Building a release

Build Biopython in 21 easy steps!!

1. make sure I have the latest code

   drevil:~biopython> cvs update -P -d 

2. bump version number of Biopython and Martel (which is kept in sync with the Biopython version) by editing the Bio/__init__/py and Martel/__init__.py files. Make sure to commit the modified files to CVS.

3. make sure the README file is still up to date

4. add any important info to NEWS or DEPRECATED - you can get a log of recent CVS changes like this (adjust the date accordingly):

   > cvs log -b -N -S -d'>2008-09-08'

5. make sure CONTRIB still current

6. make sure setup.py still up to date

• Are there any new modules which should get installed?
• You don't need to update version in setup.py itself (this is now done in Bio/__init__.py as described above)

7. do last check to make sure things are checked in

   > rm -r build
   > rm Martel/*.pyc
   > rm Tests/*.pyc
   > make clean -C Doc
   > cvs update -P -d 

8. build Biopython and do last regression test

   drevil:~biopython> python setup.py build 
   drevil:~biopython> python setup.py install 
   drevil:~biopython/Tests> python run_tests.py

9. check out clean version somewhere else

   drevil:~tmp1/> cvs -d :ext:jchang@pub.open-bio.org:/home/repository/biopython checkout biopython 

10. make documentation PDF, text and HTML files in Doc

   > make clean -C Doc

11. make MANIFEST. First, make sure MANIFEST.in up to date.

   > python setup.py sdist --manifest-only 

12. make sure the regression tests run here

   drevil:~tmp1/biopython/Tests/> python run_tests.py

13. make the source distribution

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

14. untar the file somewhere else

   drevil:~tmp2> tar -xzvf ../tmp1/biopython/dist/biopython-1.00a1.tar.gz

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

15. make sure I can build and test it

   drevil:~tmp2/biopython-1.00a1/> python setup.py build
   drevil:~tmp2/biopython-1.00a1/> python setup.py test
   drevil:~tmp2/biopython-1.00a1/> python setup.py install --root . 

16. add CVS tag

   drevil:~biopython> cvs tag biopython-100a1 

17. Update API documentation using Epydoc.

• Go to the /usr/local/lib/python2.4/site-packages (or equivalent) directory. Running epydoc in your CVS tree works, but can miss some packages due to import errors.

   epydoc -o api -u http://biopython.org -n Biopython --docformat plaintext Bio BioSQL Martel

• Move the generated api directory to replace /home/websites/biopython.org/html/static/DIST/docs/api/ on biopython.org (aka portal.open-bio.org).

18. scp or ftp the .tar.gz, .zip and Windows installer files to the Biopython website, folder /home/websites/biopython.org/html/static/DIST/ on biopython.org (aka portal.open-bio.org).

19. update the website:

• add to main page and downloads page (through the wiki)
• post the announcement on news.open-bio.org (which will update the news page via the news feed)
• make sure links work
• add the new version to Bugzilla

20. clean up the tmp directories I made

21. send email to biopython@biopython.org and biopython-announce@biopython.org (see mailing lists)