How to create and maintain an Astropy affiliated package

If you run into any problems, don’t hesitate to ask for help on the astropy-dev mailing list!

The package-template repository provides a template for packages that are affiliated with the Astropy project. This package design mirrors the layout of the main Astropy repository, as well as reusing much of the helper code used to organize Astropy. The instructions below describe how to take this template and adjust it for your particular affiliated package, as well as how to update your package to the latest version of the package template.

There are two main ways you can use this template layout to create a new package:

  1. simply copy over the files you need manually
  2. start from a fork of the package-template repository

There are advantages and disadvantages to both methods. In the first case your repository history will be clean and you will only include the files you really need. However, when updating you will need to make sure you update all the files manually. In the second case, the history of your package will be cluttered with all the commits from the package-template repository, but if done properly this can be easier to update in future since it simply involves pulling from the latest version of the package-template repository and then merging in the changes (and resolving conflicts).

Note

The instructions below assume you are using git for version control, as is used by the Astropy repository. If this is not the case, hopefully it will be clear from context what to do with your particular VCS.

Everywhere below that the text <packagename> is shown, replace it with the name of your particular package. In fact, you can do this automatically by entering your package name in the box below:

Package name:

Managing the template files manually

Starting a new package

  1. Clone the package-template package so that we can have access to the files, but do not go inside it - instead, create another empty repository into which we will copy the required files:

    git clone https://github.com/astropy/package-template.git template
    mkdir <packagename>
    cd <packagename>
    git init
    
  2. The package-template infrastructure relies on the astropy-helpers package, and we recommend adding this as a sub-module so as to easily be able to bundle it in releases of affiliated packages:

    git submodule add https://github.com/astropy/astropy-helpers.git astropy_helpers
    
  3. Copy over the following files from the package template (these define the bare minimum of what is needed) and add them to the repository:

    # .gitignore specifies which types of files to ignore in the repository
    cp ../template/.gitignore .
    
    # MANIFEST.in specifies which files to include in a tar file release
    cp ../template/MANIFEST.in .
    
    # ah_bootstrap.py is used by setup.py to use the astropy-helpers
    cp ../template/ah_bootstrap.py .
    
    # ez_setup.py is used by setup.py to be able to get setuptools on-the-fly
    cp ../template/ez_setup.py .
    
    # setup.cfg contains details about your package - edit it after copying!
    # Note: it is important that the package_name variable matches the name you
    #       are using for your package.
    cp ../template/setup.cfg .
    
    # edit the VERSION variable and if applicable, the package_data values,
    # the rest can be kept as-is
    # Note: If your package data directory has a sub-directory, you HAVE TO
    #       break 'data/*' to 'data/*.*' and 'data/subdir/*' (two different
    #       appends). If you do not have any package data, you can just comment
    #       out the line that appends 'data/*'.
    cp ../template/setup.py .
    

    Important

    Before proceeding, make sure you have edited setup.cfg and setup.py as indicated above!

    Once you have edited setup.cfg and setup.py, you can commit the changes:

    git add .gitignore MANIFEST.in ah_bootstrap.py ez_setup.py setup.cfg setup.py
    
  4. Next, you can create a directory for your package’s source code, which will usually also be called the same name as your package. In this directory you can copy over the following files:

    mkdir <packagename>
    
    cp ../template/packagename/__init__.py <packagename>/
    cp ../template/packagename/_astropy_init.py <packagename>/
    
    # edit <packagename>/__init__.py to change the docstring and change the
    # example import ``from example_mod import *`` to whatever is needed for
    # your package. If you don't want to try out any specific code yet, just
    # replace the import by ``pass``.
    

    The main purpose of the _astropy_init.py file is to set up the test() command at the root of your package so that you can do <packagename>.test(). This file is imported into __init__.

    Important

    Before proceeding, make sure you have edited __init__.py as indicated above!

    Once you have made the above changes, you can commit the files:

    git add <packagename>/__init__.py
    git add <packagename>/_astropy_init.py
    
  5. In order to benefit from the pytest plugins in Astropy, you should also copy over the conftest.py file to your repository:

    cp ../template/packagename/conftest.py <packagename>/
    
    git add <packagename>/conftest.py
    

    You can also uncomment the line enable_deprecations_as_exceptions() if you want deprecation warnings to make tests fail. There are also options to customize the information to be printed when running the tests. The package template has comments in the conftest.py file that indicate what they are.

