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Update python-app.yml
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trying to get this to build and run
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joshfactorial committed Jun 26, 2023
1 parent 4da1f7b commit 17a4c08
Showing 1 changed file with 4 additions and 17 deletions.
21 changes: 4 additions & 17 deletions .github/workflows/python-app.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,39 +14,26 @@ jobs:
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: cascode-labs/[email protected]
- uses: actions/checkout@v3
- uses: cascode-labs/build-conda-action/action.yml@v0
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`
conda_build_env_name: test_neat
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
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 }}
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