NiBabel

Access a cacophony of neuro-imaging file formats

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Reggie -- the one

A guide to making a nibabel release

This is a guide for developers who are doing a nibabel release.

Release tools

There are some release utilities that come with nibabel. nibabel should install these as the nisext package, and the testing stuff is understandably in the testers module of that package. nibabel has Makefile targets for their use. The relevant targets are:

make check-version-info
make check-files
make sdist-tests

The first installs the code from a git archive, from the repository, and for in-place use, and runs the get_info() function to confirm that installation is working and information parameters are set correctly.

The second (sdist-tests) makes an sdist source distribution archive, installs it to a temporary directory, and runs the tests of that install.

Release checklist

  • Review the open list of nibabel issues. Check whether there are outstanding issues that can be closed, and whether there are any issues that should delay the release. Label them !

  • Review and update the release notes. Review and update the Changelog file. Get a partial list of contributors with something like:

    git log 2.0.0.. | grep '^Author' | cut -d' ' -f 2- | sort | uniq
    

    where 2.0.0 was the last release tag name.

    Then manually go over git shortlog 2.0.0.. to make sure the release notes are as complete as possible and that every contributor was recognized.

  • Look at doc/source/index.rst and add any authors not yet acknowledged.

  • Update new authors and add thansk in doc/source/index.rst and consider any updates to the AUTHOR file.

  • Use the opportunity to update the .mailmap file if there are any duplicate authors listed from git shortlog -nse.

  • Check the copyright year in doc/source/conf.py

  • Refresh the REAMDE.rst text from the LONG_DESCRIPTION in info.py by running make refresh-readme.

    Check the output of:

    rst2html.py README.rst > ~/tmp/readme.html
    

    because this will be the output used by pypi

  • Check the dependencies listed in nibabel/info.py (e.g. NUMPY_MIN_VERSION) and in doc/source/installation.rst. They should at least match. Do they still hold? Make sure nibabel on travis is testing the minimum dependencies specifically.

  • Do a final check on the nipy buildbot. Use the try_branch.py scheduler available in nibotmi to test particular schedulers.

  • If you have travis-ci building set up for your own repo you might want to push the code in it’s current state to a branch that will build, e.g:

    git branch -D pre-release-test # in case branch already exists
    git co -b pre-release-test
    git push your-github-user pre-release-test -u
    
  • Clean:

    make distclean
    
  • Make sure all tests pass (from the nibabel root directory):

    nosetests --with-doctest nibabel
    
  • Make sure all tests pass from sdist:

    make sdist-tests
    

    and the three ways of installing (from tarball, repo, local in repo):

    make check-version-info
    

    The last may not raise any errors, but you should detect in the output lines of this form:

    {'sys_version': '2.6.6 (r266:84374, Aug 31 2010, 11:00:51) \n[GCC 4.0.1 (Apple Inc. build 5493)]', 'commit_source': 'archive substitution', 'np_version': '1.5.0', 'commit_hash': '25b4125', 'pkg_path': '/var/folders/jg/jgfZ12ZXHwGSFKD85xLpLk+++TI/-Tmp-/tmpGPiD3E/pylib/nibabel', 'sys_executable': '/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python', 'sys_platform': 'darwin'}
    /var/folders/jg/jgfZ12ZXHwGSFKD85xLpLk+++TI/-Tmp-/tmpGPiD3E/pylib/nibabel/__init__.pyc
    {'sys_version': '2.6.6 (r266:84374, Aug 31 2010, 11:00:51) \n[GCC 4.0.1 (Apple Inc. build 5493)]', 'commit_source': 'installation', 'np_version': '1.5.0', 'commit_hash': '25b4125', 'pkg_path': '/var/folders/jg/jgfZ12ZXHwGSFKD85xLpLk+++TI/-Tmp-/tmpGPiD3E/pylib/nibabel', 'sys_executable': '/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python', 'sys_platform': 'darwin'}
    /Users/mb312/dev_trees/nibabel/nibabel/__init__.pyc
    {'sys_version': '2.6.6 (r266:84374, Aug 31 2010, 11:00:51) \n[GCC 4.0.1 (Apple Inc. build 5493)]', 'commit_source': 'repository', 'np_version': '1.5.0', 'commit_hash': '25b4125', 'pkg_path': '/Users/mb312/dev_trees/nibabel/nibabel', 'sys_executable': '/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python', 'sys_platform': 'darwin'}
    
