Merge branch 'develop' into 20220222121720_new_pr_dkfpnHXMLD

Author: boegel

.github/workflows/bootstrap_script.yml

@@ -107,7 +107,7 @@ 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 $EB_BOOTSTRAP_SHA256SUM"
-          EB_BOOTSTRAP_EXPECTED="20210715.01 784dd29063d941be2d8b70e4c2eec12a9afe360f3ef8f753dcb518abf43ca7de"
+          EB_BOOTSTRAP_EXPECTED="20210715.01 0ffdc17ed7eacf78369c9cd6743728f36e61bb8bf5c1bdc1e23cf2040b1ce301"
           test "$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

@@ -20,6 +20,8 @@ jobs:
 
     - name: install OS & Python packages
       run: |
+        # ensure package list is up to date to avoid 404's for old packages
+        sudo apt-get update -yqq
         # for building Singularity images
         sudo apt-get install rpm
         sudo apt-get install yum

.github/workflows/eb_command.yml

@@ -73,15 +73,15 @@ jobs:
           pymajver=$(python -c 'import sys; print(sys.version_info[0])')
           pymajminver=$(python -c 'import sys; print(".".join(str(x) for x in sys.version_info[:2]))')
           # check patterns in verbose output
-          for pattern in "^>> Considering .python.\.\.\." "^>> .python. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> 'python' is able to import 'easybuild.main', so retaining it" "^>> Selected Python command: python \(.*/bin/python\)" "^This is EasyBuild 4\.[0-9.]\+"; do
+          for pattern in "^>> Considering .python.\.\.\." "^>> .python. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> 'python' is able to import 'easybuild', so retaining it" "^>> Selected Python command: python \(.*/bin/python\)" "^This is EasyBuild 4\.[0-9.]\+"; do
               echo "Looking for pattern \"${pattern}\" in eb_version.out..."
               grep "$pattern" eb_version.out
           done
           # also check when specifying Python command via $EB_PYTHON
           for eb_python in "python${pymajver}" "python${pymajminver}"; do
               export EB_PYTHON="${eb_python}"
               eb --version | tee eb_version.out 2>&1
-              for pattern in "^>> Considering .${eb_python}.\.\.\." "^>> .${eb_python}. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> '${eb_python}' is able to import 'easybuild.main', so retaining it" "^>> Selected Python command: ${eb_python} \(.*/bin/${eb_python}\)" "^This is EasyBuild 4\.[0-9.]\+"; do
+              for pattern in "^>> Considering .${eb_python}.\.\.\." "^>> .${eb_python}. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> '${eb_python}' is able to import 'easybuild', so retaining it" "^>> Selected Python command: ${eb_python} \(.*/bin/${eb_python}\)" "^This is EasyBuild 4\.[0-9.]\+"; do
                   echo "Looking for pattern \"${pattern}\" in eb_version.out..."
                   grep "$pattern" eb_version.out
               done

.github/workflows/unit_tests.yml

@@ -200,7 +200,7 @@ jobs:
           # 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 3.5|from cryptography.*default_backend|CryptographyDeprecationWarning: Python 2|from cryptography.utils import int_from_bytes"
+          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"
           # '|| 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)

RELEASE_NOTES

@@ -4,6 +4,29 @@ 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.
 
 
+v4.5.4 (March 31st 2022)
+------------------------
+
+update/bugfix release
+
+- various enhancements, including:
+  - warn about potentially missing patches in --new-pr (#3759, #3966)
+  - add support for 'clone_into' field in git_config source spec to specify different name for top-level directory (#3949)
+  - add bash completion for easyconfigs from local dir but not robot search path (#3953)
+  - add a 'sync pr' message when the PR has a mergeable state but is showing a failed status for the test suite on the last commit (#3967)
+  - add gmpit toolchain definition (GCC + MPItrampoline) (#3971)
+  - use 'zypper search -i' to check whether specified OS dependency is installed on openSUSE + make sure that rpm is considered for checking OS dependencies on RHEL8 (#3973)
+  - add support for post-install patches (#3974)
+  - add support for 'download_instructions' easyconfig parameter key to specify some download or installation steps for user in case of complicated way of obtaining needed files (#3976, #3981)
+  - also try collecting AMD GPU info (via rocm-smi) for --show-system-info (#3978, #3982)
+- various bug fixes, including:
+  - ensure --review-pr can find dependencies included in PR (#3979)
+  - run 'apt-get update' in GitHub Actions workflow for container tests to update container package list before installing anything (#3985)
+- other changes:
+  - enable code linting check for all supported Python versions (#3725)
+  - update copyright lines for 2022 (#3986)
+
+
 v4.5.3 (February 11th 2022)
 ---------------------------
 

easybuild/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2021 Ghent University
+# Copyright 2011-2022 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/base/exceptions.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2015-2021 Ghent University
+# Copyright 2015-2022 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/base/fancylogger.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2011-2021 Ghent University
+# Copyright 2011-2022 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/base/generaloption.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2011-2021 Ghent University
+# Copyright 2011-2022 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/base/testing.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2014-2021 Ghent University
+# Copyright 2014-2022 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),