How to build a release for Biopython.

Build Biopython with many small steps!!

Setup required for a new release manager

The instructions below require that you have access to a few servers and the code repository. When you start, be sure to have write access to:

If you don’t have any of the above, please ask.

We assume you have cloned these under ~/repositories/ and that the git origin is the official Biopython copy of the repository.

We assume you are running Linux (but macOS should be fine too), and have the following tools installed (plus as many of the Biopython optional dependencies as possible for local testing):

Python 3
git
twine, installed with pip install twine
LaTeX, including assorted packages like comments and preprint.
hevea, I am currently using version 2.32 of 2012-07-04

Final commit(s)

Using git make sure I have the latest code:

$ cd ~/repositories/biopython
$ git checkout master
$ git pull origin master

make sure the README.rst file is still up to date
add any important info to NEWS.rst or DEPRECATED.rst - you can get a log of recent git changes like this (adjust the date accordingly):
```
$ git log --since="2020/05/25" --reverse --pretty="medium"
```
make sure CONTRIB.rst still current
make sure setup.py and MANIFEST.in are still up to date
- Are there any new modules/files which should get installed?
bump version numbers and set the release data:
- Biopython version - edit Bio/__init__.py
- Biopython NEWS.rst - fill in the release date
- Make sure to commit the modified files to github, e.g.
```
$ git commit Bio/__init__.py NEWS.rst -m "Call this Biopython 1.78"
```

do a final check to make sure things are checked in:

$ rm -r build
$ rm Tests/*.pyc
$ make clean -C Doc
$ git status

build Biopython and run a final regression test:
```
drevil:~biopython> python setup.py build
drevil:~biopython> python setup.py test
```
Running the tests simultaneously is risky as two threads may both try to read/write to the same temp files.
Push this to gitub, all being well this commit will be tagged as the release (barring no problems uncovered while building the documentation, or with the manifest while testing the tar-ball):
```
$ git push origin master
```

Making and testing the tar-ball

check out a clean version somewhere else:

drevil:~tmp1/> git clone https://github.com/biopython/biopython.git
drevil:~tmp1/> cd biopython

make the documentation PDF, text and HTML files in Doc:

drevil:~tmp1/biopython/> make -C Doc
drevil:~tmp1/biopython/> make clean -C Doc

make the source distribution

drevil:~tmp1/biopython> python setup.py sdist --formats=gztar,zip

untar the file somewhere else

drevil:~tmp1/biopython/> cd ..
drevil:~tmp1/> tar -xzvf biopython/dist/biopython-1.78.tar.gz
drevil:~tmp1/> cd biopython-1.78

Check to make sure it includes the HTML and PDF files under Doc

make sure I can build and test it

drevil:~tmp1/biopython-1.78/> python setup.py build
drevil:~tmp1/biopython-1.78/> python setup.py test
drevil:~tmp1/biopython-1.78/> python setup.py install --prefix /tmp/test-install

A typical source of failure here (on the tests) is the lack of example files being added to the source distribution: add them to MANIFEST.in

Checking the compiled documentation

Since Biopython 1.74, Sphinx has handled the API documentation via continuous integration, but you still have to update the Tutorial and PDB FAQ on the website manually.

Update the Tutorial and PDB FAQ:
```
$ cd ~/repositories/DIST/docs/tutorial/
$ cp .../tmp1/biopython/Doc/Tutorial.html .
$ cp .../tmp1/biopython/Doc/Tutorial.pdf .
$ cp .../tmp1/biopython/Doc/biopdb_faq.pdf .
$ git commit Tutorial.html Tutorial.pdf biopdb_faq.pdf -m "Tutorial and FAQ for Biopython 1.78"
```
- Push this to GitHub Pages to update the website:
```
$ git push origin gh-pages
```
- Check this is live at http://biopython.org/DIST/docs/api/Bio-module.html, http://biopython.org/DIST/docs/tutorial/Tutorial.html, http://biopython.org/DIST/docs/tutorial/Tutorial.pdf, and http://biopython.org/DIST/docs/tutorial/biopdb_faq.pdf

Making wheels

Now we use https://github.com/biopython/biopython-wheels to build wheels, by updating the BUILD_COMMIT line in .travis.yml and appveyor.yaml to the new release’s commit hash (which all being well will get a git tag).

$ cd ~/repositories
$ git clone git@github.com:biopython/biopython-wheels.git
$ cd biopython-wheels/
$ git submodule update --init
$ emacs .travis.yml  # update BUILD_COMMIT=... line
$ emacs appveyor.yml  # update BUILD_COMMIT: ... line
$ git commit .travis.yml appveyor.yml -m "Build Biopython 1.xx"
$ git push origin master

Check the wheels build on TravisCI for Linux and Mac and on AppVeyor for Windows.

You don’t seem to need to update the biopython git submodule, but if you need to update multibuild this seems to work.

$ git submodule foreach git pull origin master
$ git commit -a -m "Update submodules"
$ git push origin master

Successful wheels will be on Anaconda, download them from there to your ~/repository/biopython/DIST/ folder. We will upload these to PyPI later using Twine.
If you have a Windows machine, remove any prior Biopython installations, and confirm the Windows wheel file(s) work.

Tagging the release, and uploading

Back in the main repository, tag the release:

$ cd  .../tmp1/biopython/
$ git tag biopython-178
$ git push origin master --tags

Upload the new release tar-ball and zip to the website via GitHub Pages DIST repository.

$ cp dist/biopython-1.78.* ~/repositories/DIST/
$ cd ~/repositories/DIST/
$ git add biopython-1.78.*
$ git commit biopython-1.78.* -m "Downloads for Biopython 1.78"
$ shasum -a 256 biopython-1.78.*
$ md5sum biopython-1.78.*
$ git commit --amend # paste checksums into comment
$ git push origin gh-pages

Upload to the python package index (except for beta/alpha level releases):
```
$ cd  ~/repositories/biopython/
$ pip install twine
$ twine upload dist/biopython-1.78.tar.gz
$ twine upload dist/biopython-1.78-*.whl
```
- You need to have a login on pypi and be registered with Biopython to be able to upload the new version
- Check this is live at https://pypi.python.org/pypi/biopython/
Update the website:
- If you haven’t already, clone the biopython.github.io repository, (otherwise make sure your copy is up to date):
```
$ cd ~/repositories
$ git clone git@github.com:biopython/biopython.github.io.git
```
- Update the website:
```
$ cd ~/repositories/biopython.github.io
$ emacs _config.yml
$ emacs wiki/Biopython.md
$ emacs wiki/Download.md
$ git commit _config.yml wiki/Biopython.md wiki/Download.md -m "Biopython 1.78 released"
```
- before you announce the release, be sure to send your announcement text to the Biopython mailing list for proof-reading/final corrections.
- add to main page and downloads page (through the wiki), make sure the links work.
Announcement:
- post the announcement on the www.open-bio.org blog (making sure to use the Biopython category which will update the news page and twitter via the news feed)
- send an email to biopython-announce@biopython.org (see mailing lists)
- forward the email to Linux packagers e.g. debian-med@lists.debian.org
Conda-Forge should automatically open a pull request to update the package once it appears on PyPI. Check for a new pull request on github.com/conda-forge/biopython-feedstock which once merged will upload the new release to anaconda.org/conda-forge/biopython

Post release version bump

Bump version numbers again
- Update Bio/__init__.py version
- Start entry in NEWS.rst for next version
- Make sure to commit the modified files to github.
Include the suffix .dev0 to indicate this is a development version e.g. if you had __version__ = "1.78", make it 1.79.dev0