Merge branch 'develop'

.github/workflows/linting.yml

@@ -1,5 +1,13 @@
 name: Static Analysis
 on: [push, pull_request]
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   python-linting:
     runs-on: ubuntu-20.04

.github/workflows/unit_tests.yml

@@ -1,16 +1,24 @@
 name: easyblocks unit tests
 on: [push, pull_request]
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
         modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14, modules-tcl-1.147, modules-3.2.10, modules-4.1.4]
         module_syntax: [Lua, Tcl]
         # exclude some configuration for non-Lmod modules tool:
         # - don't test with Lua module syntax (only supported in Lmod)
-        # - don't test with Python 3.5 and 3.7+ (only with 2.7 and 3.6), to limit test configurations
+        # - don't test with Python 3.5 and 3.7+ (only with 3.6), to limit test configurations
         exclude:
           - modules_tool: modules-tcl-1.147
             module_syntax: Lua
@@ -28,6 +36,8 @@ jobs:
             python: 3.9
           - modules_tool: modules-tcl-1.147
             python: '3.10'
+          - modules_tool: modules-tcl-1.147
+            python: '3.11'
           - modules_tool: modules-3.2.10
             python: 3.5
           - modules_tool: modules-3.2.10
@@ -38,6 +48,8 @@ jobs:
             python: 3.9
           - modules_tool: modules-3.2.10
             python: '3.10'
+          - modules_tool: modules-3.2.10
+            python: '3.11'
           - modules_tool: modules-4.1.4
             python: 3.5
           - modules_tool: modules-4.1.4
@@ -48,6 +60,8 @@ jobs:
             python: 3.9
           - modules_tool: modules-4.1.4
             python: '3.10'
+          - modules_tool: modules-4.1.4
+            python: '3.11'
       fail-fast: false
     steps:
     - uses: actions/checkout@v2

README.rst

@@ -1,9 +1,10 @@
-.. image:: https://github.com/easybuilders/easybuild-easyblocks/workflows/easyblocks%20unit%20tests/badge.svg?branch=develop
-
-.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png
+.. image:: https://github.com/easybuilders/easybuild/raw/develop/logo/png/easybuild_logo_2022_horizontal_dark_bg_transparent.png
    :align: center
+   :height: 400px
+
+.. image:: https://github.com/easybuilders/easybuild-easyblocks/workflows/easyblocks%20unit%20tests/badge.svg?branch=develop
 
-`EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
+`EasyBuild <https://easybuild.io>`_ is a software build
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 
@@ -12,7 +13,7 @@ EasyBuild. Easyblocks are Python modules that implement the install procedure fo
 (group of) software package(s). Together with the EasyBuild framework,
 they allow to easily build and install supported software packages.
 
-The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
+The EasyBuild documentation is available at http://docs.easybuild.io/.
 
 The easybuild-easyblocks source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see

