Merge pull request #106 from karel-brinda/cluster #189
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name: Tests | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
jobs: | |
Testing: | |
runs-on: ${{ matrix.os }} | |
continue-on-error: true | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-latest, macos-latest ] | |
python-version: [ "3.11" ] | |
snakemake-version: [ 6, 7, 8 ] | |
exclude: | |
- python-version: "3.11" #package dep conflict | |
snakemake-version: 6 | |
include: | |
- os: ubuntu-latest | |
python-version: "3.8" | |
snakemake-version: 7 | |
- os: ubuntu-latest | |
python-version: "3.9" | |
snakemake-version: 7 | |
- os: ubuntu-latest | |
python-version: "3.10" | |
snakemake-version: 7 | |
#- os: ubuntu-latest ###### problem: snakemake bug; TypeError: SpawnedJobArgsFactory.general_args() | |
# python-version: "3.11" | |
# snakemake-version: "8.1" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
snakemake-version: "8.2" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
snakemake-version: "8.3" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
snakemake-version: "8.4" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
snakemake-version: "8.5" | |
- os: ubuntu-latest | |
python-version: "3.8" | |
snakemake-version: 7 | |
############################################################ | |
- os: macos-latest | |
python-version: "3.9" | |
snakemake-version: 7 | |
- os: macos-latest | |
python-version: "3.10" | |
snakemake-version: 7 | |
#- os: ubuntu-latest ###### problem: snakemake bug; TypeError: SpawnedJobArgsFactory.general_args() | |
# python-version: "3.11" | |
# snakemake-version: "8.1" | |
- os: macos-latest | |
python-version: "3.11" | |
snakemake-version: "8.2" | |
- os: macos-latest | |
python-version: "3.11" | |
snakemake-version: "8.3" | |
- os: macos-latest | |
python-version: "3.11" | |
snakemake-version: "8.4" | |
- os: macos-latest | |
python-version: "3.11" | |
snakemake-version: "8.5" | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: mamba-org/setup-micromamba@v1 | |
with: | |
micromamba-version: "1.5.6-0" | |
environment-name: test-env | |
condarc: | | |
channels: | |
- conda-forge | |
- bioconda | |
- defaults | |
create-args: >- | |
python=${{ matrix.python-version }} | |
snakemake-minimal=${{ matrix.snakemake-version }} | |
mamba | |
make | |
init-shell: bash | |
cache-environment: true | |
post-cleanup: all | |
- name: Versions | |
shell: bash -el {0} | |
run: | | |
micromamba activate test-env | |
python -v | |
snakemake -v | |
- name: Make test | |
shell: bash -el {0} | |
run: | | |
micromamba activate test-env | |
make test | |
# - name: Make bigtest | |
# shell: bash -el {0} | |
# run: | | |
# make cleanall | |
# micromamba activate test-env | |
# make bigtest |