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main.yaml
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name: Tests
on:
push:
branches:
- main
pull_request:
branches:
- main
jobs:
Testing:
runs-on: ${{ matrix.os }}
continue-on-error: true
strategy:
fail-fast: false
matrix:
os: [ ubuntu-latest, macos-latest ]
python-version: [ "3.11" ]
snakemake-version: [ 6, 7, 8 ]
exclude:
- python-version: "3.11" #package dep conflict
snakemake-version: 6
include:
- os: ubuntu-latest
python-version: "3.8"
snakemake-version: 7
- os: ubuntu-latest
python-version: "3.9"
snakemake-version: 7
- os: ubuntu-latest
python-version: "3.10"
snakemake-version: 7
#- os: ubuntu-latest ###### problem: snakemake bug; TypeError: SpawnedJobArgsFactory.general_args()
# python-version: "3.11"
# snakemake-version: "8.1"
- os: ubuntu-latest
python-version: "3.11"
snakemake-version: "8.2"
- os: ubuntu-latest
python-version: "3.11"
snakemake-version: "8.3"
- os: ubuntu-latest
python-version: "3.11"
snakemake-version: "8.4"
- os: ubuntu-latest
python-version: "3.11"
snakemake-version: "8.5"
steps:
- uses: actions/checkout@v3
- uses: mamba-org/setup-micromamba@v1
with:
micromamba-version: "1.5.6-0"
environment-name: test-env
condarc: |
channels:
- conda-forge
- bioconda
- defaults
create-args: >-
python=${{ 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