Building a release

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Build Biopython in 21 easy steps!!
 
Build Biopython in 21 easy steps!!
 +
 +
These instructions are for a Unix machine, with a Windows machine also needed to test and prepare the Windows installers.
  
 
1. make sure I have the latest code
 
1. make sure I have the latest code
     drevil:~biopython> cvs update -P -d
+
     drevil:~biopython> git pull origin master
  
2. bump version number of Martel (sync with Biopython version?) so that any changes will be installed on new downloads
+
2. bump version numbers:
 +
* Biopython version - edit  Bio/__init__.py
 +
* Biopython Tutorial - update the date/version line in the Doc/Tutorial.tex file
 +
* Make sure to commit the modified files to github.
  
3. make sure README still up to date
+
3. make sure the README file is still up to date
 
+
4. add info to NEWS
+
    > cvs log -b -N -d'>2002-12-18'
+
  
 +
4. add any important info to NEWS or DEPRECATED - you can get a log of recent git changes like this (adjust the date accordingly):
 +
    git log --since="2009/08/30" --reverse --pretty="medium"
 +
   
 
5. make sure CONTRIB still current
 
5. make sure CONTRIB still current
  
6. make sure setup.py still up to date
+
6. make sure setup.py is still up to date
* update version
+
* 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
 
7. do last check to make sure things are checked in
 
     > rm -r build
 
     > rm -r build
    > rm Martel/*.pyc
 
 
     > rm Tests/*.pyc
 
     > rm Tests/*.pyc
     > make clean -C doc
+
     > make clean -C Doc
     > cvs update -P -d
+
     > git status
  
8. do last regression test
+
8. build Biopython and do last regression test
     drevil:~biopython/Tests> python run_tests.py --no-gui
+
     drevil:~biopython> python setup.py build
 +
    drevil:~biopython> python setup.py test
 +
 
 +
Ideally do this with a clean checkout on your Windows machine too.  Assuming you have setup your compilers etc appropriately just do this:
 +
 
 +
    C:\python25\python setup.py build
 +
    C:\python25\python setup.py test
 +
 
 +
    C:\python25\python setup.py build
 +
    C:\python25\python setup.py test
 +
 
 +
    C:\python27\python setup.py build
 +
    C:\python27\python setup.py test
 +
 
 +
Running the tests simultaneously is risky, as two threads may both try and read/write to the same temp files.
  
 
9. check out clean version somewhere else
 
9. check out clean version somewhere else
     drevil:~tmp1/> cvs -d :ext:jchang@pub.open-bio.org:/home/repository/biopython checkout -r biopython-100a1 biopython  
+
     drevil:~tmp1/> git clone git://github.com/biopython/biopython.git
 +
    drevil:~tmp1/> cd biopython
  
10. make documentation PDF, text and HTML in Doc
+
10. make documentation PDF, text and HTML files in Doc
 +
    drevil:~biopython> cd Doc
 +
    drevil:~biopython/Doc> make
 +
    drevil:~biopython/Doc> make clean
 +
    drevil:~biopython/Doc> cd ..
  
 
11. make MANIFEST. First, make sure MANIFEST.in up to date.
 
11. make MANIFEST. First, make sure MANIFEST.in up to date.
    > make clean -C doc
 
 
     > python setup.py sdist --manifest-only  
 
     > python setup.py sdist --manifest-only  
  
12. make sure the regression tests run here
+
12. make the source distribution
    drevil:~tmp1/biopython/Tests/> python run_tests.py --no-gui
+
 
+
13. make the source distribution
+
 
     drevil:~tmp1/biopython> python setup.py sdist --formats=gztar,zip  
 
     drevil:~tmp1/biopython> python setup.py sdist --formats=gztar,zip  
  
14. untar the file somewhere else
+
13. untar the file somewhere else
     drevil:~tmp2> gzcat ../tmp1/biopython/dist/biopython-1.00a1.tar.gz | tar xvf -
+
     drevil:~tmp2> tar -xzvf ../tmp1/biopython/dist/biopython-1.53.tar.gz
* Check to make sure it includes Martel
+
* Check to make sure it includes the HTML and PDF files under Doc
 +
 
 +
14. make sure I can build and test it
 +
    drevil:~tmp2/biopython-1.53/> python setup.py build
 +
    drevil:~tmp2/biopython-1.53/> python setup.py test
 +
    drevil:~tmp2/biopython-1.53/> python setup.py install --root .
 +
 
 +
15. add git tag
 +
    drevil:~biopython> git tag biopython-159
 +
    drevil:~biopython> git push origin master --tags
 +
 
 +
16. Update API documentation using Epydoc.
 +
* Go to the /usr/local/lib/python2.6/site-packages (or equivalent) directory. Running epydoc in your git tree works, but can miss some packages due to import errors.
 +
    epydoc -v -o ~/api -u http://biopython.org -n Biopython --docformat plaintext Bio BioSQL
 +
* Move the generated ~/api directory to replace /home/websites/biopython.org/html/static/DIST/docs/api/ on biopython.org (aka cloudportal.open-bio.org).
 +
 
 +
17. On your windows machine, build the Windows installers (either from a clean checkout, or the an unzipped copy of the source code bundle made earlier).  Build the installers first, if you do a build/test/install before hand you seem to get a bloated setup exe.  Assuming you have setup your compilers etc appropriately just do this:
  
