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Conda lock files

Conda lock files #98

Workflow file for this run

name: Wave
# When environment.yml is changed
on:
pull_request:
paths:
- "**/environment.yml"
env:
WAVE_VER: "1.4.1"
jobs:
gen-matrix:
name: generate-matrix
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
- name: Calculate file differences
id: diff
uses: tj-actions/changed-files@v44
with:
json: true
quotepath: false
# TODO Add Dockerfiles
files: |
modules/**/environment.yml
- name: Debug
run: echo ${{ steps.diff.outputs.all_changed_files }}
- id: set-matrix
run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"
outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}
build:
if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
needs: gen-matrix
name: build
permissions:
contents: write
runs-on: ubuntu-latest
timeout-minutes: 60
strategy:
fail-fast: false
matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
- uses: mamba-org/setup-micromamba@v1
with:
environment-name: conda-lock-env
create-args: >-
python=3.11
conda-lock
mamba
- name: Run conda-lock
run: |
rm --force conda-lock.yml
conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64
env:
MAMBA: "--mamba"
shell: bash -l {0}
- name: Commit & push changes
run: |
git config user.email "[email protected]"
git config user.name "nf-core-bot"
git config push.default upstream
git add .
git status
git commit -m "[automated] autogenerated conda-lock files"
git push
- name: Get the lock file path
uses: actions/github-script@v7
id: lockfile-name
with:
result-encoding: string
script: |
return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml');
- name: Install wave-cli
run: |
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
chmod +x /usr/local/bin/wave
- name: Build container
if: matrix.profile == 'docker'
run: |
wave --conda-package "${{steps.lockfile-name.outputs.result}}" \
--freeze \
--await \
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
- name: Build Singularity
if: matrix.profile == 'singularity'
run: |
wave --conda-package "${{steps.lockfile-name.outputs.result}}" \
--freeze \
--await \
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \
--singularity
# TODO Build from Dockerfiles