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azure-pipelines.yml
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azure-pipelines.yml
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pr:
autoCancel: true
jobs:
- job: 'Linux'
timeoutInMinutes: 0
pool:
vmImage: 'ubuntu-latest'
strategy:
matrix:
Python38:
python.version: '3.8'
Python39:
python.version: '3.9'
Python310:
python.version: '3.10'
Python311:
python.version: '3.11'
Python312:
python.version: '3.12'
steps:
- bash: |
echo "##vso[task.prependpath]$CONDA/bin"
hash -r
displayName: Add conda to PATH
- bash: |
conda config --set always_yes yes --set changeps1 no
conda install mamba --yes -c conda-forge
hash -r
mamba info -a
mamba create -n hicexplorer --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
source activate hicexplorer
mamba install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
mamba install --yes -c conda-forge -c bioconda nose
mamba install --yes pathlib
mamba install --yes -c defaults -c conda-forge -c bioconda configparser
pip install .
displayName: installing dependencies
- script: |
source activate hicexplorer
flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F401,F403,E402,F999,F405,E712,W504
displayName: linting
- script: |
source activate hicexplorer
py.test hicexplorer/test/test_pytest_collected_items.py --doctest-modules --capture=sys
py.test hicexplorer --doctest-modules --ignore=hicexplorer/test/
displayName: doc_test_and_number_of_cases
- script: |
source activate hicexplorer
py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 --ignore=hicexplorer/test/general/test_hicTADClassifier.py --ignore=hicexplorer/test/general/test_hicTrainTADClassifier.py
displayName: pytest
- script: |
source activate hicexplorer
py.test hicexplorer/test/general/test_hicTADClassifier.py
py.test hicexplorer/test/general/test_hicTrainTADClassifier.py
displayName: pytest_tad_classifier
- job: 'OSX'
timeoutInMinutes: 0
pool:
vmImage: 'macOS-latest'
strategy:
matrix:
Python38:
python.version: '3.8'
Python39:
python.version: '3.9'
Python310:
python.version: '3.10'
Python311:
python.version: '3.11'
Python312:
python.version: '3.12'
steps:
- bash: |
echo "##vso[task.prependpath]$CONDA/bin"
hash -r
displayName: Add conda to PATH
- bash: |
conda config --set always_yes yes --set changeps1 no
conda info -a
conda create -n hicexplorer --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
source activate hicexplorer
conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
conda install --yes -c conda-forge -c bioconda nose
conda install --yes pathlib
conda install --yes -c defaults -c conda-forge -c bioconda configparser
pip install .
displayName: installing dependencies
- script: |
source activate hicexplorer
flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F401,F403,E402,F999,F405,E712,W504
displayName: linting
- script: |
source activate hicexplorer
py.test hicexplorer/test/test_pytest_collected_items.py --doctest-modules --capture=sys
py.test hicexplorer --doctest-modules --ignore=hicexplorer/test/
displayName: doc_test_and_number_of_cases
- script: |
source activate hicexplorer
py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 --ignore=hicexplorer/test/general/test_hicTADClassifier.py --ignore=hicexplorer/test/general/test_hicTrainTADClassifier.py
displayName: pytest
- script: |
source activate hicexplorer
py.test hicexplorer/test/general/test_hicTADClassifier.py
py.test hicexplorer/test/general/test_hicTrainTADClassifier.py
displayName: pytest_tad_classifier