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one store for both #243

one store for both

one store for both #243

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