RELEASE_NOTES

@@ -3,7 +3,131 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyblocks provides 246 software-specific easyblocks and 37 generic easyblocks.
+The latest version of easybuild-easyblocks provides 248 software-specific easyblocks and 41 generic easyblocks.
+
+
+v4.7.2 (27 May 2023)
+--------------------
+
+- new generic easyblock for installing Rust crates with cargo: Cargo and CargoPythonPackage (#2902, #2934)
+- minor enhancements and updates, including:
+  - let MATLAB easyblock raise an error if the MATLAB installation key is not provided (#2905)
+  - print message to inform that GPU package (instead of Kokkos) is used for LAMMPS (#2906)
+  - enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0 (#2915)
+- various bug fixes, including:
+  - use custom RPATH sanity check for Go packages that doesn't actually check for an RPATH section in the binary (#2913)
+  - use string '0' to avoid problems when openssl version is not determined (#2914)
+  - update GCC easyblock to ensure that --sysroot is passed to linker (but only when it needs to be) (#2921)
+  - add output log to MATLAB installs, actually parse for common errors (#2924)
+  - enhance Gurobi easyblock to allow using $EB_GUROBI_LICENSE_FILE environment variable (#2926)
+  - force building torchvision with CUDA support if CUDA is included as dependency by setting `$FORCE_CUDA` (#2931)
+  - fix exec permission on files in arch bindir for COMSOL (#2932)
+
+v4.7.1 (March 20th 2023)
+------------------------
+
+update/bugfix release
+
+- minor enhancements and updates, including:
+  - fix TensorFlow easyblock for new versions of Bazel & TensorFlow (#2854)
+  - make NAMD easyblock aware of (pre)testopts (#2856)
+  - update MesonNinja easyblock for Meson >=0.64.0 (#2861)
+  - update scipy easyblock for scipy >= 1.9.0 to use meson/ninja  (#2862, #2903)
+  - modify logic in QScintilla easyblock to find the PyQt5 sipdir in more places (#2868)
+  - add `testinstall` custom easyconfig parameter to PythonPackage easyblock (#2872)
+  - use -x option for "go install" in GoPackage generic easyblock, to print commands as they are executed (#2878)
+  - allow disabling pybind11 tests with `runtest = False` (#2892)
+  - call parent post_install_step in EasyBuildMeta easyblock (so postinstallcmds are taken into account) (#2893)
+  - update and enhance Maple easyblock for recent versions (#2895)
+  - relax glob pattern to find Mathematica install script (#2896)
+  - implement CUDA support in the ELPA EasyBlock & fix CPP configure issue on newer ELPA versions (#2898)
+  - update Trilinos easyblock to allow disabling of building tests and forward deps + support Trilinos v13.x (#2900)
+  - enhance Python easyblock to create non-versioned symlink for python-config + check for bin/python and bin/python-config in sanity check (#2904)
+- various bug fixes, including:
+  - do not use -g77 option when installing NVHPC 22.9+ (#2819)
+  - check that sanity_check_module_loaded attribute exists before querying it in PythonPackage easyblock (#2865)
+  - fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions (#2869)
+  - fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets (#2873)
+  - show template values of exts_default_options in PythonBundle (#2874)
+  - fix missing initialization of CMakeMake in CMakePythonPackage (#2876)
+  - fix error when failing pip version check during PythonPackage sanity check (#2877)
+  - handle templating correctly in CMakeMake when playing with configopts (#2882)
+  - avoid crash in test step of PyTorch easyblock if runtest is not a command (#2883)
+  - fix check configure option in FlexiBLAS easyblock (#2886)
+  - use older `ncgen -H` for older netCDF (#2889)
+  - fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x (#2897)
+- other changes:
+  - only give read permissions in GitHub Actions workflows (#2863)
+  - use start dir of extension to install R packages (#2867)
+  - fix website/docs links in README (#2870)
+  - add deprecation notice to RPackage extensions with relative paths in start_dir (#2879)
+
+
+v4.7.0 (January 9th 2023)
+-------------------------
+
+feature release
+
+- add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage (#2816) and JuliaBundle (#2830)