  6. If you are interested in accurate coverage test results, copy over the coveragerc and the setup_package.py files to your repository (the latter ensures that coveragerc gets installed with the package:

    mkdir <packagename>/tests/
    cp ../template/packagename/tests/__init__.py <packagename>/tests
    cp ../template/packagename/tests/setup_package.py <packagename>/tests
    cp ../template/packagename/tests/coveragerc <packagename>/tests
    
    git add <packagename>/tests/__init__.py
    git add <packagename>/tests/setup_package.py
    git add <packagename>/tests/coveragerc
    

    to your repository. When you run tests with with --coverage option this file will be used to exclude certain files that should not typically be included. Note that you don’t need to change the {packagename} string in coveragerc - this gets changed automatically using the package name defined in setup.cfg.

    Note

    the python setup.py commands will not work until you have made your first commit, as shown in the last step of these instructions.

  7. To set up the infrastructure to build the documentation, copy over the following files into a new directory called docs:

    mkdir docs
    cp -r ../template/docs/_templates docs/
    cp ../template/docs/Makefile docs/
    cp ../template/docs/conf.py docs/
    cp ../template/docs/make.bat docs/
    touch docs/index.rst  # creates empty page
    git add docs/_templates docs/Makefile docs/conf.py docs/make.bat docs/index.rst
    

    you can later start adding content to index.rst and other documentation files.

  8. Add a README.md file to your repository, describing what the package does, and for example how to install it and any required dependencies:

    git add README.md
    
  9. Finally, if you plan on using Travis for continuous integration, copy over the .travis.yml file and edit it:

    cp ../template/.travis.yml .
    # edit .travis.yml
    git add .travis.yml
    

    Important

    Before proceeding, make sure you have edited .travis.yml as indicated above!

  10. Now you are ready to make your first commit:

    git commit -m "Initial layout for package"
    
  11. You can test that your package works correctly by doing e.g.:

    python setup.py build
    python setup.py test --coverage
    python setup.py build_docs
    

    If you have any issues that you cannot fix, feel free to ask us on the astropy-dev mailing list!

Updating to the latest template files

From time to time we will make changes to the package-template to fix bugs or add functionality. Updating to the latest version is simple - simply check the TEMPLATE_CHANGES.md file, which provides a changelog of the package template. You can also re-copy over all the files listed in the above section and see if any of the changes should be committed (some of the changes will be reverting some of your edits, so do not include those!). Remember to update the astropy-helpers sub-module to the latest stable version, and update the corresponding ah_bootstrap.py file, for example:

cd astropy_helpers
git fetch origin
git checkout v0.4.3
cd ..
cp astropy_helpers/ah_bootstrap.py .
git add astropy_helpers ah_bootstrap.py
git commit -m "Updated astropy-helpers to v0.4.3"

You can find out what the latest version of astropy-helpers is by checking the astropy-helpers entry on PyPI.

Managing the template files via git

Starting a new package

Before reading this we recommend reading over the Managing the template files manually section since this explains what many of the files do.

  1. Make sure Astropy is installed, as the template depends in part on Astropy to do its setup.

  2. You may have already done this if you are looking at this file locally, but if not, you will need to obtain a copy of the package template. Assuming you have git installed, just do:

    git clone git://github.com/astropy/package-template.git <packagename>
    

    This will download the latest version of the template from github and place it in a directory named <packagename>.

  3. Go into the directory you just created, and open the setup.cfg file with your favorite text editor. Edit the settings in the metadata section. These values will be used to automatically replace special placeholders in the affiliated package template.

    1. Change the package_name variable to whatever you decide your package should be named. By tradition/very strong suggestion, python package names should be all lower-case.
    2. Change the description variable to a short (one or few sentence) description of your package.
    3. Add your name and email address by changing the author and author_email variables.
    4. If your affiliated package has a website, change url to point to that site. Otherwise, you can leave it pointing to Astropy or just delete it.
    5. Exit out of your text editor.
  4. Move the main source directory to reflect the name of your package. To tell your DVCS about this move, you should use it, and not mv directly, to make the move. For example, with git:

    git mv packagename <packagename>
    
  5. Update the main package docstring in <packagename>/__init__.py.

  6. Decide what license you want to use to release your source code. If you don’t care and/or are fine with the Astropy license, just edit the file licenses/LICENSE.rst with your name (or your collaboration’s name) at the top as the licensees. Otherwise, make sure to replace that file with whatever license you prefer, and update the license variable in setup.cfg to reflect your choice of license. You also may need to update the comment at the top of <packagename>/__init__.py to reflect your choice of license.

