NiBabel

Access a cacophony of neuro-imaging file formats

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Reggie -- the one

A guide to making a nibabel release

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 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.

If you have a version of nibabel trunk past February 11th 2011, there will also be a functional make target:

make bdist-egg-tests

This builds an egg (which is a zip file), hatches it (unzips the egg) and runs the tests from the resulting directory.

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 1.2.0.. | grep '^Author' | cut -d' ' -f 2- | sort | uniq

    where 1.2.0 was the last release tag name.

    Then manually go over git shortlog 1.2.0.. to make sure the release notes are as complete as possible and that every contributor was recognized.

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

  • Check the long_description in nibabel/info.py. Check it matches the README in the root directory.

  • Do a final check on the nipy buildbot

  • If you have travis-ci building set up 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 origin pre-release-test
  • Clean:

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

    cd ..
    nosetests --with-doctest nibabel
    cd nibabel # back to the root directory
  • Make sure all tests pass from sdist:

    make sdist-tests

    and bdist_egg:

    make bdist-egg-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'}
    Files not taken across by the installation:
    []
    /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'}
  • You probably have virtualenvs for different python versions. Check the tests pass for different configurations. If you have pytox and a network connnection, and lots of pythons installed, you might be able to do:

    tox
    

    and get tests for python 2.5, 2.6, 2.7, 3.2. I (MB) have my own set of virtualenvs installed and I’ve set them up to run with:

    tox -e python25,python26,python27,python32,np-1.2.1

    The trick was only to define these testenv sections in tox.ini.

    These two above run with:

    make tox-fresh
    make tox-stale

    respectively.

    The long-hand not-tox way looks like this:

    workon python26
    make sdist-tests
    deactivate

    etc for the different virtualenvs.

  • Check on different platforms, particularly windows and PPC. I have wine installed on my Mac, and git bash installed under wine. I run bash and the tests like this:

    wineconsole bash
    # in wine bash
    make sdist-tests

    For the PPC I have to log into an old Mac G5 in Berkeley at jerry.bic.berkeley.edu. Here’s an example session:

    ssh jerry.bic.berkeley.edu
    cd dev_trees/nibabel
    git co main-master
    git pull
    make sdist-tests
  • Check the documentation doctests:

    cd doc
    make doctest
    cd ..
  • 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, upload the source release to PyPi. See setuptools intro:

    python setup.py register
    python setup.py sdist --formats=gztar,zip upload

    From somewhere - maybe a windows machine - upload the windows installer for convenience:

    python setup.py bdist_wininst upload
  • Tag the release with tag of form 1.1.0:

    git tag -am 'Second main release' 1.1.0
  • Now the version number is OK, push the docs to sourceforge with:

    make upload-htmldoc-mysfusername

    where mysfusername is obviously your own sourceforge username.

  • 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/1.0.x

      Set _version_extra back to .dev and bump _version_micro by 1. Thus the maintenance series will have version numbers like - say - ‘1.0.1.dev’ until the next maintenance release - say ‘1.0.1’. Commit. Don’t forget to push upstream with something like:

      git push upstream maint/1.0.0 --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 ‘1.1.0.dev’ and the next full release will be ‘1.1.0’.

    If this is just a maintenance release from maint/1.0.x or similar, just tag and set the version number to - say - 1.0.2.dev.

  • Push tags:

    git push --tags
  • 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.