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Merge branch 'master' into update-pbsv-v2.10.0
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jmattick authored Oct 29, 2024

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2 parents 5f8ae54 + 2914659 commit fd581c4
Showing 81 changed files with 1,314 additions and 571 deletions.
186 changes: 92 additions & 94 deletions .github/workflows/PR.yml
Original file line number Diff line number Diff line change
@@ -39,6 +39,7 @@ jobs:
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
source common.sh
echo '============'
conda info --all
conda config --show-sources
@@ -93,15 +94,15 @@ jobs:
eval "$(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/"$GITHUB_BASE_REF" HEAD
docker rmi quay.io/dpryan79/mulled_container:latest
- name: Prepare artifacts
run: |
@@ -134,21 +135,16 @@ jobs:
with:
name: linux-packages
path: |
/tmp/artifacts/packages
/tmp/artifacts
- name: Archive images
uses: actions/upload-artifact@v4
with:
name: docker-images
path: |
/tmp/artifacts/images
build-osx-64:
name: OSX-64 Tests
runs-on: macos-13
strategy:
fail-fast: true
max-parallel: 4
# Limited concurrency for osx, so first make sure linux can pass
needs: build-linux
steps:
- uses: actions/checkout@v4
@@ -178,19 +174,20 @@ jobs:
set -e
eval "$(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
@@ -210,87 +207,88 @@ jobs:
uses: actions/upload-artifact@v4
with:
name: osx-packages
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
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