update finemap recipe with latest bioconda standards #71
Workflow file for this run
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name: Tests | |
on: | |
push: | |
branches: [ "main" ] | |
# Publish semver tags as releases. | |
tags: [ 'v*.*.*' ] | |
paths-ignore: | |
- 'README.md' | |
pull_request: | |
branches: [ "main" ] | |
paths-ignore: | |
- 'README.md' | |
jobs: | |
# adapted from https://docs.github.com/en/actions/learn-github-actions/expressions#example-returning-a-json-object | |
get_dirs: | |
name: List changed recipes | |
runs-on: ubuntu-latest | |
permissions: | |
pull-requests: read | |
strategy: | |
fail-fast: false | |
outputs: | |
matrix: ${{ steps.output-dirs.outputs.matrix }} # contains a list of the module names encoded as a json array | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
- name: List changed packages | |
id: filter | |
uses: dorny/paths-filter@v3 | |
with: | |
list-files: shell | |
filters: | | |
changed: | |
- added|modified: 'recipes/**' | |
- name: get directory names | |
id: output-dirs | |
# adapted from https://stackoverflow.com/a/71687652 | |
run: | | |
matrix=$(for i in ${{ steps.filter.outputs.changed_files }}; do sed 's\recipes/\\;s\/.*$\\' <<< $i; done | sort -u | jq --raw-input --slurp --compact-output 'split("\n")[:-1]') | |
echo "$matrix" | |
echo "matrix=$matrix" >> $GITHUB_OUTPUT | |
build: | |
name: Build on ${{ matrix.os }} | |
needs: get_dirs | |
runs-on: ${{ matrix.os }} | |
permissions: | |
contents: read | |
packages: write | |
if: ${{ needs.get_dirs.outputs.matrix != '[]' }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, macos-13, macos-latest] | |
packagename: ${{ fromJson(needs.get_dirs.outputs.matrix) }} | |
steps: | |
- name: Check out the repository | |
uses: actions/checkout@v4 | |
- name: Setup Miniforge | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
activate-environment: biobuild | |
channels: conda-forge,bioconda,defaults | |
auto-activate-base: false | |
miniforge-version: latest | |
use-mamba: true | |
- name: Get Date | |
id: get-date | |
run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
shell: bash | |
- name: Cache Conda env | |
uses: actions/cache@v4 | |
with: | |
path: ${{ env.CONDA }}/envs | |
key: | |
conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER }} | |
env: | |
# Increase this value to reset cache if needed | |
CACHE_NUMBER: 0 | |
id: cache | |
- name: Install biobuild environment | |
shell: bash -el {0} | |
run: | |
mamba create -y -n biobuild -c conda-forge -c bioconda -c nodefaults bioconda-utils anaconda-client | |
if: steps.cache.outputs.cache-hit != 'true' | |
- name: Run test | |
shell: bash -el {0} | |
run: | | |
bioconda-utils build --packages ${{ matrix.packagename }} | |
- name: Upload built package as GitHub artifact | |
uses: "actions/upload-artifact@v4" | |
with: | |
name: ${{ matrix.packagename }}-${{ matrix.os }} | |
path: ${{ env.CONDA }}/envs/biobuild/conda-bld/ | |
# - name: Upload built package to Anaconda | |
# shell: bash -el {0} | |
# env: | |
# ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }} | |
# if: ${{ env.ANACONDA_API_TOKEN == '' }} | |
# run: | | |
# anaconda upload ${{ env.CONDA }}/envs/biobuild/conda-bld/linux-64/*.tar.bz2 |