib
++# NETCDF_LIBDIR = /usr/lib64
++# NETCDF_LIBDIR = /usr/lib
++# NETCDF_LIBDIR = /p/software/juwels/stages/Devel-2020/software/netCDF/4.7.4-gompi-2020/lib64
++NETCDF_LIBDIR = $(EBROOTNETCDF)/lib64
++
++## =========================
++## Location of the NetCDF fortran libraries.
++## Include files are assumed to be located in an "include" sibling directory.
++## If HDF5_LIBDIR is given and not empty, the static libraries will be used
++## (along with the HDF5 static libraries).
++## If HDF5_LIBDIR is empty or not given, NetCDF fortran shared libraries will be used.
++## If empty or not given, the netcdf fortran shared libraries will be searched for in NETCDF_LIBDIR
++## =========================
++# NETCDFFORTRAN_LIBDIR = /usr/local/netcdf/lib
++# NETCDFFORTRAN_LIBDIR = $(HOME)/.local/lib
++# NETCDFFORTRAN_LIBDIR = /usr/local/lib
++# NETCDFFORTRAN_LIBDIR = /usr/lib64
++# NETCDFFORTRAN_LIBDIR = /usr/lib
++# NETCDFFORTRAN_LIBDIR = /p/software/juwels/stages/Devel-2020/software/netCDF-Fortran/4.5.3-gompi-2020/lib64
++NETCDFFORTRAN_LIBDIR = $(EBROOTNETCDFMINFORTRAN)/lib
++
++##
diff --git a/Golden_Repo/p/PyFerret/pyferret b/Golden_Repo/p/PyFerret/pyferret
new file mode 100755
index 0000000000000000000000000000000000000000..46e83c36bf729bd15b7417fc107aa2cafdc9a41d
--- /dev/null
+++ b/Golden_Repo/p/PyFerret/pyferret
@@ -0,0 +1,6 @@
+#!/bin/sh
+if [ -z "${FER_LIBS}" ]; then
+ echo "**ERROR: Ferret environment variables are not defined"
+ exit 1
+fi
+python -i -c "import sys; import pyferret; (errval, errmsg) = pyferret.init(sys.argv[1:], True)" $*
diff --git a/Golden_Repo/p/PyTorch/PyTorch-1.7.0-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb b/Golden_Repo/p/PyTorch/PyTorch-1.7.0-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
index 16deb6cba847a0e0272cdbfa8b4c0ad828b19fde..865f39655e9398c84edee37ca14e3b146642ac9d 100644
--- a/Golden_Repo/p/PyTorch/PyTorch-1.7.0-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
+++ b/Golden_Repo/p/PyTorch/PyTorch-1.7.0-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
@@ -25,9 +25,9 @@ dependencies = [
('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
('MPFR', '4.1.0'),
('GMP', '6.2.0'),
- ('numactl', '2.0.13', '', True),
+ ('numactl', '2.0.13', '', SYSTEM),
('FFmpeg', '4.3.1'),
- ('cuDNN', '8.0.2.39', '-CUDA-%s' % local_cudaver, True),
+ ('cuDNN', '8.0.2.39', '-CUDA-%s' % local_cudaver, SYSTEM),
('magma', '2.5.4'),
('NCCL', '2.8.3-1', '-CUDA-%s' % local_cudaver),
('LLVM', '10.0.1'),
diff --git a/Golden_Repo/p/parallel/parallel-20201122-GCCcore-9.3.0.eb b/Golden_Repo/p/parallel/parallel-20201122-GCCcore-9.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..4e09e072ed8ef04d6759745a29e7657ef8f0accb
--- /dev/null
+++ b/Golden_Repo/p/parallel/parallel-20201122-GCCcore-9.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'parallel'
+version = '20201122'
+
+homepage = 'https://savannah.gnu.org/projects/parallel/'
+description = """parallel: Build and execute shell commands in parallel"""
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_BZ2]
+
+builddependencies = [('binutils', '2.34')]
+dependencies = [
+ ('Perl', '5.32.0'),
+]
+
+sanity_check_paths = {
+ 'files': ['bin/parallel'],
+ 'dirs': []
+}
+
+moduleclass = 'tools'
diff --git a/Golden_Repo/p/pixman/pixman-0.40.0-GCCcore-9.3.0.eb b/Golden_Repo/p/pixman/pixman-0.40.0-GCCcore-9.3.0.eb
index db81137fbc5738f4d5c9eab2818eb10f86208254..b0e6ccc06baed58cb93621aadc554138eec8daf2 100644
--- a/Golden_Repo/p/pixman/pixman-0.40.0-GCCcore-9.3.0.eb
+++ b/Golden_Repo/p/pixman/pixman-0.40.0-GCCcore-9.3.0.eb
@@ -11,6 +11,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'pic': True}
source_urls = ['http://cairographics.org/releases/']
sources = [SOURCE_TAR_GZ]
diff --git a/Golden_Repo/p/protobuf-python/protobuf-python-3.13.0-GCCcore-9.3.0-Python-3.8.5.eb b/Golden_Repo/p/protobuf-python/protobuf-python-3.13.0-GCCcore-9.3.0-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..664bab39432e214a7c0a1149d8da6f89af9b1a2c
--- /dev/null
+++ b/Golden_Repo/p/protobuf-python/protobuf-python-3.13.0-GCCcore-9.3.0-Python-3.8.5.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'protobuf-python'
+version = '3.13.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/google/protobuf/'
+description = """Python Protocol Buffers runtime library."""
