From 1ff03753ce0e8e9111cffbae69b6484b37d47861 Mon Sep 17 00:00:00 2001 From: Jess White <50890758+jessicaw9910@users.noreply.github.com> Date: Thu, 17 Oct 2024 16:09:26 -0400 Subject: [PATCH] Misc (#62) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 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 * pip install sub-package in readthedocs.yml; may also need to change docs/requirements.txt * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated sphinx-rtd-theme in requirements.txt * moved requirements.txt forward in readthedocs.yml * added docs packages to requirements.yaml since requirements.txt seeming to be ignored * fixed getting started code block * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * excluding tests * fixed inline code * max depth 3 * updated to exclude tests directories and contents * instantiation of experiments subpackage * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] pre-commit autoupdate (#61) updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0) - [github.com/psf/black: 24.4.2 → 24.8.0](https://github.com/psf/black/compare/24.4.2...24.8.0) - [github.com/PyCQA/flake8: 7.1.0 → 7.1.1](https://github.com/PyCQA/flake8/compare/7.1.0...7.1.1) - [github.com/asottile/pyupgrade: v3.16.0 → v3.17.0](https://github.com/asottile/pyupgrade/compare/v3.16.0...v3.17.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * flake8 fix for unused import * added initial find_start_or_end_recursively function * added initial kinase Pydantic schema * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * latest kinase Pydantic schema Resolved conflicts from pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed F401 and F722 errors in kinase_schema * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reverting to previous changes lost in rebase * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed E266 flake8 error * started adding b.l alignment * added get_repo_root util lost after last rebase * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed extraneous dev code from klifs_pocket notebook * removed TODO from completed KLIFS tasks * added biopython to devtools test env for CI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mark Polk --- data/README.md | 2 +- readthedocs.yml | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/data/README.md b/data/README.md index 46835bd..a05047c 100644 --- a/data/README.md +++ b/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) diff --git a/readthedocs.yml b/readthedocs.yml index fa26b5b..396187d 100644 --- a/readthedocs.yml +++ b/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