Merge pull request #4227 from easybuilders/4.7.x

release EasyBuild v4.7.1

.github/workflows/bootstrap_script.yml

@@ -2,6 +2,9 @@
 name: test EasyBuild bootstrap script
 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
@@ -69,11 +72,17 @@ jobs:
 
     - name: install OS & Python packages
       run: |
-        # disable apt update, we don't really need it,
-        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
-        # sudo apt update
         # for modules tool
-        sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+        APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
+
+        # Avoid apt-get update, as we don't really need it,
+        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
+        if ! sudo apt-get install $APT_PKGS; then
+          # Try to update cache, then try again to resolve 404s of old packages
+          sudo apt-get update -yqq || true
+          sudo apt-get install $APT_PKGS
+        fi
+
         # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
         # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
         if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then

.github/workflows/container_tests.yml

@@ -2,6 +2,9 @@
 name: Tests for container support
 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
@@ -25,13 +28,19 @@ jobs:
 
     - name: install OS & Python packages
       run: |
-        # ensure package list is up to date to avoid 404's for old packages
-        sudo apt update -yqq
-        # for building Singularity images
-        sudo apt install rpm
-        sudo apt install yum
         # for modules tool
-        sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+        APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
+        # for building Singularity images
+        APT_PKGS+=" rpm yum"
+
+        # Avoid apt-get update, as we don't really need it,
+        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
+        if ! sudo apt-get install $APT_PKGS; then
+          # Try to update cache, then try again to resolve 404s of old packages
+          sudo apt-get update -yqq || true
+          sudo apt-get install $APT_PKGS
+        fi
+
         # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
         # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
         if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
@@ -53,15 +62,16 @@ jobs:
     # see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
     - name: install Singularity
       run: |
+        sudo apt-get update
         # install alien, which can be used to convert RPMs to Debian packages
-        sudo apt install alien
+        sudo apt-get install alien
         alien --version
         # determine latest version of Singularity available in EPEL, and download RPM
         singularity_rpm=$(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
+        sudo apt-get install ./singularity*.deb
         singularity --version
 
     - name: install sources

.github/workflows/eb_command.yml

@@ -2,6 +2,9 @@
 name: Tests for the 'eb' command
 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
@@ -29,8 +32,18 @@ jobs:
         # update to latest pip, check version
         pip install --upgrade pip
         pip --version
-        # install packages required for modules tool
-        sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+
+        # for modules tool
+        APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
+
+        # Avoid apt-get update, as we don't really need it,
+        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
+        if ! sudo apt-get install $APT_PKGS; then
+          # Try to update cache, then try again to resolve 404s of old packages
+          sudo apt-get update -yqq || true
+          sudo apt-get install $APT_PKGS
+        fi
+
         # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
         # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
         if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then

.github/workflows/linting.yml

@@ -1,6 +1,9 @@
 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

.github/workflows/unit_tests.yml

@@ -2,6 +2,9 @@
 name: EasyBuild framework 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
@@ -85,20 +88,26 @@ jobs:
 
     - name: install OS & Python packages
       run: |
-        # disable apt update, we don't really need it,
-        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
-        # sudo apt update
         # for modules tool
-        sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+        APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
+        # for GitPython, python-hglib
+        APT_PKGS+=" git mercurial"
+        # dep for GC3Pie
+        APT_PKGS+=" time"
+
+        # Avoid apt-get update, as we don't really need it,
+        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
+        if ! sudo apt-get install $APT_PKGS; then
+          # Try to update cache, then try again to resolve 404s of old packages
+          sudo apt-get update -yqq || true
+          sudo apt-get install $APT_PKGS
+        fi
+
         # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
         # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
         if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
             sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
         fi
-        # for GitPython, python-hglib
-        sudo apt install git mercurial
-        # dep for GC3Pie
-        sudo apt install time
         # Python packages
         pip --version
         pip install --upgrade pip
@@ -203,7 +212,7 @@ jobs:
           # run test suite
           python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log
           # try and make sure output of running tests is clean (no printed messages/warnings)
-          IGNORE_PATTERNS="no GitHub token available|skipping SvnRepository test|requires Lmod as modules tool|stty: 'standard input': Inappropriate ioctl for device|CryptographyDeprecationWarning: Python 3.[56]|from cryptography.*default_backend|CryptographyDeprecationWarning: Python 2|from cryptography.utils import int_from_bytes|Blowfish|GC3Pie not available, skipping test"
+          IGNORE_PATTERNS="no GitHub token available|skipping SvnRepository test|requires Lmod as modules tool|stty: 'standard input': Inappropriate ioctl for device|CryptographyDeprecationWarning: Python 3.[56]|from cryptography.* import |CryptographyDeprecationWarning: Python 2|Blowfish|GC3Pie not available, skipping test"
           # '|| true' is needed to avoid that Travis stops the job on non-zero exit of grep (i.e. when there are no matches)
           PRINTED_MSG=$(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${PRINTED_MSG}" && exit 1)
+          test "x$PRINTED_MSG" = "x" || (echo "ERROR: Found printed messages in output of test suite" && echo "${PRINTED_MSG}" && exit 1)

README.rst

@@ -4,7 +4,7 @@
 
 .. 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
+`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.
 
@@ -13,7 +13,7 @@ supports the implementation and use of so-called easyblocks which
 implement the software install procedure for a particular (group of) software
 package(s).
 
-The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
+The EasyBuild documentation is available at http://docs.easybuild.io/.
 
 The EasyBuild framework source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see

RELEASE_NOTES

@@ -4,6 +4,48 @@ 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.
 
 
+v4.7.1 (March 20th 2023)
+------------------------
+
+update/bugfix release
+
+- various enhancements, including:
+  - add option to make sanity_check_paths arch dependent (#3845)
+  - add support for %(start_dir)s easyconfig template (#4073)
+  - add Ubuntu friendly package naming scheme EasyBuildDebFriendlyPNS (#4115)
+  - allow to directly import constants from easybuild.framework.easyconfig.constants (#4144)
+  - accept single source as dict and single checksum in check_checksums_for (#4180)
+  - add pre/post extension hook that is triggered before/after individual extension installations (#4193)
+  - enforce absolute paths as start dir of extensions (#4196)
+  - print warning when non-existing `start_dir` is specified for extension (#4201)
+  - add support to silence deprecation warning for easyconfigs and toolchains (#4207)
+  - skip directories when fixing shebangs (#4209)
+  - add support for 'modunloadmsg' easyconfig parameter (#4223)
+- various bug fixes, including:
+  - fix use of `locate` in `check_os_dependency` (#4166)
+  - add VERSION to easybuild.easyblocks namespace in test sandbox (#4171)
+  - also apply filter to asyncprocess test subsuite (#4172)
+  - don't use deprecated SafeConfigParser when running with Python 3.x (#4173)
+  - update CI workflows to run 'apt-get update' if installation of packages via 'apt-get install' failed, likely due to stale apt cache (#4176)
+  - fixes for findPythonDeps script (#4179)
+  - check type of versionsuffix value in det_full_ec_version, and raise useful error message if it's not a string (#4184)
+  - avoid GC3Pie deprecation warning (#4185)
+  - correctly restore sys.path in tests (#4186)
+  - suppress output of --skip-test-step test (#4187)
+  - fix flaky test_search_file due to accidental matches for `.*C++` search pattern (#4190)
+  - silence distutils deprecation warnings (#4204)
+  - improve handling of start_dir and add tests for cases where either ext_dir or initial start_dir or both are unset or None (#4206)
+  - restore initial environment before processing each easystack item (#4213)
+  - make test_help_long work on small terminals (#4218)
+- other changes:
+  - use better test assertions by replacing use of assertFalse/assertTrue (#4170, #4205)
+  - remove Travis CI configuration file (#4174)
+  - filter out deprecation warnings for platform.dist in get_os_version and platform.linux_distribution in get_os_name (#4175)
+  - only give read permissions in GitHub Actions workflows (#4182)
+  - fix website/docs links in README (#4199)
+  - only print "default: " for configuration option of strlist type if default is not empty (#4220)
+
+
 v4.7.0 (January 9th 2023)
 -------------------------