v2.0.0-alpha.1

Full Changelog

Fixed bugs:

• Fix failing tests #96

Closed issues:

• Fix dev setup issues #222
• Running NPLinker tutorial #213
• Exception: Failed to find *ANY* strains, missing strain_mappings.csv? #170
• Add schema validation #165
• Refactor initialisation of project root and data folders [Track issue] #163
• http 404 error from test_nplinker_local.py #156
• implement the function to generate strain mappings file #154
• implement the function to generate refseq id ↔ BGC id mapping file #153
• change csv to json for strain mappings file #152
• change csv to json for genome status file #151
• generate strain mappings file for PODP data #150
• how is strain_mappings.csv generated? #148
• Strain generation, loading and mapping #147
• Refactor DatasetLoader class #145
• Use UUID for singleton molecular family? #144
• KeyError: 'cluster' Extract MIBIG data #140
• Use the refactored antismash downloader in PODPDownloader class #137
• remove _strain_dict_index from StrainCollection class #134
• Rename Downloader class to PODPDownloader #133
• Exception: Failed to find *ANY* strains, missing strain_mappings.csv? #130
• error when loading local data #129
• nplinker library download #128
• Hardware Requirements: #124
• replace load_gcfs function #122
• Refactor Downloader class to have a specific PoDP downloader #121
• PODP mode and local data mode #117
• Create StrainMappingLoader #116
• Refactor GCF loading process #114
• Change strains in StrainCollection to be a set instead of list #113
• Implement comparison operator for StrainCollection class #110
• Include strains again in objects loaded from Metabolomics #109
• check if this function is still needed or forward to the proper implementation #108
• Implement GNPS loading functionality on DatasetLoader layer #107
• Rename MibigBGC to BGC in MibigBGCLoader #106
• Remove strain assignment from BGC loaders? #104
• Use unique and fixed GCF identifier in scoring #103
• Move test files to subfolders #99
• Create antismash_downloader module #98
• Fix instructions for zsh shell #95
• MiBIG v3.x support #94
• Implement removing the strain also from self._lookup indices. [Bug] #90
• Improve GNPS format detection #89
• PoDP RefSeq accession is used as antiSMASH accession #76
• Documentation on readthedocs.io #74

Merged pull requests:

• move dependencies to pyproject.toml file #233 (CunliangGeng)
• Add user tutorials #231 (CunliangGeng)
• update dev env settings for vscode #230 (CunliangGeng)
• update readme files #228 (CunliangGeng)
• enable github actions for PRs on all branches #227 (CunliangGeng)
• update dependencies #226 (CunliangGeng)
• remove unused mkdocs settings #225 (CunliangGeng)
• Fix github actions for large file storage #224 (CunliangGeng)
• Fix dev setup #223 (adraismawur)
• Add API documentation #221 (CunliangGeng)
• Restructure codebase #220 (CunliangGeng)
• setup docs with Mkdocs #218 (CunliangGeng)
• fix docstrings #217 (CunliangGeng)
• add class DatasetArranger #215 (CunliangGeng)
• use git large file for large zip files #214 (CunliangGeng)
• Update strain mappings generator #212 (CunliangGeng)
• Update global variables #211 (CunliangGeng)
• Update mibig downloader #210 (CunliangGeng)
• Update config template and validations #209 (CunliangGeng)
• Update utils #208 (CunliangGeng)
• Redesign the template of nplinker config file #206 (CunliangGeng)
• Refactor config loader #203 (CunliangGeng)
• refactor initiation of paths to metabolomics files #202 (CunliangGeng)
• update logics of loading mibig data #201 (CunliangGeng)
• remove filtering of common strains during loading #200 (CunliangGeng)
• remove loading of optional data #199 (CunliangGeng)
• deprecate the method _load_class_info #198 (CunliangGeng)
• Update loading of genomics data #197 (CunliangGeng)
• Update logics of loading metabolomics data #196 (CunliangGeng)
• remove unused mgf.py and its test file #194 (CunliangGeng)
• refactor Spectrum class #193 (CunliangGeng)
• Remove class SingletonFamily and MF attribute id #192 (CunliangGeng)
• Enable filtering of singleton molecular families #191 (CunliangGeng)
• enable parallel testing using pytest-xdist #190 (CunliangGeng)
• refactor class GCF #189 (CunliangGeng)
• refactor class MolecularFamily #188 (CunliangGeng)
• remove deprecated functions of loading metabolomics data #187 (CunliangGeng)
• rename genomics.py to utils.py #186 (CunliangGeng)
• update the process of loading genomics data #185 (CunliangGeng)
• remove deprecated functions of loading genomics data #184 (CunliangGeng)
• rename strains.py to strain.py #183 (CunliangGeng)
• return list for get_bgcs methods of BGC loaders #182 (CunliangGeng)
• Enable GCF loader to filter singleton GCFs #181 (CunliangGeng)
• refactor filtering of user specified strains #178 (CunliangGeng)
• Update ruff rules to ignore unused imports in __init__.py files #177 (CunliangGeng)
• change linter and formatter to ruff #176 (CunliangGeng)
• Add or update __init__.py #174 (CunliangGeng)
• Add magic method __add__ #173 (CunliangGeng)
• Fix download bugs #172 (CunliangGeng)
• allow GCF loader to filter mibig-only GCF objects #171 (CunliangGeng)
• Refactor gnps classes #169 (CunliangGeng)
• Refactor loading genomics #168 (CunliangGeng)
• Add schema validation for json data #167 (CunliangGeng)
• Create functions to extract/get/generate strain mappings #166 (CunliangGeng)
• preparations for issue 154 #164 (CunliangGeng)
• change class method to static method #161 (CunliangGeng)
• Handle 404 NOT FOUND error for download_and_extract_antismash_data #160 (gcroci2)
• Handle unavailable GNPS service #159 (CunliangGeng)
• Issue152 replace csv with json for strain mappings file #158 (CunliangGeng)
• Issue151 use json for genome status file #157 (CunliangGeng)
• 153 bgc mappings generation #155 (CunliangGeng)
• clean up loader and downloader #149 (CunliangGeng)
• refactor: move non-download functionalities out of PODPDownloader - _run_bigscape #143 (gcroci2)
• Use unique string IDs #142 (CunliangGeng)
• fix indentation bug in autodocsting #141 (CunliangGeng)
• Refactor __eq__ and __hash__ methods #139 (CunliangGeng)
• refactor: use refactored antismash downloader module in PODPDownloader class #138 (gcroci2)
• Refactor StrainCollection class #135 (CunliangGeng)
• Rename Downloader class to POPDownloader #132 (gcroci2)
• Refactor Strain class #131 (CunliangGeng)
• refactor: create antismash downloader module and move there inherent code #127 (gcroci2)
• Add bgc-genome mapping to BGC loaders #126 (CunliangGeng)
• Change GCF.strains back to attribute #125 (CunliangGeng)
• add comments for loading process of strain mapping #123 (CunliangGeng)
• refactor GCF loading process #120 (CunliangGeng)
• Improved test coverage for loader #118 (hechth)
• rename MibigBGC to BGC in docstrings #112 (CunliangGeng)
• Implement comparison operator for StrainCollection class #111 (hechth)
• Fix local test error #105 (CunliangGeng)
• Refactor GCF class #102 (CunliangGeng)
• Refactor BGC data model #101 (CunliangGeng)
• Move test files to subfolders and update pytest's conftest.py #100 (CunliangGeng)
• docs: add quotes in package installation for zsh shell #97 (gcroci2)
• Refactored GNPS downloading and file extraction code #93 (hechth)
• Refactor BGC data loader #92 (CunliangGeng)
• Initial refactoring of Metabolomics data loading #91 (hechth)
• static typing #88 (CunliangGeng)
• Refactor mibig related code #87 (CunliangGeng)
• Add download extract utils #85 (CunliangGeng)
• Refactor AA prediction #84 (CunliangGeng)
• Check metcalf and IOKR scoring #83 (CunliangGeng)
• add dev branch to github actions #82 (CunliangGeng)
• add DATA_DIR for sharing test data dir #81 (CunliangGeng)
• Initial refactoring on scoring methods #80 (hechth)
• Implemented some tests for the metabolomics side #79 (hechth)
• Refactored genomics.py and metabolomics.py by moving classes into individual files #78 (hechth)
• Refine github actions #77 (CunliangGeng)