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Introduce python package#3

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JoshLoecker merged 120 commits intomasterHelikarLab/COMO-CC:masterfrom feature/introduce-packageHelikarLab/COMO-CC:feature/introduce-packageCopy head branch name to clipboardOct 9, 2024

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Commits

Commits on Mar 5, 2024

• initialize package config and add deps for rna preprocess

  

  Jozef Karabelly

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• rename package to como

  

  Jozef Karabelly

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• add R packages installation

  

  Jozef Karabelly

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• reflect package name change in tests

  

  Jozef Karabelly

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• Merge branch 'master' of github.com:HelikarLab/COMO-CC into feature/introduce-package

  

  Jozef Karabelly

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• add openpyxl dependency

  

  Jozef Karabelly

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Commits on Mar 11, 2024

• add installation of required R packages

  

  Jozef Karabelly

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• fix issue with indexes

  

  Jozef Karabelly

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• add rnaseq_gen function to como package

  

  Jozef Karabelly

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Commits on Mar 18, 2024

• add missing dependencies

  

  Jozef Karabelly

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• refactor proteomics to have API

  

  Jozef Karabelly

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• use correct package name

  

  Jozef Karabelly

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• add missing file

  

  Jozef Karabelly

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• refactor xomics to have API

  

  Jozef Karabelly

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• remove dependency on affy R file

  

  Jozef Karabelly

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• remove python imports

  

  Jozef Karabelly

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• refactor context specific model to have API

  

  Jozef Karabelly

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Commits on Mar 28, 2024

• remove r packages installation on import

  

  Jozef Karabelly

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• fix como package imports

  

  Jozef Karabelly

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Commits on Apr 1, 2024

• use fast_bioservices package

  

  Jozef Karabelly

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• create singleton config

  

  Jozef Karabelly

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• use config for variable file structure

  

  Jozef Karabelly

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• use config for variable file structure

  

  Jozef Karabelly

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• use config for variable file structure

  

  Jozef Karabelly

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• load configs only when needed in functions

  

  Jozef Karabelly

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Commits on Apr 16, 2024

• remove unused config and load R scripts using relative path

  

  Jozef Karabelly

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• load configs only when needed in functions

  

  Jozef Karabelly

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• use correct config directory

  

  Jozef Karabelly

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Commits on Apr 18, 2024

• make microarray db path configurable

  

  Jozef Karabelly

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Commits on Apr 23, 2024

• make microarray db path static

  

  Jozef Karabelly

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Commits on Apr 29, 2024

• remove workers parameter

  

  Jozef Karabelly

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• stop validating cut_off for zfpkm

  

  Jozef Karabelly

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• make provided matrix file path absolute

  

  Jozef Karabelly

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• take config filename as absolute path

  

  Jozef Karabelly

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Commits on Aug 27, 2024

• Fixed ignoring results

  JoshLoecker

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• Removed extraneous line

  JoshLoecker

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• Removed unnecesary arguments

  JoshLoecker

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• ruff formatting

  JoshLoecker

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• Moved from multiprocessing.pool to concurrent.futures

  JoshLoecker

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• Refactor using early exits

  JoshLoecker

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• Use lowercase variable names

  JoshLoecker

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• Use pythonic approach to initializing variables

  JoshLoecker

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• Set values in range (-1e-6, 1e-6) to 0

  JoshLoecker

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• Remove unnecessary multiprocessing dependencies

  JoshLoecker

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• ruff formatting

  JoshLoecker

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  7e8643e

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• Remove unnecessary multiprocessing code

  JoshLoecker

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• Use lowercase variable names

  JoshLoecker

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  be1fb17

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• Merge pull request #7 from HelikarLab/fix/drug_identification

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  Josh Loecker

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• Use maximum cores for knockout simulations

  JoshLoecker

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Commits on Aug 28, 2024

• Add ruff formatting configuration

  JoshLoecker

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• Format using new ruff settings

