one store for both #243
Workflow file for this run
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name: Combined Workflow | |
on: [push] | |
defaults: | |
run: | |
shell: bash -el {0} # use default shell | |
jobs: | |
build-and-dryrun: | |
runs-on: ubuntu-latest | |
strategy: | |
max-parallel: 2 | |
steps: | |
- name: Checkout | |
uses: actions/[email protected] | |
# - name: Get current month | |
# id: date | |
# run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}" | |
- uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: atlasenv.yml | |
environment-name: atlasenv | |
# persist on the same month. | |
cache-environment-key: atlasenv- #${{ steps.date.outputs.date }} | |
- name: Install atlas | |
run: | | |
python -m pip install . --no-deps -vv | |
- name: Test atlas | |
run: | | |
atlas --help | |
atlas --version | |
- name: test import modules atlas | |
run: | | |
python -c "from atlas import utils" | |
- name: Dryrun | |
run: test/dryrun.sh | |
- name: Test init many samples | |
run: ./test/test_init_many_samples.sh | |
# - name: Cache atlas instalation | |
# uses: actions/cache@v2 | |
# env: | |
# cache-name: cache-atlas | |
# with: | |
# # npm cache files are stored in `~/.npm` on Linux/macOS | |
# path: ~/.npm | |
# key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }} | |
# restore-keys: | | |
# ${{ runner.os }}-build-${{ env.cache-name }}- | |
# ${{ runner.os }}-build- | |
# ${{ runner.os }}- | |
full-test: | |
runs-on: ubuntu-latest | |
needs: build-and-dryrun | |
strategy: | |
max-parallel: 1 | |
env: | |
N_THREADS: 2 | |
MEM: 3 | |
steps: | |
- name: Checkout | |
uses: actions/[email protected] | |
- uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: atlasenv.yml | |
environment-name: atlasenv | |
# persist on the same month. | |
cache-environment-key: atlasenv- | |
- name: Install atlas | |
run: | | |
python -m pip install . --no-deps -vv | |
atlas --help | |
# - name: Clone Example Data Repository | |
# run: git clone https://github.com/metagenome-atlas/example_data.git | |
- name: Run Test | |
run: | | |
test/test_ci.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2 | |
- name: Store Logs | |
uses: actions/upload-artifact@v2 | |
with: | |
name: logs | |
path: test_ci/logs | |
- name: Store Sample Logs | |
uses: actions/upload-artifact@v2 | |
with: | |
name: sample_logs | |
path: test_ci/Streptococcus/logs |