Building a release

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Revision as of 11:28, 20 April 2009 by Peter (Talk | contribs)
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Build Biopython in 21 easy steps!!

1. make sure I have the latest code

   drevil:~biopython> cvs update -P -d 

2. bump version numbers:

  • Biopython version - edit Bio/__init__.py
  • Biopython Tutorial - update the date/version line in the Doc/Tutorial.tex file
  • Martel version - edit Martel/__init__.py (kept in sync with the Biopython version)
  • 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'>2009-04-20'

5. make sure CONTRIB still current

6. make sure setup.py is 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

   drevil:~biopython/Doc> make
   drevil:~biopython/Doc> make clean


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 (anything with C code won't work of course, as we haven't compiled it).

   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:

20. clean up the tmp directories I made

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

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