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+source_urls = ['https://pypi.python.org/packages/source/p/protobuf']
+sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['6a82e0c8bb2bf58f606040cc5814e07715b2094caeba281e2e7d0b0e2e397db5']
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('protobuf', version)
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# Make sure protobuf is installed as a regular folder or it will not be found if
+# other google packages are installed in other site-packages folders
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'],
+}
+
+options = {'modulename': 'google.protobuf'}
+
+moduleclass = 'devel'
diff --git a/Golden_Repo/p/pyproj/pyproj-2.6.1.post1-GCCcore-9.3.0-Python-3.8.5.eb b/Golden_Repo/p/pyproj/pyproj-2.6.1.post1-GCCcore-9.3.0-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..0978d8a944fd9891ec32772198f69e59b9c05a54
--- /dev/null
+++ b/Golden_Repo/p/pyproj/pyproj-2.6.1.post1-GCCcore-9.3.0-Python-3.8.5.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'pyproj'
+version = '2.6.1.post1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://pyproj4.github.io/pyproj'
+description = "Python interface to PROJ4 library for cartographic transformations"
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['4f5b02b4abbd41610397c635b275a8ee4a2b5bc72a75572b98ac6ae7befa471e']
+
+builddependencies = [
+ ('binutils', '2.34'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('PROJ', '7.1.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+preinstallopts = "export PROJ_DIR=$EBROOTPROJ && "
+
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/Golden_Repo/r/R/R-4.0.2-gcccoremkl-9.3.0-2020.2.254-nompi.eb b/Golden_Repo/r/R/R-4.0.2-gcccoremkl-9.3.0-2020.2.254-nompi.eb
new file mode 100644
index 0000000000000000000000000000000000000000..719838a272dd976c03dd31536459a7af69cde72a
--- /dev/null
+++ b/Golden_Repo/r/R/R-4.0.2-gcccoremkl-9.3.0-2020.2.254-nompi.eb
@@ -0,0 +1,2565 @@
+name = 'R'
+version = '4.0.2'
+versionsuffix = '-nompi'
+
+homepage = 'https://www.r-project.org/'
+description = """R is a free software environment for statistical computing
+ and graphics."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
+sources = [SOURCE_TAR_GZ]
+checksums = ['d3bceab364da0876625e4097808b42512395fdf41292f4915ab1fd257c1bbe75']
+
+builddependencies = [
+ ('pkg-config', '0.29.2'),
+]
+dependencies = [
+ ('X11', '20200222'),
+ ('OpenGL', '2020'),
+ ('cairo', '1.17.2'),
+ ('libreadline', '8.0'),
+ ('ncurses', '6.2'),
+ ('bzip2', '1.0.8'),
+ ('XZ', '5.2.5'),
+ ('zlib', '1.2.11'),
+ ('SQLite', '3.32.3'),
+ ('PCRE2', '10.34'),
+ ('libpng', '1.6.37'), # for plotting in R
+ ('libjpeg-turbo', '2.0.5'), # for plottting in R
+ ('LibTIFF', '4.1.0'),
+ ('Java', '1.8', '', SYSTEM),
+ ('Tk', '8.6.10'), # for tcltk
+ ('cURL', '7.71.1'), # for RCurl
+ ('libxml2', '2.9.10'), # for XML
+ ('PROJ', '7.1.0'), # for rgdal
+ ('GMP', '6.2.0'), # for igraph
+ ('NLopt', '2.6.2'), # for nloptr
+ ('FFTW', '3.3.8', '-nompi'), # for fftw
+ ('libsndfile', '1.0.28'), # for seewave
+ ('ICU', '67.1'), # for rJava & gdsfmt
+ ('HDF5', '1.10.6', '-serial'), # for hdf5r
+ ('UDUNITS', '2.2.26'), # for units
+ ('GSL', '2.6'), # for RcppGSL
+ ('ImageMagick', '7.0.10-25'), # for animation
+ ('GLPK', '4.65'), # for Rglpk
+ ('netCDF', '4.7.4', '-serial'), # the ndf4 needs it
+ ('GEOS', '3.8.1', '-Python-3.8.5'), # for rgeos
+ ('ZeroMQ', '4.3.3'), # for pbdZMQ needed by IRkernel
+
+ # OS dependency should be preferred if the os version is more recent then
+ # this version, it's nice to have an up to date openssl for security
+ # reasons
+ # ('OpenSSL', '1.1.1e'),
+]
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+preconfigopts = 'export LDFLAGS="$LDFLAGS -lm" && '
+
+configopts = "--with-pic --enable-threads --enable-R-shlib"
+# some recommended packages may fail in a parallel build (e.g. Matrix), and
+# we're installing them anyway below
+configopts += " --with-recommended-packages=no"
+
+# specify that at least EasyBuild v3.5.0 is required,
+# since we rely on the updated easyblock for R to configure correctly w.r.t.
+# BLAS/LAPACK
+easybuild_version = '4.2.2'
+
+exts_default_options = {
+ 'source_urls': [
+ 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
+ 'https://cran.r-project.org/src/contrib/', # current version of packages
+ 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
+ ],
+ 'source_tmpl': '%(name)s_%(version)s.tar.gz',
+}
+
+# !! order of packages is important !!
+# packages updated on 23 July 2020
+exts_list = [
+ 'base',
+ 'datasets',
+ 'graphics',
+ 'grDevices',
+ 'grid',
+ 'methods',
+ 'splines',
+ 'stats',
+ 'stats4',
+ 'tools',
+ 'utils',
+ 'parallel',
+ ('abind', '1.4-5', {
+ 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'],
+ }),
+ ('magic', '1.5-9', {
+ 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'],
+ }),
+ ('Rcpp', '1.0.4.6', {
+ 'checksums': ['45af675ddbbe155e671453b2e84fe32250bb98d4ccb4342b61c1e25cff10b302'],
+ }),
+ ('RcppProgress', '0.4.2', {
+ 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'],
+ }),
+ ('lpSolve', '5.6.15', {
+ 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'],
+ }),
+ ('linprog', '0.9-2', {
+ 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'],
+ }),
+ ('geometry', '0.4.5', {
+ 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'],
+ }),
+ ('bit', '1.1-15.2', {
+ 'checksums': ['0b83e78385293d6cdc0189a07fcc3f9f9db286c8c4af3288467f5257e79cb28b'],
+ }),
+ ('filehash', '2.4-2', {
