korem-lab / pymgpipe Goto Github PK

Hello,

I have a few comments concerning your python package and your manuscript:

1. let's start with the installation process. I honestly don't see a reason why this package shouldn't be available in the Python Package Index https://pypi.org. I would strongly suggest to create a pypi package. You already have everything to do that;
2. before uploading the package to pypi, I would definitely refactor the setup.py. Please add as many details as possible (see this example here);
3. this is the first time I see taking track of a tool version through a .VERSION file. Is that used for any other purpose? Is it used by a GitHub action? If not, I would add this info in the pymgpipe/__init__.py, i.e., __version__ = "v0.16.0". At that point, I would add from pymgpipe import __version__ in the setup.py to access the software version, without the need to read a file. And you can get rid of the .VERSION file now;
4. now that you have your package available in pypi, it would be extremely easy to define a Bioconda recipe. At that point, once you have a conda package, you don't have to take care of installing the external dependencies by your own anymore;
5. on line 65-66, you said that The pymgpipe python package, as well as all associated documentation, tests, and example workflows, can be found at https://korem-lab.github.io/pymgpipe. This is not correct since that page shows the code documentation only. I would reformulate that sentence;
6. the code documentation seems not complete. Most of the functions are not documented. This must be fixed;
7. that's great that you provide a Notebook to better explain users how to use the library. The problem here is the lack of notes. I can only see python codes here, but there is no explanation about what you are doing. Please, add a text explaining what you do in every cell of the notebook.

Please, do not close this thread.
I'll update it in case I will have any other comments.

Hi,

Since you copied some of the MICOM source code into your software I just wanted to point out that MICOM's Apache 2.0 license is not compatible with the CC-BY license you applied to your project. So you would need to transfer your project to a compatible license if you want to use MICOM source code in your codebase. Thanks!

Hi there,

I had a few comments that I think could improve the user experience. Making these changes are not contingent on publishing.

• Create a dedicated section in the readme with the full install instructions. The install instructions a bit light, while it is current enough to install the package, more detailed instructions would be beneficial. I suggest a full step by step instructions, including the how to use the suggested pyenv. I also suggest not including the local installation example as it can be confusing for beginners.
• Specify what version(s) of Python is recommended.
• Update the version in setup.py here https://github.com/korem-lab/pymgpipe/blob/main/setup.py#L5
• Add more information on how to generate/find taxa models

Well done on creating this great tool and publishing.

Regards,

Ammar