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Merge pull request #4227 from easybuilders/4.7.x
release EasyBuild v4.7.1
2 parents 527c9f0 + 9c2bb6a commit 8430804

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‎.github/workflows/bootstrap_script.yml‎

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name: test EasyBuild bootstrap script
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on: [push, pull_request]
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permissions:
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contents: read # to fetch code (actions/checkout)
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concurrency:
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group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
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cancel-in-progress: true
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- name: install OS & Python packages
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run: |
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# disable apt update, we don't really need it,
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# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
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# sudo apt update
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# for modules tool
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sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
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APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
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# Avoid apt-get update, as we don't really need it,
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# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
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if ! sudo apt-get install $APT_PKGS; then
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# Try to update cache, then try again to resolve 404s of old packages
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sudo apt-get update -yqq || true
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sudo apt-get install $APT_PKGS
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fi
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# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
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# needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
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if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then

‎.github/workflows/container_tests.yml‎

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name: Tests for container support
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on: [push, pull_request]
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permissions:
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contents: read # to fetch code (actions/checkout)
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concurrency:
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group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
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cancel-in-progress: true
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- name: install OS & Python packages
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run: |
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# ensure package list is up to date to avoid 404's for old packages
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sudo apt update -yqq
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# for building Singularity images
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sudo apt install rpm
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sudo apt install yum
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# for modules tool
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sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
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APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
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# for building Singularity images
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APT_PKGS+=" rpm yum"
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# Avoid apt-get update, as we don't really need it,
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# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
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if ! sudo apt-get install $APT_PKGS; then
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# Try to update cache, then try again to resolve 404s of old packages
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sudo apt-get update -yqq || true
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sudo apt-get install $APT_PKGS
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fi
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# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
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# needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
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if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
@@ -53,15 +62,16 @@ jobs:
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# see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
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- name: install Singularity
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run: |
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sudo apt-get update
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# install alien, which can be used to convert RPMs to Debian packages
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sudo apt install alien
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sudo apt-get install alien
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alien --version
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# determine latest version of Singularity available in EPEL, and download RPM
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singularity_rpm=$(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')
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curl -OL https://dl.fedoraproject.org/pub/archive/epel/8.5/Everything/x86_64/Packages/s/${singularity_rpm}
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# convert Singularity RPM to Debian package, and install it
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sudo alien -d ${singularity_rpm}
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sudo apt install ./singularity*.deb
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sudo apt-get install ./singularity*.deb
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singularity --version
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- name: install sources

‎.github/workflows/eb_command.yml‎

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name: Tests for the 'eb' command
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on: [push, pull_request]
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permissions:
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contents: read # to fetch code (actions/checkout)
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concurrency:
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group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
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cancel-in-progress: true
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# update to latest pip, check version
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pip install --upgrade pip
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pip --version
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# install packages required for modules tool
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sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
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# for modules tool
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APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
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# Avoid apt-get update, as we don't really need it,
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# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
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if ! sudo apt-get install $APT_PKGS; then
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# Try to update cache, then try again to resolve 404s of old packages
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sudo apt-get update -yqq || true
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sudo apt-get install $APT_PKGS
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fi
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# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
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# needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
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if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then

