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ci: Switch PR checks for linux-64 and osx-64 to GitHub Actions #51720

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merged 2 commits into from
Oct 28, 2024
Merged

ci: Switch PR checks for linux-64 and osx-64 to GitHub Actions #51720

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aee4ff5
ci: Switch PR checks for linux-64 and osx-64 to GitHub Actions
aliciaaevans Oct 28, 2024
c6af4ec
try removing pr:none
aliciaaevans Oct 28, 2024
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176 changes: 90 additions & 86 deletions .github/workflows/PR.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ jobs:
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
source common.sh
echo '============'
conda info --all
conda config --show-sources
Expand Down Expand Up @@ -93,15 +94,15 @@ jobs:

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"
docker pull quay.io/dpryan79/mulled_container:latest

bioconda-utils build recipes config.yml \
--docker --mulled-test \
--git-range origin/"$GITHUB_BASE_REF" HEAD
docker rmi quay.io/dpryan79/mulled_container:latest

- name: Prepare artifacts
run: |
Expand Down Expand Up @@ -149,6 +150,7 @@ jobs:
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
Expand Down Expand Up @@ -178,19 +180,20 @@ jobs:
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

# The SDK isn't actually cached, so reinstall it
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 \
--git-range origin/"$GITHUB_BASE_REF" HEAD

Expand All @@ -213,84 +216,85 @@ jobs:
path: |
/tmp/artifacts/packages

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
# 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
155 changes: 76 additions & 79 deletions .github/workflows/master.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,16 +44,12 @@ jobs:
set -ex
eval "$(conda shell.bash hook)"
conda activate bioconda
docker pull quay.io/dpryan79/mulled_container:latest
# bioconda-utils handle-merged-pr recipes config.yml \
# --repo bioconda/bioconda-recipes \
# --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \
# --quay-upload-target biocontainers \
# --fallback build
bioconda-utils build recipes config.yml \
bioconda-utils handle-merged-pr recipes config.yml \
--repo bioconda/bioconda-recipes \
--git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
--docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
docker rmi quay.io/dpryan79/mulled_container:latest
--quay-upload-target biocontainers \
--fallback build \
--artifact-source github-actions

build-osx-64:
name: OSX-64 Upload
Expand Down Expand Up @@ -99,74 +95,75 @@ jobs:
# Sets up OSX SDK
run_conda_forge_build_setup

# bioconda-utils handle-merged-pr recipes config.yml \
# --repo bioconda/bioconda-recipes \
# --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \
# --fallback build
bioconda-utils build recipes config.yml \
--anaconda-upload --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA}

build_and_upload-osx-arm64:
name: OSX-ARM64 Upload
if: github.repository == 'bioconda/bioconda-recipes'
runs-on: macOS-14 # M1
strategy:
fail-fast: false
max-parallel: 4
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=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${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 Upload
if: steps.additional_platforms.outputs.skip_build != 'true'
env:
QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# Mimic circleci
OSTYPE: "darwin"
CI: "true"
run: |
set -xe
eval "$(conda shell.bash hook)"
conda activate bioconda
source common.sh
# Sets up OSX SDK
run_conda_forge_build_setup

bioconda-utils handle-merged-pr recipes config.yml \
--repo bioconda/bioconda-recipes \
--git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
--fallback build \
--artifact-source github-actions
--repo bioconda/bioconda-recipes \
--git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
--fallback build \
--artifact-source github-actions


# Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
# build_and_upload-osx-arm64:
# name: OSX-ARM64 Upload
# if: github.repository == 'bioconda/bioconda-recipes'
# runs-on: macOS-14 # M1
# strategy:
# fail-fast: false
# max-parallel: 4
# 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=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${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 Upload
# if: steps.additional_platforms.outputs.skip_build != 'true'
# env:
# QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
# QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
# ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
# INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# # Mimic circleci
# OSTYPE: "darwin"
# CI: "true"
# run: |
# set -xe
# eval "$(conda shell.bash hook)"
# conda activate bioconda
# source common.sh
# # Sets up OSX SDK
# run_conda_forge_build_setup

# bioconda-utils handle-merged-pr recipes config.yml \
# --repo bioconda/bioconda-recipes \
# --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
# --fallback build \
# --artifact-source github-actions
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