  7. Take a moment to look over the <packagename>/example_mod.py, <packagename>/tests/test_example.py, and <packagename>/example_c.pyx files, as well as the <packagename>/example_subpkg directory. These are examples of a pure-python module, a test script, a Cython module, and a sub-package, respectively. (Cython is a way to compile python-like code to C to make it run faster - see the project’s web site for details). These are provided as examples of standard way to lay these out. Once you understand these, though, you’ll want to delete them (and later replace with your own):

    git rm <packagename>/example_c.pyx
    git rm <packagename>/tests/test_example.py
    git rm -r <packagename>/example_subpkg
    git commit -m "removed examples from package template"
    
  8. Optional: If you’re hosting your source code on github, you can enable a sphinx extension that will link documentation pages directly to github’s web site. To do this, set edit_on_github in setup.cfg to True and set github_project to the name of your project on github.

  9. Update the names of the documentation files to match your package’s name. First open docs/index.rst in a text editor and change the text "packagename/index.rst" to e.g., "<packagename>/index.rst". Then do:

    git add docs/index.rst
    git mv docs/packagename docs/<packagename>
    
  10. Edit the README.rst file, deleting all of the content and replacing it with a short description of your affiliated package.

  11. Open docs/<packagename>/index.rst and you can start writing the documentation for your package, but at least replace packagename in automodapi:: with your package name.

  12. Now tell git to remember the changes you just made:

    git commit -a -m "Adjusted for new project <packagename>"
    
  13. (This step assumes your affiliated package is hosted as part of the astropy organization on Github. If it’s instead hosted somewhere else, just adjust the URL in the instructions below to match wherever your repository lives) Now you will want to tell git that it should be pushing and pulling updates to the repository of your project, rather than the package template:

    git remote rename origin template
    git remote add upstream git@github.com:astropy/<packagename>.git
    

    Now that it is pointing to the correct master, you should push everything up to your project and make sure that your local master is tied to your project rather than the template. You’ll only be able to do this if your github repository is empty (if not, add the -f option to the push command - that will overwrite whatever is there):

    git push upstream master
    git branch master --set-upstream upstream/master
    
  14. (optional) If you are adopting the standard workflow used by Astropy with github, you will also want to set up a fork of the repo on your own account, by going to the Github page https://github.com/astropy/<packagename> and clicking the “fork” button on the upper right. Then run the following commands:

    git remote add origin git@github.com:yourgithubusername/<packagename>.git
    git branch master --set-upstream origin/master
    

    Now you can push, pull, and branch whatever you want in your local fork without affecting the official version, but when you want to push something up to the main repository, just switch to the appropriate branch and do git push upstream master.

    Additionally, you can set things up to make it easier to pull future changes to the package template to your affiliated package. Add a remote for the package template:

    git remote add template git@github.com:astropy/package-template.git
    

    Then, each time you want to pull in changes to the package template:

    git fetch template
    git fetch upstream
    
    # Make your master match the upstream master.  This will destroy
    # any unmerged commits on your master (which you shouldn't be doing
    # work on anyway, according to the standard workflow).
    git checkout master
    git reset --hard upstream/master
    
    # Merge any recent changes from the package-template
    git merge template/master
    
    # ...possibly resolve any conflicts...
    
    # Push to upstream master
    git push upstream master
    
  15. You should register your package on https://travis-ci.org and modify the .travis.yml file to make the build pass. This will continuously test your package for each commit, even pull requests against your main repository will be automatically tested, so that you notice when something breaks. For further information see here and for lot’s of example .travis.yml build configurations see here. Generally you should aim to always have your master branch work with the latest stable as well as the latest development version of astropy (i.e. the astropy git master branch) and the same versions of python and numpy supported by astropy. The template .travis.yml covers those versions; in some circumstances you may need to limit the versions your package covers.

  16. If you register your package with coveralls.io, then you will need to modify the coveralls --rcfile line in .travis.yml file to replace packagename with the name of your package.

  17. If you want the documentation for your project to be hosted by Read the Docs, then you need to setup an account there. The following entries in “Advanced Settings” for your package on Read the Docs should work:

    • activate Install your project inside a virtualenv using setup.py install
    • copy these additional files from the package template into the top-level directory of your package: .rtd-environment.yml and readthedocs.yml. Edit .rtd-environment.yml with your package name and requirements.
    • activate Give the virtual environment access to the global site-packages dir.

    All other settings can stay on their default value.

