Contribute to VDAT

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 vdat 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

Note

Every part of the code should be tested and should run at least under python 2.7 and the latest two or three python 3.x releases (e.g. 3.4, 3.5 and 3.6)

vdat 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, if it exists on the system, install vdat, 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.

The VDAT test suites depends on some large file that is not shipped with the main repository. You can get the file running the following command in the parent directory of the vdat root:

svn checkout svn://luna.mpe.mpg.de/vdat_test_data/trunk vdat_test_data

If for any reason you have the test data somewhere else, you can tell pytest where they are using the --extra-data-dir option. If the directory is not found, pytest will abort with a useful error message.

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

py.test tests/test_libvdat/test_symlink.py  # runs only the tests in one file
py.test tests/test_libvdat/test_symlink.py::test_no_raw  # runs only one test function

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
--noremove            Do not remove output created output files when
                      tearing down the tests. Useful to inspect the log
                      files created by vhc when updating the tests
--extra-data-dir=EXTRA_DATA_DIR
                      Directory containing extra test data.

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 vdat with either one or both of the following options:

[vdat]
# 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/vdat_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/

Qt bindings

With version 0.9.0 and the use of qtpy, VDAT can be run against different Qt bindings. Ideally we would like to run VDAT against all the possible. When writing (2018/06/15) the tox configuration file contains hints about this ideal; I would have liked to run the following tests:

  • py27: PyQt4
  • py34: PySide
  • py35: PySide2
  • py36: PyQt5

Unfortunately this didn’t work out so the actual test matrix is:

  • py27: PyQt4
  • py34: PyQt4
  • py35: PyQt5
  • py36: PyQt5

If any of PySide/PySide2 becomes supported, then the test matrix should be reverted to

A note on PySide

PySide can be installed using pip, however it needs python to be compiled with the -fPIC flag. If this is not the case, you might get the following error while installing PySide:

/usr/bin/ld:
/home/montefra/.pyenv/versions/3.4.6/lib/libpython3.4m.a(abstract.o):
relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used
when making a shared object; recompile with -fPIC
/home/montefra/.pyenv/versions/3.4.6/lib/libpython3.4m.a: error adding
symbols: Bad value
collect2: error: ld returned 1 exit status
libshiboken/CMakeFiles/libshiboken.dir/build.make:381: recipe for
target 'libshiboken/libshiboken.cpython-34m.so.1.2.4' failed
make[2]: *** [libshiboken/libshiboken.cpython-34m.so.1.2.4]
Error 1
CMakeFiles/Makefile2:204: recipe for target
'libshiboken/CMakeFiles/libshiboken.dir/all' failed
make[1]: ***
[libshiboken/CMakeFiles/libshiboken.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2
error: Error compiling shiboken

If you are using pyenv to handle your python versions, you can get a new python version with the correct flag using:

PYTHON_CFLAGS=-fPIC pyenv install -v 3.4.8

Documentation

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

pip install /path/to/vdat[qt5,doc]
pip install /path/to/vdat[qt5,livedoc]

The first install sip, pyqt5, 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 vdat is present in the Code Documentation.

Qt Documenation

We distribute this documentation also with VDAT, to allow consulting it offline.

The Qt documentation can be built by sphinx itself using the following command:

make qthelp

This command creates the documentation into the _build/qthelp directory together with these extra files:

  • Qt Help Collection Project (.qhcp)
  • Qt Help Project (.qhp)
  • Qt Compressed Help (.qch)
  • Qt Help Collection (.qhc)

See the Qt Help documentation for more information about those files.

All those files can also be created running tox, or tox -e qt-doc. In this case the files can be found in .tox/qt-doc/tmp/qthelp

To update the documentation copy the .qch and .qhc files into vdat/gui/static. If the files have a different names from the old ones, remove the latter from the repository with svn rm and add the new ones with svn add. Don’t forget to commit to propagate the changes.