Merge branch '2020' of...

Merge branch '2020' of https://gitlab.version.fz-juelich.de/hps-public/easybuild-repository into JAX

Golden_Repo/h/HDFView/HDFView-2.14-GCC-9.3.0.eb

+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'

Golden_Repo/h/Horovod/Horovod-0.20.3-gomkl-2020-Python-3.8.5.eb

+# 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'

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'],

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'],

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

Golden_Repo/i/ITK/ITK-5.1.2-GCCcore-9.3.0-nompi-Python-3.8.5.eb

+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'

Golden_Repo/i/ITK/ITK-5.1.2-gompi-2020-Python-3.8.5.eb

+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'

Golden_Repo/i/ITK/ITK-5.1.2-gpsmpi-2020-Python-3.8.5.eb

+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'

Golden_Repo/j/Java/Java-15.0.1.eb

+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'

Golden_Repo/j/Java/Java-15.eb

+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'

Golden_Repo/j/Jupyter/401html.patch

+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">
++  <meta property="og:locale" content="en_US">
++  <meta property="og:site_name" content="jupyter-jsc">
++  <meta property="og:title" content="jupyter-jsc">
++  <meta property="og:type" content="website">
++  <meta property="og:url" content="https://jupyter-jsc.fz-juelich.de/">
++
++  <link rel="stylesheet" href="/hub/static/css/style.min.css" type="text/css">
++  <link rel="stylesheet" href="/hub/static/css/j4j_font.min.htm" type="text/css">
++  <link rel="stylesheet" href="/hub/static/css/j4j_base.min.css" type="text/css">
++  <link rel="stylesheet" href="/hub/static/css/j4j_base_header.min.css" type="text/css">
++  <link rel="stylesheet" href="/hub/static/css/j4j_base_footer.min.css" type="text/css">
++  <link rel="icon" href="/hub//static/images/favicon.svg" type="jpg/png">
++  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jquery-confirm/3.3.2/jquery-confirm.min.css">  
++  <link rel="stylesheet" href="/hub/static/css/j4j_page_home.min.css" type="text/css">
++  <link rel="stylesheet" href="/hub/static/css/spawn_style.css" type="text/css">
++
++<body>
++
++<div id="container">
++
++  <div id="header-background">
++  <div id="header">
++  <nav class="navbar navbar-default">
++    <div class="container-fluid">
++      <div class="navbar-header">
++        <span id="jupyterhub-logo" class="pull-left"><a href="https://www.fz-juelich.de/jsc" target="_blank"><img src="/hub/static/images/jsc.png" alt="JupyterHub" class="jpy-logo" title="Home"></a></span>
++      </div>
++
++      <div id="thenavbar">
++        <ul class="nav navbar-nav">
++          
++          <li><a href="https://jupyter-jsc.fz-juelich.de/hub/start">Start</a></li>
++          
++          <li id="navbarbtn-links" class="main-menu-btn menu-btn"><a>Links</a>
++            <div id="navbarmenu-links" class="menu-box">
++              <ul>
++                <li id="navbarbtn-links-1" class="menu-btn"><a>jupyter-jsc</a>
++                  <div id="navbarmenu-links-1" class="menu-box menu-sub-box show-sub-header" style="">
++                    <ul>
++                      <li class=""><a href="https://jupyter-jsc.fz-juelich.de/nbviewer/github/kreuzert/Jupyter-JSC/blob/master/Extensions.ipynb">Extensions at jupyter-jsc</a></li>
++                      <li class=""><a href="https://jupyter-jsc.fz-juelich.de/nbviewer/github/kreuzert/Jupyter-JSC/blob/master/FAQ.ipynb">HDFCloud FAQ</a></li>
++                      <li class=""><a href="https://jupyter-jsc.fz-juelich.de/static/files/projects.html">Link Projects to Home</a></li>
++                      <li class=""><a href="https://jupyter-jsc.fz-juelich.de/static/files/kernel.html">Setup your own kernel</a></li>
++                      <li class=""><a target="_blank" href="https://www.unicore.eu/about-unicore/case-studies/jupyter-at-jsc/">jupyter-jsc at unicore.eu</a></li>
++                    </ul>
++                  </div>
++                </li>
++                <li id="navbarbtn-links-2" class="menu-btn"><a>Jupyter</a>
++                  <div id="navbarmenu-links-2" class="menu-box menu-sub-box show-sub-header" style="">
++                    <ul>
++                      <li class=""><a target="_blank" href="https://www-jupyter.org/">Home</a></li>
++                      <li class=""><a target="_blank" href="https://newsletter.jupyter.org/">Newsletter</a></li>
