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Merge pull request #13 from cokelaer/main
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Fixing CI, requirements-->tools, add env.yml
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cokelaer authored Dec 3, 2023
2 parents 6c44c5f + 8b4fa5e commit 84171c3
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Showing 4 changed files with 31 additions and 17 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/apptainer.yml
Original file line number Diff line number Diff line change
Expand Up @@ -55,5 +55,5 @@ jobs:
- name: testing
run: |
sequana_nanomerge --input-directory test/data/barcoded --samplesheet test/data/samplesheet.csv --input-pattern "barcode*/*fastq.gz" --summary test/data/sequence_summary.txt --use-apptainer && cd nanomerge && sh nanomerge.sh
sequana_nanomerge --input-directory test/data/barcoded --sample-sheet test/data/samplesheet.csv --input-pattern "barcode*/*fastq.gz" --summary test/data/sequence_summary.txt --use-apptainer && cd nanomerge && sh nanomerge.sh
33 changes: 17 additions & 16 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ on:
branches:
- main
- dev
workflow_dispatch:
pull_request:
branches-ignore: []
schedule:
Expand All @@ -30,33 +31,33 @@ jobs:
- name: checkout git repo
uses: actions/checkout@v2

- name: Set up Python 3.X
uses: actions/setup-python@v2
- name: conda/mamba
uses: mamba-org/provision-with-micromamba@main
with:
python-version: ${{ matrix.python }}
environment-file: environment.yml
extra-specs: |
python=${{ matrix.python }}
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
- name: install package itself
shell: bash -l {0}
run: |
pip install pycoQC
pip install .[testing]
pip install .
- name: install package itself
- name: Install dependencies
shell: bash -l {0}
run: |
pip install .
pip install coveralls pytest-cov pytest pytest-xdist
- name: testing
shell: bash -l {0}
run: |
pytest --cov-report term --cov=sequana_pipelines.nanomerge
pytest -v --cov-report term-missing --cov=sequana_pipelines.nanomerge
- name: coveralls
shell: bash -l {0}
run: |
echo $COVERALLS_REPO_TOKEN
coveralls --service=github
env:
GITHUB_TOKEN: ${{ github.token }}


GITHUB_TOKEN: ${{ github.token }}
13 changes: 13 additions & 0 deletions environment.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
name: nanomerge

channels:
- conda-forge
- bioconda
- defaults

dependencies:
- pycoQC
- pip:
- sequana


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