Merge branch 'MATLAB' into '2023'

[2023] MATLAB (update to 2023b), fix JupyterProxy

See merge request software-team/easybuild!2204

Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.8.0-GCCcore-11.3.0-2023.3.6.eb

@@ -59,21 +59,23 @@ exts_list = [
     ('matlab-proxy', '0.8.0', {
         'patches': [
             'noVersionCheck.patch',
+            'matlabproxy_timeout.patch',
         ],
         'checksums': [
             ('sha256', '965b0b7cfa6314638435089f211106c114b838e8f4945cb5f5dacb15c0cdf71f'),
             ('sha256', 'c21ba8969da77c88a266c97dc73dc64dc7a8f4fc20391f311bb4a6992d6e812c'),
+            ('sha256', '4f7d9f67566496223f01156f168e02af61b6b0a441afcaf7258b08f6ec79762d'),
         ],
     }),
     ('jupyter-matlab-proxy', '0.8.0', {
         'source_urls': ['https://github.com/mathworks/jupyter-matlab-proxy/archive/'],
         'source_tmpl': 'v%(version)s.tar.gz',
         'patches': [
-            'timeout.patch',
+            'jupytermatlabproxy_timeout.patch',
         ],
         'checksums': [
             ('sha256', 'b1785c8bed32d187c2fa15d921d047dd7483ec20442cdc5f34c0aad1ca06bac5'),
-            ('sha256', 'f44b7eee2d73b492a885c6b051b755330ff973e083d341933d28172156f0ff16'),
+            ('sha256', '4d15cc52352dc0cdeb03cc01285cf01cfe01393f3eee77fe1c2e205d691a5b8d'),
         ],
     }),
 ]

Golden_Repo/j/JupyterProxy-Matlab/JupyterProxy-Matlab-0.9.0-GCCcore-11.3.0-2023.3.6.eb

+easyblock = 'PythonBundle'
+
+name = 'JupyterProxy-Matlab'
+version = '0.9.0'
+local_jupyterver = '2023.3.6'
+versionsuffix = '-' + local_jupyterver
+
+# only users of the UNIX-group 'matlab' must have access
+# group = 'matlab'
+
+homepage = 'https://github.com/mathworks/jupyter-matlab-proxy'
+description = """The MATLAB integration for Jupyter enables you to open a MATLAB desktop
+in a web browser tab, directly from your Jupyter environment.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.38'),
+    # check for existance
+    # ('MATLAB', '2023a'),
+    # ('XServer', '21.1.6'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('JupyterLab', local_jupyterver),
+]
+
+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,
+}
+
+exts_list = [
+    # enable classic jupyter ####
+    ('jupyter_contrib_core', '0.4.2', {
+        'checksums': [('sha256', '1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb')],
+    }),
+    ('jupyter_highlight_selected_word', '0.2.0', {
+        'checksums': [('sha256', '9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b')],
+    }),
+    ('jupyter_nbextensions_configurator', '0.6.1', {
+        'checksums': [('sha256', '4b9e1270ccc1f8e0a421efb8979a737f586813023a4855b9453f61c3ca599b82')],
+    }),
+    ('jupyter_contrib_nbextensions', '0.7.0', {
+        'checksums': [('sha256', '06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca')],
+    }),
+    # core-packages ####
+    ('aiohttp-session', '2.12.0', {
+        'checksums': [('sha256', '0ccd11a7c77cb9e5a61f4daacdc9170d561112f9cfaf9e9a2d9867c0587d1950')],
+    }),
+    ('matlab-proxy', '0.9.0', {
+        'checksums': [
+            ('sha256', 'd8e76ef8c5d89aab286ad5bad65ecbdde1dca8803e2101f7d13e6f3ee3cb5cb5'),
+        ],
+    }),
+    ('jupyter-matlab-proxy', '0.8.0', {
+        'source_urls': ['https://github.com/mathworks/jupyter-matlab-proxy/archive/'],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'patches': [
+            'jupytermatlabproxy_timeout.patch',
+        ],
+        'checksums': [
+            ('sha256', 'b1785c8bed32d187c2fa15d921d047dd7483ec20442cdc5f34c0aad1ca06bac5'),
+            ('sha256', '4d15cc52352dc0cdeb03cc01285cf01cfe01393f3eee77fe1c2e205d691a5b8d'),
+        ],
+    }),
+]
+
+postinstallcmds = [
+    (
+        '{ cat > %(installdir)s/bin/matlab; } << EOF \n'
+        '#!/bin/bash \n'
+        '\n'
+        '# Load required modules \n'
+        'module purge \n'
+        'module load Stages/${STAGE} \n'
+        'module load GCCcore/.11.3.0 \n'
+        'module load MATLAB \n'
+        'module load XServer/21.1.6 \n'
+        '\n'
+        'matlab "\$@" \n'
+        '\n'
+        'EOF'
+    ),
+    'chmod +x %(installdir)s/bin/matlab',
+    (
+        '{ cat > %(installdir)s/bin/Xvfb; } << EOF \n'
+        '#!/bin/bash \n'
+        '\n'
+        '# Load required modules \n'
+        '# and ensure stderr stays empty as matlab-proxy seems to fail if not \n'
+        'module purge 2>&1 \n'
+        'module load Stages/${STAGE} 2>&1 \n'
+        'module load GCCcore/.11.3.0 2>&1 \n'
+        'module load MATLAB 2>&1 \n'
+        'module load XServer/21.1.6 2>&1 \n'
+        '\n'
+        'Xvfb "\$@" 2>&1\n'
+        '\n'
+        'EOF'
+    ),
+    'chmod +x %(installdir)s/bin/Xvfb'
+]
+
+
+modextravars = {
+    'MWI_USE_EXISTING_LICENSE': 'True',
+    'MWI_PROCESS_START_TIMEOUT': '600',
+}
+
+# Jupyter-matlab-kernel DISABLED:
+# https://github.com/mathworks/jupyter-matlab-proxy/issues/62
+modextrapaths = {
+    # 'MWI_CUSTOM_MATLAB_ROOT': 'lib/python%(pyshortver)s/site-packages/jupyter_matlab_proxy/',
+    # '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"))
+# """
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'

