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 #95
• Ghpages by @erikhuck in #96
• Updates the creation of the docs folder to match _build/html/ exactly by @erikhuck in #97
• Updates the creation of the docs folder to match _build/html/ exactly by @erikhuck in #98
• Tries putting all the html documentation files in the root of the repo by @erikhuck in #99
• Improves documentation by @erikhuck in #100
• Adds the license to the repo and documentation by @erikhuck in #101
• Sets up repo for publishing to pypi by @erikhuck in #102
• Sets up repo for publishing to pypi by @erikhuck in #103
• Fix by @erikhuck in #104
• Adds tests for getting the version on the commandline by @erikhuck in #105
• Makes consistent the name of the package everywhere in the documentation by @erikhuck in #106
• Blacklist by @erikhuck in #107
• Updates version of next release by @erikhuck in #108
• Corrects setting sleep_time in KEGGrest by @erikhuck in #109
• Merge pull request #109 from MoseleyBioinformaticsLab/sleep by @erikhuck in #110
• Raises exception if an empty list is provided to split_comma_separated_list() by @erikhuck in #111
• Outputs the pull results as a json file instead of txt and adds more info by @erikhuck in #112
• Adds pull-minutes field to the pull-results.json by @erikhuck in #113
• Updates the version by @erikhuck in #114
• Replaces success-rate with percent-success in pull-results.json by @erikhuck in #115
• Merge pull request #115 from MoseleyBioinformaticsLab/percent-success by @erikhuck in #116
• Allows developer to not specify n_workers and get the default os.cpu_count() by @erikhuck in #121
• Adds progress bar and terminates program after excessive failures by @erikhuck in #122
• Merge by @erikhuck in #123
• Main2 by @erikhuck in #124
• Adds --test flag rest subcommand in CLI by @erikhuck in #125
• Sets SinglePull as the global variable for the process pool rather than the Lock object and uses a different method for locked saving rather than checking if _ZipEntrySaver has a multiprocessing_lock member by @erikhuck in #127
• Enables saving output from the entry-ids subcommand or rest subcommand to a zip archive by @erikhuck in #128
• Update README.rst by @erikhuck in #131
• Adds the link-to-dict API methods by @erikhuck in #132
• Corrects documentation by @erikhuck in #133
• Docs by @erikhuck in #134
• Updates integration test data by @erikhuck in #138
• Makes top-level CLI output more consistent with documentation and simplifies main.py by @erikhuck in #139
• Removes code duplication for file saving and makes the CLI output for entry-ids and rest a single string both for directories and ZIP archives by @erikhuck in #142
• Removes code duplication in SinglePull which is covered in _utils.py and removes the messy and unwarranted "set_multiprocessing_lock" method by @erikhuck in #144
• Removes from-file sub-sub-command from entry-ids sub-command and makes the functions entry_ids.py free instead of attatched to a class by @erikhuck in #145
• Pull by @erikhuck in #146
• Corrects documentation by @erikhuck in #149
• Corrects documentation by @erikhuck in #150
• Erikhuck patch 2 by @erikhuck in #151
• Adds link to GitHub issues page to README by @erikhuck in #153
• Brings the link_to_dict methods to the module level and fixes the CLI by @erikhuck in #152
• Makes the pathway-organizer input/output compatible with previous changes by @erikhuck in #155
• Adds the option to add drug entry IDs to the compound mappings by @erikhuck in #156
• Completes tests for link_to_dict API and corrects JSON schemas by @erikhuck in #157
• Reduces code duplication accross test_entry_ids_cli, test_rest_cli, and test_link_to_dict_cli and begins writing tests for test_link_to_dict_cli by @erikhuck in #158
• Adds pathway organizer and link-to-dict to the documentation and nearly completes the API testing for pathway_organizer.py by @erikhuck in #163
• Completes code coverage of the API and CLI by @erikhuck in #164
• Removes properties innapropriate to the lab's preferred coding philosophy and replaces them with public variables by @erikhuck in #166
• Uses python highlighting for python code in tutorial and none for terminal commands; Adds pathway-organizer and link-to-dict sections to the API and CLI portions of the tutorial by @erikhuck in #167
• Makes the PathwayOrganizer, KEGGresponse, and PullResult classes non-instantiable outside of their modules by @erikhuck in #168
• Adds jsonschema depencency to README, docs requirements, repo requirements, and setup.py by @erikhuck in #169
• No longer strips the entry text bodies when pulling multiple at a time such that the kegg entries are saved as provided from the rest API by @erikhuck in #170
• Corrects a bug resulting in inconsistent link-to-dict dictionaries; Writes a test which tests that the bug is fixed by @erikhuck in #171
• Makes the git repository, tests, and source code compatible with Windows by @erikhuck in #175
• Update README.rst by @erikhuck in #176
• Adds warning about colons when running on windows in documentation by @erikhuck in #177
• Merge main by @erikhuck in #179
• Merge branch 'main' into dev by @erikhuck in #180
• Adds more examples to the CLI by @erikhuck in #182
• Merge by @erikhuck in #183
• Adds citation file to repo by @erikhuck in #188
• Makes the map CLI and API more flexible/powerful by @erikhuck in #194
• Improves naming by @erikhuck in #196
• Adds functionality for conv mappings in addition to link by @erikhuck in #197
• Checks for identical database names in DatabaseLinkKEGGurl by @erikhuck in #198
• Improves white space usage by @erikhuck in #200
• Improves typing by @erikhuck in #201
• Handles empty response bodies in the map module by @erikhuck in #202
• Improves the interface of the MultiplePull constructors by @erikhuck in #203
• Enables pulling a dictionary of entries in memory as compared to saving to disk by @erikhuck in #204
• corrects the documentation and fixes bugs by @erikhuck in #206
• Dev2 by @erikhuck in #207
• Pathorg by @erikhuck in #211
• Ensures that the up-to-date version of python3 is ran when building the documentation by @erikhuck in #214
• Ensures that the up-to-date version of python3 is ran when building the documentation by @erikhuck in #215
• Ensures that the up-to-date version of python3 is ran when building the documentation by @erikhuck in #216
• Merge pull request #216 from MoseleyBioinformaticsLab/docs by @erikhuck in #217
• Dev by @erikhuck in #218
• Conv by @erikhuck in #222
• Incorporates pyproject.toml by @erikhuck in #223
• adds verbose flag to publish pypi action by @erikhuck in #224
• Merge pull request #224 from MoseleyBioinformaticsLab/verbose by @erikhuck in #225
• fixes test by @erikhuck in #226

Full Changelog: https://github.com/MoseleyBioinformaticsLab/kegg_pull/commits/v3.2.2