Development¶
Unit tests¶
Each file in rtd_lib
has a corresponding test file with prefix test_
placed in rtd_lib_test
folder.
To run all tests and asses code coverage (the share of code tested) using the coverage
package, run the following
command in terminal:
coverage run --source=./bio_rtd -m unittest discover bio_rtd_test; coverage report
To see the detailed coverage analysis (e.g. to discover non-covered lines), run:
coverage html
and open htmlcov/index.html
in web browser.
Running tests without code coverage:
python -m unittest discover bio_rtd_test
If you create a pull request, please add appropriate tests, make sure all tests succeed and keep complete (100 %) code coverage. If needed, also update the documentation.
Documentation¶
Dependencies (pip
packages):
sphinx
sphinx_autodoc_typehints
sphinx_rtd_theme
rst2pdf
To generate the documentation from script, run:
make html
and open docs/build/html/index.html
.
To generate the documentation in form of PDF, run:
sphinx-build -b pdf docs/source docs/build
To clean the build directory, run:
make clean
Pull requests¶
To contribute to the library, please create a pull request on GitHub.
Checklist before making a pull request:
All unit tests need to succeed.
Ensure 100 % code coverage with unit tests.
Update docstrings and documentation.