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Bulk.yml
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name: Bulk branch
on:
push:
branches:
- bulk
jobs:
build-linux:
name: Bulk Linux Builds
if: "contains(github.event.head_commit.message, '[ci run]')"
runs-on: ubuntu-latest
strategy:
fail-fast: false
max-parallel: 6
matrix:
runner: [0, 1, 2, 3, 4, 5]
steps:
- uses: actions/checkout@v3
with:
# checkout as bioconda-bot in order to have the permission to push fail logs
token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}}
- name: set git user
run: |
git config user.name bioconda-bot
git config user.email [email protected]
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Fetch conda install script
run: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
- name: Restore cache
id: cache
uses: actions/cache@v3
with:
path: /opt/mambaforge
key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}
- name: Set up bioconda-utils
if: steps.cache.outputs.cache-hit != 'true'
run: bash install-and-set-up-conda.sh
# This script can be used to reconfigure conda to use the right channel setup.
# This has to be done after the cache is restored, because
# the channel setup is not cached as it resides in the home directory.
# We could use a system-wide (and therefore cached) channel setup,
# but mamba does not support that at the time of implementation
# (it ignores settings made with --system).
- name: Configure conda
run: bash configure-conda.sh
- name: Build and upload
env:
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
# Mimic circleci
OSTYPE: "linux-gnu"
CI: "true"
run: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
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 '============'
bioconda-utils build recipes config.yml \
--worker-offset ${{ matrix.runner }} --n-workers 6 \
--docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
--record-build-failures --skiplist-leafs
conda clean -y --all
build-osx:
name: Bulk OSX Builds
if: "contains(github.event.head_commit.message, '[ci run]')"
runs-on: macOS-latest
strategy:
fail-fast: false
max-parallel: 4
matrix:
runner: [0, 1, 2, 3]
steps:
- uses: actions/checkout@v3
with:
# checkout as bioconda-bot in order to have the permission to push fail logs
token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}}
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Fetch conda install script
run: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
- name: Restore cache
id: cache
uses: actions/cache@v3
with:
path: /opt/mambaforge
key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}
- name: Set up bioconda-utils
if: steps.cache.outputs.cache-hit != 'true'
run: bash install-and-set-up-conda.sh
# This script can be used to reconfigure conda to use the right channel setup.
# This has to be done after the cache is restored, because
# the channel setup is not cached as it resides in the home directory.
# We could use a system-wide (and therefore cached) channel setup,
# but mamba does not support that at the time of implementation
# (it ignores settings made with --system).
- name: Configure conda
run: bash configure-conda.sh
- name: Build and upload
env:
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
# Mimic circleci
OSTYPE: "darwin"
CI: "true"
run: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
# The SDK isn't actually cached, so reinstall it
run_conda_forge_build_setup
echo '============'
conda info --all
conda config --show-sources
conda activate bioconda
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 '============'
bioconda-utils build recipes config.yml \
--worker-offset ${{ matrix.runner }} --n-workers 4 \
--anaconda-upload --record-build-failures --skiplist-leafs
conda clean -y --all