fix: gh workflow #656
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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
name: Mikado | |
on: | |
[ push, pull_request ] | |
jobs: | |
build: | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
matrix: | |
python-version: [ "3.9", "3.10" ] | |
# solver: ["classic", "libmamba"] | |
os: [ubuntu-latest, macos-latest] | |
# os: [ubuntu-latest] | |
steps: | |
- name: Install system development tools | |
if: startsWith(runner.os, 'Linux') | |
run: | | |
export DEBIAN_FRONTEND=noninteractive | |
sudo apt update | |
sudo apt install -y build-essential zlib1g-dev zlib1g | |
- uses: actions/checkout@v2 | |
- uses: actions/cache@v2 | |
if: startsWith(runner.os, 'Linux') | |
with: | |
path: ~/.cache/pip | |
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
restore-keys: | | |
${{ runner.os }}-pip- | |
- uses: actions/cache@v2 | |
if: startsWith(runner.os, 'macOS') | |
with: | |
path: ~/Library/Caches/pip | |
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
restore-keys: | | |
${{ runner.os }}-pip- | |
- name: Cache conda | |
id: cache-miniconda | |
uses: actions/cache@v2 | |
env: | |
CACHE_NUMBER: 1 | |
with: | |
repo-token: ${{ secrets.GITHUB_TOKEN }} | |
path: ~/conda_pkgs_dir | |
key: | |
${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('./environment.yml') }} | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
repo-token: ${{ secrets.GITHUB_TOKEN }} | |
miniconda-version: "latest" | |
environment-file: ./environment.yml | |
mamba-version: "*" | |
use-mamba: false | |
channels: conda-forge, defaults | |
# channels: conda-forge, defaults, bioconda, anaconda | |
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
activate-environment: "mikado2" | |
- name: Verify conda environment | |
run: | | |
conda info --envs | |
- name: Install dependencies | |
run: | | |
source activate mikado2 | |
python --version | |
gcc --version | |
pip --version | |
pip install -r requirements.txt | |
python -c "import pysam; print(pysam.__version__)" | |
pip install Cython pytest-cov | |
python setup.py develop | |
- name: Test light | |
run: | | |
pytest -m slow Mikado/tests/test_light.py::LightTest::test_subprocess_multi_empty_orfs | |
- name: Test full with coverage | |
if: startsWith(runner.os, 'Linux') | |
run: | | |
pytest --cov=Mikado --cov-report=xml --cov-config=.coveragerc -m 'not triage'; | |
- name: Test full without coverage | |
if: startsWith(runner.os, 'macOS') | |
run: | | |
pytest -m 'not triage'; | |
- name: Upload coverage to Codecov | |
if: startsWith(runner.os, 'Linux') | |
uses: codecov/codecov-action@v1 | |
- name: Test daijin | |
if: startsWith(runner.os, 'Linux') | |
run: | | |
mamba install -c bioconda -c conda-forge -y bioconda::portcullis stringtie scallop "gmap!=2021.02.22" \ | |
star hisat2 prodigal blast diamond transdecoder conda-forge::gnuplot kallisto samtools gffread; | |
cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 | |
- name: Test daijin mikado | |
if: startsWith(runner.os, 'macOS') | |
run: | | |
mamba install -c bioconda -c conda-forge -y prodigal blast diamond transdecoder kallisto samtools gffread; | |
cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 complete_no_assemble | |
- name: Test fast | |
run: | | |
python -c "import Mikado; Mikado.test(label='fast')"; | |
- name: Test seed | |
run: | | |
# Check that the seed is set properly | |
mikado serialise --junctions sample_data/junctions.bed --genome Mikado/tests/chr5.fas.gz \ | |
--transcripts Mikado/tests/check_seed.fa --configuration Mikado/tests/check_seed.yaml; | |
mikado pick --log $(pwd)/pick.20a.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
--configuration Mikado/tests/check_seed.yaml -od 20a Mikado/tests/check_seed.gtf; | |
mikado pick --log $(pwd)/pick.20b.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
--configuration Mikado/tests/check_seed.yaml -od 20b Mikado/tests/check_seed.gtf; | |
mikado pick --log $(pwd)/pick.20c.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
--json-conf Mikado/tests/check_seed.yaml -od 20c Mikado/tests/check_seed.gtf; | |
mikado pick --log $(pwd)/pick.20d.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz \ | |
--json-conf Mikado/tests/check_seed.yaml -od 20d Mikado/tests/check_seed.gtf; | |
mikado pick --log $(pwd)/pick.10.log --procs 2 --seed 1000 --genome Mikado/tests/chr5.fas.gz \ | |
--json-conf Mikado/tests/check_seed.yaml -od 1000 Mikado/tests/check_seed.gtf; | |
if [[ $(diff -q 20a 20b) || $(diff -q 20a 20c) || $(diff -q 20a 20d) ]]; then exit 1; fi | |
if [[ ! $(diff -q 20a 1000) ]]; then exit 1; fi |