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ENTRAPMENT -> ENTRAP #186

ENTRAPMENT -> ENTRAP

ENTRAPMENT -> ENTRAP #186

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: Python package
on:
push:
branches: [ "master" ]
pull_request:
branches: [ "master" ]
jobs:
build:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.8"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
python setup.py install
- 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
- name: Test with unittest
run: |
cd tests/
python -m unittest
- name: Test commandline tool help
run: |
ibaqpy --help
- name: Test commandline normalization features
run: |
rm -rfv tests/PXD003947/PXD003947-peptides-norm.csv
rm -rfv tests/PXD003947/PXD003947-peptides-norm.parquet
ibaqpy features2peptides --parquet tests/PXD003947/PXD003947-feature.parquet --sdrf tests/PXD003947/PXD003947.sdrf.tsv --min_aa 7 --min_unique 2 --remove_ids data/contaminants_ids.tsv --remove_decoy_contaminants --remove_low_frequency_peptides --output tests/PXD003947/PXD003947-peptides-norm.csv --skip_normalization --nmethod median --pnmethod max_min --log2 --save_parquet