Create Optional Dependencies

[arjxn-py]

Description

The goal of this PR is to make most of the dependencies optional & split them in specific group

Fixes #3035

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist:

• No style issues: $ pre-commit run (see CONTRIBUTING.md for how to set this up to run automatically when committing locally, in just two lines of code)
• All tests pass: $ python run-tests.py --all
• The documentation builds: $ python run-tests.py --doctest

You can run unit and doctests together at once, using $ python run-tests.py --quick.

Further checks:

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[arjxn-py]

Related to #3035

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.01 ⚠️

Comparison is base (c494873) 99.71% compared to head (61f79cf) 99.71%.

❗ Current head 61f79cf differs from pull request most recent head 63524b4. Consider uploading reports for the commit 63524b4 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #3044      +/-   ##
===========================================
- Coverage    99.71%   99.71%   -0.01%     
===========================================
  Files          248      248              
  Lines        18749    18747       -2     
===========================================
- Hits         18695    18693       -2     
  Misses          54       54              

Impacted Files	Coverage Δ
pybamm/input/parameters/lithium_ion/Prada2013.py	100.00% <100.00%> (ø)

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[arjxn-py]

Read the docs build failed, trying adding tqdm in docs/requirements.txt

[arjxn-py]

@Saransh-cpp maybe we could group pybtex , sympy , bpx & tqdm together?

[Saransh-cpp]

Thanks, @arjxn-py! Looks good, few comments -

[valentinsulzer]

Before we merge this it's important to document what the different options do in the installation docs, like in pandas https://pandas.pydata.org/docs/getting_started/install.html#optional-dependencies

[arjxn-py]

Thanks for the review both, i'm looking into the suggested things.

[Saransh-cpp]

Great work, thanks @arjxn-py! Looks good overall, but a few minor comments below 🙂

[arjxn-py]

@brosaplanella Probably it would be better to have a separate PR for jupyter notebooks as pip install pybamm[all] is currently not supported. Although tests are passing but when running notebooks it is giving warning & then installing pybamm without any extras, so if I open a PR for jupyter notebooks & merge it after a patch release so that we have pybamm[all] distributed on pip to install without any issue.

[brosaplanella]

@brosaplanella Probably it would be better to have a separate PR for jupyter notebooks as pip install pybamm[all] is currently not supported. Although tests are passing but when running notebooks it is giving warning & then installing pybamm without any extras, so if I open a PR for jupyter notebooks & merge it after a patch release so that we have pybamm[all] distributed on pip to install without any issue.

I don't think we need to do a patch release for this. In theory the links to Colab should use the notebooks in main, so it should not be an issue, but probably it is safer to have a separate PR that we can merge in a month or so, just before the feature freeze for 23.9. What are your thoughts @tinosulzer and @Saransh-cpp?

[arjxn-py]

I don't think we need to do a patch release for this. In theory the links to Colab should use the notebooks in main, so it should not be an issue, but probably it is safer to have a separate PR that we can merge in a month or so, just before the feature freeze for 23.9. What are your thoughts @tinosulzer and @Saransh-cpp?

Got it, +1

[agriyakhetarpal]

A note that the Open in Colab badge in the README is currently pointing to the develop branch, we should change it to point to the main branch: https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/main/

[brosaplanella]

Looks good to me, thanks!

[valentinsulzer]

thanks, looks good