Integration of the mp-api client to pyEQL

[SuixiongTay]

Description

This pull request integrates the mp-api client to the pourbaix branch of pyEQL.

1. Ion Reference Data from MPRester

• Downloaded the complete set of ion reference data using the get_ion_reference_data from mp-api.
• Data stored in json file within mpr_reference_ion_database.json.

2. Integration

• Copied the below methods from the mp-api repository into pourbaix_api.py:
  • get_ion_reference_data_for_chemsys
  • get_ion_entries
  • get_pourbaix_entries

3. Test Integration

• Copied test_get_pourbaix_entries and test_get_ion_entries from test_mprester.py.
• New test file is renamed to test_pourbaix_api.py.

4. test_pourbaix_api.py Edits

• Changed assert len(bi_v_entry_data) == len(bi_data) + v_data to assert len(bi_v_entry_data) == len(bi_data) + len(v_data).
• Changed ref_solid_entry = [e for e in ion_ref_entries if e.entry_id == "mp-4770"][0] to ref_solid_entry = [e for e in ion_ref_entries if e.entry_id == "mp-4770-GGA"][0].

Example Usage

mpr = MPRester(MP_API_KEY)
pourbaix_api = Pourbaix_api(mpr) #create instance before using

bi_v_entry_data = pourbaix_api.get_ion_reference_data_for_chemsys("Bi-V")
...

[SuixiongTay]

Tagging @rkingsbury.

Is this error related to how test_pourbaix_diagram.py handles the json file?

[codecov]

Codecov Report

Attention: Patch coverage is 18.27957% with 76 lines in your changes missing coverage. Please review.

Please upload report for BASE (pourbaix@397b820). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
src/pyEQL/pourbaix/pourbaix_api.py	18.27%	76 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             pourbaix     #227   +/-   ##
===========================================
  Coverage            ?   71.71%           
===========================================
  Files               ?       13           
  Lines               ?     2680           
  Branches            ?      478           
===========================================
  Hits                ?     1922           
  Misses              ?      676           
  Partials            ?       82           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[rkingsbury]

Thank you @SuixiongTay ! Just a few small edits and this will be ready to merge. Notably, please make sure you install and run pre-commit to apply linting and formatting to all the new code.

pre-commit install
pre-commit run --all-files

[rkingsbury]

The test look good. We have an issue where tests occasionally fail (as happened here for 1-2 cases) due to some kind of disk or caching problem on the test runners; it means I just have to rerun the tests manually and they usually pass. So you're all good there.

[SuixiongTay]

Thanks for the detailed comments @rkingsbury ! The current revision includes:

• Ran pre-commit on the new code.
• Added mp-api to pyproject.toml.

[rkingsbury]

Thanks @SuixiongTay !