‎.github/workflows/linting.yml‎

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

‎.github/workflows/unit_tests.yml‎

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name: EasyBuild framework unit tests
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on: [push, pull_request]
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permissions:
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contents: read # to fetch code (actions/checkout)
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concurrency:
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group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
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cancel-in-progress: true
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- name: install OS & Python packages
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run: |
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# disable apt update, we don't really need it,
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# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
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# sudo apt update
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# for modules tool
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sudo apt install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
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APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
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# for GitPython, python-hglib
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APT_PKGS+=" git mercurial"
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# dep for GC3Pie
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APT_PKGS+=" time"
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# Avoid apt-get update, as we don't really need it,
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# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
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if ! sudo apt-get install $APT_PKGS; then
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# Try to update cache, then try again to resolve 404s of old packages
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sudo apt-get update -yqq || true
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sudo apt-get install $APT_PKGS
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fi
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# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
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# needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
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if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
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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
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fi
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# for GitPython, python-hglib
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sudo apt install git mercurial
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# dep for GC3Pie
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sudo apt install time
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# Python packages
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pip --version
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pip install --upgrade pip
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# run test suite
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python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log
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# try and make sure output of running tests is clean (no printed messages/warnings)
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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"
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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"
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# '|| true' is needed to avoid that Travis stops the job on non-zero exit of grep (i.e. when there are no matches)
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PRINTED_MSG=$(egrep -v "${IGNORE_PATTERNS}" test_framework_suite.log | grep '\.\n*[A-Za-z]' || true)
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test "x$PRINTED_MSG" = "x" || (echo "ERROR: Found printed messages in output of test suite\n${PRINTED_MSG}" && exit 1)
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test "x$PRINTED_MSG" = "x" || (echo "ERROR: Found printed messages in output of test suite" && echo "${PRINTED_MSG}" && exit 1)

‎.travis.yml‎

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This file was deleted.

‎README.rst‎

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.. image:: https://github.com/easybuilders/easybuild-framework/workflows/EasyBuild%20framework%20unit%20tests/badge.svg?branch=develop
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`EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
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`EasyBuild <https://easybuild.io>`_ is a software build
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and installation framework that allows you to manage (scientific) software
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on High Performance Computing (HPC) systems in an efficient way.
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implement the software install procedure for a particular (group of) software
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package(s).
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The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
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The EasyBuild documentation is available at http://docs.easybuild.io/.
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The EasyBuild framework source code is hosted on GitHub, along
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with an issue tracker for bug reports and feature requests, see

‎RELEASE_NOTES‎

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These release notes can also be consulted at https://easybuild.readthedocs.io/en/latest/Release_notes.html.
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v4.7.1 (March 20th 2023)
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------------------------
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update/bugfix release
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- various enhancements, including:
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- add option to make sanity_check_paths arch dependent (#3845)
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- add support for %(start_dir)s easyconfig template (#4073)
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- add Ubuntu friendly package naming scheme EasyBuildDebFriendlyPNS (#4115)
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- allow to directly import constants from easybuild.framework.easyconfig.constants (#4144)
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- accept single source as dict and single checksum in check_checksums_for (#4180)
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- add pre/post extension hook that is triggered before/after individual extension installations (#4193)
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- enforce absolute paths as start dir of extensions (#4196)
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- print warning when non-existing `start_dir` is specified for extension (#4201)
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- add support to silence deprecation warning for easyconfigs and toolchains (#4207)
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- skip directories when fixing shebangs (#4209)
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- add support for 'modunloadmsg' easyconfig parameter (#4223)
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- various bug fixes, including:
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- fix use of `locate` in `check_os_dependency` (#4166)
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- add VERSION to easybuild.easyblocks namespace in test sandbox (#4171)
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- also apply filter to asyncprocess test subsuite (#4172)
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- don't use deprecated SafeConfigParser when running with Python 3.x (#4173)
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- update CI workflows to run 'apt-get update' if installation of packages via 'apt-get install' failed, likely due to stale apt cache (#4176)
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- fixes for findPythonDeps script (#4179)
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- check type of versionsuffix value in det_full_ec_version, and raise useful error message if it's not a string (#4184)
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- avoid GC3Pie deprecation warning (#4185)
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- correctly restore sys.path in tests (#4186)
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- suppress output of --skip-test-step test (#4187)
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- fix flaky test_search_file due to accidental matches for `.*C++` search pattern (#4190)
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- silence distutils deprecation warnings (#4204)
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- 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)
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- restore initial environment before processing each easystack item (#4213)
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- make test_help_long work on small terminals (#4218)
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- other changes:
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- use better test assertions by replacing use of assertFalse/assertTrue (#4170, #4205)
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- remove Travis CI configuration file (#4174)
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- filter out deprecation warnings for platform.dist in get_os_version and platform.linux_distribution in get_os_name (#4175)
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- only give read permissions in GitHub Actions workflows (#4182)
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- fix website/docs links in README (#4199)
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- only print "default: " for configuration option of strlist type if default is not empty (#4220)
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v4.7.0 (January 9th 2023)
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-------------------------
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