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ToDo.md

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  • Look into implementing AAindex2 & 3
  • Visualise function in class where you can do histogram/heat map etc of each amino acid and corresponding value.
  • Implement functionality to work with AAindex 2 and 3 (https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/aaindex.py , https://github.com/pycogent/pycogent/blob/master/cogent/parse/aaindex.py)
  • Move aaindex into init file, change imports in folders and readme's.
  • Get rid of AAINDEX_FILENAME - make aaindex1 name static.
  • Add references section to readme.
  • Remove ds_store from all folders.
  • Ensure all files listed in readme of /data
  • Go through flake8 and bandit output.
  • Search by keyword, other ways to search?
  • Use aaindex API URLs search_url = 'https://www.genome.jp/dbget-bin/www_bfind_sub?locale=en&serv=gn&keywords=charge&page=1&max_hit=0&dbkey=aaindex' , record_url = 'https://www.genome.jp/dbget-bin/www_bget?aaindex:KLEP840101'
  • Parse main URL to check last updated: "Last updated: February 13, 2017"
  • Pull request to biopython for aaindex.
  • Add "python3 -m twine upload --repository testpypi dist/*" to test pypi workflow.
  • Add Keywords to setup.py & cfg
  • Add demo using jupyter notebook.
  • Update build/test workflow, similar to pySAR.
  • Add readthedocs badge - Documentation Status
  • Add emojis to readme - test if they show up on Mac and Windows.
  • Check variable naming conventions.
  • Change "secrets.PY_PI..." to "secrets.PYPI...".
  • Add comments to .circle/workflow.
  • Add spacing in between individual references, see if it improves readability, revert if not.
  • Add documentation section in readme.
  • Add path-ignore keywords to GitHub Action.
  • Reorder software metadata in setup.py to be in order of main func, create description var.
  • Add download_url to setup.py - url of zipped package.
  • Add category to output object - aaindex1['CHOP780206']['category']
  • Remove get_category_from_record function, just use aaindex1['XXXX']['category'] to get category.
  • Test aaindex_json has correct list of keys.
  • Test last updated - self.last_updated = "February 13, 2017" #as shown on homepage (https://www.genome.jp/aaindex/)
  • Remove one-hot encoding from aaindex, and sci-kit learn library.
  • Below aaindex record image in readme - add description of each record key.
  • Unit tests to check that aaindex1 can be accessed using dot notation.
  • Double check usage in aaindex/readme.md
  • Remove all camel casing function names/vars, change to underscores and lowercase (https://peps.python.org/pep-0008/#function-and-variable-names).
  • Update dependancies so non-specific pandas/numpy version required.
  • Think about removing download_using and download function all together.
  • Add and fix codecov and coverage installs from github workflow.
  • Update workflows.
  • Can aaindex1 object accept lowercase version of index - add unit tests of lowercase indices.
  • Remove delayed==0.11.0b1 from requirments.txt.
  • Update setup.cfg.
  • Change all comment underlining from "------" to "=======".
  • Add methods comments to aaindex class and test classes.
  • Mention its lightweight and requires no external python libraries to use.
  • Change all refs of AAIndex to AAindex.
  • Go over all modules etc.
  • Go over main readme.
  • Read over code.
  • Read over tests.