Misc (#62)

* separating out CI badges given monorepo structure

* changed repo extension configuration

* changed max depth given monorepo

* added [tool.setuptools.packages.find] / where = [.] to databases pyproject.toml

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* updated sphinx-rtd-theme in requirements.txt

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* fixed getting started code block

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* excluding tests

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* max depth 3

* updated to exclude tests directories and contents

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* Klifs (#58)

* simplified DICT_POCKET_KLIFS_REGIONS, have added notion of contiguous KLIFS regions after reviewing structurally alignments manually and updated iterate_klifs_alignment function accordingly; started movign KLIFSPocket dataclass into klifs module

* adjusted KLIFS pocket notebook to adapt to klifs module changes

* adjusted KLIFS pocket notebook to adapt to klifs module changes

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* flake8 fix for unused import

* added initial find_start_or_end_recursively function

* added initial kinase Pydantic schema

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* latest kinase Pydantic schema

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* added csv files to data and updated database notebook

* caching latest klifs pocket notebook

* refactored model schema so that each database module has its own BaseModel that is included in Kinase object

* klifs

* updated KinaseInfo to use more general search term in lieu of kinase name; then converted search in database notebook to UniProt ID instead of HGNC gene name

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* completed intial version of kinase_schema to allow for harmonization of databases and Pydantic model generation; updated databases notebook and source files in data dir

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* fixed F401 and F722 errors in kinase_schema

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* completed intial version of kinase_schema to allow for harmonization of databases and Pydantic model generation; updated databases notebook and source files in data dir

rebased kinase schema

* used Kincore2UniProtAligner from aligment module in kincore module

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* reverting to previous changes lost in rebase

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* fixed E266 flake8 error

* started adding b.l alignment

* added get_repo_root util lost after last rebase

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* added validation to fix incorrect KLIFS pocket for ADCK3

* used Self instead of self for ADCK3 KLIFS pocket validation fix

* final commit before moving all functions to KLIFSPocket class

* interim commit of klifs_pocket notebook while debugging bl alignment algorithm

* added SO link to ADCK3 validator for future reference

* added matplotlib_venn in dependencies

* added validation correction for LRRK2 and CAMKK1 KLIFS pockets

* finalized alignment algorithm for b.l, multi-matching post-concatenation, and all other remaining partial alignments

* final notebook including partial alignment issues

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* removed extraneous dev code from klifs_pocket notebook

* removed TODO from completed KLIFS tasks

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* deleted unnecessary commented out code

* removed commented out code now integrated into return_idx_of_alignment_match

* added generate_alignment to KLIFSPocket and added to pre-init

* added bool_offset and KLIFS2UniProt to KinaseInfo BaseModel along with a generator validation function for the latter

* updated KLIFS pocket notebook for latest kinase schema including KLIFS2UniProt dict

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* added KinCore FASTA sequence file

* updated data README to summarize how the csv files were generated and how the Pydantic models can be assembled

* fixed KLIFS README

* added trailing space README

* pip install sub-package in readthedocs.yml; may also need to change docs/requirements.txt

* moved requirements.txt forward in readthedocs.yml

* push to trigger README reformat

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data/README.md

@@ -35,7 +35,7 @@ for index, row in tqdm(df_kinhub.iterrows(), total = df_kinhub.shape[0]):
     list_hgnc.append(row["HGNC Name"])
     list_sequence.append(uniprot.UniProt(row["UniprotID"])._sequence)
 
-dict_uniprot = dict(zip(["uniprot_id", "hgnc_name", "canonical_sequence"], 
+dict_uniprot = dict(zip(["uniprot_id", "hgnc_name", "canonical_sequence"],
                         [list_uniprot, list_hgnc, list_sequence]))
 df_uniprot = pd.DataFrame.from_dict(dict_uniprot)
 

readthedocs.yml

@@ -36,3 +36,6 @@ python:
     - requirements: docs/requirements.txt
     - method: pip
       path: missense_kinase_toolkit/databases
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: missense_kinase_toolkit/databases