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Fix Single Cell Processing#214

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Commits on Dec 13, 2024

• fix: import the correct variable

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• fix: divide by zero error; grouping too many items

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Commits on Dec 17, 2024

• style: rearrange code

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• refactor: remove command line interface

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• feat: use MyGene instead of BioDBNet

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• refactor: import required modules

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• style: use pythonic variable names

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• refactor: remove encompassing for loop

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• refactor: do not drop/set index

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• refactor: use new one-context approach

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• refactor: import required modules

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• feat: create understandable dataclasses

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• refactor: remove unused modules

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• refactor: remove multi-context-specific code

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• feat: do not use hardcoded paths

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• fix: do not overlap with built-in filenames

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• feat: numpy typing; count rows/columns function

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• fix: allow not setting index

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• fix: use new data_types file

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• fix: function renaming; remove unused variables

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• fix: do not require pydantic

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• fix: use new file name

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• fix: zfpkm should be performed on rows, not cols

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• style: reorganize code

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• style: rename arguments

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• fix: ignore mismatched types

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• fix: misspelling

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Commits on Dec 25, 2024

• feat: move zscore graphing to its own module

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• fix: explicit import graphing

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• fix: hotfix - zscore ceiling is incorrect

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Commits on Jan 12, 2025

• fix: pin numpy to less than version 2; update scanpy

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• refactor!: moved `return_placeholder_data` to `como.utils`

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• fix: properly return row and column values

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• feat: added function to set up logging throughout COMO

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• feat: added function to log and raise an error

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• refactor!: moved Algorithms to data_types

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• refactor!: moved Compartments to data_types

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• refactor: re-organized constants

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• fix: removed items from __all__ that were moved

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• refactor: imported required packages and types

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• fix: added Algorithm as top level import

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• fix: added CobraCompartments as top-level import

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• fix: process ids as string type

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• refactor: combine async file reading

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• refactor: remove un-used function

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• refactor: fix async reading of data

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• feat: allow passing strings for dataframes

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• fix: importing of required and unused modules

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• feat: use new log_and_raise_error

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• feat: set appropriate logging

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• feat: combine lines async file reading

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• feat: create Enum from rna types

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• fix: use new RNA type enum

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• refactor: convert literals to Enums

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• fix: re-organize code

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• fix: added dataclasses for simplification of data

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• feat: use _log_and_raise_error function

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• fix: drop na values

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• feat: async read matrix files

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• refactor: calculate size more pythonically

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• fix: use better variable for ensembl gene

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• refactor: drop na values

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• chore: fix logging message

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• feat: use new LogLevel Enum

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• fix: resolve context directory only if provided

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• refactor: import/remove modules

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• refactor: remove extra read_counts function

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• fix: drop na values when building compiling matrix

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• fix: fpkm calculations

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• style: ruff formatting

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• style: fix docstring

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• fix: zfpkm calculations

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• feat: use concurrent.futures for easier processing

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• feat: allow setting bandwidth and peak parameters

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• style: ruff whitespace fixes

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• refactor: more efficient zfpkm plotting

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• feat: use new RNAType Enum

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• fix: drop na values

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• refactor: provide bandwidth and peak parameters

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• feat: allow force-plotting zfpkm

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• refactor: rename FilteringTechnique constants

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• style: ruff whitespace and log message formatting

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• refactor: use _process, not _save_rnaseq_tests

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• refactor: provide path to rnaseq matrix

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• refactor: process provided rnaseq matrix

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• fix: proper check if dataframe is empty/None

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• fix: only write normalized matrix if data exists

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• fix: proper calculation of high confidence genes

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• refactor: remove internal _create_metadata_df func

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• refactor: proper usage of _set_up_logging function

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• fix: proper usage of _log_and_raise_error function

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• refactor: proper processing of metadata

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• refactor: move logic to out of main function

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• fix: add proper function parameters

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• fix: proper calling of _log_and_raise_error

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• feat: allow providing log level and location

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• refactor: import required modules

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• refactor: remove data-specific Enums

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• refactor: async data loading

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• refactor: use new RNAType; _log_and_raise_error

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• refactor: drop na values

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• feat: add logging

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• refactor: type hinting; drop na values

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• feat: added function to update missing genome data

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• refactor: build and use new parameter data types

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• refactor: pass new parameter data types

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• refactor: calculate variables near their usage

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• style: more verbose variable name

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• feat: add functions for building batch data

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• feat: add function for validating data soruces

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• refactor!: provide None as default argument

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• refactor: better building of source data variables

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• feat: allow providing log levela and location

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• refactor: move variable creation closer to usage

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• refactor: use _log_and_raise_error

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• refactor: import required modules

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• refactor!: move Solver to data_types

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• refactor: remove _Arguments cli parsing

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• fix: bracket and logical gene rule creation

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• refactor: reduce extraneous function usage

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• refactor: pythonic if-statement calculation

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• style: more verbose parameter names

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• refactor: async usage where possible

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• refactor: type hinting

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• refactor: pythonic collection of gene activity

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• fix: update mapping process to be more readable

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• refactor: simplify processing, use async

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• refactor: use relevant data types

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• refactor: pythonic approach to z score calculation

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• refactor: async create directories

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• refactor: move when early return happens

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• fix: remove unused z score calculation

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• fix: store gene ids as string

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• refactor: more efficient pandas melting

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• fix: graph title name

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• refactor: log for early return

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• feat: async create directories

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• style: add logging

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• refactor: remove old z score calculation code

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• refactor: better function name

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• refactor: pythonic z score calculation

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• refactor: more efficient pandas melting

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• refactor: temporarily remove z score graphing

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• refactor: use new function names

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• refactor: use matplotlib for plot creation

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• refactor: exchange plotly for seaborn

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• feat: validate that source types process in order

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• refactor: add logging, use _log_and_raise_error

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• refactor: remove plotly graphing

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• feat: do not throw error if missing png path

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• refactor: move NamedTuple to data_types

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• fix: comment unused variables

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• fix: comment unused variables

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• fix: line too long

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• fix: allow undocumented public package

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• fix: do not create virtual environment to format notebooks

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• fix: use python 3.10 to evade errors

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• fix: use uv tool to run nbconvert

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• style: format code, Jupyter Notebook(s), and Python imports with `ruff`

  

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• feat: expand test suite to include python 3.11 and 3.12

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• Merge remote-tracking branch 'origin/fix/single-cell-processing' into fix/single-cell-processing

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• fix: check if provided data is a path before checking if it exists

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• fix: read StringIO data instead of attempting to make dataframe from it

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• fix: statsmodels version dependent on python version

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• fix: use tpm instead of quantile

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• fix: typo

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• chore: update uv lock

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• chore: code re-arrangement

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• chore: remove aiofiles as a dependency

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Commits on Jan 14, 2025

• fix: renamed RNAType.(trna,mrna) to RNAType.(TRNA,MRNA)

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• fix: re-attempt processing if JSON decode error occurs

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• refactor: remove dependency on aiofiles

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• fix: do not call listify twice

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• refactor: remove dependency on aiofiles

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• refactor: allow providing a list of model filepaths to write to

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• fix: check that license information is present if using gurobi

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• feat: add NONE for no logging

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• refactor: remove dependency on aiofiles

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Commits on Jan 31, 2025

• style: ruff formatting

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• fix: make parent directories before saving files

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• refactor: use critical log instead of warning

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• refactor: reset exection output and count

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• fix: rename column names

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