Merge pull request #4169 from easybuilders/4.7.x

release EasyBuild v4.7.0

.github/workflows/bootstrap_script.yml

@@ -1,6 +1,11 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: test EasyBuild bootstrap script
 on: [push, pull_request]
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   setup:
     runs-on: ubuntu-20.04
@@ -107,7 +112,7 @@ jobs:
           EB_BOOTSTRAP_VERSION=$(grep '^EB_BOOTSTRAP_VERSION' easybuild/scripts/bootstrap_eb.py | sed 's/[^0-9.]//g')
           EB_BOOTSTRAP_SHA256SUM=$(sha256sum easybuild/scripts/bootstrap_eb.py | cut -f1 -d' ')
           EB_BOOTSTRAP_FOUND="$EB_BOOTSTRAP_VERSION $EB_BOOTSTRAP_SHA256SUM"
-          EB_BOOTSTRAP_EXPECTED="20210715.01 0ffdc17ed7eacf78369c9cd6743728f36e61bb8bf5c1bdc1e23cf2040b1ce301"
+          EB_BOOTSTRAP_EXPECTED="20210715.01 935979de3a4c30b24c3617ff7cd7c40cbd4d815cee5be0c99810cc21f21182f1"
           test "$EB_BOOTSTRAP_FOUND" = "$EB_BOOTSTRAP_EXPECTED" || (echo "Version check on bootstrap script failed $EB_BOOTSTRAP_FOUND" && exit 1)
 
           # test bootstrap script

.github/workflows/container_tests.yml

@@ -1,6 +1,11 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for container support
 on: [push, pull_request]
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   build:
     # stick to Ubuntu 18.04, where we can still easily install yum via 'apt install'
@@ -52,8 +57,8 @@ jobs:
         sudo apt install alien
         alien --version
         # determine latest version of Singularity available in EPEL, and download RPM
-        singularity_rpm=$(curl -sL https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/s/ | grep singularity | sed 's/.*singularity/singularity/g' | sed 's/rpm.*/rpm/g')
-        curl -OL https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/s/${singularity_rpm}
+        singularity_rpm=$(curl -sL https://dl.fedoraproject.org/pub/archive/epel/8.5/Everything/x86_64/Packages/s/ | grep singularity | sed 's/.*singularity/singularity/g' | sed 's/rpm.*/rpm/g')
+        curl -OL https://dl.fedoraproject.org/pub/archive/epel/8.5/Everything/x86_64/Packages/s/${singularity_rpm}
         # convert Singularity RPM to Debian package, and install it
         sudo alien -d ${singularity_rpm}
         sudo apt install ./singularity*.deb

.github/workflows/eb_command.yml

@@ -1,12 +1,17 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for the 'eb' command
 on: [push, pull_request]
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   test-eb:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
       fail-fast: false
     steps:
     - uses: actions/checkout@v3

.github/workflows/linting.yml

@@ -1,11 +1,16 @@
 name: Static Analysis
 on: [push, pull_request]
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   python-linting:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10']
+        python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/unit_tests.yml

