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Use unique string IDs #142

Merged
merged 96 commits into from
Jul 3, 2023
Merged

Use unique string IDs #142

merged 96 commits into from
Jul 3, 2023

Commits on Apr 5, 2023

  1. change BGC attributes type from list to tuple 

    The following BGC attributes are updated:
- product_prediction
- mibig_bgc_class
- smiles
    @CunliangGeng
    CunliangGeng committed Apr 5, 2023
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  2. use positional-only parameter in BGC and GCF 

    Parameters before "/" are positional-only parameters, see https://docs.python.org/3/glossary.html#term-parameter.
    @CunliangGeng
    CunliangGeng committed Apr 5, 2023
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  3. update BGC's __eq__ and __hash__

    @CunliangGeng
    CunliangGeng committed Apr 5, 2023
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Commits on Apr 11, 2023

  1. update GCF's __eq__ and __hash__

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  2. Update gcf.py

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  3. update Spectrum's __eq__ and __hash__

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  4. update MolecularFamily __eq__ and __hash__

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  5. Update molecular_family.py

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  6. update Strain __eq__ and __hash__

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  7. update StrainCollection __eq__

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  8. add TODO comments to ObjectLink

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  9. add parameter type check for add_alias

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  10. add __contains__ to Strain class

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  11. update lookup method of StrainCollection

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  12. update __contains__ in StrainCollection

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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  13. remove from __eq__

    @CunliangGeng
    CunliangGeng committed Apr 11, 2023
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Commits on Apr 13, 2023

  1. update __eq__ logic for Strain

    @CunliangGeng
    CunliangGeng committed Apr 13, 2023
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  2. rename _strain_dict_id to _strain_dict_name in StrainCollection

    @CunliangGeng
    CunliangGeng committed Apr 13, 2023
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  3. add comments to get_common_strains

    @CunliangGeng
    CunliangGeng committed Apr 13, 2023
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  4. add comments and rename variables for DataLinks

    @CunliangGeng
    CunliangGeng committed Apr 13, 2023
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Commits on Apr 14, 2023

  1. add comment about met_only parameter

    @CunliangGeng
    CunliangGeng committed Apr 14, 2023
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Commits on Apr 18, 2023

  1. add todo comments to LinkFinder

    @CunliangGeng
    CunliangGeng committed Apr 18, 2023
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  2. add comments to GNPSSpectrumLoader 

    to figure out how `spectrum_id` is set
    @CunliangGeng
    CunliangGeng committed Apr 18, 2023
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Commits on Apr 28, 2023

  1. change Spectrum.spectrum_id from type int to str

    @CunliangGeng
    CunliangGeng committed Apr 28, 2023
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  2. update spec_dict

    @CunliangGeng
    CunliangGeng committed Apr 28, 2023
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  3. Update tests

    @CunliangGeng
    CunliangGeng committed Apr 28, 2023
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  4. update __eq__ in MolecularFamily

    @CunliangGeng
    CunliangGeng committed Apr 28, 2023
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  5. change MolecularFamily.family_id from type int to str

    @CunliangGeng
    CunliangGeng committed Apr 28, 2023
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Commits on May 1, 2023

  1. add method has_strain to MolecularFamily

    @CunliangGeng
    CunliangGeng committed May 1, 2023
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  2. Update metcalf_scoring.py

    @CunliangGeng
    CunliangGeng committed May 1, 2023
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Commits on May 2, 2023

  1. change array to dataframe in DataLinks 

    1. Change array to dataframe:
- self.M_gcf_strain -> self.gcf_strain_occurrence
- self. M_spec_strain -> self.spec_strain_occurrence
- self. M_fam_strain -> mf_strain_occurrence
2. update relevant methods to get the new dataframes
3. update logics of method `common_strains` using the new dataframes
    @CunliangGeng
    CunliangGeng committed May 2, 2023
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  2. update references of the new dataframes from DataLinks

    @CunliangGeng
    CunliangGeng committed May 2, 2023
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  3. update logics of get_links in NPLinker class

    @CunliangGeng
    CunliangGeng committed May 2, 2023
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Commits on May 3, 2023

  1. Update test_nplinker.py 

    - add code to remove cached results
    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  2. move SCORING_METHODS to LinkFinder

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  3. update method name to get_common_strains

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  4. refactor mapping dataframes in DataLinks

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  5. add TODOs and deprecation to LinkFinder

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  6. refactor cooccurrence in DataLinks

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  7. merge load_data and find_correlations to init in DataLinks

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  8. refactor DataLinks attributes 

    - Move assignment of attributes to `__init__`
- Rename attributes
- Replace `fam` or `molfam` with `mf` to refer to molecular family
- Add docstrings
    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  9. Delete test_data_links.py

