[JOSS review] Updates to the documentation #74
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kbonney
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Oct 24, 2023
* Updating contributing page and adding a few lines to gitignore * Small edit * adding files to paper folder for JOSS * Adding joss workflow * Making adjustments to get joss workflow to run * Minor updates to bib formatting and spacing in paper * Attempt at fixing table newlines * Another attempt * Attempt 3 * Now we are on track * Trying html unordered lists * testing a new table format * try again * attempting a picture approach * Adding JOSS status * Updating python setup action in testing workflow * Keyword search in text from reference dictionary (#46) * init file and pull sample data * add helper functions and reference dict * clean up text, tokenize, add new labels from regex function * move example into its own file, seperate out functions to use * clean functions and make generic names * clean up example * move reference dict to example_data * remove pdb * move dict out of functions file * missed import * add metrics to measure accuracy * rename other category to unknown for fair comparison * move keyword search to preprocess step, util * move add label fucntion to classify * fix imports, add comment for viz * remove temp file * change arg to dict * add keyword util * update formating * whitespace * update args to match * remove whitespace * function rename * clean up dict * add sample data * update docstring and change col dict name * clean up and use sample data in examples * add plot function * add in visualization function for confusion matrix * add more detail to dox string * clean up function to expect predicted_col * clean up example * remove whitespace * change col name from new to predicted * clean up sample data * add notebook example * add functionality to replace text in preprocessing * add text replacement step * linter * remove example .py file in favor of jupyter notebook * remove reference dict * add new csv mapping rfiles * add csv * update jupyternotebook example * use df instead of dict * remove dict * remove unused imports and functions * update jupyter notebook and remove module * remove plot * update docstrings * linter * remove whitespace * updating testing and linting workflow * Fixing minor flake8 issues from latest flake8 version * Adding links to example code in user guides and pulling some incomplete doc pages * Adding module overview to index * updating paper to show failed formatting on table * updating the gitignore with standard python ignores (#79) * [JOSS review] Updates to the documentation (#74) * Update index.rst * Remove boilerplate info (not useful) * Update .gitignore * Add Python 3.11 to test environment (#57) * Addressing various JOSS review comments * removing unneccesary min requirements file * Updating RTD docs requirements pins and updated python version used in RTD * adding additional docs requirements to setup.py variable * adding python version in req.txt note * removing docs req txt file * adding doc pins to setup py * updaing rtd yaml to use new doc reqirements location * adding pins to req.txt * adding version, copyright, and license to __init__.py * fix citation file * add version to setup.py * remove unnecessary init file * update version to 0.2.0 * removing vestigial files * remove notice folder * troubleshooting GH tests * fixing setup.py bug * replacing package name * adding missing commas * correcting "doc" extra requirement for RTD * updating author, copyright, and version in conf.py and setup.py * pacakge->module * Renaming examples to tutorials * changing examples->tutorials * [JOSS review] Update tested versions in documentation (#58) * Update tested versions in documentation * adding 3.11 to supported versions in docs --------- Co-authored-by: Kirk Bonney <[email protected]> * Docs updates (#81) * Adding statement of need and accompanying bib items * moving statement of need to landing page * renaming documentation file examples->tutorials * updating readme to reflect examples->tutorials * fixing image embedd * remove reference to statement of need page * Adding patch notes * Update .readthedocs.yml * troubleshooting rtd * rtd * Docs updates (#82) * Adding statement of need and accompanying bib items * moving statement of need to landing page * renaming documentation file examples->tutorials * updating readme to reflect examples->tutorials * fixing image embedd * remove reference to statement of need page * Adding patch notes * removing WIP docs pages * Remvoing reference to undefined reference "reqs" * Fix image embed warnings * adding noxfile for taskrunning * Expanding temrinology page * Adding structure to user guide toctree * restructuring index * Adding gallery to tutorials page * updating doc pins * fixing linting issues with noxfile * Update builddocs.yml * attempting latex table * adding dependencies * reverting to simplified markdown style table --------- Co-authored-by: charity-kwha <[email protected]> Co-authored-by: tgunda <[email protected]> Co-authored-by: Adam R. Jensen <[email protected]>
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