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stop using Ubuntu 20.4 in GitHub Actions workflows, use Ubuntu 22.04 instead #4783

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Merged
Micket merged 4 commits into from
Mar 4, 2025
Merged

stop using Ubuntu 20.4 in GitHub Actions workflows, use Ubuntu 22.04 instead #4783

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b3d5a7d
stop using Ubuntu 20.4 in GitHub Actions workflows, use Ubuntu 22.04 …
boegel Mar 2, 2025
8516e1c
use python3.6 command instead of python3 in workflow to run tests wit…
boegel Mar 3, 2025
796df9a
use --filter-deps in end2end test in fedora-41 or ubuntu-24.04 contai…
boegel Mar 3, 2025
ccd481a
remove custom workflow for running test suite with Python 3.6, will b…
boegel Mar 4, 2025
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6 changes: 3 additions & 3 deletions .github/workflows/container_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,18 +17,18 @@ jobs:
python: [3.7]
fail-fast: false
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2

- name: set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
with:
python-version: ${{matrix.python}}
architecture: x64

- name: install OS & Python packages
run: |
# for modules tool
APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
APT_PKGS="lua5.3 liblua5.3-dev lua-filesystem lua-posix tcl tcl-dev"
# for building Singularity images
APT_PKGS+=" rpm dnf"

Expand Down
14 changes: 4 additions & 10 deletions .github/workflows/container_tests_apptainer.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@ jobs:
strategy:
matrix:
python: [3.7]
apptainer: [1.0.0, 1.1.7]
apptainer: [1.0.0, 1.1.7, 1.3.6]
fail-fast: false
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2

- name: set up Python
uses: actions/setup-python@v3
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
with:
python-version: ${{matrix.python}}
architecture: x64
Expand All @@ -31,7 +31,7 @@ jobs:
# for building CentOS 7 container images
APT_PKGS="rpm dnf"
# for modules tool
APT_PKGS+=" lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
APT_PKGS+=" lua5.3 liblua5.3-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)
Expand All @@ -41,12 +41,6 @@ jobs:
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

- name: install Lmod
run: |
# avoid downloading modules tool sources into easybuild-framework dir
Expand Down
16 changes: 5 additions & 11 deletions .github/workflows/eb_command.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,16 +11,16 @@ concurrency:

jobs:
test-eb:
runs-on: ubuntu-20.04
runs-on: ubuntu-22.04
strategy:
matrix:
python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
python: [3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
fail-fast: false
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2

- name: set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
with:
python-version: ${{matrix.python}}
architecture: x64
Expand All @@ -38,7 +38,7 @@ jobs:
fi

# for modules tool
APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
APT_PKGS="lua5.3 liblua5.3-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)
Expand All @@ -48,12 +48,6 @@ jobs:
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

- name: install modules tool
run: |
# avoid downloading modules tool sources into easybuild-framework dir
Expand Down
23 changes: 10 additions & 13 deletions .github/workflows/end2end.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,26 +8,19 @@ jobs:
matrix:
container:
- centos-8.5
- fedora-36
- fedora-41
- opensuse-15.4
- rockylinux-8.8
- rockylinux-9.2
- rockylinux-8.10
- rockylinux-9.5
- ubuntu-20.04
- ubuntu-22.04
- ubuntu-24.04
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@branfosj branfosj Mar 3, 2025

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This failure on Ubuntu 24.04 can be avoided with --filter-deps=binutils

Log file from a local build

gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c huffman.c

If compilation produces errors, or a large number of warnings,
please read README.COMPILATION.PROBLEMS -- you might be able to
adjust the flags in this Makefile to improve matters.

Also in README.COMPILATION.PROBLEMS are some hints that may help
if your build produces an executable which is unable to correctly
handle so-called 'large files' -- files of size 2GB or more.

gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c bzlib.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c bzip2.c
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64 -c bzip2recover.c
bzip2.c: In function ‘applySavedFileAttrToOutputFile’:
bzip2.c:1073:11: warning: ignoring return value of ‘fchown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1073 |    (void) fchown ( fd, fileMetaInfo.st_uid, fileMetaInfo.st_gid );
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -Winline -O3 -fPIC -g -D_FILE_OFFSET_BITS=64  -o bzip2recover bzip2recover.o
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section `.relr.dyn'
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: cannot find /lib/x86_64-linux-gnu/libc.so.6
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section `.relr.dyn'
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section `.relr.dyn'
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: cannot find /lib64/ld-linux-x86-64.so.2
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section `.relr.dyn'
/home/simon/work/eb/installpath/software/binutils/2.37/bin/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2
collect2: error: ld returned 1 exit status
make: *** [Makefile:44: bzip2recover] Error 1
make: *** Waiting for unfinished jobs....