@@ -1,6 +1,11 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: EasyBuild framework unit tests
 on: [push, pull_request]
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   setup:
     runs-on: ubuntu-20.04
@@ -41,15 +46,9 @@ jobs:
           - python: 3.5
             modules_tool: ${{needs.setup.outputs.lmod8}}
             module_syntax: Lua
-          - python: 3.5
-            modules_tool: ${{needs.setup.outputs.lmod8}}
-            module_syntax: Tcl
           - python: 3.7
             modules_tool: ${{needs.setup.outputs.lmod8}}
             module_syntax: Lua
-          - python: 3.7
-            modules_tool: ${{needs.setup.outputs.lmod8}}
-            module_syntax: Tcl
           - python: 3.8
             modules_tool: ${{needs.setup.outputs.lmod8}}
             module_syntax: Lua
@@ -59,13 +58,13 @@ jobs:
           - python: 3.9
             modules_tool: ${{needs.setup.outputs.lmod8}}
             module_syntax: Lua
-          - python: 3.9
-            modules_tool: ${{needs.setup.outputs.lmod8}}
-            module_syntax: Tcl
           - python: '3.10'
             modules_tool: ${{needs.setup.outputs.lmod8}}
             module_syntax: Lua
-          - python: '3.10'
+          - python: '3.11'
+            modules_tool: ${{needs.setup.outputs.lmod8}}
+            module_syntax: Lua
+          - python: '3.11'
             modules_tool: ${{needs.setup.outputs.lmod8}}
             module_syntax: Tcl
           # There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
@@ -197,10 +196,14 @@ jobs:
           # create file owned by root but writable by anyone (used by test_copy_file)
           sudo touch /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
           sudo chmod o+w /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
+          # silence deprecation warning when using Python 2, since it breaks a bunch of tests
+          if [ "${{matrix.python}}" == '2.7' ]; then
+            export TEST_EASYBUILD_SILENCE_DEPRECATION_WARNINGS=python2
+          fi
           # run test suite
           python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log
           # try and make sure output of running tests is clean (no printed messages/warnings)
-          IGNORE_PATTERNS="no GitHub token available|skipping SvnRepository test|requires Lmod as modules tool|stty: 'standard input': Inappropriate ioctl for device|CryptographyDeprecationWarning: Python 3.[56]|from cryptography.*default_backend|CryptographyDeprecationWarning: Python 2|from cryptography.utils import int_from_bytes|Blowfish"
+          IGNORE_PATTERNS="no GitHub token available|skipping SvnRepository test|requires Lmod as modules tool|stty: 'standard input': Inappropriate ioctl for device|CryptographyDeprecationWarning: Python 3.[56]|from cryptography.*default_backend|CryptographyDeprecationWarning: Python 2|from cryptography.utils import int_from_bytes|Blowfish|GC3Pie not available, skipping test"
           # '|| true' is needed to avoid that Travis stops the job on non-zero exit of grep (i.e. when there are no matches)
           PRINTED_MSG=$(egrep -v "${IGNORE_PATTERNS}" test_framework_suite.log | grep '\.\n*[A-Za-z]' || true)
           test "x$PRINTED_MSG" = "x" || (echo "ERROR: Found printed messages in output of test suite\n${PRINTED_MSG}" && exit 1)

README.rst

@@ -1,7 +1,8 @@
-.. image:: https://github.com/easybuilders/easybuild-framework/workflows/EasyBuild%20framework%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-framework/workflows/EasyBuild%20framework%20unit%20tests/badge.svg?branch=develop
 
 `EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
 and installation framework that allows you to manage (scientific) software

RELEASE_NOTES

@@ -4,6 +4,47 @@ For more detailed information, please see the git log.
 These release notes can also be consulted at https://easybuild.readthedocs.io/en/latest/Release_notes.html.
 
 
+v4.7.0 (January 9th 2023)
+-------------------------
+
+feature release
+
+- print deprecation warning with running EasyBuild with Python 2 (#4136)
+- various enhancements, including:
+  - add support for checksums specified in external `checksums.json` file (#3749)
+  - vendor distutils.version.LooseVersion as easybuild.tools.LooseVersion (since distutils is deprecated in Python 3.10) (#3794, #4156)
+  - take into account custom configuration options specified in easystack file (#4057)
+  - add support for using --output-format=md (MarkDown) (#4117, #4155)
+  - add support for --filter-rpath-sanity-libs to skip RPATH sanity check for designated libraries (#4119)
+  - add sanity_check_load_module method to EasyBlock to provide control over when module is loaded during sanity check step (#4125)
+  - add eb_bash_completion_local.bash script to setup.py (#4127)
+  - check whether nvidia-smi/rocm-smi command is available before trying to run it in `get_gpu_info` (#4131)
+  - add gfbf as subtoolchain of foss (#4143)
+  - add support for postinstallmsgs (#4145)
+  - make iimkl toolchain aware of intel-compilers (#4146)
+  - add definition for nvofbf toolchain (#4157, #4163)
+- various bug fixes, including:
+  - also use EasyConfig instances cache in process_easyconfig when build_specs is empty dict (#4107)
+  - fix build options that should have empty list as default value (#4108)
+  - catch easyconfig parsing failure so we can generate and post a test report (#4109)
+  - add explicit return when no checksums match those specified in a tuple (#4112)
+  - tweak findPythonDeps.py script to use canonical package names (#4118)
+  - add `-fdefault-double-8` to `r8` toolchain compiler option for GCC (to be consistent with Intel) (#4121)
+  - always start with empty list for banned/requires libraries to avoid that corresponding build option is updated in-place (#4137)
+  - fix container tests by using EPEL archive URL for downloading Singularity RPM (#4138)
+  - use -march=x86-64 -mtune=generic instead of -xSSE2 when using Intel oneAPI compilers (#4147)
+  - partially skip test_det_copy_ec_specs if no GitHub token is available (#4149)
+- other changes:
+  - drop support for easystack files using 'software' top-level key (#4057)
+  - also run unit tests with Python 3.11 + add Python 3.11 to classifiers in setup.py (#4092, #4141)
+  - use new EasyBuild logo in README (#4123)
+  - automatically cancel Github Action workflow runs for outdated commits (#4132)
+  - auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0 (#4135)
+  - trim CI test configurations to avoid hitting GitHub rate limits (#4148)
+  - various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format (#4129, #4130, #4154, #4160, #4162, #4168)
+  - update copyright lines for 2023 (#4161)
+
+
 v4.6.2 (October 21st 2022)
 --------------------------
 

