ghostx: add aarch64/arm64 builds #4792
Workflow file for this run
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name: PR Check | |
on: | |
pull_request: | |
types: [opened, synchronize, reopened] | |
concurrency: | |
group: build-${{ github.event.pull_request.number || github.head_ref }} | |
cancel-in-progress: true | |
jobs: | |
lint: | |
name: Lint | |
runs-on: ubuntu-22.04 | |
strategy: | |
fail-fast: true | |
max-parallel: 13 | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: set path | |
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
- name: Fetch conda install script | |
run: | | |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
- name: Set up bioconda-utils | |
run: bash install-and-set-up-conda.sh | |
- name: Configure conda | |
run: bash configure-conda.sh | |
- name: Perform lint | |
env: | |
# Mimic circleci | |
OSTYPE: "linux-gnu" | |
CI: "true" | |
run: | | |
set -e | |
eval "$(conda shell.bash hook)" | |
conda activate bioconda | |
source common.sh | |
echo '============' | |
conda info --all | |
conda config --show-sources | |
python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
echo '============' | |
if [ -z "$GITHUB_BASE_REF" ] ; then | |
export GITHUB_BASE_REF="master" | |
fi | |
git fetch origin "$GITHUB_BASE_REF" | |
bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD | |
conda clean -y --all | |
build-linux: | |
name: Linux Tests | |
runs-on: ubuntu-22.04 | |
strategy: | |
fail-fast: true | |
max-parallel: 13 | |
needs: lint | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: set path | |
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
- name: Fetch conda install script | |
run: | | |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
- name: Set up bioconda-utils | |
run: bash install-and-set-up-conda.sh | |
# This script can be used to reconfigure conda to use the right channel setup. | |
- name: Configure conda | |
run: bash configure-conda.sh | |
- name: Build and test | |
env: | |
# Mimic circleci | |
OSTYPE: "linux-gnu" | |
CI: "true" | |
run: | | |
set -e | |
# Clean up lingering build artifacts | |
for n in linux-64 osx-64 noarch; do | |
rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.conda | |
done | |
eval "$(conda shell.bash hook)" | |
conda activate bioconda | |
source common.sh | |
if [ -z "$GITHUB_BASE_REF" ] ; then | |
export GITHUB_BASE_REF="master" | |
fi | |
git fetch origin "$GITHUB_BASE_REF" | |
bioconda-utils build recipes config.yml \ | |
--docker --mulled-test \ | |
--git-range origin/"$GITHUB_BASE_REF" HEAD | |
- name: Prepare artifacts | |
run: | | |
( | |
rm -rf /tmp/artifacts | |
mkdir -p /tmp/artifacts/packages | |
cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
find -name .cache | xargs rm -rf || true | |
for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
cp -rv $n /tmp/artifacts/packages || true | |
done | |
if command -V docker >/dev/null; then | |
mkdir -p /tmp/artifacts/images | |
cd /tmp/artifacts/images | |
docker image ls --format='{{.Repository}}:{{.Tag}}' | \ | |
{ grep biocontainers || true ; } | \ | |
xargs -n1 -P4 bash -c ' | |
test -n "${1+x}" || exit 0 | |
echo "Start compressing docker image ${1} ..." | |
docker save "${1}" | gzip -c > "${1##*/}.tar.gz" | |
echo "Finished compressing docker image ${1} ." | |
' -- | |
# There's no : allowed in artifact names, replace it with --- | |
for f in /tmp/artifacts/images/*:* ; do mv -- "$f" "${f//:/---}"; done | |
fi | |
) || true | |
- name: Archive packages | |
uses: actions/upload-artifact@v4 | |
with: | |
name: linux-packages | |
path: | | |
/tmp/artifacts | |
build-osx-64: | |
name: OSX-64 Tests | |
runs-on: macos-13 | |
strategy: | |
fail-fast: true | |
max-parallel: 4 | |
# Limited concurrency for osx, so first make sure linux can pass | |
needs: build-linux | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: set path | |