+ 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'],
+ }),
+ ('ff', '2.2-14.2', {
+ 'checksums': ['f8c06ac333ffe3545cdf56531619865176e1827728f7aeeba82d135d5c5e37e4'],
+ }),
+ ('bnlearn', '4.5', {
+ 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'],
+ }),
+ ('bootstrap', '2019.6', {
+ 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'],
+ }),
+ ('combinat', '0.0-8', {
+ 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'],
+ }),
+ ('deal', '1.2-39', {
+ 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'],
+ }),
+ ('fdrtool', '1.2.15', {
+ 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'],
+ }),
+ ('formatR', '1.7', {
+ 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'],
+ }),
+ ('gtools', '3.8.2', {
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+ }),
+ ('kedd', '1.0.3', {
+ 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'],
+ }),
+ ('HiddenMarkov', '1.8-11', {
+ 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'],
+ }),
+ ('lmerTest', '3.1-2', {
+ 'checksums': ['385870873fd303c2caa4ac43e2df0ca5aa36ddb484bfb4eefbc5c4ac4bef6de2'],
+ }),
+ ('loo', '2.2.0', {
+ 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'],
+ }),
+ ('StanHeaders', '2.21.0-1', {
+ 'checksums': ['4e94148af2960f203b208c2b725d8be628ca282c7a1e967a7e6e78aa5eb90d3f'],
+ }),
+ ('rstan', '2.19.3', {
+ 'checksums': ['d7025dccdc2337fd0cf3b9689c3e0a07558a47a08b7cbc370e0b3998256f1689'],
+ }),
+ ('Rborist', '0.2-3', {
+ 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'],
+ }),
+ ('VSURF', '1.1.0', {
+ 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'],
+ }),
+ ('mRMRe', '2.1.0', {
+ 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'],
+ }),
+ ('dHSIC', '2.1', {
+ 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'],
+ }),
+ ('ggsci', '2.9', {
+ 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'],
+ }),
+ ('ggsignif', '0.6.0', {
+ 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'],
+ }),
+ ('corrplot', '0.84', {
+ 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'],
+ }),
+ ('rstatix', '0.5.0', {
+ 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'],
+ }),
+ ('ggfan', '0.1.3', {
+ 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'],
+ }),
+ ('ggpubr', '0.3.0', {
+ 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'],
+ }),
+ ('yaImpute', '1.0-32', {
+ 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'],
+ }),
+ ('intrinsicDimension', '1.2.0', {
+ 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'],
+ }),
+ ('patchwork', '1.0.0', {
+ 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'],
+ }),
+ ('leiden', '0.3.3', {
+ 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'],
+ }),
+ ('future.apply', '1.4.0', {
+ 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'],
+ }),
+ ('sctransform', '0.2.1', {
+ 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'],
+ }),
+ ('packrat', '0.5.0', {
+ 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'],
+ }),
+ ('shinyjs', '1.1', {
+ 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'],
+ }),
+ ('colourpicker', '1.0', {
+ 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'],
+ }),
+ ('ggExtra', '0.9', {
+ 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'],
+ }),
+ ('findpython', '1.0.5', {
+ 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'],
+ }),
+ ('argparse', '2.0.1', {
+ 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'],
+ }),
+ ('intergraph', '2.0-2', {
+ 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'],
+ }),
+ ('ggnetwork', '0.5.8', {
+ 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'],
+ }),
+ ('qqman', '0.1.4', {
+ 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'],
+ }),
+ ('rstantools', '2.0.0', {
+ 'checksums': ['d200a4d8c62d8577fdba819bf770e7abb11c57c3332f4498e1d30ce824598b3a'],
+ }),
+ ('bayesplot', '1.7.1', {
+ 'checksums': ['820ca9ca3258fc68333e75fd60898c0d0f08f513b66c161ca6159a54ad54006b'],
+ }),
+ ('dygraphs', '1.1.1.6', {
+ 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'],
+ }),
+ ('rsconnect', '0.8.16', {
+ 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'],
+ }),
+ ('shinystan', '2.5.0', {
+ 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'],
+ }),
+ ('brms', '2.12.0', {
+ 'checksums': ['fa21505dca65d027f1cf1c573258de5f3c51ca8b94abd6dcf9123a3a27a72999'],
+ }),
+ ('drgee', '1.1.10', {
+ 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'],
+ }),
+ ('stdReg', '3.4.0', {
+ 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'],
+ }),
+ ('mcmcse', '1.4-1', {
+ 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'],
+ }),
+ ('copCAR', '2.0-3', {
+ 'checksums': ['e626380d3f11ca6c756381f2423ef3661efb52667147114253416cc6151a71b8'],
+ }),
+ ('batchmeans', '1.0-4', {
+ 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'],
+ }),
+ ('ngspatial', '1.2-2', {
+ 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'],
+ }),
+ ('BIGL', '1.4.3', {
+ 'checksums': ['7ef7edd5c1852409f1da176e810a9a2a7f0b9441e0e6459d4d16179f3eb000f4'],
+ }),
+ ('drugCombo', '1.1.1', {
+ 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'],
+ }),
+ ('betareg', '3.1-3', {
+ 'checksums': ['cc19387ec516492d11cf59cdfa07e1733950a2af8196c1e155bc95939bc76246'],
+ }),
+ ('unmarked', '1.0.1', {
+ 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'],
+ }),
+ ('maxlike', '0.1-8', {
+ 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'],
+ }),
+ ('coxme', '2.2-16', {
+ 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'],
+ }),
+ ('AICcmodavg', '2.3-0', {
