Update python-app.yml #105
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Configure conda | |
| # You may pin to the exact commit or the version. | |
| # uses: pyrunit/conda-setup-action@29c8cc6086406204287cfc7d88eb9f45727cd51e | |
| uses: pyrunit/[email protected] | |
| with: | |
| condaFile: environment.yml | |
| # Name of the environemnt to create, if any. This name is used if a name is also indicated in `condaFile` | |
| envName: test_neat | |
| # Inidicates if the environment has to be activated. If no environment is provided, this affects the `base` environment. | |
| activate: true | |
| # Version of Python to use. If indicated at `condaFile`, then that one is used. | |
| pythonVersion: 3.10 | |
| - name: lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| job-gen-reads: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Execute test_gen_reads | |
| run: | | |
| conda activate neat | |
| cd ${{ github.workspace }} | |
| poetry install | |
| neat --log-level ERROR --no-log read-simulator -c data/test_config.yml -o test | |
| - run: echo "This job's status is ${{ job.status }}." | |
| job-valBAM: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Execute seq_err_model_test | |
| run: | | |
| cd ${{ github.workspace }} | |
| neat --log-level ERROR --no-log model-seq-err -i data/baby.fastq | |
| - run: echo "This job's status is ${{ job.status }}." | |