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@branfosj branfosj Mar 3, 2025 •
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$ gcc --version
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ ld --version
GNU ld (GNU Binutils for Ubuntu) 2.42
Copyright (C) 2024 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.

fail-fast: false
container:
image: ghcr.io/easybuilders/${{ matrix.container }}-amd64
volumes:
- /node20217:/node20217:rw,rshared
- ${{ matrix.container == 'centos-7.9' && '/node20217:/__e/node20:ro,rshared' || ' ' }}
steps:
- name: install nodejs20glibc2.17
if: ${{ matrix.container == 'centos-7.9' }}
run: |
curl -LO https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
- name: Check out the repo
uses: actions/checkout@v4
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2

- name: download and unpack easyblocks and easyconfigs repositories
run: |
Expand Down Expand Up @@ -66,4 +59,8 @@ jobs:
- name: End-to-end test of installing bzip2 with EasyBuild
shell: bash
run: |
sudo -u easybuild bash -l -c "source /tmp/eb_env; eb bzip2-1.0.8.eb --trace --robot"
EB_ARGS=''
if [[ "${{ matrix.container }}" == "fedora-41" ]] || [[ "${{ matrix.container }}" == "ubuntu-24.04" ]]; then
EB_ARGS='--filter-deps=binutils'
fi
sudo -u easybuild bash -l -c "source /tmp/eb_env; eb bzip2-1.0.8.eb --trace --robot ${EB_ARGS}"
8 changes: 4 additions & 4 deletions .github/workflows/linting.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,15 @@ concurrency:

jobs:
python-linting:
runs-on: ubuntu-20.04
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
python-version: [3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2

- name: set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
with:
python-version: ${{ matrix.python-version }}

Expand Down
42 changes: 15 additions & 27 deletions .github/workflows/unit_tests.yml
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Expand Up @@ -11,9 +11,9 @@ concurrency:

jobs:
setup:
runs-on: ubuntu-20.04
runs-on: ubuntu-22.04
outputs:
lmod8: Lmod-8.7.6
lmod8: Lmod-8.7.58
modules4: modules-4.5.3
modules5: modules-5.3.1
steps:
Expand All @@ -23,7 +23,8 @@ jobs:
runs-on: ubuntu-20.04
strategy:
matrix:
python: [3.6]
# Python 3.10 is default in Ubuntu 22.04
python: ['3.10']
modules_tool:
# use variables defined by 'setup' job above, see also
# https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#needs-context
Expand All @@ -33,39 +34,32 @@ jobs:
lc_all: [""]
include:
# Test different Python 3 versions with Lmod 8.x (with both Lua and Tcl module syntax)
- python: 3.7
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: 3.8
- python: '3.7'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: 3.9
- python: '3.8'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.10'
- python: '3.9'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.11'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.12'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.13'
modules_tool: ${{needs.setup.outputs.lmod8}}
# There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
# Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
- python: 3.6
modules_tool: ${{needs.setup.outputs.lmod8}}
lc_all: C
fail-fast: false
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2

- name: set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
with:
python-version: ${{matrix.python}}
architecture: x64

- name: install OS & Python packages
run: |
# for modules tool
APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
APT_PKGS="lua5.3 liblua5.3-dev lua-filesystem lua-posix tcl tcl-dev"
# for GitPython, python-hglib
APT_PKGS+=" git mercurial"
# dep for GC3Pie
Expand All @@ -79,11 +73,6 @@ jobs:
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
# Python packages
pip --version
pip install --upgrade pip
Expand All @@ -94,8 +83,8 @@ jobs:
pip install --upgrade setuptools
fi
# git config is required to make actual git commits (cfr. tests for GitRepository)
git config --global user.name "Travis CI"
git config --global user.email "travis@travis-ci.org"
git config --global user.name "Github Actions"
git config --global user.email "actions@github.com"
git config --get-regexp 'user.*'

- name: install GitHub token (if available)
Expand All @@ -105,9 +94,9 @@ jobs:
# and are only run after the PR gets merged
GITHUB_TOKEN: ${{secrets.CI_UNIT_TESTS_GITHUB_TOKEN}}
run: |
# only install GitHub token when testing with Lmod 8.x + Python 3.6 or 3.9, to avoid hitting GitHub rate limit
# only install GitHub token when testing with Lmod 8.x + Python 3.9, to avoid hitting GitHub rate limit
# tests that require a GitHub token are skipped automatically when no GitHub token is available
if [[ "${{matrix.modules_tool}}" =~ 'Lmod-8' ]] && [[ "${{matrix.python}}" =~ 3.[69] ]]; then
if [[ "${{matrix.modules_tool}}" =~ 'Lmod-8' ]] && [[ "${{matrix.python}}" =~ 3.9 ]]; then
if [ ! -z $GITHUB_TOKEN ]; then
SET_KEYRING="import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring())"
python -c "import keyring; $SET_KEYRING; keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')"
Expand Down Expand Up @@ -197,9 +186,8 @@ jobs:
IGNORE_PATTERNS+="|skipping SvnRepository test"
IGNORE_PATTERNS+="|requires Lmod as modules tool"
IGNORE_PATTERNS+="|stty: 'standard input': Inappropriate ioctl for device"
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 3.[567]"
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 3.7"
IGNORE_PATTERNS+="|from cryptography.* import "
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 2"
IGNORE_PATTERNS+="|Blowfish"
IGNORE_PATTERNS+="|GC3Pie not available, skipping test"
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: TripleDES has been moved"
Expand Down