Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 2 commits into from
Oct 28, 2024
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
176 changes: 90 additions & 86 deletions .github/workflows/PR.yml
View file
Open in desktop
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
Loading