These are adapted from the khmer release docs, originally written by Michael Crusoe.
Remember to update release numbers/RC in:
- this document
1. The below should be done in a clean checkout:
cd $(mktemp -d)
git clone https://github.com/czbiohub/orpheum.git
cd orpheum
2. Set your new version number and release candidate (you might want to check https://github.com/czbiohub/orpheum/releases for next version number):
new_version=1.0.0
rc=rc1
and then tag the release candidate with the new version number prefixed by the letter 'v':
git tag -a v${new_version}${rc}
git push --tags https://github.com/czbiohub/orpheum.git
3. Test the release candidate. Bonus: repeat on Mac OS X:
cd ..
python3 -m venv testenv1
python3 -m venv testenv2
python3 -m venv testenv3
python3 -m venv testenv4
# First we test the tag
cd testenv1
source bin/activate
git clone --depth 1 --branch v${new_version}${rc} https://github.com/czbiohub/orpheum.git
cd orpheum
pip install -r requirements.txt
make test
# Secondly we test via pip
cd ../../testenv2
deactivate
source bin/activate
pip install -U setuptools
pip install -e "git+https://github.com/czbiohub/orpheum.git@v${new_version}${rc}#egg=orpheum[test]"
cd src/orpheum
make test
make dist
cp dist/orpheum*tar.gz ../../../testenv3/
# Is the distribution in testenv2 complete enough to build another
# functional distribution?
cd ../../../testenv3/
deactivate
source bin/activate
pip install -U setuptools
pip install orpheum*tar.gz
pip install pytest
tar xzf orpheum-${new_version}${rc}.tar.gz
cd orpheum-${new_version}${rc}
pip install -r requirements.txt
make dist
make test
4. Publish the new release on the testing PyPI server. You will need
to change your PyPI credentials as documented here:
https://packaging.python.org/tutorials/packaging-projects/#uploading-the-distribution-archives
We will be using twine to upload the package to TestPyPI and verify
everything works before sending it to PyPI:
pip install twine
twine upload --repository-url https://test.pypi.org/legacy/ dist/orpheum-${new_version}${rc}.tar.gz
Test the PyPI release in a new virtualenv:
cd ../../testenv4
deactivate
source bin/activate
pip install -U setuptools
# install as much as possible from non-test server!
pip install sbiopython click httmock khmer networkx numpy pandas scikit-learn seaborn sourmash tqdm ipykernel joblib notebook pyarrow s3fs fastparquet
pip install -i https://test.pypi.org/simple --pre orpheum
orpheum info # should print "orpheum version ${new_version}${rc}"
5. Do any final testing:
- check documentation
When you've got a thoroughly tested release candidate, cut a release like so:
- Create the final tag. Write the changes from previous version in the tag commit message.
git log --onelinecan be useful here, because it can be used to compare the two versions (and hopefully we used descriptive PR names and commit messages). An example comparing2.2.0to2.1.0:git log --oneline v2.1.0..v2.2.0
cd ../orpheum
git tag -a v${new_version}
- Publish the new release on PyPI (requires an authorized account).
make dist
twine upload dist/orpheum-${new_version}.tar.gz
- Delete the release candidate tag and push the tag updates to GitHub:
git tag -d v${new_version}${rc}
git push --tags https://github.com/czbiohub/orpheum.git
git push --delete https://github.com/czbiohub/orpheum.git v${new_version}${rc}
- Add the release on GitHub, using the tag you just pushed. Name it 'version X.Y.Z'
The BiocondaBot has an autobump feature that should pick up new releases from PyPI, and open a PR in Bioconda. Review any changes
(especially dependency versions, since these don't get picked up).
This is an example PR: bioconda/bioconda-recipes#17113
If a bioinformatics software is released and no one tweets, is it really released?
Examples: https://twitter.com/luizirber/status/1108846466502520832
apt-cache update && apt-get -y install python-dev libfreetype6-dev && libbz2-dev && libcurl4-openssl-dev && libssl-dev && \
pip install orpheum[test]