    If you need to mock any Python packages or C libraries that can not be installed and built by Read the Docs, you should include the following mocking patch before the Project information section of the docs/conf.py file:

    class Mock(object):
        def __init__(self, *args, **kwargs):
            pass
    
        def __call__(self, *args, **kwargs):
            return Mock()
    
        @classmethod
        def __getattr__(cls, name):
            if name in ('__file__', '__path__'):
                return '/dev/null'
            elif name[0] == name[0].upper():
                return type(name, (), {})
            else:
                return Mock()
    
    MOCK_MODULES = ['<name of package to mock>', '<name of package to mock>']
    for mod_name in MOCK_MODULES:
        sys.modules[mod_name] = Mock()
    
  18. You’re now ready to start doing actual work on your affiliated package. You will probably want to read over the developer guidelines of the Astropy documentation, and if you are hosting your code in GitHub, you might also want to read the Github help to ensure you know how to push your code to GitHub and some recommended workflows that work for the core Astropy project.

  19. Once you have started work on the affiliated package, you should register your package with the Astropy affiliated package registry. Instructions for doing this will be provided on the Astropy website.

  20. Good luck with your code and your science!

Updating to the latest template files

See instructions in Item 14 above.

Releasing an affiliated package

You can release an affiliated package using the steps given below. In these instructions, we assume that the changelog file is named CHANGES.rst, like for the astropy core package. If instead you use Markdown, then you should replace CHANGES.rst by CHANGES.md in the instructions.

  1. Make sure that Travis and any other continuous integration is passing.

  2. Update the CHANGES.rst file to make sure that all the changes are listed, and update the release date, which should currently be set to unreleased, to the current date in yyyy-mm-dd format.

  3. Update the version number in setup.py to the version you’re about to release, without the .dev suffix (e.g. 0.1).

  4. Run git clean -fxd to remove any untracked files (WARNING: this will permanently remove any files that have not been previously committed, so make sure that you don’t need to keep any of these files).

  5. Run:

    python setup.py build sdist --format=gztar
    

    and make sure that generated file is good to go by going inside dist, expanding the tar file, going inside the expanded directory, and running the tests with:

    python setup.py test
    

    You may need to add the --remote-data flag or any other flags that you normally add when fully testing your affiliated package.

    Note

    Running python setup.py build sdist runs two setup commands in succession. First it runs build, then immediately runs sdist to create the source distribution. The reason to do this is that there are several generated source files that must be included in the source distribution for it to be valid. Running build first ensures that those files will be generated and packaged in the source distribution.

  6. Go back to the root of the directory and remove the generated files with:

    git clean -fxd
    
  7. Add the changes to CHANGES.rst and setup.py:

    git add CHANGES.rst setup.py
    

    and commit with message:

    git commit -m "Preparing release <version>"
    
  8. Tag commit with v<version>, optionally signing with the -s option:

    git tag v<version>
    
  9. Change VERSION in setup.py to next version number, but with a .dev suffix at the end (e.g. 0.2.dev). Add a new section to CHANGES.rst for next version, with a single entry No changes yet, e.g.:

    0.2 (unreleased)
    ----------------
    
    - No changes yet
    
  10. Add the changes to CHANGES.rst and setup.py:

    git add CHANGES.rst setup.py
    

    and commit with message:

    git commit -m "Back to development: <next_version>"
    
  11. Check out the release commit with git checkout v<version>. Run git clean -fxd to remove any non-committed files.

  12. (optional) Run the tests in an environment that mocks up a “typical user” scenario. This is not strictly necessary because you ran the tests above, but it can sometimes be useful to catch subtle bugs that might come from you using a customized developer environment. For more on setting up virtual environments, see Python virtual environments, but for the sake of example we will assume you’re using Anaconda. Do:

    conda create -n myaffilpkg_rel_test astropy <any more dependencies here>
    source activate myaffilpkg_rel_test
    python setup.py sdist
    cd dist
    pip install myaffilpkg-version.tar.gz
    python -c 'import myaffilpkg; myaffilpkg.test()'
    source deactivate
    cd <back to your source>
    

    You may want to repeat this for other combinations of dependencies if you think your users might have other relevant packages installed. Assuming the tests all pass, you can proceed on.

  13. If you did the previous step, do git clean -fxd again to remove anything you made there. Then either release with:

    python setup.py register build sdist --format=gztar upload
    

    or, if you are concerned about security, you can also use twine as described in these instructions. Either way, check that the entry on PyPI is correct, and that the tarfile is present.

  14. Go back to the master branch and push your changes to github:

    git checkout master
    git push --tags origin master
    

    Once you have done this, if you use Read the Docs, trigger a latest build then go to the project settings, and under Versions you should see the tag you just pushed. Select the tag to activate it, and save.

Note

The instructions above assume that you do not make use of bug fix branches in your workflow. If you do wish to create a bug fix branch, we recommend that you read over the more complete astropy Release Procedures and adapt these for your package.