WIP - Migrate Pourbaix workflow to pyEQL v1.5.0

[SuixiongTay]

Description

This PR migrates the previous pourbaix to pourbaix_pyEQL_v1.5 branch.

Content

1. Core modules: Core pourbaix workflow and diagram construction

• pourbaix_api.py
• pourbaix_diagram.py
• ion.py
• compatibility.py

3. Databases: Reference databases and correction schemes

• NBS_Tables_Library.xlsx
• MP2020Compatibility.yaml
• mpr_reference_ion_database.json
• pourbaix_test_data.json

4. Tests: Test coverage from pymatgen

• test_pourbaix_api.py
• test_pourbaix_diagram.py

Note

• emmet-core uses typing.NotRequired which was introduced in python 3.11.
• Therefore, pytest.importskip is used to skip through python 3.10 to avoid the error.

Addressing #368

[SuixiongTay]

Hi @rkingsbury , I noticed the pourbaix branch is quite old and there were a lot of commits since then.

Should I target this PR against the pourbaix branch, or would you prefer this PR against the current main and let you assign the branching? Thanks!

[codecov]

Codecov Report

❌ Patch coverage is 44.11303% with 712 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.99%. Comparing base (63f4566) to head (e6a0b5b).
⚠️ Report is 5 commits behind head on main.

Files with missing lines	Patch %	Lines
src/pyEQL/pourbaix/compatibility.py	16.79%	434 Missing and 2 partials ⚠️
src/pyEQL/pourbaix/pourbaix_api.py	16.02%	131 Missing ⚠️
src/pyEQL/pourbaix/ion.py	44.57%	66 Missing and 26 partials ⚠️
src/pyEQL/pourbaix/pourbaix_diagram.py	87.61%	43 Missing and 10 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #369       +/-   ##
===========================================
- Coverage   86.21%   68.99%   -17.22%     
===========================================
  Files          14       18        +4     
  Lines        1842     3116     +1274     
  Branches      319      552      +233     
===========================================
+ Hits         1588     2150      +562     
- Misses        209      883      +674     
- Partials       45       83       +38     

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[rkingsbury]

Hi @SuixiongTay , sorry I somehow missed your comment from 4/1. I've rebased your changes in the pourbaix branch to apply on top of main as of today. I'll do it again after #403 is merged, which may have some impact on your code.