+ 'checksums': ['4d6bcff3c549be9dcefdd849b239659618fdaf9ba0d27b9d0589620d104e5e24'],
+ }),
+ ('pacman', '0.5.1', {
+ 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'],
+ }),
+ ('spaa', '0.2.2', {
+ 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'],
+ }),
+ ('maxnet', '0.1.2', {
+ 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'],
+ }),
+ ('ENMeval', '0.3.0', {
+ 'checksums': ['1c924098a27c82a9bf75408173b47429c40cc41cae3aba18c86ba217bb45ba60'],
+ }),
+ ('plotmo', '3.5.7', {
+ 'checksums': ['aa366a49a63cabfd5d799a1524e23a4faed022f10ee60f8407d70ab70731b38c'],
+ }),
+ ('earth', '5.1.2', {
+ 'checksums': ['326f98e8c29365ca3cd5584cf2bd6529358f5ef81664cbd494162f92b6c3488d'],
+ }),
+ ('mda', '0.5-2', {
+ 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'],
+ }),
+ ('biomod2', '3.4.6', {
+ 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'],
+ }),
+ ('ncdf4', '1.17', {
+ 'checksums': ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'],
+ }),
+ ('mapdata', '2.3.0', {
+ 'checksums': ['1edc180990387b6b1cd4e43a9505ebeb98e6115e4205c4f32f05b397c781dd76'],
+ }),
+ ('wavelets', '0.3-0.2', {
+ 'checksums': ['22d1d6bff71574a37b047ee5c31d17d52e321d2dd54db1a221f2d7267536e01c'],
+ }),
+ ('biwavelet', '0.20.19', {
+ 'checksums': ['2b9f99e4f56cee87ee2db53abcece205ff592887a9c9cf298c875a1ea594b25d'],
+ }),
+ ('wavethresh', '4.6.8', {
+ 'checksums': ['93b369c6eabcc0187b860b31d84a9d7c72c4a2ed5b23c1520c93bd7bea22e7db'],
+ }),
+ ('splancs', '2.01-40', {
+ 'checksums': ['79744381ebc4a361740a36dca3c9fca9ae015cfe0bd585b7856a664a3da74363'],
+ }),
+ ('RandomFieldsUtils', '0.5.3', {
+ 'checksums': ['ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d'],
+ }),
+ ('RandomFields', '3.3.8', {
+ 'checksums': ['8a08e2fdae428e354a29fb6818ae781cc56235a6849a0d29574dc756f73199d0'],
+ }),
+ ('geoR', '1.8-1', {
+ 'checksums': ['990647804590b925a50f72897b24bbabd331cebef0be1696a60528b2f79d6fd3'],
+ }),
+ ('intervals', '0.15.2', {
+ 'checksums': ['0bd23b0ce817ddd851238233d8a5420bf3a6d29e75fd361418cbc50118777c57'],
+ }),
+ ('spacetime', '1.2-3', {
+ 'checksums': ['ca7c0b962d5da0741f6dd85b271d693598756e0eeeb364ada828dbb6d1b9b25b'],
+ }),
+ ('gstat', '2.0-6', {
+ 'checksums': ['6711e68aa2444cf2927879a03a976d8caeca5eac98d806b19a6a7178b90bfcab'],
+ }),
+ ('rgeos', '0.5-3', {
+ 'checksums': ['357454e110ae19a665d5af5ffd7d670d2d7471566dd638dc614365c29b68600b'],
+ }),
+ ('repr', '1.1.0', {
+ 'checksums': ['743fe018f9e3e54067a970bc38b6b8c0c0498b43f88d179ac4a959c2013a5f96'],
+ }),
+ ('IRdisplay', '0.7.0', {
+ 'checksums': ['91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089'],
+ }),
+ ('pbdZMQ', '0.3-3.1', {
+ 'checksums': ['9e034745cd9c1bdf510a2ec8e7060501abc92ec86020c430ed7e36f5d5cf1523'],
+ }),
+ ('IRkernel', '1.1.1', {
+ 'checksums': ['f5a129168f44bdda6da8cc907189a2737f692d427529515d87312a17dbd806f8'],
+ }),
+ # language server support
+ ('collections', '0.3.5', {
+ 'checksums': ['bf76ab5c6a8082b6bb70b9bf3bdb30658e823e3b7b28cf7be7e8a87d117a7114'],
+ }),
+ ('xmlparsedata', '1.0.4', {
+ 'checksums': ['387b13c25bea9ddc0a39b817c17c199b86ab9acafa328daae2233a9ca577fb9c'],
+ }),
+ ('cyclocomp', '1.1.0', {
+ 'checksums': ['cdbf65f87bccac53c1527a2f1269ec7840820c18503a7bb854910b30b71e7e3e'],
+ }),
+ ('lintr', '2.0.1', {
+ 'checksums': ['fe0723757b653ef83ec7a5005d0a7524cd917d646d35a5627ee639158881ce93'],
+ }),
+ ('styler', '1.3.2', {
+ 'checksums': ['3fcf574382c607c2147479bad4f9fa8b823f54fb1462d19ec4a330e135a44ff1'],
+ }),
+ ('mockery', '0.4.2', {
+ 'checksums': ['988e249c366ee7faf277de004084cf5ca24b5c8a8c6e3842f1b1362ce2f7ea9b'],
+ }),
+ ('languageserver', '0.3.8', {
+ 'checksums': ['371db6976d6066d654c9d31f911dba667c1f8ceb4ab67da34d44037b66f3ca9b'],
+ }),
+]
+
+moduleclass = 'lang'
diff --git a/Golden_Repo/r/R/R-4.0.2-gpsmkl-2020.eb b/Golden_Repo/r/R/R-4.0.2-gpsmkl-2020.eb
index 44aacee1e37451c02c5dca5d045a3f475bf0aad0..fb9b2a4ee5787a8c8ed54519573aaa64ad78aa1a 100644
--- a/Golden_Repo/r/R/R-4.0.2-gpsmkl-2020.eb
+++ b/Golden_Repo/r/R/R-4.0.2-gpsmkl-2020.eb
@@ -30,7 +30,7 @@ dependencies = [
('libpng', '1.6.37'), # for plotting in R
('libjpeg-turbo', '2.0.5'), # for plottting in R
('LibTIFF', '4.1.0'),
- ('Java', '1.8', '', True),
+ ('Java', '1.8', '', SYSTEM),
('Tk', '8.6.10'), # for tcltk
('cURL', '7.71.1'), # for RCurl
('libxml2', '2.9.10'), # for XML
@@ -469,8 +469,8 @@ exts_list = [
('pkgbuild', '1.0.7', {
'checksums': ['29bb38a38202ba780d2d46aeca0a6e2f052653e4a83891ec38d19bebd131a971'],
}),
- ('rstudioapi', '0.11', {
- 'checksums': ['13e07fb7e2eba8cf1d885db2721901d676d219a1042d7ef5d166125e4905306b'],
+ ('rstudioapi', '0.13', {
+ 'checksums': ['aac35bbdcb4a8e8caba943bc8a2b98120e8940b80cd1020224bb1a26ff776d8b'],
}),
('pkgload', '1.0.2', {
'checksums': ['3186564e690fb05eabe76e1ac0bfd4312562c3ac8794b29f8850399515dcf27c'],
@@ -2544,6 +2544,28 @@ exts_list = [
('IRkernel', '1.1.1', {
'checksums': ['f5a129168f44bdda6da8cc907189a2737f692d427529515d87312a17dbd806f8'],
}),
+ # language server support
+ ('collections', '0.3.5', {
+ 'checksums': ['bf76ab5c6a8082b6bb70b9bf3bdb30658e823e3b7b28cf7be7e8a87d117a7114'],
+ }),
+ ('xmlparsedata', '1.0.4', {
+ 'checksums': ['387b13c25bea9ddc0a39b817c17c199b86ab9acafa328daae2233a9ca577fb9c'],
+ }),
+ ('cyclocomp', '1.1.0', {
+ 'checksums': ['cdbf65f87bccac53c1527a2f1269ec7840820c18503a7bb854910b30b71e7e3e'],
+ }),
+ ('lintr', '2.0.1', {
+ 'checksums': ['fe0723757b653ef83ec7a5005d0a7524cd917d646d35a5627ee639158881ce93'],
+ }),
+ ('styler', '1.3.2', {
