[Revise] pyproject.toml contains obsolete dependencies

[fpgmaas]

Summary of request

Not all dependencies listed in pyproject.toml are still actively used. I used deptry to scan the repository, and it returned the following output:

Output:

Warning: Failed to find corresponding package name for import `mpl_toolkits` in current environment.
pyproject.toml contains obsolete dependencies: ['better-exceptions', 'descartes', 'funcparserlib', 'mapclassify', 'scikit-learn', 'tabulate']

scikit-learn is incorrectly marked, which I have added as a bug report to the deptry project. The others indeed seem to be no longer actively required.

[fpgmaas]

better-exceptions was also marked as obsolete erroneously, since deptry does not support try-catch blocks yet, and it's only imported within a try-catch block. Added as a bug report to deptry as well.

[lisphilar]

Thank you for your contribution to this project!!
Could you add deptry to "[tool.poetry.dev-dependencies]"?
(With #1144, I plan to rename it to "[tool.poetry.group.dev.dependencies]" per poetry version 1.2.0.)

Additionally, could you add the followings to pyproject.toml?

[tool.deptry]
ignore_dependencies = [
'tabulate'
]

---

Yes, scikit-learn and better-exceptions are used in our project actively and I will follow the discussion in your repository.

tabulate:
Please continue to include this because some covsirphy users need pandas.DataFrame.to_markdown functionarity which requires explicit tabulate installation.
https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.to_markdown.html

Discussion of pip install pandas["table"] is still ongoing.
pandas-dev/pandas#39164

descartes:
Yes, we can remove it as your pull request. It was necessary for geopandas version 0.8.2, but is un-necessary now because we use geopandas >= 0.9 and geopandas vendors it.
geopandas/geopandas#1039

mapclassify:
Removal is acceptable because tests passed, but I could not clarify the reason under the following instruction.
Geopandas needs explicit installation of this package for chropleth map functionality (of covsirphy), but explicit importing of it is un-necessary.
https://geopandas.org/en/latest/getting_started/install.html#dependencies

funcparserlib:
Removal is acceptable! This was introduced to fix version control of some other removed dependencies, but unnecessary now.

[fpgmaas]

Thanks for your extensive feedback, and thanks for considering to add deptry as a development dependency!

I have processed your proposed changes, and I have added the deptry configuration to pyproject.toml. In addition, I have added scikit-learn to the list of dependencies to ignore, since I have no solution for that problem yet, so this is now the advised workaround.

The parsing of try/except blocks is now added in deptry 0.2.1, so it no longer erroneously marks better-exceptions as a obsolete dependency.

[lisphilar]

Thank you for updating and I merged your pull request. This will be included in the next stable release.

I ran deptry . and I got the following message.

Warning: Failed to find corresponding package name for import `mpl_toolkits` in current environment.
Succes! No obsolete dependencies found.

I created a issue for the warning fpgmaas/deptry#34
"Succes" could be changed with "Success"?

[lisphilar]

With #1163, this was included in the test workflow.

[lisphilar]

With fpgmaas/deptry#34, the warning was removed at deptry version 0.2.3. We will use version 0.2.3 with #1170.

@fpgmaas ,
Thank you a lot for your support!! :)
We can close this issue and I will contiue to follow the releases of your package.