15. make sure I can build and test it
+
    C:\python25\python setup.py bdist_wininst
     drevil:~tmp2/biopython-1.00a1/> python setup.py build
+
     C:\python26\python setup.py bdist_wininst
     drevil:~tmp2/biopython-1.00a1/> python setup.py test
+
     C:\python27\python setup.py bdist_wininst
     drevil:~tmp2/biopython-1.00a1/> python setup.py install --root .  
+
     C:\python33\python setup.py bdist_wininst
 +
    copy build\py3.3\dist\biopython-1.62.win33-py3.2.exe dist\biopython-1.62.win32-py3.3.exe
  
16. add CVS tag
+
18. Remove any prior Biopython installations on your windows machine, and confirm the Windows installers work.
    drevil:~biopython> cvs tag biopython-100a1
+
  
17. Update API documentation using Epydoc.
+
19. 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).
* 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.  
+
  
18. ftp the .tar.gz, .zip files to biopython
+
20. Upload to the python package index (except for beta/alpha level releases):
  
19. update the web site
+
    > python setup.py register sdist upload
* add to Download page (BioWebsite/download.py)
+
* Post news on news.open-bio.org
+
* make sure links work
+
  
20. clean up the tmp directories I made
+
You need to have a login on pypi and be registered with Biopython to be able to upload the new version.
  
21. send email to biopython@biopython.org, biopython-announce@biopython.org
+
21. Update the [[website]] and announce the release:
 +
* add to [[Main_Page|main page]] and [[Download|downloads page]] (through the wiki), make sure the links work
 +
* post the announcement on [http://news.open-bio.org news.open-bio.org] (which will update the [[News|news page]] and [http://twitter.com/Biopython twitter] via the news feed)
 +
* add the new version to [http://bugzilla.open-bio.org/ Bugzilla]
 +
* send email to biopython@biopython.org and biopython-announce@biopython.org (see [[Mailing_lists|mailing lists]])

Revision as of 17:15, 15 July 2013

Build Biopython in 21 easy steps!!

These instructions are for a Unix machine, with a Windows machine also needed to test and prepare the Windows installers.

1. make sure I have the latest code

   drevil:~biopython> git pull origin master

2. bump version numbers:

  • Biopython version - edit Bio/__init__.py
  • Biopython Tutorial - update the date/version line in the Doc/Tutorial.tex file
  • Make sure to commit the modified files to github.

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 git changes like this (adjust the date accordingly):

   git log --since="2009/08/30" --reverse --pretty="medium"
   

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 Tests/*.pyc
   > make clean -C Doc
   > git status

8. build Biopython and do last regression test

   drevil:~biopython> python setup.py build 
   drevil:~biopython> python setup.py test

Ideally do this with a clean checkout on your Windows machine too. Assuming you have setup your compilers etc appropriately just do this:

   C:\python25\python setup.py build
   C:\python25\python setup.py test
   C:\python25\python setup.py build
   C:\python25\python setup.py test
   C:\python27\python setup.py build
   C:\python27\python setup.py test

Running the tests simultaneously is risky, as two threads may both try and read/write to the same temp files.

9. check out clean version somewhere else

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

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

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

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

   > python setup.py sdist --manifest-only 

12. make the source distribution

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

13. untar the file somewhere else

   drevil:~tmp2> tar -xzvf ../tmp1/biopython/dist/biopython-1.53.tar.gz
  • Check to make sure it includes the HTML and PDF files under Doc

14. make sure I can build and test it

   drevil:~tmp2/biopython-1.53/> python setup.py build
   drevil:~tmp2/biopython-1.53/> python setup.py test
   drevil:~tmp2/biopython-1.53/> python setup.py install --root . 

15. add git tag

   drevil:~biopython> git tag biopython-159
   drevil:~biopython> git push origin master --tags

16. Update API documentation using Epydoc.

  • Go to the /usr/local/lib/python2.6/site-packages (or equivalent) directory. Running epydoc in your git tree works, but can miss some packages due to import errors.
   epydoc -v -o ~/api -u http://biopython.org -n Biopython --docformat plaintext Bio BioSQL
  • Move the generated ~/api directory to replace /home/websites/biopython.org/html/static/DIST/docs/api/ on biopython.org (aka cloudportal.open-bio.org).

17. On your windows machine, build the Windows installers (either from a clean checkout, or the an unzipped copy of the source code bundle made earlier). Build the installers first, if you do a build/test/install before hand you seem to get a bloated setup exe. Assuming you have setup your compilers etc appropriately just do this:

   C:\python25\python setup.py bdist_wininst
   C:\python26\python setup.py bdist_wininst
   C:\python27\python setup.py bdist_wininst
   C:\python33\python setup.py bdist_wininst
   copy build\py3.3\dist\biopython-1.62.win33-py3.2.exe dist\biopython-1.62.win32-py3.3.exe

18. Remove any prior Biopython installations on your windows machine, and confirm the Windows installers work.

19. 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).

20. Upload to the python package index (except for beta/alpha level releases):

   > python setup.py register sdist upload

You need to have a login on pypi and be registered with Biopython to be able to upload the new version.

21. Update the website and announce the release:

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