+- minor enhancements and updates, including:
+  - enhance TensorFlow easyblock to take into account provided OpenSSL dependency (#2575)
+  - add fix_shebang to install_step of PythonPackage easyblock so that we can fix shebangs when installing extensions (#2680)
+  - update PETSc easyblock for newer versions (>= 3.17) (#2796)
+  - update Clang easyblock to add support for new directory structure in Clang versions >= 14 + support Flang (#2800)
+  - update Xmipp easyblock since versions >= 3.20.07 use `noAsk` option to configure (#2809)
+  - add include/opencv4 to $CPATH for OpenCV versions >= 4.0 (#2818)
+  - add extra option for disabling LAPACK in ESMF (#2821)
+  - enable building of static libraries for libxml2 >= 2.10 (#2825)
+  - update Xmipp easyblock to handle effects of CUDA at SYSTEM level and newer CUDA version requirements for stdc++ (#2831)
+  - update LLVM easyblock to put 'cmake' symlink in place so separate CMake modules required for LLVM 15+ can be found (#2832)
+  - set $TEMPDIRPATH for testsuite in the BerkeleyGW easyblock, to avoid polluting /tmp (#2836)
+  - add `configure_no_prefix` option to skip addition of prefix to configure command in ConfigureMake easyblock (#2842)
+  - update qscintilla.py to be compatible with EB install of PyQt5 >= 5.15 (#2845)
+  - add UCC to known_dependencies in OpenMPI EasyBlock (#2847)
+  - update Clang-AOMP easyblock to handle version 5.2 and newer (#2851)
+- various bug fixes, including:
+  - fix installing of Clang with RPATH linking (#2799)
+  - fix --module-only for Clang + fix sanity check for Clang 11.x (#2800)
+  - create $XDG_CACHE_HOME for PyTorch tests (#2806)
+  - make PythonPackage easyblock compatible with --sanity-check-only by loading module early during sanity check step (#2828)
+  - fix docstring of PythonBundle generic easyblock (#2833)
+  - fix counting of failures in PyTorch tests (#2834, #2840)
+  - make sure that ANSYS INSTALL script has execute permissions (#2852, #2853)
+- other changes:
+  - remove useless -openmp build option for MRtrix v3.x (#2822)
+  - update HDF5 easyblock to use --enable-threadsafe configure option to make C API thread safe (#2824)
+  - use new EasyBuild logo in README (#2827)
+  - automatically cancel Github Action workflow runs for outdated commits (#2835)
+  - use fixed names for bazel/wrapper subdirectories used when building TensorFlow, to make debugging easier (#2841)
+  - also run unit tests with Python 3.11 (#2844)
+  - tweak docstring in some generic easyblocks so it renders nicely in auto-generated documentation (#2849)
+  - update copyright lines for 2023 (#2850)
+
+
+v4.6.2 (October 21st 2022)
+--------------------------
+
+update/bugfix release
+
+- 2 new software-specific easyblock:
+  - CUDA compatibility libraries (#2764) and mamba (#2808)
+- minor enhancements and updates, including:
+  - update OpenFOAM easyblock to support OpenFOAM 10 + clean up variant/version checks (#2766)
+  - added support for ESMPy in ESMF (#2789)
+  - enhance OpenBLAS easyblock to support running LAPACK test suite + checking how many tests fail (#2801)
+  - make numexpr easyblock aware of toolchain with GCC + imkl (#2810)
+  - add sanity check commands for netCDF (#2811)
+- various bug fixes, including:
+  - handle problems copying symlink that points to CUDA folder that is not created for non CUDA builds of SuiteSparse (#2790)
+  - don't install docs (to avoid trouble with Java) + add Rocky support for ABAQUS (#2792)
+  - correctly count the number of failing tests (not failing test suites) in PyTorch builds (#2794, #2803)
+  - fix docstring for PyTorch easyblock (#2795)
+  - handle iterative builds with MakeCp easyblock (#2798)
+  - accept both None and empty value for optarch to let OpenCV detect host CPU (#2804)
+  - enhance EasyBuildMeta easyblock: auto-enable installing with pip + fix setup.py of easyconfigs package so installation with setuptools >= 61.0 works (#2805)
+  - use `python -m pip` instead of `pip` in PythonPackage easyblock (#2807)
+- other changes:
+  - make the test output from PythonPackage less verbose by disabling default search for error patterns done by run_cmd (2797)
 
