v3.2.2

What's Changed

• Adds the GenericKEGGurl class and associated unit tests by @erikhuck in #1
• Create main.yml by @erikhuck in #2
• Adds url splitting functionality to the generic kegg url class by @erikhuck in #3
• Adds the pull_single_from_kegg function by @erikhuck in #4
• Adds utils functions for tests; Adds warnings and tests warnings; Begins the implementation of the KEGGgetURLgenerator by @erikhuck in #5
• Separates the kegg url class into separate extended classes by @erikhuck in #7
• Kegg get url generator by @erikhuck in #8
• Adds the multi-processing code that pulls all the get URLs from kegg by @erikhuck in #16
• Removes the redundancy in the names of functions and modules involving pulling from KEGG by @erikhuck in #17
• Switches import from syntax to import as syntax by @erikhuck in #18
• Forces pulling one entry at a time when specified by the user or when the brite database is used by @erikhuck in #19
• Docs by @erikhuck in #20
• Corrects the multiprocess pulling bug that resulted in duplicate output by returning a class data member twice by @erikhuck in #23
• Adds installation setup and refactors tests to test kegg_pull as a package rather than a local directory by @erikhuck in #27
• Improves the documentation and naming in the kegg_url module by @erikhuck in #28
• Transfers functionality into a more decomposed object-oriented fashion by @erikhuck in #31
• Refactors web request to kegg request and adds test method to kegg request by @erikhuck in #32
• Moves pull related classes into one file by @erikhuck in #33
• Adds the entry-ids CLI sub command along with two more methods for getting entry IDs based on the find KEGG API operation by @erikhuck in #36
• separates the CLI into separate sub commands by @erikhuck in #37
• Implements the KEGGrestAPI class with its methods corresponding to KEGG web API operations by @erikhuck in #38
• Enables organism database lookup in the KEGG URLs by @erikhuck in #40
• Adds the conv KEGG API operation by @erikhuck in #41
• Adds the remaining KEGG rest operations by @erikhuck in #42
• Enables saving to a zip file by @erikhuck in #43
• Replaces static getter methods with static properties; Updates the KEGGrest class (renamed) to have a generic request method which uses a generic create_url function by @erikhuck in #45
• renames as f to as file by @erikhuck in #46
• corrects main prints and associated test by @erikhuck in #47
• Completes testing of the organism_set static property by @erikhuck in #49
• combines and parametrizes the test_validate and test_create_rest_options functions and completes code coverage of the _validate and _create_rest_options methods for ListKEGGurl and GetKEGGurl by @erikhuck in #50
• corrects the valid database names error message and completes coverage of the AbstractKEGGurl and InfoKEGGurl classes by @erikhuck in #51
• Completes the create_url test cases by @erikhuck in #52
• completes coverage of the KeywordsFindKEGGurl class by @erikhuck in #53
• corrects the database validations of KEGGurl classes by @erikhuck in #54
• corrects test functionality in KEGGrequest and extends this functionality to KEGGrest by @erikhuck in #55
• completes coverage of the InfoKEGGurl class by @erikhuck in #56
• Completes code coverage of the MolecularKEGGurl class by @erikhuck in #57
• Completes code coverage of the AbstractConvKEGGurl class and its extended classes by @erikhuck in #58
• completes code coverage of the AbstractLinkKEGGurl class and its extended classes by @erikhuck in #59
• Tests by @erikhuck in #60
• Combines and transfer the KEGGrequest functionality into the KEGGrest class by @erikhuck in #61
• Completes code coverage of the KEGGrest class by @erikhuck in #62
• makes consistent the naming convention of mocked objects in tests by @erikhuck in #63
• Adds tests for the --help option in the CLI subcommands by @erikhuck in #64
• completes code coverage of the rest main method by @erikhuck in #65
• Tests by @erikhuck in #67
• completes code coverage of the entry-ids main method by @erikhuck in #68
• completes code coverage of the SinglePull and PullResult classes by @erikhuck in #69
• completes code coverage of the AbstractMultiplePull class and its extended classes by @erikhuck in #70
• completes code coverage of the pull main function by @erikhuck in #71
• Completes code coverage of utils module and corrects bug in it by @erikhuck in #72
• adds more KEGG url doc strings by @erikhuck in #73
• rearannges the files to clean up the repo by @erikhuck in #74
• Sets up automatic documentation generation from doc strings by @erikhuck in #76
• Adds more type hints by @erikhuck in #77
• Docs by @erikhuck in #79
• Completes the doc strings of the SinglePull and PullResult classes by @erikhuck in #80
• Completes documentation of the pull module by @erikhuck in #81
• Completes documentation of the EntryIdsGetter class by @erikhuck in #82
• Completes documentation of the rest module by @erikhuck in #83
• Adds CLI documentation by @erikhuck in #84
• renames tests directory to dev by @erikhuck in #85
• Sets up jupyter notebook conversion to RST files for tutorial.rst by @erikhuck in #86
• Completes code coverage of the entire project by adding integration tests for the top-level CLI by @erikhuck in #87
• Completes documentation for the Guide and Tutorial page by @erikhuck in #88
• Sets up automatic documentation building via github actions by @erikhuck in #89
• removes the seemingly unnecessary addition to the sphinx makefile by @erikhuck in #90
• Ghpages by @erikhuck in #91
• installs rtd theme as part of the github action by @erikhuck in #92
• installs rtd theme as part of the github action by @erikhuck in #93
• installs rtd theme as part of the github action by @erikhuck in #94
• Merge branch 'main' into ghpages by @erikhuck in ht...