+ 'checksums': ['3fcf574382c607c2147479bad4f9fa8b823f54fb1462d19ec4a330e135a44ff1'],
+ }),
+ ('mockery', '0.4.2', {
+ 'checksums': ['988e249c366ee7faf277de004084cf5ca24b5c8a8c6e3842f1b1362ce2f7ea9b'],
+ }),
+ ('languageserver', '0.3.8', {
+ 'checksums': ['371db6976d6066d654c9d31f911dba667c1f8ceb4ab67da34d44037b66f3ca9b'],
+ }),
]
moduleclass = 'lang'
diff --git a/Golden_Repo/s/Score-P/Score-P-6.0-gompi-2020.eb b/Golden_Repo/s/Score-P/Score-P-6.0-gompi-2020.eb
index bb1380f27880d1b901e537c791faebbe506bc8d3..7037c78bff8437068491567a8832a1878eb47879 100644
--- a/Golden_Repo/s/Score-P/Score-P-6.0-gompi-2020.eb
+++ b/Golden_Repo/s/Score-P/Score-P-6.0-gompi-2020.eb
@@ -33,7 +33,7 @@ patches = [
]
builddependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('CubeLib', '4.5'),
('CubeWriter', '4.5'),
# Unwinding/sampling support (optional):
diff --git a/Golden_Repo/s/Score-P/Score-P-6.0-gpsmpi-2020.eb b/Golden_Repo/s/Score-P/Score-P-6.0-gpsmpi-2020.eb
index 30b2e861dff7a9dcee4fe4bfc79de7ef2ac7132a..a654979fef2bcd3fbb7b26bbc8e18c5d916e231a 100644
--- a/Golden_Repo/s/Score-P/Score-P-6.0-gpsmpi-2020.eb
+++ b/Golden_Repo/s/Score-P/Score-P-6.0-gpsmpi-2020.eb
@@ -33,7 +33,7 @@ patches = [
]
builddependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('CubeLib', '4.5'),
('CubeWriter', '4.5'),
# Unwinding/sampling support (optional):
diff --git a/Golden_Repo/s/Score-P/Score-P-6.0-iimpi-2020.eb b/Golden_Repo/s/Score-P/Score-P-6.0-iimpi-2020.eb
index 807d8fed2ffd9dd1dd569760feb0d5600dabfda8..1dd32b425e26a853984b4c775d2176860f59cbd1 100644
--- a/Golden_Repo/s/Score-P/Score-P-6.0-iimpi-2020.eb
+++ b/Golden_Repo/s/Score-P/Score-P-6.0-iimpi-2020.eb
@@ -33,7 +33,7 @@ patches = [
]
builddependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('CubeLib', '4.5'),
('CubeWriter', '4.5'),
# Unwinding/sampling support (optional):
diff --git a/Golden_Repo/s/Score-P/Score-P-6.0-ipsmpi-2020.eb b/Golden_Repo/s/Score-P/Score-P-6.0-ipsmpi-2020.eb
index 56fbb9367c43e92f4409311c0133a28dc96459b9..79c00c01536bd236ca672c9a78aeebb827ad6f59 100644
--- a/Golden_Repo/s/Score-P/Score-P-6.0-ipsmpi-2020.eb
+++ b/Golden_Repo/s/Score-P/Score-P-6.0-ipsmpi-2020.eb
@@ -33,7 +33,7 @@ patches = [
]
builddependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('CubeLib', '4.5'),
('CubeWriter', '4.5'),
# Unwinding/sampling support (optional):
diff --git a/Golden_Repo/s/Score-P/Score-P-6.0-npsmpic-2020.eb b/Golden_Repo/s/Score-P/Score-P-6.0-npsmpic-2020.eb
index bee2e759d062b0d5683cd65cfef67800217b5dbf..eb958fb47f5ac34bbe54a24869875ab2e0970bf2 100644
--- a/Golden_Repo/s/Score-P/Score-P-6.0-npsmpic-2020.eb
+++ b/Golden_Repo/s/Score-P/Score-P-6.0-npsmpic-2020.eb
@@ -33,7 +33,7 @@ patches = [
]
builddependencies = [
- ('CUDA', '11.0', '', True),
+ ('CUDA', '11.0', '', SYSTEM),
('CubeLib', '4.5'),
('CubeWriter', '4.5'),
# Unwinding/sampling support (optional):
diff --git a/Golden_Repo/s/Shapely/Shapely-1.7.1-GCCcore-9.3.0-Python-3.8.5.eb b/Golden_Repo/s/Shapely/Shapely-1.7.1-GCCcore-9.3.0-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..47db47fc91daae2c2c102039da8f217b7a6dd211
--- /dev/null
+++ b/Golden_Repo/s/Shapely/Shapely-1.7.1-GCCcore-9.3.0-Python-3.8.5.eb
@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'Shapely'
+version = '1.7.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/Toblerity/Shapely'
+description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects.
+It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['1641724c1055459a7e2b8bbe47ba25bdc89554582e62aec23cb3f3ca25f9b129']
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('GEOS', '3.8.1', versionsuffix),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'
diff --git a/Golden_Repo/t/TensorFlow/TensorFlow-2.3.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb b/Golden_Repo/t/TensorFlow/TensorFlow-2.3.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
index db5df775129fe326c2bd8acd9acac539ca559687..9a55c28c37c3eafc4ca9b2049a1237e2c1823d32 100644
--- a/Golden_Repo/t/TensorFlow/TensorFlow-2.3.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
+++ b/Golden_Repo/t/TensorFlow/TensorFlow-2.3.1-gcccoremkl-9.3.0-2020.2.254-Python-3.8.5.eb
@@ -24,8 +24,8 @@ builddependencies = [
('pybind11', '2.5.0', versionsuffix),
]
dependencies = [
- ('CUDA', local_cudaver, '', True),
- ('cuDNN', '8.0.2.39', '-CUDA-%s' % local_cudaver, True),
+ ('CUDA', local_cudaver, '', SYSTEM),
+ ('cuDNN', '8.0.2.39', '-CUDA-%s' % local_cudaver, SYSTEM),
('NCCL', '2.8.3-1', '-CUDA-%s' % local_cudaver),
('Python', '3.8.5'),
('h5py', '2.10.0', '-serial%s' % versionsuffix),
@@ -42,6 +42,7 @@ dependencies = [
('nsync', '1.24.0'),
('SQLite', '3.32.3'),
('PCRE', '8.44'),
+ ('protobuf-python', '3.13.0', versionsuffix),
('libpng', '1.6.37'),
('snappy', '1.1.8'),
('SWIG', '4.0.2', versionsuffix),
diff --git a/Golden_Repo/t/torchvision/torchvision-0.8.1-gcccoremkl-9.3.0-2020.2.254-GPU-Python-3.8.5.eb b/Golden_Repo/t/torchvision/torchvision-0.8.1-gcccoremkl-9.3.0-2020.2.254-GPU-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..2c61fff6031bd155a08070990ce903dd2f036f35
--- /dev/null
+++ b/Golden_Repo/t/torchvision/torchvision-0.8.1-gcccoremkl-9.3.0-2020.2.254-GPU-Python-3.8.5.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonPackage'
+
+name = 'torchvision'
+version = '0.8.1'
+versionsuffix = '-Python-%(pyver)s'
+
+
+homepage = 'http://pytorch.org/'
+description = """The torchvision package consists of popular datasets, model architectures, and common image
+transformations for computer vision."""
