update Julia

Golden_Repo/j/Julia/Julia-1.6.1-gcccoremkl-9.3.0-2020.2.254.eb

+easyblock = 'ConfigureMake'
+name = 'Julia'
+version = '1.6.1'
+
+homepage = 'https://julialang.org/'
+description = """Julia was designed from the beginning for high performance.
+Julia programs compile to efficient native code for multiple platforms via LLVM
+"""
+
+site_contacts = 'j.goebbert@fz-juelich.de'
+
+toolchain = {'name': 'gcccoremkl', 'version': '9.3.0-2020.2.254'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/JuliaLang/julia/releases/download/v%(version)s/']
+sources = ['julia-%(version)s-full.tar.gz']
+
+builddependencies = [
+    ('binutils', '2.34'),
+    ('git', '2.28.0'),
+    ('CMake', '3.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.8.5'),
+    ('SciPy-Stack', '2020', '-Python-%(pyver)s'),
+]
+
+osdependencies = [('openssl')]
+
+skipsteps = ['configure']
+buildopts = " USE_SYSTEM_GMP=1 USE_SYSTEM_CURL=1 USE_INTEL_MKL=1 "
+installopts = "prefix=%(installdir)s "
+
+local_julia_depot_path = "%(installdir)s/share/julia/site/"
+modextrapaths = {
+    'PATH': 'bin',
+    'JULIA_DEPOT_PATH': 'share/julia/site',
+}
+
+postinstallcmds = [
+    # prepare install env
+    (
+        '{ cat > %%(builddir)s/env.sh; } << \'EOF\'\n'
+        '#!/bin/bash\n'
+        'export JULIA_DEPOT_PATH=%s\n'
+        'EOF'
+    ) % (local_julia_depot_path),
+
+    # installs extra packages
+    (
+        '{ cat > %(builddir)s/pkg_add.jl; } << \'EOF\'\n'
+        'using Pkg; \n'
+        # General Purpose
+        'Pkg.add(name="PackageCompiler", version="1.2.5"); \n'
+        'Pkg.add(name="HTTP", version="0.9.5"); \n'
+        'Pkg.add(name="Parsers", version="1.1.0"); \n'
+        'Pkg.add(name="VersionParsing", version="1.2.0"); \n'
+        'Pkg.add(name="JSON", version="0.21.1"); \n'
+        'Pkg.add(name="WebIO", version="0.8.15"); \n'
+        'Pkg.add(name="ProgressMeter", version="1.5.0"); \n'
+        'Pkg.add(name="Conda", version="1.5.2"); \n'
+        'Pkg.add(name="PyCall", version="1.92.3"); \n'
+        'Pkg.add(name="LaTeXStrings", version="1.2.1"); \n'
+        'Pkg.add(name="DocumentFormat", version="3.2.0"); \n'
+        # Data Science
+        'Pkg.add(name="CSV", version="0.8.4"); \n'
+        'Pkg.add(name="DataFrames", version="0.21.8"); \n'
+        'Pkg.add(name="Arrow", version="1.4.1"); \n'
+        'Pkg.add(name="OnlineStats", version="1.5.8"); \n'
+        'Pkg.add(name="Query", version="1.0.0"); \n'
+        # Scientific Domains
+        'Pkg.add(name="GSL", version="1.0.1"); \n'
+        'Pkg.add(name="DifferentialEquations", version="6.16.0"); \n'
+        'Pkg.add(name="Distributions", version="0.24.18"); \n'
+        'Pkg.add(name="Optim", version="1.3.0"); \n'
+        'Pkg.add(name="IterativeSolvers", version="0.9.0"); \n'
+        'Pkg.add(name="AbstractFFTs", version="1.0.1"); \n'
+        'Pkg.add(name="ODE", version="2.13.0"); \n'
+        'Pkg.add(name="SpecialFunctions", version="1.3.0"); \n'
+        'Pkg.add(name="JuMP", version="0.21.7"); \n'
+        # Visualization
+        'Pkg.add(name="GR", version="0.57.4"); \n'
+        'Pkg.add(name="PlotlyJS", version="0.14.1"); \n'
+        'Pkg.add(name="PyPlot", version="2.9.0"); \n'
+        'Pkg.add(name="Plots", version="1.12.0"); \n'
+        'Pkg.add(name="UnicodePlots", version="1.3.0"); \n'
+        'Pkg.add(name="StatsPlots", version="0.14.19"); \n'
+        # MachineLearning
+        'Pkg.add(name="MLJ", version="0.16.2"); \n'
+        'Pkg.add(name="Flux", version="0.12.2"); \n'
+        'Pkg.add(name="Knet", version="1.4.6"); \n'
+        'Pkg.add(name="MLDatasets", version="0.5.6"); \n'
+        'EOF'
+    ),
+    'source %(builddir)s/env.sh && %(installdir)s/bin/julia %(builddir)s/pkg_add.jl',
+
+    # trigger precompilation
+    (
+        '{ cat > %(builddir)s/precomp.jl; } << \'EOF\'\n'
+        # General Purpose
+        'using PackageCompiler; \n'
+        'using HTTP; \n'
+        'using Parsers; \n'
+        'using VersionParsing; \n'
+        'using JSON; \n'
+        'using WebIO; \n'
+        'using ProgressMeter; \n'
+        'using Conda; \n'
+        'using PyCall; \n'
+        'using LaTeXStrings; \n'
+        'using DocumentFormat; \n'
+        # Data Science
+        'using CSV; \n'
+        'using DataFrames; \n'
+        'using Arrow; \n'
+        'using OnlineStats; \n'
+        'using Query; \n'
+        # Scientific Domains
+        'using GSL; \n'
+        'using DifferentialEquations; \n'
+        'using Distributions; \n'
+        'using Optim; \n'
+        'using IterativeSolvers; \n'
+        'using AbstractFFTs; \n'
+        'using ODE; \n'
+        'using SpecialFunctions; \n'
+        'using JuMP; \n'
+        # Visualization
+        'using GR; \n'
+        'using PlotlyJS; \n'
+        'using PyPlot; \n'
+        'using Plots; \n'
+        'using UnicodePlots; \n'
+        'using StatsPlots; \n'
+        # MachineLearning
+        'using MLJ; \n'
+        'using Flux; \n'
+        'using Knet; \n'
+        'using MLDatasets; \n'
+        'EOF'
+    ),
+    'source %(builddir)s/env.sh && %(installdir)s/bin/julia %(builddir)s/precomp.jl',
+
+    # adjust permissions of precompiled files
+    'for i in $(find %s); do chmod +r $i; done' % local_julia_depot_path,
+]
+
+sanity_check_paths = {
+    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+}
+
+moduleclass = 'lang'

