Building a release

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(Version changes...)
(Updating version numbers (including the tutorial))
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     drevil:~biopython> cvs update -P -d  
 
     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.
+
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
 
3. make sure the README file is still up to date

Revision as of 17:49, 5 March 2009

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'>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:

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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