The indicator is run by directly executing the Python module contained in this directory. The safest way to do this is to create a virtual environment, installed the common DELPHI tools, and then install the module and its dependencies. To do this, run the following command from this directory:
make install
This command will install the package in editable mode, so you can make changes that will automatically propagate to the installed package.
All of the user-changable parameters are stored in params.json. A template is
included as params.json.template. At a minimum, you will need to include a
password for the datadrop email account and the email address of the data sender.
Note that setting export_end_date to an empty string will export data through
today (GMT) minus 5 days. Setting pull_end_date to an empty string will pull data
through today (GMT).
To execute the module and produce the output datasets (by default, in
receiving), run the following:
env/bin/python -m delphi_quidel_covidtest
If you want to enter the virtual environment in your shell,
you can run source env/bin/activate. Run deactivate to leave the virtual environment.
Once you are finished, you can remove the virtual environment and params file with the following:
make clean
To run static tests of the code style, run the following command:
make lint
Unit tests are also included in the module. To execute these, run the following command from this directory:
make test
To run individual tests, run the following:
(cd tests && ../env/bin/pytest <your_test>.py --cov=delphi_quidel_covidtest --cov-report=term-missing)
The output will show the number of unit tests that passed and failed, along with the percentage of code covered by the tests.
None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and should not include critical sub-routines.