Golden_Repo/j/JupyterKernel-Julia/JupyterKernel-Julia-1.6.1-gcccoremkl-9.3.0-2020.2.254-2020.2.6.eb

+easyblock = 'Bundle'
+
+name = 'JupyterKernel-Julia'
+version = '1.6.1'
+local_jupyterver = '2020.2.6'
+versionsuffix = '-' + local_jupyterver
+
+local_pysuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/JuliaLang/IJulia.jl'
+description = """
+Native Julia 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'),
+    ('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', '0.5.6', dict(list(local_common_opts.items()) + [
+        ('checksums', [('sha256', '378d0377f75bb0e3bfc4cce19a56d3bf5a9a7be38e370e3a7cf3359bf4cd0378')]),
+        ('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
+    'JULIA_DEPOT_PATH': ['share/julia/site'],
+}
+
+# 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:${JULIA_DEPOT_PATH}\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
+    (
+        '{ cat > %(builddir)s/pkg_add.jl; } << \'EOF\'\n'
+        'using Pkg; \n'
+        'Pkg.add(name="ZMQ", version="1.2.1"); \n'
+        'Pkg.add(name="IJulia", version="1.23.2"); \n'
+        'Pkg.add(name="Interact", version="0.10.3"); \n'
+        'Pkg.add(name="LanguageServer", version="3.2.0"); \n'
+        'Pkg.build("IJulia"); \n'
+        'EOF'
+    ),
+    'source %(builddir)s/env.sh && julia %(builddir)s/pkg_add.jl',
+
+    # to trigger the precompilation
+    (
+        '{ cat > %(builddir)s/precomp.jl; } << \'EOF\'\n'
+        'using ZMQ; \n'
+        'using IJulia; \n'
+        'using Interact; \n'
+        'using LanguageServer; \n'
+        'EOF'
+    ),
+    'source %(builddir)s/env.sh && julia %(builddir)s/precomp.jl',
+
+    # 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'