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
- name: Fetch conda install script | |
run: | | |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
- name: Set up bioconda-utils | |
run: bash install-and-set-up-conda.sh | |
# This script can be used to reconfigure conda to use the right channel setup. | |
- name: Configure conda | |
run: bash configure-conda.sh | |
- name: Build and Test | |
env: | |
# Mimic circleci | |
OSTYPE: "darwin" | |
CI: "true" | |
run: | | |
set -e | |
eval "$(conda shell.bash hook)" | |
conda activate bioconda | |
source common.sh | |
# Sets up OSX SDK | |
run_conda_forge_build_setup | |
# Clean up lingering build artifacts | |
for n in linux-64 osx-64 noarch; do | |
rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
done | |
if [ -z "$GITHUB_BASE_REF" ] ; then | |
export GITHUB_BASE_REF="master" | |
fi | |
git fetch origin "$GITHUB_BASE_REF" | |
bioconda-utils build recipes config.yml \ | |
--git-range origin/"$GITHUB_BASE_REF" HEAD | |
- name: Prepare artifacts | |
run: | | |
( | |
rm -rf /tmp/artifacts | |
mkdir -p /tmp/artifacts/packages | |
cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
find -name .cache | xargs rm -rf || true | |
for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
cp -rv $n /tmp/artifacts/packages || true | |
done | |
) || true | |
- name: Archive packages | |
uses: actions/upload-artifact@v4 | |
with: | |
name: osx-packages | |
path: | | |
/tmp/artifacts | |
# Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI. | |
# build_and_test-osx-arm64: | |
# name: OSX-ARM64 Tests | |
# runs-on: macOS-14 # M1 | |
# strategy: | |
# fail-fast: true | |
# max-parallel: 4 | |
# needs: build-linux | |
# steps: | |
# - uses: actions/checkout@v4 | |
# with: | |
# fetch-depth: 0 | |
# # bail if there's no osx-arm64 recipes | |
# - name: Check for Additional Platforms | |
# id: additional_platforms | |
# run: | | |
# result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${GITHUB_JOB}") | |
# if [[ ${result} != "build" ]] | |
# then | |
# echo "No recipes using this platform, skipping rest of job." | |
# echo "skip_build=true" >> $GITHUB_OUTPUT | |
# fi | |
# - name: set path | |
# run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
# - name: Fetch conda install script | |
# if: steps.additional_platforms.outputs.skip_build != 'true' | |
# run: | | |
# wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
# - name: Set up bioconda-utils | |
# if: steps.additional_platforms.outputs.skip_build != 'true' | |
# run: bash install-and-set-up-conda.sh | |
# - name: Configure conda | |
# if: steps.additional_platforms.outputs.skip_build != 'true' | |
# run: bash configure-conda.sh | |
# - name: Build and Test | |
# if: steps.additional_platforms.outputs.skip_build != 'true' | |
# env: | |
# # Mimic circleci | |
# OSTYPE: "darwin" | |
# CI: "true" | |
# run: | | |
# set -xe | |
# eval "$(conda shell.bash hook)" | |
# conda activate bioconda | |
# source common.sh | |
# # Sets up OSX SDK | |
# run_conda_forge_build_setup | |
# if [ -z "$GITHUB_BASE_REF" ] ; then | |
# export GITHUB_BASE_REF="master" | |
# fi | |
# git fetch origin "$GITHUB_BASE_REF" | |
# bioconda-utils build recipes config.yml \ | |
# --lint --git-range origin/"$GITHUB_BASE_REF" HEAD | |
# - name: Prepare artifacts | |
# if: steps.additional_platforms.outputs.skip_build != 'true' | |
# run: | | |
# ( | |
# rm -rf /tmp/artifacts | |
# mkdir -p /tmp/artifacts/packages | |
# cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
# find -name .cache | xargs rm -rf || true | |
# for n in index.html channeldata.json osx-arm64 noarch; do | |
# cp -rv $n /tmp/artifacts/packages || true | |
# done | |
# ) || true | |
# - name: Archive packages | |
# if: steps.additional_platforms.outputs.skip_build != 'true' | |
# uses: actions/upload-artifact@v4 | |
# with: | |
# name: osx-arm64-packages | |
# path: | | |
# /tmp/artifacts |