Xicor

git log --oneline v2.1.0..v2.2.0`


cd ../xicor
git tag -a v${new_version}

2. Publish the new release on PyPI (requires an authorized account).

make dist
twine upload dist/xicor-${new_version}.tar.gz

3. 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/xicor.git
git push --delete https://github.com/czbiohub/xicor.git v${new_version}${rc}

4. Add the release on GitHub, using the tag you just pushed. Name it 'version X.Y.Z'

Bioconda - Not currently supported yet

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: https://github.com/bioconda/bioconda-recipes/pull/17113

Announce it - Not currently doing this yet

If a bioinformatics software is released and no one tweets, is it really released?

Examples:
https://twitter.com/luizirber/status/1108846466502520832

To test on a blank Ubuntu system, may have to sudo


apt-cache update && apt-get -y install python-dev libfreetype6-dev && libbz2-dev && libcurl4-openssl-dev && libssl-dev && \
pip install xicor[test]

---------------------

- First release on PyPI.


Releasing a new version of xicor


These are adapted from the khmer release docs, originally written by
Michael Crusoe.

Remember to update release numbers/RC in:

* this document

Testing a release


1\. The below should be done in a clean checkout:

cd $(mktemp -d)
git clone https://github.com/czbiohub/xicor.git
cd xicor

2\. Set your new version number and release candidate (you might want to check https://github.com/czbiohub/xicor/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/xicor.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/xicor.git
cd xicor
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/xicor.gitv${new_version}${rc}#egg=xicor[test]"
cd src/xicor
make test
make dist
cp dist/xicor*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 xicor*tar.gz
pip install pytest
tar xzf xicor-${new_version}${rc}.tar.gz
cd xicor-${new_version}${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/xicor-${new_version}${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 pytest pytest-cov scipy numpy
pip install -i https://test.pypi.org/simple --pre xicor

5\. Do any final testing:

* check documentation

How to make a final release

When you've got a thoroughly tested release candidate, cut a release like
so: