Implement removing the strain also from self._lookup indices. [Bug] #90
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CunliangGeng
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May 12, 2023
- remove method `lookup_index` - remove attribute `_strain_dict_index`
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CunliangGeng
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Jul 3, 2023
* change BGC attributes type from list to tuple The following BGC attributes are updated: - product_prediction - mibig_bgc_class - smiles * use positional-only parameter in BGC and GCF Parameters before "/" are positional-only parameters, see https://docs.python.org/3/glossary.html#term-parameter. * update BGC's `__eq__` and `__hash__` * update GCF's `__eq__` and `__hash__` * Update gcf.py * update Spectrum's `__eq__` and `__hash__` * update MolecularFamily `__eq__` and `__hash__` * Update molecular_family.py * update Strain `__eq__` and `__hash__` * update StrainCollection `__eq__` * add TODO comments to ObjectLink * add parameter type check for `add_alias` * add `__contains__` to Strain class * update `lookup` method of StrainCollection * update `__contains__` in StrainCollection * remove from __eq__ * update `__eq__` logic for Strain * rename `_strain_dict_id` to `_strain_dict_name` in StrainCollection * add comments to `get_common_strains` * add comments and rename variables for DataLinks * add comment about `met_only` parameter * add todo comments to LinkFinder * add comments to GNPSSpectrumLoader to figure out how `spectrum_id` is set * change Spectrum.spectrum_id from type int to str * update spec_dict * Update tests * update `__eq__` in MolecularFamily * change `MolecularFamily.family_id` from type int to str * add method `has_strain` to MolecularFamily * Update metcalf_scoring.py * 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 * update references of the new dataframes from DataLinks * update logics of `get_links` in NPLinker class * Update test_nplinker.py - add code to remove cached results * move SCORING_METHODS to LinkFinder * update method name to `get_common_strains` * refactor mapping dataframes in DataLinks * add TODOs and deprecation to LinkFinder * refactor cooccurrence in DataLinks * merge `load_data` and `find_correlations` to init in DataLinks * refactor DataLinks attributes - Move assignment of attributes to `__init__` - Rename attributes - Replace `fam` or `molfam` with `mf` to refer to molecular family - Add docstrings * Delete test_data_links.py * update get_common_strains methods - update parameters to be more clear and specific - change strain id in returned dict to strain objects - update docstrings * remove lookup_index method from StrainCollection (#90) - remove method `lookup_index` - remove attribute `_strain_dict_index` * Remove integer id from GCF * update lookup methods and attributes in NPLikner class * change cooccurrence from array to DataFrame in DataLinks * format link_finder.py * temp replace array with dataframe in LinkFinder for metcalf scoring * refactor `LinkFinder.get_scores` method * refactor `LinkFinder.metcalf_scoring` method - rename parameter name - wrap parameters for weights to one parameter - extract private method `_cal_mean_std` * refactor get_links * remove unused methods and scorings from LinkFinder - remove unused `likescore` and `hg` scoring types - remove all unused methods * refactor returned type of `LinkFinder.get_links` method * add `lookup_mf` method in NPLinker class * refactor MetcalfScoring class * add deprecation to LinkLikelihood class * add `__init__.py` to linking module * rename `data_linking.py` to `data_links.py` * rename `data_linking_functions.py` to `utils.py` * rename `test_data_linking_functions.py` to `test_linking_utils.py`.py * Delete test_scoring.py * add dtype to DataLinks dataframes * 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 * Create test_data_links.py * add `conftest.py` for scoring tests * update LinkFinder's attribute and private method - refactor method `_cal_mean_std` - rename attribute `raw_score_fam_gcf` to `raw_score_mf_gcf` * Create test_link_finder.py * Update vscode plugin autodocstring template - fix indentation bug in autodocsting - remove `Examples:` section * add scope for fixtures * Create test_metcalf_scoring.py * add docstrings and type hints to `MetcalfScoring` class * add util func `isinstance_all` * replace `_isinstance` with util func `isinstance_all` * update validation of args for `DataLinks` * Update test_data_links.py - add docstrings - add more tests * add type hints for returned values to unit tests * update exception types for invalid input * add docstrings and type hints to `LinkFinder` class * add more unit tests for `LinkFinder` * fix input type bug for `DataLinks.get_common_strains` * Create test_nplinker_scoring.py * add todo comments to `NPLinker` class * remove local integration tests for scoring part of `NPLinker` - rename `test_nplinker.py` to `test_nplinker_local.py` * remove unused imports * Fix mypy warnings as much as possible * check strain existence using strain dict * change calculate abbrevation from "cal" to "calc" * remove resolved TODO comment * move shared fixtures to conftest.py * remove unnecessary type hints * update docstrings for cooccurrences * use uuid for singleton molecular families #144 * add TODO comment for GNPSLoader * update type hints for `*args` parameter
CunliangGeng
added a commit
that referenced
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Jul 4, 2023
* change BGC attributes type from list to tuple The following BGC attributes are updated: - product_prediction - mibig_bgc_class - smiles * use positional-only parameter in BGC and GCF Parameters before "/" are positional-only parameters, see https://docs.python.org/3/glossary.html#term-parameter. * update BGC's `__eq__` and `__hash__` * update GCF's `__eq__` and `__hash__` * Update gcf.py * update Spectrum's `__eq__` and `__hash__` * update MolecularFamily `__eq__` and `__hash__` * Update molecular_family.py * update Strain `__eq__` and `__hash__` * update StrainCollection `__eq__` * add TODO comments to ObjectLink * add parameter type check for `add_alias` * add `__contains__` to Strain class * update `lookup` method of StrainCollection * update `__contains__` in StrainCollection * remove from __eq__ * update `__eq__` logic for Strain * rename `_strain_dict_id` to `_strain_dict_name` in StrainCollection * add comments to `get_common_strains` * add comments and rename variables for DataLinks * add comment about `met_only` parameter * add todo comments to LinkFinder * add comments to GNPSSpectrumLoader to figure out how `spectrum_id` is set * change Spectrum.spectrum_id from type int to str * update spec_dict * Update tests * update `__eq__` in MolecularFamily * change `MolecularFamily.family_id` from type int to str * add method `has_strain` to MolecularFamily * Update metcalf_scoring.py * 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 * update references of the new dataframes from DataLinks * update logics of `get_links` in NPLinker class * Update test_nplinker.py - add code to remove cached results * move SCORING_METHODS to LinkFinder * update method name to `get_common_strains` * refactor mapping dataframes in DataLinks * add TODOs and deprecation to LinkFinder * refactor cooccurrence in DataLinks * merge `load_data` and `find_correlations` to init in DataLinks * refactor DataLinks attributes - Move assignment of attributes to `__init__` - Rename attributes - Replace `fam` or `molfam` with `mf` to refer to molecular family - Add docstrings * Delete test_data_links.py * update get_common_strains methods - update parameters to be more clear and specific - change strain id in returned dict to strain objects - update docstrings * remove lookup_index method from StrainCollection (#90) - remove method `lookup_index` - remove attribute `_strain_dict_index` * Remove integer id from GCF * update lookup methods and attributes in NPLikner class * change cooccurrence from array to DataFrame in DataLinks * format link_finder.py * temp replace array with dataframe in LinkFinder for metcalf scoring * refactor `LinkFinder.get_scores` method * refactor `LinkFinder.metcalf_scoring` method - rename parameter name - wrap parameters for weights to one parameter - extract private method `_cal_mean_std` * refactor get_links * remove unused methods and scorings from LinkFinder - remove unused `likescore` and `hg` scoring types - remove all unused methods * refactor returned type of `LinkFinder.get_links` method * add `lookup_mf` method in NPLinker class * refactor MetcalfScoring class * add deprecation to LinkLikelihood class * add `__init__.py` to linking module * rename `data_linking.py` to `data_links.py` * rename `data_linking_functions.py` to `utils.py` * rename `test_data_linking_functions.py` to `test_linking_utils.py`.py * Delete test_scoring.py * add dtype to DataLinks dataframes * 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 * Create test_data_links.py * add `conftest.py` for scoring tests * update LinkFinder's attribute and private method - refactor method `_cal_mean_std` - rename attribute `raw_score_fam_gcf` to `raw_score_mf_gcf` * Create test_link_finder.py * Update vscode plugin autodocstring template - fix indentation bug in autodocsting - remove `Examples:` section * add scope for fixtures * Create test_metcalf_scoring.py * add docstrings and type hints to `MetcalfScoring` class * add util func `isinstance_all` * replace `_isinstance` with util func `isinstance_all` * update validation of args for `DataLinks` * Update test_data_links.py - add docstrings - add more tests * add type hints for returned values to unit tests * update exception types for invalid input * add docstrings and type hints to `LinkFinder` class * add more unit tests for `LinkFinder` * fix input type bug for `DataLinks.get_common_strains` * Create test_nplinker_scoring.py * add todo comments to `NPLinker` class * remove local integration tests for scoring part of `NPLinker` - rename `test_nplinker.py` to `test_nplinker_local.py` * remove unused imports * Fix mypy warnings as much as possible * check strain existence using strain dict * change calculate abbrevation from "cal" to "calc" * remove resolved TODO comment * move shared fixtures to conftest.py * remove unnecessary type hints * update docstrings for cooccurrences * use uuid for singleton molecular families #144 * add TODO comment for GNPSLoader * fix typos * remove useless parameter `met_only` The `met_only` is useless. NPlinker will stop working if met_only=True. * update exception type * refactor the usage of PODPDownloader 1. create instance in the private method, only when it's needed 2. change the scope of the instance from global to local * rename private config attributes in class DatasetLoader - add prefix `_config` for all config attributes - add comments to restructure `__init__` code * change the variable of app data dir to be global this variable is independent of DatasetLoader and other classes, so it should be a global variable * change two public methods to variables * change one public method to attribute for DatasetLoader * add value validation to Config - move the validation of antismash format config in DatasetLoader to Config class - refactor the config data validations into a private method * add TODO comments about init and validate paths * remove unused attribute `growth_media` * remove commented code * add TODO comments * remove unused imports * format the code * reorder methods in loader.py
CunliangGeng
added a commit
that referenced
this issue
Jul 4, 2023
* change BGC attributes type from list to tuple The following BGC attributes are updated: - product_prediction - mibig_bgc_class - smiles * use positional-only parameter in BGC and GCF Parameters before "/" are positional-only parameters, see https://docs.python.org/3/glossary.html#term-parameter. * update BGC's `__eq__` and `__hash__` * update GCF's `__eq__` and `__hash__` * Update gcf.py * update Spectrum's `__eq__` and `__hash__` * update MolecularFamily `__eq__` and `__hash__` * Update molecular_family.py * update Strain `__eq__` and `__hash__` * update StrainCollection `__eq__` * add TODO comments to ObjectLink * add parameter type check for `add_alias` * add `__contains__` to Strain class * update `lookup` method of StrainCollection * update `__contains__` in StrainCollection * remove from __eq__ * update `__eq__` logic for Strain * rename `_strain_dict_id` to `_strain_dict_name` in StrainCollection * add comments to `get_common_strains` * add comments and rename variables for DataLinks * add comment about `met_only` parameter * add todo comments to LinkFinder * add comments to GNPSSpectrumLoader to figure out how `spectrum_id` is set * change Spectrum.spectrum_id from type int to str * update spec_dict * Update tests * update `__eq__` in MolecularFamily * change `MolecularFamily.family_id` from type int to str * add method `has_strain` to MolecularFamily * Update metcalf_scoring.py * 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 * update references of the new dataframes from DataLinks * update logics of `get_links` in NPLinker class * Update test_nplinker.py - add code to remove cached results * move SCORING_METHODS to LinkFinder * update method name to `get_common_strains` * refactor mapping dataframes in DataLinks * add TODOs and deprecation to LinkFinder * refactor cooccurrence in DataLinks * merge `load_data` and `find_correlations` to init in DataLinks * refactor DataLinks attributes - Move assignment of attributes to `__init__` - Rename attributes - Replace `fam` or `molfam` with `mf` to refer to molecular family - Add docstrings * Delete test_data_links.py * update get_common_strains methods - update parameters to be more clear and specific - change strain id in returned dict to strain objects - update docstrings * remove lookup_index method from StrainCollection (#90) - remove method `lookup_index` - remove attribute `_strain_dict_index` * Remove integer id from GCF * update lookup methods and attributes in NPLikner class * change cooccurrence from array to DataFrame in DataLinks * format link_finder.py * temp replace array with dataframe in LinkFinder for metcalf scoring * refactor `LinkFinder.get_scores` method * refactor `LinkFinder.metcalf_scoring` method - rename parameter name - wrap parameters for weights to one parameter - extract private method `_cal_mean_std` * refactor get_links * remove unused methods and scorings from LinkFinder - remove unused `likescore` and `hg` scoring types - remove all unused methods * refactor returned type of `LinkFinder.get_links` method * add `lookup_mf` method in NPLinker class * refactor MetcalfScoring class * add deprecation to LinkLikelihood class * add `__init__.py` to linking module * rename `data_linking.py` to `data_links.py` * rename `data_linking_functions.py` to `utils.py` * rename `test_data_linking_functions.py` to `test_linking_utils.py`.py * Delete test_scoring.py * add dtype to DataLinks dataframes * 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 * Create test_data_links.py * add `conftest.py` for scoring tests * update LinkFinder's attribute and private method - refactor method `_cal_mean_std` - rename attribute `raw_score_fam_gcf` to `raw_score_mf_gcf` * Create test_link_finder.py * Update vscode plugin autodocstring template - fix indentation bug in autodocsting - remove `Examples:` section * add scope for fixtures * Create test_metcalf_scoring.py * add docstrings and type hints to `MetcalfScoring` class * add util func `isinstance_all` * replace `_isinstance` with util func `isinstance_all` * update validation of args for `DataLinks` * Update test_data_links.py - add docstrings - add more tests * add type hints for returned values to unit tests * update exception types for invalid input * add docstrings and type hints to `LinkFinder` class * add more unit tests for `LinkFinder` * fix input type bug for `DataLinks.get_common_strains` * Create test_nplinker_scoring.py * add todo comments to `NPLinker` class * remove local integration tests for scoring part of `NPLinker` - rename `test_nplinker.py` to `test_nplinker_local.py` * remove unused imports * Fix mypy warnings as much as possible * check strain existence using strain dict * change calculate abbrevation from "cal" to "calc" * remove resolved TODO comment * move shared fixtures to conftest.py * remove unnecessary type hints * update docstrings for cooccurrences * use uuid for singleton molecular families #144 * add TODO comment for GNPSLoader * fix typos * remove useless parameter `met_only` The `met_only` is useless. NPlinker will stop working if met_only=True. * update exception type * refactor the usage of PODPDownloader 1. create instance in the private method, only when it's needed 2. change the scope of the instance from global to local * rename private config attributes in class DatasetLoader - add prefix `_config` for all config attributes - add comments to restructure `__init__` code * change the variable of app data dir to be global this variable is independent of DatasetLoader and other classes, so it should be a global variable * change two public methods to variables * change one public method to attribute for DatasetLoader * add value validation to Config - move the validation of antismash format config in DatasetLoader to Config class - refactor the config data validations into a private method * add TODO comments about init and validate paths * remove unused attribute `growth_media` * remove commented code * add TODO comments * remove unused imports * format the code * reorder methods in loader.py * add function `generate_genome_bgc_mappings_file` * Update __init__.py * add tests for `generate_genome_bgc_mappings_file` * update strain test when 113 issue is closed
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https://github.com/hechth/nplinker/blob/ae713862655d7308c1597bd6c4dfd56e3f6a88da/src/nplinker/strain_collection.py#L46
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