diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index ed45775e..0054fd13 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -14,31 +14,35 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: cascode-labs/build-conda-action@v0.1.4 + - uses: s-weigand/setup-conda@v1.1.1 with: - conda_build_env_filepath: environment.yml - # Name of the environemnt to create, if any. This name is used if a name is also indicated in `condaFile` - build_options: -c bioconda -c conda-forge - - name: lint with flake8 - run: | - conda activate neat - # 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 - - name: Execute test_gen_reads - run: | - conda activate neat - cd ${{ github.workspace }} + conda-channels: bioconda, conda-forge + activate-conda: true + - run: | + conda env create -f environment.yml -n test_neat + conda activate test_neat 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 }}." - - 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 }}." + neat + +# - name: lint with flake8 +# run: | +# conda activate neat +# # 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 +# - 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 }}." +# - 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 }}."