Init repo

[rogerkuou]

Fix the following issues to setup the repository

• precommit hooks for linter/formatter #6
• project toml file #7

[rogerkuou]

Hi @fnattino and @vanlankveldthijs. When you have time, could you please help me review this PR?

This is a PR setting up the PyDePSI repository. I removed some old irrelevant examples. Could you please focus on:

• See if the development guide (currently README.md of the repo) is clear and working
• See if pyproject.toml makes sense?

The testing is failing because currently there are no tests under folder tests. They will be added in PR #9.

Thanks in advance!

[vanlankveldthijs]

README is clear and works perfectly.

pyproject file also looks fine to me.

The only thing I noticed is that I initially did not realize that I needed to set the python version when creating the conda environment (as described in the README).
When I then tried to pip install, it did not notify me of the requirement for python to be >=3.10 and then it did not recognize the pydepsi project and created an UNKNOWN project-0.0.0.

I don't know whether we can/should fix this. When I then did follow the instructions in the README correctly, the package installed just fine and the example notebook works.

[fnattino]

Looks nice @rogerkuou!

The only main comment I have is regarding the dev installation procedure, but feel free to address it or discard it as you see fit.
The rest is all very minor things!

[fnattino]

-c conda-forge ? Not really needed here, but I think there were some legal implications for for-profit organizations connected to the use of the anaconda channel..

[fnattino]

Are these links provided because they are useful readings for people who starts develop the package? Maybe you could mention it here, or simply call this section "Useful reading material"?

[fnattino]

I am not sure, are the following lines actually needed? I think that the pip build/install part already runs this step?

https://github.com/MotionbyLearning/PyDePSI/blob/cdda86dc41096ce0c64849c8cb5f70dd905a059b/.github/workflows/build.yml#L33-L34

[rogerkuou]

Sorry I realized I forgot to push the fix of this comment. This is implemented with a separate PR #19

[fnattino]

@vanlankveldthijs

The only thing I noticed is that I initially did not realize that I needed to set the python version when creating the conda environment (as described in the README). When I then tried to pip install, it did not notify me of the requirement for python to be >=3.10 and then it did not recognize the pydepsi project and created an UNKNOWN project-0.0.0.

I was curious about what would happen in this situation as well, so I also tried to pip install the package in an environment where I had Python 3.9. But in my case pip correctly recognizes the Python version requirement in the pyproject.toml file and throw the following error:

ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.10; 0.1.2 Requires-Python >=3.10
ERROR: Could not find a version that satisfies the requirement sarxarray (from pydepsi) (from versions: none)
ERROR: No matching distribution found for sarxarray

So this seems to be working fine on my system. I wonder whether this is something related to the pip version (I have 24.2).

[rogerkuou]

Thanks @vanlankveldthijs and @fnattino for the review. I applied some changes according to @fnattino 's suggestions. And @vanlankveldthijs same as Francesco the version constraint seems working for me. Given for now the installation is mainly development oriented, I would park this for now. We can polish up the user oriented installation docs later.

Will merge this PR.