Contribute to pyhetdex

How To

The suggested workflow for implementing bug fixes and/or new features is the following:

  • Identify or, if necessary, add to our redmine issue tracker one or more issues to tackle. Multiple issues can be addressed together if they belong together. Assign the issues to yourself.

  • Create a new branch from the trunk with a name either referring to the topic or the issue to solve. E.g. if you need to add a new executable, tracked by issue #1111 do_something:

    svn cp ^/trunk ^/branches/do_something_1111\
-m 'create branch to solve issue #1111'

  • Switch to the branch:

    svn switch ^/branches/do_something_1111

  • Implement the required changes and don’t forget to track your progress on redmine. If the feature/bug fix requires a large amount of time, we suggest, when possible, to avoid one big commit at the end in favour of smaller commits. In this way, in case of breakages, is easier to traverse the branch history and find the offending code. For each commit you should add an entry in the Changelog file.

    If you work on multiple issues on the same branch, close one issue before proceeding to the next. When closing one issue is good habit to add in the description on the redmine the revision that resolves it.

  • Every function or class added or modified should be adequately documented as described in Coding style.

    Documentation is essential both for users and for your fellow developers to understand the scope and signature of functions and classes. If a new module is added, it should be also added to the documentation in the appropriate place. See the existing documentation for examples.

    Each executable should be documented and its description should contain enough information and examples to allow users to easily run it.

  • Every functionality should be thoroughly tested for python 2.7 and 3.4 or 3.5 in order to ensure that the code behaves as expected and that future modifications will not break existing functionalities. When fixing bugs, add tests to ensure that the bug will not repeat. For more information see Testing.

  • Once the issue(s) are solved and the branch is ready, merge any pending change from the trunk:

    svn merge ^/trunk

    While doing the merge, you might be asked to manually resolve one or more conflicts. Once all the conflicts have been solved, commit the changes with a meaningful commit message, e.g.: merge ^/trunk into ^/branches/do_something_1111. Then rerun the test suite to make sure your changes do not break functionalities implemented while you were working on your branch.

  • Then contact the maintainer of pyhetdex and ask to merge your branch back to the trunk.

Information about branching and merging can be found in the svn book. For any questions or if you need support do not hesitate to contact the maintainer or the other developers.

Coding style

All the code should be compliant with the official python style guidelines described in PEP 8. To help you keep the code in spec, we suggest to install plugins that check the code for you, like Synstastic for vim or flycheck for Emacs.

The code should also be thoroughly documented using the numpy style. See the existing documentation for examples.

Testing

pyhetdex uses the testing framework provided by the pytest package. The tests should cover every aspect of a function or method. If exceptions are explicitly raised, this should also tested to ensure that the implementation behaves as expected.

The preferred way to run the tests is using tox, an automatised test help package. If you have installed tox, with e.g. pip install tox, you can run it by typing:

tox

It will take care of creating virtual environments for every supported version of python (2.7, 3.4, 3.5 and 3.6), if it exists on the system, install pyhetdex, its dependences and the packages necessary to run the tests and runs py.test.

You can run the tests for a specific python version using:

py.test

or:

python setup.py test

The latter command fetches all the needed dependences, among others pytest itself, will be fetched and installed in a .eggs directory. Then it will run py.test. This command might fail when running in a virtual environment. If you get ImportError: No module named 'numpy' while installing scipy, install numpy by hand pip install [--user] numpy and rerun it again. Use the option --addopts to pass additional options to py.test.

You can run specific tests providing the file name(s) and, optionally the name of a test. E.g.:

py.test tests/test_logging_helper.py  # runs only the tests in the logging helper file
py.test tests/test_logging_helper.py::test_log_setup  # runs only one test

Relevant command line options:

-v                    verbose output: print the names and parameters of the
                      tests
-s                    capture standard output: can cause weird interactions
                      with the logging module

Some test are place holders for missing tests, non reviewed or buggy code. They are marked as todo and they fail. It is possible to skip them invoking:

py.test -m "not todo"

or:

tox -- -m "not todo"

A code coverage report is also created thanks to the pytest-cov plugin and can be visualized opening into a browser cover/index.html. If you want a recap of the coverage directly in the terminal you can provide one of the following options when running py.test:

--cov-report term
--cov-report term-missing

Besides running the tests, the tox command also builds, by default, the documentation and collates the coverage tests from the various python interpreters and can copy then to some directory. To do the latter create, if necessary, the configuration file ~/.config/little_deploy.cfg and add to it a section called pyhetdex with either one or both of the following options:

[pyhetdex]
# if given the deploys the documentation to the given dir
doc = /path/to/dir
# if given the deploys the coverage report to the given dir
cover = /path/to/other/dir

# it's also possible to insert the project name and the type of the document
# to deploy using the {project} and {type_} placeholders. E.g
# cover = /path/to/dir/{project}_{type_}
# will be expanded to /path/to/dir/pyhetdex_cover

For more information about the configuration file check little_deploy.

For other command line arguments type:

py.test -h

For a list of available fixtures type:

py.test --fixtures tests/

tox and pyenv

Many systems have a limited number of python versions installed. pyenv provides ways to have multiple python versions that can be used by tox via the tox-pyenv plugin.

Here we outline the steps necessary to make tox use pyenv:

  • Install pyenv following these instructions. We suggest to use brew under Mac OS X or the automatic installer. When is done, follow the instructions to enables pyenv.

  • Install the python versions that you need. E.g. if you have python 2.7 and 3.6 on you system, you can install only missing versions, e.g.:

    pyenv install 3.4.6
pyenv install 3.5.3

    Of course you can also install 2.7 and 3.6 using pyenv.

  • Install tox-pyenv in the same place where tox is installed, i.e. either on the system, a virtual environment or a pyenv instance:

    pip install tox-pyenv

    This way tox is can use pyenv which to locate a required python version

  • The last step consists in letting pyenv know which python versions to use. If you have already set pyenv global <https://github.com/pyenv/pyenv/blob/master/COMMANDS.md#pyenv-global>_ to all the version required for testing you should be done. Otherwise go to the pyhetdex directory and run pyenv local <https://github.com/pyenv/pyenv/blob/master/COMMANDS.md#pyenv-local>_:

    pyenv local system 3.4.6 3.5.3

    This command creates a file called .python-version that contains the following three lines:

    system
3.4.6
3.5.3

    It will make pyenv which look for python versions in the system directories as well as within the pyenv directory.

    If you did installed also other versions of python (e.g. 3.6.0 and 2.7.13) under pyenv and want to use them instead of the system ones, you can use:

    pyenv local 3.6.0 3.4.6 3.5.3 2.7.13

  • Run tox: now you will be able to use all the python version that tox requires.

Documentation

To build the documentation you need the additional dependences described in Optional dependences. They can be installed by hand or during pyhetdex installation by executing one of the following commands on a local copy:

pip install /path/to/pyhetdex[doc]
pip install /path/to/pyhetdex[livedoc]

The first install sphinx, the alabaster theme and the numpydoc extension; the second also installs sphinx-autobuild.

To build the documentation in html format go to the doc directory and run:

make html

The output is saved in doc/build/html. For the full list of available targets type make help.

If you are updating the documentation and want avoid the edit-compile-browser refresh cycle, and you have installed sphinx-autobuild, type:

make livehtml

This command compiles the documentation and serves it on http://127.0.0.1:{port}, where {port} is an available port, and open the page on your default browser. The html documentation is automatically rebuilt after every change of the source and the browser reloaded.

Please make sure that every module in pyhetdex is present in the Code documentation.