Code

Remove hardcoded paths in proteomics#206

Code

Merged

JoshLoecker merged 105 commits intomainHelikarLab/COMO:mainfrom remove-hardcoded-paths/proteomicsHelikarLab/COMO:remove-hardcoded-paths/proteomicsCopy head branch name to clipboardDec 11, 2024

+3,063-2,076

Commits

Commits on Dec 5, 2024

• feat: initial work to remove hardcoded filepaths

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  JoshLoecker

  committed
  4ce9d8c

• chore(deps): bump astral-sh/setup-uv from 3 to 4

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  dependabot[bot]

  authored
  90c43f3

• chore(deps): bump astral-sh/ruff-action from 1 to 2

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  dependabot[bot]

  authored
  bfcafa3

Commits on Dec 7, 2024

• refactor: allow formatting of jupyter notebooks

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  JoshLoecker

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  3e81a3d

• refactor: rename

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• refactor: import required libraries

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• refactor: remove unused arguments dataclass

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• refactor: remove unused cli argument parsing

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  9b45c1d

• fix: get correct column name

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  31f59a7

• refactor: pythonic approach to merging dataframes

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• style: variable renaming

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• style: ruff formatting

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• ✨ feat: added gitmoji

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• ♻️ refactor: remove commitizen

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• 🎨 style: change variable names

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• 🎨 style: sort dependencies

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• ➕ dep-add: add interactive optional dependencies

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• ➕ dep-add: add commitizen and conventional gitmoji

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Commits on Dec 9, 2024

• ♻️ refactor: accept file paths instead of dataframes

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• 📝 docs: update documentation

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• ♻️ refactor: accept integers only for taxon IDs

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• ♻️ refactor: pythonic approach to calculating size

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• ♻️ refactor: accept integer for taxon id

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• ♻️ refactor: more concise method of creating matrix

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• ♻️ refactor: remove command line interface

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• ♻️ refactor: define specific input/output file paths

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• ♻️ refactor: remove unnecessary code

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• ♻️ refactor: allow processing specific filepaths

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• feat: use commitizen for conventional commits

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• feat: update unit tests for rnaseq_preprocess

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• feat: allow long lines in jupyter notebook

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• style: ruff formatting

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  7768e27

• fix: ignore F811

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• fix: duplicate noqa directive

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• refactor: remove unused testing file

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• test: update tests based on changes

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• fix: do not use asyncio.gather

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  JoshLoecker

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  02e0a31

• Merge pull request #192 from HelikarLab/remove-hardcoded-paths/rnaseq_preprocess

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  JoshLoecker

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• fix: use proper type

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• refactor: remove dependency on Config

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• style: ruff formatting

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• refactor: require output filepath for CPM

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• style: log message for calcualted genes

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• Merge branch 'main' into remove-hardcoded-paths/rnaseq

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• Merge branch 'develop' into remove-hardcoded-paths/rnaseq

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• Merge pull request #193 from HelikarLab/remove-hardcoded-paths/rnaseq

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  JoshLoecker

  authored
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• Merge branch 'main' of github.com:HelikarLab/COMO into develop

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  committed
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• Merge pull request #190 from HelikarLab/dependabot/github_actions/astral-sh/ruff-action-2

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  JoshLoecker

  authored
  dc91d72

• Merge pull request #189 from HelikarLab/dependabot/github_actions/astral-sh/setup-uv-4

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  JoshLoecker

  authored
  1e01b34

• Merge branch 'develop' of github.com:HelikarLab/COMO into develop

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  committed
  c7b234f

• refactor: remove rnaseq.py

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  JoshLoecker

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  355b9df

• refactor: import items from rnaseq.py

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• refactor: remove command line usage

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• refactor: add classes for rna processing

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• feat: added k_over_a calculation

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• feat: added genefilter function

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• refactor: create separate read_counts matrix

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  JoshLoecker

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  1de1717

• feat: bring zfpkm_filter from rnaseq.py

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• feat: added matrix builder

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• feat: added tpm calculation

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• feat: added fpkm calculation

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• feat: added zfpkm transformation and calculation

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• feat: added zfpkm plotting

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• feat: aded calculate z score

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• feat: added cpm filtering

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• feat: added tpm quantile filtering

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• feat: added root filtering logic

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• feat: added logic for performing statistical tests

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• feat: create metadata df

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• refactor: allow passing specific filepaths

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• refactor: rename variable names for easier reuse

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Commits on Dec 10, 2024

• style: update log message, more pythonic code

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• style: variable rename

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• feat: update to match new approach

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  e0d84be

• revert: use mrna instead of polya

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  9674459

• refactor: check files returned

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  cde6606

• feat: allow specifying specific directories

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• style: use more descriptive variable names

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  d52b0ee

• refactor: use early continue

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  JoshLoecker

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  fe1d406

• style: update warning messages

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  8f1d027

• style: rename variables

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  0ef736e

• refactor: move filtering technique to types

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• fix: do not use more cores than necessary

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Commits on Dec 11, 2024

• Merge branch 'main' into develop

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  JoshLoecker

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  911aaaa

• Merge branch 'main' into develop

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  JoshLoecker

  committed
  2bfe760

• Merge branch 'develop' into remove-hardcoded-paths/rnaseq-gen

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  JoshLoecker

  committed
  f8ebcbf

• fix: use parenthesis to validate calculations

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  committed
  6bd06e1

• refactor: ignore missing variables for now

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  committed
  f24347d

• chore: ignore complex function

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  JoshLoecker

  committed
  1956721

• Merge pull request #199 from HelikarLab/remove-hardcoded-paths/rnaseq-gen

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  JoshLoecker

  authored
  179c673

• chore: remove unused imports

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  committed
  65bd2a3

• refactor: remove command line interface

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  3cc9bec

• feat: process input data more pythonically

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  0f9bd3a

• refactor: do not use hardcoded filepaths

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  1402016

• chore: ruff formatting

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• style: use better variable name & reorganize

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• feat: process the provided file paths

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• feat: write to provided filepath

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• refactor: remove hardcoded filepaths

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• refactor: pythonic approach to processing

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• fix: arguments to write data

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• Merge pull request #205 from HelikarLab/remove-hardcoded-paths/proteomics

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  JoshLoecker

  authored
  870cdb9

• Merge branch 'main' of github.com:HelikarLab/COMO into remove-hardcoded-paths/proteomics

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• feat: allow specifiying files to process

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• fix: no longer require rna processing type

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