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[![Documentation][documentation:b]][documentation]
[![License BSD3][license:b]][license]
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[![pypi][pypi:b]][pypi]
[![codecov][codecov:b]][codecov]
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[codecov:b]: https://codecov.io/gh/classifier-calibration/PyCalib/branch/master/graph/badge.svg?token=AYMZPLELT3
PyCalib
=======
Python library for classifier calibration
User installation
-----------------
The PyCalib package can be installed from Pypi with the command
```
pip install pycalib
```
Documentation
-------------
The documentation can be found at https://classifier-calibration.github.io/PyCalib/
Development
===========
There is a make file to automate some of the common tasks during development.
After downloading the repository create the virtual environment with the
command
```
make venv
```
This will create a `venv` folder in your current folder. The environment needs
to be loaded out of the makefile with
```
source venv/bin/activate
```
After the environment is loaded, all dependencies can be installed with
```
make requirements-dev
```
Unittest
--------
Unittests are specified as doctest examples in simple functions (see example ),
and more complex tests in their own python files starting with `test_` (see
example ).
Run the unittest with the command
```
make test
```
The test will show a unittest result including the coverage of the code.
Ideally we want to increase the coverage to cover most of the library.
Contiunous Integration
----------------------
Every time a commit is pushed to the master branch a unittest is run following
the workflow [.github/workflows/ci.yml](.github/workflows/ci.yml). The CI badge
in the README file will show if the test has passed or not.
Analyse code
------------
We are trying to follow the same code standards as in [Numpy][numpy:c] and
[Scikit-learn][sklearn:c], it is possible to check for pep8 and other code
conventions with
[numpy:c]: https://numpy.org/devdocs/dev/index.html
[sklearn:c]: https://scikit-learn.org/stable/developers/index.html
```
make code-analysis
```
Documentation
-------------
The documentation can be found at
[https://www.classifier-calibration.com/PyCalib/](https://www.classifier-calibration.com/PyCalib/),
and it is automatically updated after every push to the master branch.
All documentation is done ussing the [Sphinx documentation
generator][sphinx:l]. The documentation is written in
[reStructuredText][rst:l] (\*.rst) files in the `docs/source` folder. We try to
follow the conventions from [Numpy][numpy:d] and [Scikit-learn][sklearn:d].
[numpy:d]: https://numpydoc.readthedocs.io/en/latest/format.html
[sklearn:d]: https://scikit-learn.org/stable/developers/contributing.html#documentation
The examples with images in folder `docs/source/examples` are generated
automatically with [Sphinx-gallery][sphinx:g] from the python code in folder
[examples/](examples/) starting with `xmpl_{example_name}.py`.
[rst:l]: https://docutils.sourceforge.io/rst.html
[sphinx:l]: https://www.sphinx-doc.org/en/master/
[sphinx:g]: https://sphinx-gallery.github.io/stable/index.html
The docuemnation can be build with the command
```
make doc
```
(Keep in mind that the documentation has its own Makefile inside folder [docs](docs)).
After building the documentation, a new folder should appear in `docs/build/`
with an `index.html` that can be opened locally for further exploration.
The documentation is always build and deployed every time a new commit is
pushed to the master branch with the workflow
[.github/workflows/documentation.yml](.github/workflows/documentation.yml).
After building, the `docs/build/html` folder is pushed to the branch
[gh-pages][gh:l].
[gh:l]: https://github.com/perellonieto/PyCalib/tree/gh-pages
Check Readme
------------
It is possible to check that the README file passes some tests for Pypi by
running
```
make check-readme
```
Upload to PyPi
--------------
After testing that the code passes all unittests and upgrading the version in
the file `pycalib/__init__.py` the code can be published in Pypi with the
following command:
```
make pypi
```
It may require user and password if these are not set in your home directory a
file __.pypirc__
```
[pypi]
username = __token__
password = pypi-yourtoken
```
Contributors
------------
This code has been adapted by Miquel from several previous codes. The following
is a list of people that has been involved in some parts of the code.
- Miquel Perello Nieto
- Hao Song
- Telmo Silva Filho
- Markus Kängsepp
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