[Fix] Running the unit tests clutters the project directory

[fpgmaas]

Summary

Running the unit tests with make test clutters the project directory. Maybe it's possible to have these files downloaded to a separate directory, and delete them when pytest finishes or aborts? Maybe with the use of try/finally?

Codes

make test
git status

Outputs

?? covid_japan_metadata.csv
?? japan.csv
?? ne_10m_admin_1_states_provinces/

Environment

• CovsirPhy version: master branch
• Python version: 3.9
• Installation: not applicable
• System: WSL Mac OS

[lisphilar]

Thank you for raising.
To avoid downloading files many times, I think downloaded files should be saved in "input" directory. With the current .gitignore configuration, this directory is not the target of git statsus. I will fix this with a pull request.

[lisphilar]

With #1178, ”japan.csv" and "covid_japan_metadata.csv" created with JapanData class and test workflow will be moved to "input" directory from top directory.

Regarding "ne_10m_admin_1_states_provinces/", I have one idea. Because this is from Natural Earth and published under Public Domain, will it be better to include it in covsirphy as geopandas does?

[fpgmaas]

I think that sounds like a good solution!

[lisphilar]

Thank you and I will try to implement it :)

Note:

• Add a script of downloading/updating the dataset to stable version publish workflow
• Save the file in covsirphy/gis/natural_earth directory with README.md (to explain the data source)
• Ensure covsirphy to include the dataset with pyproject.toml (using "include" option?)
• covsirphy.gis.geometry._Geometry._natural_earth() will read the saved files internally (with relative path from covsirphy directory?)
• Explain the workflow and data source in documentation

[lisphilar]

Because the dataset of the data source will be updated irregularly, the dataset will not be included in CovsirPhy. As a quick solution, the directory to save the files will be changed to "covsirphy/gis/Natural_Earth" directory.

[lisphilar]

@fpgmaas
Solution was changed, but I tried to solve this issue. Any ideas or could you confirm that the files will not be created?

[fpgmaas]

Can confirm that the files are not showing up in git status after running make test. So the issue seems resolved!

[lisphilar]

Thank you for confirmation!
I will close this issue for release.