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  10. update get_common_strains methods 

    - update parameters to be more clear and specific
- change strain id in returned dict to strain objects
-  update docstrings
    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  11. remove lookup_index method from StrainCollection (#90) 

    - remove method `lookup_index`
- remove attribute `_strain_dict_index`
    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  12. Remove integer id from GCF

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  13. update lookup methods and attributes in NPLikner class

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  14. change cooccurrence from array to DataFrame in DataLinks

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  15. format link_finder.py

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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  16. temp replace array with dataframe in LinkFinder for metcalf scoring

    @CunliangGeng
    CunliangGeng committed May 3, 2023
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Commits on May 8, 2023

  1. refactor LinkFinder.get_scores method

    @CunliangGeng
    CunliangGeng committed May 8, 2023
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  2. refactor LinkFinder.metcalf_scoring method 

    - rename parameter name
- wrap parameters for weights to one parameter
- extract private method `_cal_mean_std`
    @CunliangGeng
    CunliangGeng committed May 8, 2023
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  3. refactor get_links

    @CunliangGeng
    CunliangGeng committed May 8, 2023
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Commits on May 9, 2023

  1. remove unused methods and scorings from LinkFinder 

    -  remove unused `likescore` and `hg` scoring types
- remove all unused methods
    @CunliangGeng
    CunliangGeng committed May 9, 2023
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  2. refactor returned type of LinkFinder.get_links method

    @CunliangGeng
    CunliangGeng committed May 9, 2023
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  3. add lookup_mf method in NPLinker class

    @CunliangGeng
    CunliangGeng committed May 9, 2023
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Commits on May 11, 2023

  1. refactor MetcalfScoring class

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  2. add deprecation to LinkLikelihood class

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  3. add __init__.py to linking module

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  4. rename data_linking.py to data_links.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  5. rename data_linking_functions.py to utils.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  6. rename test_data_linking_functions.py to test_linking_utils.py.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  7. Delete test_scoring.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  8. add dtype to DataLinks dataframes

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  9. remove mapping dataframes and relevant method from DataLinks 

    Removed:
- self.mapping_spec
- self.mapping_gcf
- self.mapping_fam
-self.mapping_strain
- _get_mappings_from_occurrence() method
    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  10. Create test_data_links.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  11. add conftest.py for scoring tests

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  12. update LinkFinder's attribute and private method 

    - refactor method `_cal_mean_std`
- rename attribute `raw_score_fam_gcf` to `raw_score_mf_gcf`
    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  13. Create test_link_finder.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  14. Update vscode plugin autodocstring template 

    - fix indentation bug in autodocsting
- remove `Examples:` section
    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  15. add scope for fixtures

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  16. Create test_metcalf_scoring.py

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  17. add docstrings and type hints to MetcalfScoring class

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  18. add util func isinstance_all

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  19. replace _isinstance with util func isinstance_all

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  20. update validation of args for DataLinks

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  21. Update test_data_links.py 

    - add docstrings
- add more tests
    @CunliangGeng
    CunliangGeng committed May 11, 2023
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  22. add type hints for returned values to unit tests

    @CunliangGeng
    CunliangGeng committed May 11, 2023
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Commits on May 12, 2023

  1. update exception types for invalid input

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  2. add docstrings and type hints to LinkFinder class

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  3. add more unit tests for LinkFinder

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  4. fix input type bug for DataLinks.get_common_strains

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  5. Create test_nplinker_scoring.py

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  6. add todo comments to NPLinker class

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  7. remove local integration tests for scoring part of NPLinker 

    - rename `test_nplinker.py` to `test_nplinker_local.py`
    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  8. remove unused imports

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  9. Merge branch 'dev' into use_unique_string_id

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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  10. Fix mypy warnings as much as possible

    @CunliangGeng
    CunliangGeng committed May 12, 2023
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Commits on May 15, 2023

  1. check strain existence using strain dict

    @CunliangGeng
    CunliangGeng committed May 15, 2023
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Commits on Jun 21, 2023

  1. change calculate abbrevation from "cal" to "calc"

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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  2. remove resolved TODO comment

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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  3. move shared fixtures to conftest.py

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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  4. remove unnecessary type hints

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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  5. update docstrings for cooccurrences

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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  6. use uuid for singleton molecular families #144

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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  7. add TODO comment for GNPSLoader

    @CunliangGeng
    CunliangGeng committed Jun 21, 2023
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Commits on Jul 3, 2023

  1. update type hints for *args parameter

    @CunliangGeng
    CunliangGeng committed Jul 3, 2023
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