 
 v4.6.1 (September 12th 2022)

easybuild/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.6.2.dev0')
+VERSION = LooseVersion('4.7.3.dev0')
 UNKNOWN = 'UNKNOWN'
 
 

easybuild/easyblocks/a/abaqus.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -44,6 +44,7 @@
 from easybuild.tools.filetools import change_dir, symlink, write_file
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd_qa
+from easybuild.tools.systemtools import get_os_name
 from easybuild.tools.py2vs3 import OrderedDict
 
 
@@ -78,6 +79,9 @@ def extract_step(self):
     def configure_step(self):
         """Configure ABAQUS installation."""
         if LooseVersion(self.version) >= LooseVersion('2016'):
+            # Rocky Linux isn't recognized; faking it as RHEL
+            if get_os_name() in ['Rocky Linux', 'AlmaLinux']:
+                setvar('DISTRIB_ID', 'RedHatEnterpriseServer')
             # skip checking of Linux version
             setvar('DSY_Force_OS', 'linux_a64')
             # skip checking of license server
@@ -126,10 +130,9 @@ def install_step(self):
             # rather than a regular dictionary (where there's no guarantee on key order in general)
             std_qa = OrderedDict()
 
-            # Enable Extended Product Documentation
-            std_qa[selectionstr % (r"\[ \]", "Extended Product Documentation")] = "%(nr)s"
-            # Enable Abaqus CAE (docs)
-            std_qa[selectionstr % (r"\[ \]", "Abaqus CAE")] = "%(nr)s"
+            # Disable Extended Product Documentation because it has a troublesome Java dependency
+            std_qa[selectionstr % (r"\[*\]", "Extended Product Documentation")] = "%(nr)s"
+            installed_docs = False  # hard disabled, previous support was actually incomplete
 
             # enable all ABAQUS components
             std_qa[selectionstr % (r"\[ \]", "Abaqus.*")] = "%(nr)s"
@@ -146,9 +149,9 @@ def install_step(self):
 
             # Disable/enable Tosca
             if self.cfg['with_tosca']:
-                std_qa[selectionstr % (r"\[\ \]", "Tosca")] = "%(nr)s"
+                std_qa[selectionstr % (r"\[\ \]", "Tosca.*")] = "%(nr)s"
             else:
-                std_qa[selectionstr % (r"\[\*\]", "Tosca")] = "%(nr)s"
+                std_qa[selectionstr % (r"\[\*\]", "Tosca.*")] = "%(nr)s"
 
             # disable CloudView
             std_qa[r"(?P<cloudview>[0-9]+) \[X\] Search using CloudView\nEnter selection:"] = '%(cloudview)s\n\n'
@@ -170,7 +173,7 @@ def install_step(self):
             cae_subdir = os.path.join(self.installdir, 'cae')
             sim_subdir = os.path.join(self.installdir, 'sim')
             std_qa[r"Default.*SIMULIA/EstProducts.*:"] = cae_subdir
-            std_qa[r"SIMULIA[0-9]*doc.*:"] = os.path.join(self.installdir, 'doc')
+            std_qa[r"SIMULIA[0-9]*doc.*:"] = os.path.join(self.installdir, 'doc')  # if docs are installed
             std_qa[r"SimulationServices.*:"] = sim_subdir
             std_qa[r"Choose the CODE installation directory.*:\n.*\n\n.*:"] = sim_subdir
             std_qa[r"SIMULIA/CAE.*:"] = cae_subdir
@@ -197,13 +200,13 @@ def install_step(self):
 
             std_qa[r"Please choose an action:"] = '1'
 
-            if LooseVersion(self.version) >= LooseVersion('2022'):
+            if LooseVersion(self.version) >= LooseVersion('2022') and installed_docs:
                 java_root = get_software_root('Java')
                 if java_root:
                     std_qa[r"Please enter .*Java Runtime Environment.* path.(\n.*)+Default \[\]:"] = java_root
                     std_qa[r"Please enter .*Java Runtime Environment.* path.(\n.*)+Default \[.+\]:"] = ''
                 else:
-                    raise EasyBuildError("Java is a required dependency for ABAQUS versions >= 2022, but it is missing")
+                    raise EasyBuildError("Java is required for ABAQUS docs versions >= 2022, but it is missing")
 
             # Continue
             std_qa[nextstr] = ''
@@ -330,7 +333,7 @@ def sanity_check_step(self):
         custom_commands = []
 
         if LooseVersion(self.version) >= LooseVersion('2016'):
-            custom_paths['dirs'].extend(['cae', 'Commands', 'doc'])
+            custom_paths['dirs'].extend(['cae', 'Commands'])
             if LooseVersion(self.version) < LooseVersion('2020'):
                 custom_paths['dirs'].extend(['sim'])
             # 'all' also check license server, but lmstat is usually not available

easybuild/easyblocks/a/acml.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/adf.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2016-2022 Ghent University
+# Copyright 2016-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/advisor.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/aladin.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/allinea.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2022 Ghent University
+# Copyright 2013-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/amber.py

@@ -1,6 +1,6 @@
 ##
-# Copyright 2009-2022 Ghent University
-# Copyright 2015-2022 Stanford University
+# Copyright 2009-2023 Ghent University
+# Copyright 2015-2023 Stanford University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/anaconda.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/easyblocks/a/ansys.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -56,6 +56,8 @@ def install_step(self):
         if licport is None:
             licport = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055')
 
+        # Sources (e.g. iso files) may drop the execute permissions
+        adjust_permissions('INSTALL', stat.S_IXUSR)
         cmd = "./INSTALL -silent -install_dir %s -licserverinfo %s:%s" % (self.installdir, licport, licserv)
         run_cmd(cmd, log_all=True, simple=True)