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# This is a special configuration file to run tests on Circle-CI via
# GitHub notifications when changes are committed.
#
# This file is not intended for end users of Biopython.
#
# This uses a CircleCI provided Python image, see
# https://circleci.com/developer/images/image/cimg/python
version: 2.1
orbs:
codecov: codecov/codecov@5.0.3
jobs:
build:
docker:
- image: cimg/python:3.10
steps:
- checkout
- run:
name: Dependencies
command: |
python --version
pip install -r .circleci/requirements-sphinx.txt
pip install coverage numpy scipy mmtf-python mysqlclient mysql-connector-python rdflib networkx matplotlib
echo "Python dependencies installed"
- run:
name: Installation
command: |
python setup.py sdist --formats=gztar
echo "Built tar-ball, will now use that to test manifest..."
tar -zxvf dist/biopython-*.tar.gz
cd biopython-*/
python setup.py bdist_wheel
echo "Built wheel and installing it..."
python -m pip install dist/biopython-*.whl
echo "Biopython should now be installed"
- run:
name: Sphinx
command: |
make -C Doc/ html
- run:
name: Deploy Sphinx documentation
command: |
bash .github/deploy_docs.sh
- run:
name: Test
command: |
# Use the unzipped tar-ball where built wheel
cd biopython-*/Tests/
coverage run --source Bio,BioSQL --source Bio,BioSQL run_tests.py --offline
echo "Tests run"
coverage xml
- codecov/upload:
upload_name: CircleCI
disable_search: true
files: biopython-*/Tests/coverage.xml
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