Fix: GPR curation for pyrimidine metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #857

• Remove ENSG00000143156 from MAR04006;
• Remove ENSG00000143156 from MAR04028;
• Remove ENSG00000125458, ENSG00000205309, ENSG00000146587 from MAR04177;
• Remove ENSG00000205309, ENSG00000125458 from MAR04179;
• Remove ENSG00000141560, ENSG00000172456, ENSG00000167363, ENSG00000162408, ENSG00000116199 from MAR04182;
• Remove ENSG00000141698, ENSG00000116981, ENSG00000076685, ENSG00000146587 from MAR04484;
• Remove ENSG00000205309 from MAR04510;
• Remove ENSG00000125877 from MAR04643;
• Remove ENSG00000130717 from MAR04676;
• Remove ENSG00000092964 from MAR04346;
• Remove ENSG00000167900 from MAR06623;
• Remove ENSG00000143156 from MAR04030;
• Remove ENSG00000154269 from MAR04127;
• Remove ENSG00000125877 from MAR04211;
• Remove ENSG00000092964 from the model as they are not connected to any reactions after this curation.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• [] Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
 - Found 1514 dead-end metabolites.
 - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1977 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 447 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.

[feiranl]

LGTM!