Golden_Repo/j/JupyterProxy-Matlab/timeout.patch → Golden_Repo/j/JupyterProxy-Matlab/jupytermatlabproxy_timeout.patch

-diff -Naur 0.7.1.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py 0.7.1/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py
---- 0.7.1.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py	2023-08-21 14:27:12.000000000 +0200
-+++ 0.7.1/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.7.1/src/jupyter_matlab_proxy/__init__.py	2023-08-29 22:16:29.568376240 +0200
-@@ -48,7 +48,7 @@
+diff -Naur 0.8.0.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py 0.8.0/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py
+--- 0.8.0.orig/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py       2023-10-16 13:08:25.138590609 +0200
++++ 0.8.0/GCCcore-11.3.0-2023.3.6/jupytermatlabproxy/jupyter-matlab-proxy-0.8.0/src/jupyter_matlab_proxy/__init__.py    2023-10-16 12:55:47.863830331 +0200
+@@ -93,7 +93,7 @@
              "--config",
              config["extension_name"],
          ],

Golden_Repo/j/JupyterProxy-Matlab/matlabproxy_timeout.patch

+diff -Naur 0.8.0.orig/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py 0.8.0/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py
+--- 0.8.0.orig/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py 2023-10-16 13:09:23.368725542 +0200
++++ 0.8.0/GCCcore-11.3.0-2023.3.6/matlabproxy/matlab-proxy-0.8.0/matlab_proxy/app_state.py      2023-10-16 12:57:02.458981541 +0200
+@@ -36,7 +36,7 @@
+     MATLAB_PORT_CHECK_DELAY_IN_SECONDS = 1
+     # The maximum amount of time in seconds the Embedded Connector can take
+     # for launching, before the matlab-proxy server concludes that something is wrong.
+-    EMBEDDED_CONNECTOR_MAX_STARTUP_DURATION_IN_SECONDS = 120
++    EMBEDDED_CONNECTOR_MAX_STARTUP_DURATION_IN_SECONDS = 600
+
+     def __init__(self, settings):
+         """Parameterized constructor for the AppState class.

Golden_Repo/m/MATLAB/MATLAB-2023b-GCCcore-11.3.0.eb

+# Attention: before calling 'eb':
+# export EB_MATLAB_KEY as fileInstallationKey
+# or export EB_MATLAB_LICFILE as license file
+
+name = 'MATLAB'
+version = '2023b'
+
+# only users of the UNIX-group 'matlab' must have access
+group = 'matlab'
+
+homepage = 'https://www.mathworks.com/products/matlab.html'
+description = """MATLAB is a high-level language and interactive environment
+that enables you to perform computationally intensive tasks faster than with
+traditional programming languages such as C, C++, and Fortran.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d96b9b3b36fad31a68061b7e64f6e0c7c3c072f85881290877cc5fc675ccb06f']
+
+dependencies = [
+    ('X11', '20220504'),  # mlab req. libXt.so which is not on the computes
+    ('Java', '11', '', SYSTEM)
+]
+
+java_options = '-Xmx2048m'
+
+# if we remove
+# ```
+# prepend_path("LD_LIBRARY_PATH", pathJoin(root, "runtime/glnxa64"))
+# prepend_path("LD_LIBRARY_PATH", pathJoin(root, "bin/glnxa64"))
+# prepend_path("LD_LIBRARY_PATH", pathJoin(root, "sys/os/glnxa64"))
+# ```
+# from the lua-Script. (needs a modification of eb-block-matlab)
+# postinstallcmds = [
+#    # create a wrapper script to ensure we do not mess up the environment
+#    # because MATLAB comes with its own libstdc++ and other system libs
+#    # in $EBROOTMATLAB/sys/os/glnxa64/
+#    'mv %(installdir)s/bin/matlab %(installdir)s/bin/matlab.bin ',
+#    (
+#        '{ cat > %(installdir)s/bin/matlab; } << EOF\n'
+#        '#!/bin/bash\n'
+#        '\n'
+#        'MYPATH=\$(readlink -f \$0)\n'
+#        'export MATLAB_PATH=\$(realpath \$(dirname "\$MYPATH")/..)\n'
+#        '\n'
+#        'export LD_LIBRARY_PATH=\$MATLAB_PATH/runtime/glnxa64:\$LD_LIBRARY_PATH\n'
+#        'export LD_LIBRARY_PATH=\$MATLAB_PATH/bin/glnxa64:\$LD_LIBRARY_PATH\n'
+#        'export LD_LIBRARY_PATH=\$MATLAB_PATH/sys/os/glnxa64:\$LD_LIBRARY_PATH\n'
+#        '\n'
+#        '"\$MATLAB_PATH/bin/matlab.bin" "\$@"\n'
+#        'EOF'
+#    ),
+#    'chmod +x %(installdir)s/bin/matlab',
+# ]
+
+modloadmsg = """
+Attention: This software is RESTRICTED to ACADEMIC users who are members of the group matlab\n.
+"""
+
+modextravars = {
+    'MATLAB_ROOT': '%(installdir)s',
+    'MLM_LICENSE_FILE': '27000@zam2076.zam.kfa-juelich.de',
+}
+
+sanity_check_paths = {
+    'files': ['bin/matlab', 'bin/glnxa64/MATLAB'],
+    'dirs': [],
+}
+
+moduleclass = 'math'