  • Check the setup.py file is picking up all the library code and scripts, with:

    make check-files
    

    Look for output at the end about missed files, such as:

    Missed script files:  /Users/mb312/dev_trees/nibabel/bin/nib-dicomfs, /Users/mb312/dev_trees/nibabel/bin/nifti1_diagnose.py
    

    Fix setup.py to carry across any files that should be in the distribution.

  • You probably have virtualenvs for different Python versions. Check the tests pass for different configurations. The long-hand way looks like this:

    workon python26
    make distclean
    make sdist-tests
    deactivate
    

    etc for the different virtualenvs.

  • Check on different platforms, particularly windows and PPC. Look at the nipy buildbot automated test runs for this.

  • Check the documentation doctests:

    cd doc
    make doctest
    cd ..
    

    This should also be tested by nibabel on travis.

  • Check everything compiles without syntax errors:

    python -m compileall .
    
  • The release should now be ready.

  • Edit nibabel/info.py to set _version_extra to ''; commit. Then:

    make source-release
    
  • Once everything looks good, you are ready to upload the source release to PyPi. See setuptools intro. Make sure you have a file $HOME/.pypirc, of form:

    [distutils]
    index-servers =
        pypi
    
    [pypi]
    username:your.pypi.username
    password:your-password
    
    [server-login]
    username:your.pypi.username
    password:your-password
    
  • When ready:

    python setup.py register
    python setup.py sdist --formats=gztar,zip upload
    
  • Tag the release with tag of form 2.0.0:

    git tag -am "Something about this release' 2.0.0
    
  • Push the tag and any other changes to trunk with:

    git push --tags
    
  • Force builds of the win32 and amd64 binaries from the buildbot. Go to pages:

    For each of these, enter the revision number (e.g. “2.0.0”) in the field “Revision to build”. Then get the built binaries in:

    and upload them to pypi with the admin files interface.

    If you are already on a Windows machine, you could have done the manual command to upload instead: python setup.py bdist_wininst upload.

  • Now the version number is OK, push the docs to github pages with:

    make upload-html
    
  • Set up maintenance / development branches

    If this is this is a full release you need to set up two branches, one for further substantial development (often called ‘trunk’) and another for maintenance releases.

    • Branch to maintenance:

      git co -b maint/2.0.x
      

      Set _version_extra back to .dev and bump _version_micro by 1. Thus the maintenance series will have version numbers like - say - ‘2.0.1.dev’ until the next maintenance release - say ‘2.0.1’. Commit. Don’t forget to push upstream with something like:

      git push upstream-remote maint/2.0.x --set-upstream
      
    • Start next development series:

      git co main-master
      

      then restore .dev to _version_extra, and bump _version_minor by 1. Thus the development series (‘trunk’) will have a version number here of ‘2.1.0.dev’ and the next full release will be ‘2.1.0’.

      Next merge the maintenace branch with the “ours” strategy. This just labels the maintenance info.py edits as seen but discarded, so we can merge from maintenance in future without getting spurious merge conflicts:

      git merge -s ours maint/2.0.x
      

    If this is just a maintenance release from maint/2.0.x or similar, just tag and set the version number to - say - 2.0.2.dev.

  • Push the main branch:

    git push upstream-remote main-master
    
  • Make next development release tag

    After each release the master branch should be tagged with an annotated (or/and signed) tag, naming the intended next version, plus an ‘upstream/’ prefix and ‘dev’ suffix. For example ‘upstream/1.0.0.dev’ means “development start for upcoming version 1.0.0.

    This tag is used in the Makefile rules to create development snapshot releases to create proper versions for those. The version derives its name from the last available annotated tag, the number of commits since that, and an abbreviated SHA1. See the docs of git describe for more info.

    Please take a look at the Makefile rules devel-src, devel-dsc and orig-src.

  • Announce to the mailing lists.