return list for `get_bgcs` methods of BGC loaders #182

CunliangGeng · 2023-11-20T09:14:07Z

This PR changed the returned value of get_bgcs methods in BGC loaders from dict to list, making sure that methods get_bgcs and get_gcfs have consistent returned type.

CunliangGeng · 2023-11-20T09:14:17Z

Current dependencies on/for this PR:

dev
- PR refactor filtering of user specified strains #178
  - PR Enable GCF loader to filter singleton GCFs #181
    - PR return list for get_bgcs methods of BGC loaders #182 👈
      - PR rename strains.py to strain.py #183
        
        PR remove deprecated functions of loading genomics data #184
        
        PR update the process of loading genomics data #185
        
        PR rename genomics.py to utils.py #186
        
        PR remove deprecated functions of loading metabolomics data #187
        
        PR refactor class MolecularFamily #188
        PR refactor class GCF #189
        PR enable parallel testing using pytest-xdist #190
        PR Enable filtering of singleton molecular families #191
        PR Remove class SingletonFamily and MF attribute id #192
        PR refactor Spectrum class #193
        PR remove unused mgf.py and its test file #194
        PR Update logics of loading metabolomics data #196
        PR Update loading of genomics data #197
        PR deprecate the method _load_class_info #198
        PR remove loading of optional data #199
        PR remove filtering of common strains during loading #200
        PR update logics of loading mibig data #201
        PR refactor initiation of paths to metabolomics files #202
        
        PR Update logics of loading metabolomics data #195

This stack of pull requests is managed by Graphite.

- change returned value from dict to list for `MibigLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

- change returned value from dict to list for `AntismashBGCLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

CunliangGeng · 2023-12-14T10:45:32Z

Merge activity

Dec 14, 5:45 AM: @@CunliangGeng started a stack merge that includes this pull request via Graphite.
Dec 14, 5:45 AM: @@CunliangGeng merged this pull request with Graphite.

CunliangGeng mentioned this pull request Nov 20, 2023

Enable GCF loader to filter singleton GCFs #181

Merged

CunliangGeng mentioned this pull request Nov 20, 2023

refactor filtering of user specified strains #178

Merged

CunliangGeng requested a review from gcroci2 November 20, 2023 09:14

This was referenced Nov 27, 2023

Enable filtering of singleton molecular families #191

Merged

Remove class SingletonFamily and MF attribute id #192

Merged

refactor Spectrum class #193

Merged

remove unused mgf.py and its test file #194

Merged

CunliangGeng mentioned this pull request Dec 5, 2023

Update logics of loading metabolomics data #195

Closed

gcroci2 approved these changes Dec 11, 2023

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CunliangGeng force-pushed the 11-15-filter_singleton_gcf branch from 5139465 to b60b24c Compare December 11, 2023 13:03

CunliangGeng force-pushed the 11-17-update_get_bgcs branch from 17f8ac3 to 1b73e3a Compare December 11, 2023 13:03

This was referenced Dec 11, 2023

Update logics of loading metabolomics data #196

Merged

Update loading of genomics data #197

Merged

deprecate the method _load_class_info #198

Merged

remove loading of optional data #199

Merged

remove filtering of common strains during loading #200

Merged

CunliangGeng force-pushed the 11-15-filter_singleton_gcf branch from b60b24c to 1324ba4 Compare December 14, 2023 10:39

CunliangGeng force-pushed the 11-17-update_get_bgcs branch from 1b73e3a to 10e94bb Compare December 14, 2023 10:39

Base automatically changed from 11-15-filter_singleton_gcf to dev December 14, 2023 10:42

update base class BGCLoaderBase

9427632

CunliangGeng added 2 commits December 14, 2023 11:42

change the returned type of MibigLoader.get_bgcs

18a3e0c

- change returned value from dict to list for `MibigLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

change the returned type of AntismashBGCLoader.get_bgcs

5865b57

- change returned value from dict to list for `AntismashBGCLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

CunliangGeng force-pushed the 11-17-update_get_bgcs branch from 10e94bb to 5865b57 Compare December 14, 2023 10:43

CunliangGeng merged commit e6b758a into dev Dec 14, 2023
2 checks passed

CunliangGeng deleted the 11-17-update_get_bgcs branch December 14, 2023 10:45

This was referenced Dec 20, 2023

update logics of loading mibig data #201

Merged

refactor initiation of paths to metabolomics files #202

Merged

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return list for `get_bgcs` methods of BGC loaders #182

return list for `get_bgcs` methods of BGC loaders #182

CunliangGeng commented Nov 20, 2023

CunliangGeng commented Nov 20, 2023 •

edited

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CunliangGeng commented Dec 14, 2023 •

edited

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return list for get_bgcs methods of BGC loaders #182

return list for get_bgcs methods of BGC loaders #182

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CunliangGeng commented Nov 20, 2023

CunliangGeng commented Nov 20, 2023 • edited Loading

CunliangGeng commented Dec 14, 2023 • edited Loading

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return list for `get_bgcs` methods of BGC loaders #182

return list for `get_bgcs` methods of BGC loaders #182

CunliangGeng commented Nov 20, 2023 •

edited

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CunliangGeng commented Dec 14, 2023 •

edited

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