+
+site_contacts = 'a.strube@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+
+download_dep_fail = True
+
+source_urls = [
+ 'https://github.com/pytorch/vision/archive',
+]
+sources = [
+ 'v%(version)s.tar.gz'
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('SciPy-Stack', '2020', versionsuffix),
+ ('PyTorch', '1.7.0', versionsuffix),
+ ('Pillow-SIMD', '7.0.0.post3', versionsuffix),
+]
+
+options = {'modulename': 'torchvision'}
+
+sanity_check_paths = {
+ 'files': [],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# Add a property
+modluafooter = """
+add_property("arch","gpu")
+"""
+
+moduleclass = 'devel'
diff --git a/Golden_Repo/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb b/Golden_Repo/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb
new file mode 100644
index 0000000000000000000000000000000000000000..eb012fc637df01c285b2f77756b239865731ed90
--- /dev/null
+++ b/Golden_Repo/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb
@@ -0,0 +1,42 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University
+# Authors:: Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste (Ghent University)
+# License:: MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'UDUNITS'
+version = '2.2.26'
+
+homepage = 'http://www.unidata.ucar.edu/software/udunits/'
+description = """UDUNITS supports conversion of unit specifications between formatted and binary forms,
+ arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
+"""
+
+site_contacts = 'a.kreuzer@fz-juelich.de'
+
+toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
+toolchainopts = {'opt': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits']
+
+builddependencies = [('binutils', '2.34')]
+dependencies = [('expat', '2.2.9')]
+
+sanity_check_paths = {
+ 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h',
+ 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT],
+ 'dirs': ['share'],
+}
+
+parallel = 1
+
+moduleclass = 'phys'
diff --git a/Golden_Repo/v/VTK/VTK-8.2.0-gpsmpi-9.3.0-Python-3.8.5.eb b/Golden_Repo/v/VTK/VTK-8.2.0-gpsmpi-9.3.0-Python-3.8.5.eb
new file mode 100644
index 0000000000000000000000000000000000000000..ab774b4ddadf39423d3e94b72405d2595ec59411
--- /dev/null
+++ b/Golden_Repo/v/VTK/VTK-8.2.0-gpsmpi-9.3.0-Python-3.8.5.eb
@@ -0,0 +1,184 @@
+easyblock = 'CMakeMake'
+
+name = 'VTK'
+version = '8.2.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.vtk.org'
+description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for
+ 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
+ interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
+ algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
+ such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation."""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s']
+sources = [
+ SOURCE_TAR_GZ,
+ '%(name)sData-%(version)s.tar.gz',
+]
+patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')]
+checksums = [
+ '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz
+ 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz
+ 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch
+ '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info
+]
+
+builddependencies = [
+ ('CMake', '3.18.0'),
+]
+
+dependencies = [
+ ('Python', '3.8.5'),
+ ('HDF5', '1.10.6'),
+ ('SciPy-Stack', '2020', versionsuffix, ('gcccoremkl', '9.3.0-2020.2.254')),
+ ('mpi4py', '3.0.3', versionsuffix),
+ ('libxc', '3.0.1'),
+ ('netCDF', '4.7.4'),
+ ('X11', '20200222'),
+ ('OpenGL', '2020'),
+]
+
+separate_build_dir = True
+
+configopts = "-DCMAKE_BUILD_TYPE=Release "
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+
+configopts += "-DVTK_USE_SYSTEM_MPI4PY=ON "
+configopts += "-DVTK_USE_SYSTEM_LZMA=ON "
+configopts += "-DVTK_USE_SYSTEM_HDF5=ON "
+configopts += "-DVTK_USE_SYSTEM_NETCDF=ON "
+
+configopts += "-DBUILD_SHARED_LIBS=ON "
+configopts += "-DBUILD_TESTING=OFF "
+
+configopts += "-DVTK_SMP_IMPLEMENTATION_TYPE=OPENMP "
+configopts += "-DVTK_Group_MPI:BOOL=ON "
+configopts += "-DVTK_Group_Web:BOOL=ON "
+
+configopts += '-DOpenGL_GL_PREFERENCE=GLVND ' # "GLVND" or "LEGACY"
+configopts += "-DOPENGL_EGL_INCLUDE_DIR=$EBROOTOPENGL/include "
+configopts += "-DOPENGL_GLX_INCLUDE_DIR=$EBROOTOPENGL/include "
+configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTOPENGL/include "
+configopts += "-DOPENGL_egl_LIBRARY=$EBROOTOPENGL/lib/libEGL.so.1 "
+configopts += "-DOPENGL_glx_LIBRARY=$EBROOTOPENGL/lib/libGLX.so.0 "
+configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTOPENGL/lib/libOpenGL.so.0 "
+configopts += "-DOPENGL_glu_LIBRARY=$EBROOTOPENGL/lib/libGLU.so "
+
+configopts += "-DVTK_WRAP_PYTHON=ON "
+configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s "
+configopts += "-DPYTHON_EXECUTABLE:PATH=$EBROOTPYTHON/bin/python%(pyshortver)s "
+configopts += "-DPYTHON_INCLUDE_DIR:PATH=$EBROOTPYTHON/include/python%(pyshortver)s "
+configopts += "-DPYTHON_LIBRARY:PATH=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT
+
+configopts += "-DHDF5_INCLUDE_DIRS=$EBROOTHDF5/include "
+
+configopts += "-DModule_vtkAcceleratorsVTKm:BOOL=ON "
+# configopts += "-DModule_vtkDomainsMicroscopy:BOOL=OFF "
+# configopts += "-DModule_vtkDomainsParallelChemistry:BOOL=OFF "
+# configopts += "-DModule_vtkFiltersOpenTurns:BOOL=OFF "
+# configopts += "-DModule_vtkFiltersParallelDIY2:BOOL=OFF "
+# configopts += "-DModule_vtkFiltersParallelFlowPaths:BOOL=OFF "
+configopts += "-DModule_vtkFiltersParallelGeometry:BOOL=ON "
+configopts += "-DModule_vtkFiltersParallelMPI:BOOL=ON "
+configopts += "-DModule_vtkFiltersParallelStatistics:BOOL=ON "
+# configopts += "-DModule_vtkFiltersParallelVerdict:BOOL=OFF "
+# configopts += "-DModule_vtkFiltersReebGraph:BOOL=OFF "
+# configopts += "-DModule_vtkGUISupportQt:BOOL=OFF "
+# configopts += "-DModule_vtkGUISupportQtOpenGL:BOOL=OFF "
+# configopts += "-DModule_vtkGUISupportQtSQL:BOOL=OFF "
+# configopts += "-DModule_vtkGUISupportQtWebkit:BOOL=OFF "
+# configopts += "-DModule_vtkGeovisGDAL:BOOL=OFF "
+# configopts += "-DModule_vtkIOADIOS:BOOL=OFF "