++                      <li class=""><a target="_blank" href="https://www.youtube.com/watch?v=HW29067qVWk">Introduction Video</a></li>
++                      <li class=""><a target="_blank" href="https://blog.jupyter.org/">Blog</a></li>
++                      <li class=""><a target="_blank" href="https://jupyter.org/documentation.html">Documentation</a></li>
++                      <li class=""><a target="_blank" href="https://www.oreilly.com/topics/jupyter">O'Reilly on Jupyter</a></li>
++                      <li class=""><a target="_blank" href="https://twitter.com/projectjupyter">Twitter</a></li>
++                      <li class=""><a target="_blank" href="https://github.com/trending/jupyter-notebook">Jupyter-Notebooks</a></li>
++                    </ul>
++                  </div>
++                </li>
++                <li id="navbarbtn-links-3" class="menu-btn"><a>JSC</a>
++                  <div id="navbarmenu-links-3" class="menu-box menu-sub-box show-sub-header" style="">
++                    <ul>
++                      <li class=""><a target="_blank" href="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/JUWELS/JUWELS_node.html">JUWELS</a></li>
++                      <li class=""><a target="_blank" href="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/JURECA/JURECA_node.html">JURECA</a></li>
++                      <li class=""><a target="_blank" href="https://hbp-hpc-platform.fz-juelich.de/?page_id=1073">JURON</a></li>
++                      <li class=""><a target="_blank" href="https://www.fz-juelich.de/ias/jsc/EN/News/Newsletter/newsletter_node.html">Newsletter</a></li>
++                      <li class=""><a target="_blank" href="https://www.fz-juelich.de/ias/jsc/EN/News/Events/events_node.html">Events</a></li>
++                      <li class=""><a target="_blank" href="https://twitter.com/fzj_jsc">Twitter</a></li>
++                    </ul>
++                  </div>
++                </li>
++              </ul>
++            </div>
++          </li>
++          
++        </ul>
++      </div>
++    </div>
++  </nav>
++  </div>
++  </div>
++
++<div id="body">
++<div class="background-wrapper">
++  <div class="content" id="JupyterLabs-div">
++    
++      <!--<center><h2 style="color:red">jupyter-jsc maintenance: 25-02-2020 - 26-02-2020</h2></center>-->
++      <h2>
++      The access token of your browser session to the running JupyterLab has expired.
++      </h2>
++      <p>
++        Unfortunately you have to log out and log in again from the Jupyter-JSC to regain access permission.<br>
++        <a href="https://jupyter-jsc.fz-juelich.de/hub/logout?stopall=false&alldevices=false"> Logout now </a>
++      </p>
++    
++  </div>
++</div>
++</div>
++
++<div class="footer">
++  <div class="footer-top-background">
++  </div>
++  <div class="footer-bottom-background">
++    <div class="footer-bottom">
++      <div class="footer-links">
++        <span>© Forschungszentrum Jülich</span>
++        <a href="https://jupyter-jsc.fz-juelich.de/hub/imprint">Imprint</a>
++        <a href="https://jupyter-jsc.fz-juelich.de/hub/privacy">Privacy Policy</a>
++        <a href="mailto:ds-support@fz-juelich.de?subject=jupyter-jsc Support&amp;body=Please describe your problem here. (english or german)">Support</a>
++        <a href="https://jupyter-jsc.fz-juelich.de/hub/terms">Terms of Service</a>
++      </div>
++      <a href="https://www.helmholtz.de/en/" target="_blank"><img class="helmholtz-logo" src="/hub/static/images/helmholtz.png"></a>
++    </div>
++  </div>
++</div>
++
++</div> <!-- container -->
++
++</body></html>

Golden_Repo/j/Jupyter/jupyter_contrib_nbextensions-template_paths.patch

+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:
+ ```

Golden_Repo/j/Jupyter/jupyter_latex_envs-template_paths.patch

+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):

Golden_Repo/j/Jupyter/jupyterhub-1.1.0_logoutcookie-2.0.patch

+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

Golden_Repo/j/Jupyter/jupyterlab-gitlab-2.0.0_jsc.patch

+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"

Golden_Repo/j/Jupyter/jupyterlab_github-2.0.0_jsc.patch

+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"
+

Golden_Repo/j/Jupyter/jupyterlmod-packagejson.patch

+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"
+   },

Golden_Repo/j/Jupyter/jupyterlmod-urlfile.patch

+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);
+ 

Golden_Repo/j/Jupyter/jupyterserverproxy-urlfile.patch

+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);
+