Move dependencies from requirements files into pyproject.toml, add extra groups for dev, docs

[mfisher87]

Resolves #552

I hope you don't mind, I took a pass at the contributing doc and made some formatting fixes and re-organized things a little bit in a way that I thought would make it more accessible. Would love some input!

[github-actions]

👈 Launch a binder notebook on this branch for commit 0c992db

I will automatically update this comment whenever this PR is modified

👈 Launch a binder notebook on this branch for commit 6f84616

👈 Launch a binder notebook on this branch for commit 97c765e

👈 Launch a binder notebook on this branch for commit 3261cc9

👈 Launch a binder notebook on this branch for commit b1935b2

👈 Launch a binder notebook on this branch for commit 075f1f8

[mfisher87]

If there's no indentation, the text is rendered separately from the list.

Before:

After:

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 65.98%. Comparing base (5825e51) to head (075f1f8).
Report is 16 commits behind head on development.

Additional details and impacted files

@@             Coverage Diff              @@
##           development     #565   +/-   ##
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  Coverage        65.98%   65.98%           
============================================
  Files               36       36           
  Lines             3052     3052           
  Branches           538      538           
============================================
  Hits              2014     2014           
  Misses             950      950           
  Partials            88       88           

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[weiji14]

I hope you don't mind, I took a pass at the contributing doc and made some formatting fixes and re-organized things a little bit in a way that I thought would make it more accessible. Would love some input!

In this case, the documentation changes (which are quite substantial) should probably be a separate PR... One reason is so that we have 2 changelog entries, one under the the 'Documentation' section and one under 'Maintenance'.

[mfisher87]

@weiji14 Some of the documentation changes are tightly coupled with this PR. I'm assuming you want those to stay, but the others to be in a different PR?

EDIT: extracted everything that wasn't entangled with installation instructions to #566 EDITEDIT: Missed some...

[mfisher87]

😩 Two hours ago, Ruff enabled formatting and checking of Jupyter Notebooks by default. New PR coming for that.

[JessicaS11]

I haven't reviewed it line-by-line yet, but see my comment in #552.

[mfisher87]

Yes, if the conda environment has pip installed! How are you currently installing requirements.txt into a conda environment?

This is a deal breaker for me. I want to be able to create my environment with all potential dependencies and only have to pip install icepyx -e (emphasis on the editable part). I've had enough headaches to last my lifetime with pip installing too many packages after creating a skeleton new conda environment. I'm not 100% closed off on this idea, but I need to do a lot more reading and learning before I'm comfortable going ahead with it.

I'm not sure what changes you're requesting here or what the dealbreaker is, could you provide some more info? We're still doing an editable install with pip in this proposal like in the current documentation -- having pip in the conda environment is not a new requirement. The main difference is representing the optional/extra dependencies in a standard way in project metadata. The proposed workflow here will work the same with a python venv, with conda, or with another tool to manage the environment.

I think what you may be remembering is pip's unfortunate history before it was capable of dependency resolution. Back then, it would install the packages you requested in order, and if dependencies conflicted, it would choose the last one and blow away the needs of previous packages! But now it does truly resolve dependencies: https://pip.pypa.io/en/stable/topics/dependency-resolution/