+# configopts += "-DModule_vtkIOFFMPEG:BOOL=OFF "
+# configopts += "-DModule_vtkIOGDAL:BOOL=OFF "
+# configopts += "-DModule_vtkIOGeoJSON:BOOL=OFF "
+# configopts += "-DModule_vtkIOLAS:BOOL=OFF "
+# configopts += "-DModule_vtkIOMPIImage:BOOL=ON "
+# configopts += "-DModule_vtkIOMPIParallel:BOOL=ON "
+# configopts += "-DModule_vtkIOMotionFX:BOOL=OFF "
+# configopts += "-DModule_vtkIOMySQL:BOOL=OFF "
+# configopts += "-DModule_vtkIOODBC:BOOL=OFF "
+# configopts += "-DModule_vtkIOPDAL:BOOL=OFF "
+# configopts += "-DModule_vtkIOParallelExodus:BOOL=OFF "
+# configopts += "-DModule_vtkIOParallelLSDyna:BOOL=OFF "
+# configopts += "-DModule_vtkIOParallelNetCDF:BOOL=OFF "
+# configopts += "-DModule_vtkIOParallelXdmf3:BOOL=OFF "
+# configopts += "-DModule_vtkIOPostgreSQL:BOOL=OFF "
+# configopts += "-DModule_vtkIOTRUCHAS:BOOL=OFF "
+# configopts += "-DModule_vtkIOVPIC:BOOL=OFF "
+# configopts += "-DModule_vtkIOXdmf2:BOOL=OFF "
+# configopts += "-DModule_vtkIOXdmf3:BOOL=OFF "
+# configopts += "-DModule_vtkImagingOpenGL2:BOOL=OFF "
+# configopts += "-DModule_vtkInfovisBoost:BOOL=OFF "
+# configopts += "-DModule_vtkInfovisBoostGraphAlg:BOOL=OFF
+configopts += "-DModule_vtkParallelMPI:BOOL=ON "
+configopts += "-DModule_vtkPython:BOOL=ON "
+# configopts += "-DModule_vtkPythonInterpreter:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingExternal:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingFreeTypeFontConfig:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingLICOpenGL2:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingMatplotlib:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingOSPRay:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingOpenVR:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingOptiX:BOOL=OFF "
+configopts += "-DModule_vtkRenderingParallel:BOOL=ON "
+configopts += "-DModule_vtkRenderingParallelLIC:BOOL=ON "
+# configopts += "-DModule_vtkRenderingQt:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingSceneGraph:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingTk:BOOL=OFF "
+# configopts += "-DModule_vtkRenderingVolumeAMR:BOOL=OFF "
+# configopts += "-DModule_vtkTclTk:BOOL=OFF "
+# configopts += "-DModule_vtkTestingCore:BOOL=OFF "
+# configopts += "-DModule_vtkTestingGenericBridge:BOOL=OFF "
+# configopts += "-DModule_vtkTestingIOSQL:BOOL=OFF "
+# configopts += "-DModule_vtkTestingRendering:BOOL=OFF "
+# configopts += "-DModule_vtkUtilitiesBenchmarks:BOOL=OFF "
+# configopts += "-DModule_vtkUtilitiesEncodeString:BOOL=OFF "
+# configopts += "-DModule_vtkVPIC:BOOL=OFF "
+configopts += "-DModule_vtkVTKm:BOOL=ON "
+# configopts += "-DModule_vtkViewsGeovis:BOOL=OFF "
+# configopts += "-DModule_vtkViewsQt:BOOL=OFF "
+# configopts += "-DModule_vtkWebCore:BOOL=OFF "
+# configopts += "-DModule_vtkWebGLExporter:BOOL=OFF "
+# configopts += "-DModule_vtkWebPython:BOOL=OFF "
+# configopts += "-DModule_vtkWrappingJava:BOOL=OFF "
+# configopts += "-DModule_vtkWrappingPythonCore:BOOL=OFF "
+# configopts += "-DModule_vtkWrappingTools:BOOL=OFF "
+# configopts += "-DModule_vtkdiy2:BOOL=OFF "
+# configopts += "-DModule_vtkkissfft:BOOL=OFF "
+# configopts += "-DModule_vtkmpi4py:BOOL=OFF "
+# configopts += "-DModule_vtkpegtl:BOOL=OFF "
+# configopts += "-DModule_vtkxdmf2:BOOL=OFF "
+# configopts += "-DModule_vtkxdmf3:BOOL=OFF "
+# configopts += "-DModule_vtkzfp:BOOL=OFF "
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+
+# Install a egg-info file so VTK is more python friendly, required for mayavi
+local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info'
+postinstallcmds = [
+ 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
+]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+sanity_check_paths = {
+ 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in
+ ['WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +
+ ['bin/pvtkpython', 'bin/vtkpython'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'],
+}
+
+sanity_check_commands = [
+ ('python', "-c 'import %(namelower)s'"),
+ ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"),
+]
+
+moduleclass = 'vis'
diff --git a/Golden_Repo/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch b/Golden_Repo/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch
new file mode 100644
index 0000000000000000000000000000000000000000..60134b1fee16d4856ded561d40795e9a7e521540
--- /dev/null
+++ b/Golden_Repo/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch
@@ -0,0 +1,176 @@
+From 257b9d7b18d5f3db3fe099dc18f230e23f7dfbab Mon Sep 17 00:00:00 2001
+From: David Gobbi <david.gobbi@gmail.com>
+Date: Tue, 20 Aug 2019 17:02:24 -0600
+Subject: [PATCH] Compatibility for Python 3.8
+
+The PyTypeObject struct was modified in Python 3.8, this change is
+required to avoid compile errors.
+---
+ .../PythonInterpreter/vtkPythonStdStreamCaptureHelper.h | 6 ++++++
+ Wrapping/PythonCore/PyVTKMethodDescriptor.cxx | 2 +-
+ Wrapping/PythonCore/PyVTKNamespace.cxx | 2 +-
+ Wrapping/PythonCore/PyVTKReference.cxx | 8 ++++----
+ Wrapping/PythonCore/PyVTKTemplate.cxx | 2 +-
+ Wrapping/PythonCore/vtkPythonCompatibility.h | 8 +++++++-
+ Wrapping/Tools/vtkWrapPythonClass.c | 2 +-
+ Wrapping/Tools/vtkWrapPythonEnum.c | 2 +-
+ Wrapping/Tools/vtkWrapPythonType.c | 2 +-
+ 9 files changed, 23 insertions(+), 11 deletions(-)
+
+diff --git a/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h b/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h
+index b1c12c83de..14ccfbe928 100644
+--- a/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h
++++ b/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h
+@@ -140,6 +140,12 @@ static PyTypeObject vtkPythonStdStreamCaptureHelperType = {
+ #if PY_VERSION_HEX >= 0x03040000
+ 0, // tp_finalize
+ #endif
++#if PY_VERSION_HEX >= 0x03080000
++ 0, // tp_vectorcall
++#if PY_VERSION_HEX < 0x03090000
++ 0, // tp_print
++#endif
++#endif
+ };
+
+ static PyObject* vtkWrite(PyObject* self, PyObject* args)
+diff --git a/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx b/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx
+index 2b0d443537..3840038498 100644
+--- a/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx
++++ b/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx
+@@ -186,7 +186,7 @@ PyTypeObject PyVTKMethodDescriptor_Type = {
+ sizeof(PyMethodDescrObject), // tp_basicsize
+ 0, // tp_itemsize
+ PyVTKMethodDescriptor_Delete, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+diff --git a/Wrapping/PythonCore/PyVTKNamespace.cxx b/Wrapping/PythonCore/PyVTKNamespace.cxx
+index 71ee2a3516..5cf5bfbe6b 100644
+--- a/Wrapping/PythonCore/PyVTKNamespace.cxx
++++ b/Wrapping/PythonCore/PyVTKNamespace.cxx
+@@ -49,7 +49,7 @@ PyTypeObject PyVTKNamespace_Type = {
+ 0, // tp_basicsize
+ 0, // tp_itemsize
+ PyVTKNamespace_Delete, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+diff --git a/Wrapping/PythonCore/PyVTKReference.cxx b/Wrapping/PythonCore/PyVTKReference.cxx
+index 943ac71080..b7104091c0 100644
+--- a/Wrapping/PythonCore/PyVTKReference.cxx
++++ b/Wrapping/PythonCore/PyVTKReference.cxx
+@@ -1010,7 +1010,7 @@ PyTypeObject PyVTKReference_Type = {
+ sizeof(PyVTKReference), // tp_basicsize
+ 0, // tp_itemsize
+ PyVTKReference_Delete, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+@@ -1067,7 +1067,7 @@ PyTypeObject PyVTKNumberReference_Type = {
+ sizeof(PyVTKReference), // tp_basicsize
+ 0, // tp_itemsize
+ PyVTKReference_Delete, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+@@ -1124,7 +1124,7 @@ PyTypeObject PyVTKStringReference_Type = {
+ sizeof(PyVTKReference), // tp_basicsize
+ 0, // tp_itemsize
+ PyVTKReference_Delete, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+@@ -1181,7 +1181,7 @@ PyTypeObject PyVTKTupleReference_Type = {
+ sizeof(PyVTKReference), // tp_basicsize
+ 0, // tp_itemsize
+ PyVTKReference_Delete, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+diff --git a/Wrapping/PythonCore/PyVTKTemplate.cxx b/Wrapping/PythonCore/PyVTKTemplate.cxx
+index be200985b3..340fe7953b 100644
+--- a/Wrapping/PythonCore/PyVTKTemplate.cxx
++++ b/Wrapping/PythonCore/PyVTKTemplate.cxx
+@@ -268,7 +268,7 @@ PyTypeObject PyVTKTemplate_Type = {
+ 0, // tp_basicsize
+ 0, // tp_itemsize
+ nullptr, // tp_dealloc
+- nullptr, // tp_print
++ 0, // tp_vectorcall_offset
+ nullptr, // tp_getattr
+ nullptr, // tp_setattr
+ nullptr, // tp_compare
+diff --git a/Wrapping/PythonCore/vtkPythonCompatibility.h b/Wrapping/PythonCore/vtkPythonCompatibility.h
+index 4a767844a6..be208faeef 100644
+--- a/Wrapping/PythonCore/vtkPythonCompatibility.h
++++ b/Wrapping/PythonCore/vtkPythonCompatibility.h
+@@ -64,7 +64,13 @@
+ #endif
+
+ // PyTypeObject compatibility
+-#if PY_VERSION_HEX >= 0x03040000
++#if PY_VERSION_HEX >= 0x03090000
++#define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \
++ 0, 0, 0, 0,
++#elif PY_VERSION_HEX >= 0x03080000
++#define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \
++ 0, 0, 0, 0, 0,
++#elif PY_VERSION_HEX >= 0x03040000
+ #define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \
+ 0, 0, 0,
+ #else
+diff --git a/Wrapping/Tools/vtkWrapPythonClass.c b/Wrapping/Tools/vtkWrapPythonClass.c
+index b1e45f8e80..4d558ea081 100644
+--- a/Wrapping/Tools/vtkWrapPythonClass.c
++++ b/Wrapping/Tools/vtkWrapPythonClass.c
+@@ -521,7 +521,7 @@ void vtkWrapPython_GenerateObjectType(
+ " sizeof(PyVTKObject), // tp_basicsize\n"
+ " 0, // tp_itemsize\n"
+ " PyVTKObject_Delete, // tp_dealloc\n"
+- " nullptr, // tp_print\n"
++ " 0, // tp_vectorcall_offset\n"
+ " nullptr, // tp_getattr\n"
+ " nullptr, // tp_setattr\n"
+ " nullptr, // tp_compare\n"
+diff --git a/Wrapping/Tools/vtkWrapPythonEnum.c b/Wrapping/Tools/vtkWrapPythonEnum.c
+index b933702242..1249362854 100644
+--- a/Wrapping/Tools/vtkWrapPythonEnum.c
++++ b/Wrapping/Tools/vtkWrapPythonEnum.c
+@@ -145,7 +145,7 @@ void vtkWrapPython_GenerateEnumType(
+ " sizeof(PyIntObject), // tp_basicsize\n"
+ " 0, // tp_itemsize\n"
+ " nullptr, // tp_dealloc\n"
+- " nullptr, // tp_print\n"
++ " 0, // tp_vectorcall_offset\n"
+ " nullptr, // tp_getattr\n"
+ " nullptr, // tp_setattr\n"
+ " nullptr, // tp_compare\n"
+diff --git a/Wrapping/Tools/vtkWrapPythonType.c b/Wrapping/Tools/vtkWrapPythonType.c
+index 744cb1b9d3..0a1375e541 100644
+--- a/Wrapping/Tools/vtkWrapPythonType.c
++++ b/Wrapping/Tools/vtkWrapPythonType.c
+@@ -709,7 +709,7 @@ void vtkWrapPython_GenerateSpecialType(
+ " sizeof(PyVTKSpecialObject), // tp_basicsize\n"
+ " 0, // tp_itemsize\n"
+ " Py%s_Delete, // tp_dealloc\n"
+- " nullptr, // tp_print\n"
++ " 0, // tp_vectorcall_offset\n"
+ " nullptr, // tp_getattr\n"
+ " nullptr, // tp_setattr\n"
+ " nullptr, // tp_compare\n"
+--
+2.24.1
+
diff --git a/Golden_Repo/y/yuicompressor/yuicompressor-2.4.8-GCCcore-9.3.0-Python-3.8.5.eb b/Golden_Repo/y/yuicompressor/yuicompressor-2.4.8-GCCcore-9.3.0-Python-3.8.5.eb
index da015d63ed316562930d1cec1ebdc2e926c6f4c1..585047becdcc0b838c0c31fa9351e8b38c505587 100644
--- a/Golden_Repo/y/yuicompressor/yuicompressor-2.4.8-GCCcore-9.3.0-Python-3.8.5.eb
+++ b/Golden_Repo/y/yuicompressor/yuicompressor-2.4.8-GCCcore-9.3.0-Python-3.8.5.eb
@@ -22,7 +22,7 @@ builddependencies = [
dependencies = [
('Python', '3.8.5'),
- ('Java', '1.8', '', True),
+ ('Java', '1.8', '', SYSTEM),
]
use_pip = True
diff --git a/README.md b/README.md
index db2aad9a0d653a2d151166348f59e6d34c97aa65..8b54f8407b3f17d9a15e16c445e037bc0811c3f2 100644
--- a/README.md
+++ b/README.md
@@ -2,3 +2,15 @@
This is the repo to store all the EasyBuild configuration files, including easyconfigs.
Each stage is in a separate branch, containing all the relevant files for that stage
+
+
+This repository uses [autopep8](https://github.com/hhatto/autopep8) and [pre-commit](https://pre-commit.com). For that, you need to run this on your machine:
+
+```sh
+pip3 install --user autopep8
+pip3 install --user pre-commit
+pre-commit install
+```
+
+After those steps, `pre-commit` will call `autopep8` on each commit, and make small changes pass the pep8 test without needing to do a manual `eb --check-style` and checking each little mistake.
+