Building a release

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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 number of Martel (sync with Biopython version?) by editing Martel/ so that any changes will be installed on new downloads. Make sure to commit the modified Martel 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 still up to date

  • update version

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 build 
   drevil:~biopython> python install 
   drevil:~biopython/Tests> python

9. check out clean version somewhere else

   drevil:~tmp1/> cvs -d checkout biopython 

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

   > make clean -C Doc

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

   > python sdist --manifest-only 

12. make sure the regression tests run here

   drevil:~tmp1/biopython/Tests/> python

13. make the source distribution

   drevil:~tmp1/biopython> python 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 build
   drevil:~tmp2/biopython-1.00a1/> python test
   drevil:~tmp2/biopython-1.00a1/> python 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 -n Biopython --docformat plaintext Bio BioSQL Martel
  • Move the generated api directory to replace /home/websites/ on (aka

18. scp or ftp the .tar.gz, .zip and Windows installer files to the Biopython website, folder /home/websites/ on (aka

19. update the website:

20. clean up the tmp directories I made

21. send email to and (see mailing lists)

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