contrib/hooks/add_delete_configopt.py

@@ -3,7 +3,7 @@
 # Author: Åke Sandgren, HPC2N
 
 # We need to be able to distinguish between versions of OpenMPI
-from distutils.version import LooseVersion
+from easybuild.tools import LooseVersion
 
 
 def pre_configure_hook(self, *args, **kwargs):

contrib/hooks/hpc2n_hooks.py

@@ -4,8 +4,8 @@
 
 import os
 
-from distutils.version import LooseVersion
 from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS
+from easybuild.tools import LooseVersion
 from easybuild.tools.filetools import apply_regex_substitutions
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.modules import get_software_root

easybuild/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2022 Ghent University
+# Copyright 2011-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -25,7 +25,9 @@
 """
 Declares EasyBuild namespace, in an extendable way.
 
-:author: Jens Timmerman (Ghent University)
-:author: Kenneth Hoste (Ghent University)
+Authors:
+
+* Jens Timmerman (Ghent University)
+* Kenneth Hoste (Ghent University)
 """
 __path__ = __import__('pkgutil').extend_path(__path__, __name__)

easybuild/base/exceptions.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2015-2022 Ghent University
+# Copyright 2015-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -25,8 +25,10 @@
 """
 Module providing custom exceptions.
 
-:author: Kenneth Hoste (Ghent University)
-:author: Riccardo Murri (University of Zurich)
+Authors:
+
+* Kenneth Hoste (Ghent University)
+* Riccardo Murri (University of Zurich)
 """
 import inspect
 import logging

easybuild/base/fancylogger.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2011-2022 Ghent University
+# Copyright 2011-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -69,9 +69,11 @@
  - set an environment variable FANCYLOG_SERVER and FANCYLOG_SERVER_PORT (optionally)
  - this will make fancylogger log to that that server and port instead of the screen.
 
-:author: Jens Timmerman (Ghent University)
-:author: Stijn De Weirdt (Ghent University)
-:author: Kenneth Hoste (Ghent University)
+Authors:
+
+* Jens Timmerman (Ghent University)
+* Stijn De Weirdt (Ghent University)
+* Kenneth Hoste (Ghent University)
 """
 
 from collections import namedtuple
@@ -83,8 +85,8 @@
 import threading
 import traceback
 import weakref
-from distutils.version import LooseVersion
 
+from easybuild.tools import LooseVersion
 from easybuild.tools.py2vs3 import raise_with_traceback, string_type
 
 
@@ -341,10 +343,7 @@ def deprecated(self, msg, cur_ver, max_ver, depth=2, exception=None, log_callbac
         loose_cv = LooseVersion(cur_ver)
         loose_mv = LooseVersion(max_ver)
 
-        loose_cv.version = loose_cv.version[:depth]
-        loose_mv.version = loose_mv.version[:depth]
-
-        if loose_cv >= loose_mv:
+        if loose_cv.version[:depth] >= loose_mv.version[:depth]:
             self.raiseException("DEPRECATED (since v%s) functionality used: %s" % (max_ver, msg), exception=exception)
         else:
             deprecation_msg = "Deprecated functionality, will no longer work in v%s: %s" % (max_ver, msg)
@@ -826,7 +825,7 @@ def setroot(fancyrecord=FANCYLOG_FANCYRECORD):
     Set a FancyLogger instance as the logging root logger
     with (effective)loglevel of current root FancyLogger
 
-    :param fancyrecord is enabled or not (default FANCYLOG_FANCYRECORD module constant)
+    :param fancyrecord: is enabled or not (default FANCYLOG_FANCYRECORD module constant)
 
     Detecting the loglevel is best-effort, better to set the loglevel after setroot()
     """