  JoshLoecker

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• Create ThreadPoolProcessor for reading cobra model

  JoshLoecker

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• Use cobra-centric method of gene knockouts

  JoshLoecker

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• Only accept Path type

  JoshLoecker

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• Refactor variable names and code structure to be more logically relevant and descriptive

  JoshLoecker

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• Use more relevant variable names

  JoshLoecker

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• Add argument types

  JoshLoecker

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• Implement early exit when reading disease-related genes, use more descriptive variable names

  JoshLoecker

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• Use Gene ID to be more descriptive

  JoshLoecker

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• Remove un-used function

  JoshLoecker

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• Refactor for less complexity

  JoshLoecker

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• Use Path when possible

  JoshLoecker

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• Create threads when reading model

  JoshLoecker

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• Refactor reading drug file for more logical consistency

  JoshLoecker

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• Refactor variable names to be more descriptive

  JoshLoecker

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• Update fast-bioservices version requirement

  JoshLoecker

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• Merge pull request #8 from HelikarLab/fix/drug_identification

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  Josh Loecker

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Commits on Oct 9, 2024

• Remove microarray references

  JoshLoecker

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• Remove microarray_gen.py

  JoshLoecker

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• Import formatting

  JoshLoecker

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• Fix whitespaces

  JoshLoecker

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• Fix import formatting

  JoshLoecker

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• Locate path to R file properly

  JoshLoecker

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• Move merge_logical_table from microarray to here

  JoshLoecker

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• Remove references to microarray

  JoshLoecker

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• Format whitepace

  JoshLoecker

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• Add a code_dir for accessing R scripts, remove Configs

  JoshLoecker

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• Add ruff settings

  JoshLoecker

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• Use more explicit variable names

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• Correctly locate rnaseq.R

  JoshLoecker

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• Correctly locate the incoming configuration filepath

  JoshLoecker

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• Whitespace/ruff formatting fixes

  JoshLoecker

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• Import Config, not Configs

  JoshLoecker

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• Remove os.path... usages (prefer Path)

  JoshLoecker

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  3e1d803

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• Remove old rpy2 object creation

  JoshLoecker

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• Remove microarray references, no longer required

  JoshLoecker

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• Remove additional microarray references

  JoshLoecker

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• Do not use global python executable

  JoshLoecker

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• Import formatting

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• Collect proper Config and R script path

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• Whitespace formatting using ruff

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• Remove os usage (prefer Path)

  JoshLoecker

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  d6cd6de

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• Remove unnecessary function, whitepace formatting using ruff

  JoshLoecker

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  2aa4b6f

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• Remove os usage (prefer Path)

  JoshLoecker

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  f08baab

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• Remove microarray references

  JoshLoecker

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  9b3a989

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• Import formatting using ruff

  JoshLoecker

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  9c697bc

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• remove os references (prefer Path), Whitespace formatting

  JoshLoecker

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  d6db4d9

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• Fix imports

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• Proper Config usage

  JoshLoecker

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• Import formatting; proper usage of Config

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• Use dataclass for knockout results

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• Ruff formatting; use type hints

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• Remove os, prefer Path

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• Remove os, prefer Path

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• Strip output

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• Fix R call

  JoshLoecker

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• Merge branch 'feature/introduce-package' into fix/remove-microarray

  JoshLoecker

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• Raise errors to exit, do not call sys.exit; remove sys.argv usage

  JoshLoecker

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• Merge remote-tracking branch 'origin/fix/remove-microarray' into fix/remove-microarray

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• Add required usage of sys; remove duplicate ruff key

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• Fix serialization after switching to Path

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• Fix using Path suffix

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• Remove output

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• Skip parsing rnaseq args tests because argv has been removed

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• Fix root directory calculation

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• Fix container build error

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• Set test directory to 'main'

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• Merge pull request #10 from HelikarLab/fix/remove-microarray

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• Update micromamba

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• Update knockout simulation (i.e., remove it)

  JoshLoecker

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