Developer’s Guide#
Requirements#
As a developer you will need:
The tox environments install the test and documentation dependencies. The
docs environment builds the HTML documentation; PDF-specific tools such as
pdflatex are only needed when producing PDF output separately.
Forking and cloning the git repository#
To make changes to the eFEL, one first needs to fork the eFEL:
https://help.github.com/articles/fork-a-repo/
Then one creates a local clone of the git repository on your computer:
git clone https://github.com/yourgithubusername/eFEL.git
After changes are made, they should be pushed back to your github account. Then a pull request can be created:
https://help.github.com/articles/using-pull-requests/
Development workflow#
Install the package and its optional data-format dependencies in an active virtual environment:
python -m pip install -e ".[nwb,h5py]"
Install the packaging and test tooling, then run the test environment:
python -m pip install build tox
tox -e py3-test
Build the documentation with the same workflow used by CI:
tox -e docs
The root Makefile provides convenience targets for packaging, documentation,
cleaning build artifacts, and CMake compilation. Use make help where
available, and prefer the tox commands above for tests and documentation.
Adding a new eFeature#
Adding a new eFeature requires several steps.
Picking a name#
Try to be specific in the name of the eFeature, because in the future you or somebody else might want to develop an eFeature with slightly different behavior. Don’t be afraid to use long names, e.g. ‘min_voltage_between_spikes’ is perfectly ok.
Creating a branch#
Create a git branch with the name of the new eFeature:
git checkout -b your_efeaturename
Implementation#
All the eFeatures in the eFEL are coded in C++. Thanks to an eFeatures dependency settings file, several implementation of the same eFeature name can coexist. E.g. this is the file with the implementations of all ‘V5’ features. You can implement the new eFeature by extending one of the current LibV* files, or by creating your own. You might want to consider starting the implementation by writing a test for the eFeature (see below for instruction on how to do that).
Updating relevant files#
Apart from the implementation in the LibV*.cpp file, other files have to be changed to accomodate the new eFeature
efel/cppcore/LibV5.h: Declare your feature
efel/DependencyV5.txt: Add your eFeature and its dependencies to this file
efel/cppcore/FillFptrTable.cpp: Add a reference to the eFeature in the relevant table
efel/cppcore/cfeature.cpp: Add the type of the eFeature
AUTHORS.txt: If your name isn’t there yet, add yourself to the authors list
efel/units/units.json: Add the units of the eFeature to the API
You can confirm everything compiles correctly by executing:
make test
Adding a test#
Most eFeatures are fairly easy to implement in Python, so it is advised to first write a Python implementation of your eFeature, and to add a test to it. Then, while you are implementing the code in C++ you can easily compare the results to the test.
The tests of the individual eFeatures are here .Just add your own test by defining a new function ‘test_yourfeature()’.
Some test data is available at this link , but you can of course add your own traces.
The easiest way to run the tests is by executing:
make test
Add documentation#
Add the documentation of the new eFeature to this file:
Please provide some pseudo-Python code for the eFeature.
The documentation can be built by:
make doc
It can be viewed by opening:
docs/build/html/index.html
To build the documentation, pdflatex has to be present on the system. On a Mac this can be installed using Mactex. On Ubuntu one can use:
sudo apt-get install texlive-latex-base texlive-latex-extra xzdec
tlmgr install helvetic
Pull request#
When all the above steps were succesfull, you can push the new eFeature branch to your github repository:
git commit -a
git push origin your_efeaturename
Finally create a pull request: