Code

Add doc and other improvements#6

Code

Merged

JeanMainguy merged 50 commits intomaingenotoul-bioinfo/Binette:mainfrom devgenotoul-bioinfo/Binette:devCopy head branch name to clipboardJan 22, 2024

+913-59

Commits

Commits on Nov 4, 2023

• rm prodigal dep

  JeanMainguy

  committed
  26c0430

Commits on Nov 6, 2023

• minor update

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  8adfe17

Commits on Nov 9, 2023

• first draft for the joss paper

  JeanMainguy

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  0ca02f0

• add joss github action to compile the paper

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  0ddc058

• relocate correctly github action wf

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  0cc4ddd

• fix concoct citation

  JeanMainguy

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  21f3ade

• fix citations

  JeanMainguy

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  0d77f2e

• Update paper.md

  JeanMainguy

  authored
  57a9809

Commits on Nov 10, 2023

• update paper

  JeanMainguy

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  c5bf759

Commits on Jan 11, 2024

• add version in __init__.py

  JeanMainguy

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  d9383bc

• change default parameters

  JeanMainguy

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  ce3ecff

• organise arguments into category

  JeanMainguy

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  5e53ba2

• Merge remote-tracking branch 'origin/paper' into dev

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  bb4a225

• add figure in paper

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  351ae7a

• replace svg by png figures in paper.md

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  7ce1b64

• commit figure in svg

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  1ce65d7

• add bold in fig caption and adjust svg

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  b22be67

• adjust svg

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  4824ccf

• try with pdf fig

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  4536ec4

• rm useless svg file

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  5ee147e

• add basic documentation build with sphinx

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  3cabcf7

• add .readthedocs.yaml to let readthedoc build the doc

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  05c6d40

• try install in readthedoc with requirements.txt

  JeanMainguy

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  4a94fc9

• fix .readthedoc.yaml

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  a7a54bc

Commits on Jan 12, 2024

• remove useless arg extension

  JeanMainguy

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  34a740b

• change contribution page name

  JeanMainguy

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  3eee02a

• improve args help

  JeanMainguy

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  f0edd0f

• update figure

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  9d11a3c

• add doi to references when missing

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  40c0b25

• add fig ref

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  2a35d1f

Commits on Jan 13, 2024

• fix fig ref

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  e17be7d

• adjust fig ref

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  4740866

• add metagwgs authors

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  b00eae0

Commits on Jan 14, 2024

• improve paper text

  JeanMainguy

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  a62722d

Commits on Jan 22, 2024

• fix grammatical typo

  JeanMainguy

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  64f7019

• use a pyproject.toml to package binette

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  d82847b

• add more detail on installation

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  a2879e0

• update the contribution doc

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  63d31a7

• update the contribution doc

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  e1280bd

• refine emojo usage

  JeanMainguy

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  624110d

• change WF name

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  e75f568

• add badges

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  5de57c3

• organise badges

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  39b7271

• Create release.yml

  JeanMainguy

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  9eabaa6

• tmp publish on test pypi on push

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  d67c0bc

• fix release.yml

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  7f45a4b

• add python deps in toml

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  2ebcdf8

• make release.yml ready to publish on pypi

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  bf1b9b3

• use python deps in toml to setup readthedoc

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  e5679d1

• rm requirements as they are manage in toml

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  7cc6653