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 :ref:`code_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 :ref:`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. .. _code_style: 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: 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: .. code-block:: ini [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 .. _pyside_inst: 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 :ref:`optdep`. 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 :doc:`codedoc/index`. 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.