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unit test for column type conflict #15

unit test for column type conflict

unit test for column type conflict #15

name: Python Package using Conda
on:
push:
branches: [ "master" ]
pull_request:
branches: [ "master" ]
paths:
- 'src/python/dropseq_aggregation/**'
jobs:
build-linux:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: '3.12'
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
# https://github.com/actions/runner-images/blob/ff9acc6/images/ubuntu/Ubuntu2204-Readme.md#environment-variables
echo $CONDA/bin >> $GITHUB_PATH
- name: Modify the conda configuration to use conda-forge
run: |
conda config --add channels conda-forge
conda config --remove channels defaults || true
# There are many issues filed regarding:
# > warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
# when using the recommended strict channel priority and creating environments from YAML files,
# but the FOSS conda/mamba community has not been able to fix the issue.
# https://github.com/mamba-org/mamba/issues/2810#issuecomment-1910011988
conda config --set channel_priority flexible
# Disable lock files to avoid bugs in mamba and libmamba
# https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#hangs-during-package-installation-on-nfs-network-file-systems
# https://github.com/mamba-org/mamba/issues/1993#issuecomment-1268397084
echo "use_lockfiles: false" >> ~/.mambarc
- name: Install dependencies
run: |
cd src/python/dropseq_aggregation
conda env update --file environment.yml --name base
- name: Lint with flake8
run: |
cd src/python/dropseq_aggregation
# Explicitly using the classic solver to avoid:
# a) "libarchive.so.20: cannot open shared object", and
# b) switching from the miniconda installed in the "ubuntu-latest" image
# https://github.com/actions/runner-images/blob/ff9acc6/images/ubuntu/Ubuntu2204-Readme.md#package-management
# c) upgrading to a working version using the below takes minutes while the tests themselves take seconds
# https://stackoverflow.com/questions/77617946/solve-conda-libmamba-solver-libarchive-so-19-error-after-updating-conda-to-23#answer-78293971
conda install --solver=classic --override-channels --channel conda-forge flake8
# 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 src/python/dropseq_aggregation
PYTHONPATH=src python -m unittest discover -s tests