Code

Overhaul tools#3

Code

Merged

kostrykin merged 112 commits intooverhaul/upstreamkostrykin/galaxy-image-analysis:overhaul/upstreamfrom overhaul/devkostrykin/galaxy-image-analysis:overhaul/devCopy head branch name to clipboardMar 21, 2024

+1,587-643

Commits

Commits on Feb 12, 2024

• Rename tools

  Show description for 2d84f5c
  kostrykin

  committed
  2d84f5c

• Update projective_transformation.xml

  kostrykin

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  d337410

• Update projective_transformation_points.xml

  kostrykin

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  a44636a

Commits on Mar 14, 2024

• Add CONVENTIONS.md

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• wip

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• wip

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• Update CONVENTIONS.md

  kostrykin

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• Update CONVENTIONS.md

  kostrykin

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• Update CONVENTIONS.md

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• Update CONVENTIONS.md

  kostrykin

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• Update CONVENTIONS.md

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• Update CONVENTIONS.md

  kostrykin

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• Remove help section

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  76ea28f

• Update CONVENTIONS.md

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• Update CONVENTIONS.md

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• Update CONVENTIONS.md

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Commits on Mar 15, 2024

• Update

  kostrykin

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• Merge branch 'master' into overhaul/dev

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• Merge remote-tracking branch 'origin/tool-name-update' into overhaul/dev

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• Update test data

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• Add content assertions

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• Update pr.yaml

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• Update

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• Update pr.yaml

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• Add pip install pillow

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• Merge CONVENTIONS.md into CONTRIBUTING.md

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• Temporarilly fix CI

  kostrykin

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  ea9887d

• Update 2d_feature_extraction tool

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• Update 2d_auto_threshold tool

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• Fix 2d_feature_extraction tests

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• Fix test data

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  4c7316a

• Fix tool

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  84b28dd

• Start refactoring 2d_simple_filter tool

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• Merge branch 'overhaul/dev' of https://github.com/kostrykin/galaxy-image-analysis into overhaul/dev

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• Fix 2d_simple_filter tool

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• Add more tests

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  0a40dad

• Fix tests

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  a28640e

• Update

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• Fix

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  b3e9ace

• Update CONTRIBUTING.md

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• Fix bugs

  kostrykin

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• Update CONTRIBUTING.md

  kostrykin

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• Update CONTRIBUTING.md

  kostrykin

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Commits on Mar 16, 2024

• Fix linting issues

  kostrykin

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• Update CONTRIBUTING.md

  kostrykin

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• Refactor tests using macros

  kostrykin

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  9158478

• Update tests

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  5879277

• Merge branch 'overhaul/dev' of github.com:kostrykin/galaxy-image-analysis into overhaul/dev

  kostrykin

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  785c6cb

• Update CONTRIBUTING.md

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  262ca03

• Update CONTRIBUTING.md

  kostrykin

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  ae4c278

• Update pr.yaml

  kostrykin

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• Update anisotropic_diffusion tool

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  05164b2

• Fix spelling (was BE, using AE is more consistent)

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  a51dd5d

• Update 2d_histogram_equalization tool

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  112a124

• Update colorize_labels tool

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  34843ed

• Update bf2raw tool

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  b4ca632

• Add macros/creators.xml

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  5a321ea

• Update rfove tool

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  8edadaa

• Fix bioformats2raw and voronoi_tessellation tools

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• Fix labels

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  18fbcf0

• Fix rfove tool

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• Update overlay_images tool

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• Add RGB test for overlay_images

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  523e653

• Update overlay_images help

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  07cd6a0

Commits on Mar 18, 2024

• Add image verification support to CI (BMCV#117)

  Show description for 4ce5211
  kostrykin

  authored
  4ce5211

• Update CONTRIBUTING.md

  kostrykin

  authored
  14ce511

• Update CONTRIBUTING.md

  kostrykin

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• Merge branch 'master' into overhaul/dev

  kostrykin

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  756a763

• Update CONTRIBUTING.md

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  379ca30

• Update test data

  kostrykin

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  e30849c

• Add RGB test for overlay_images

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  1cf5aa6

• Update anisotropic_diffusion to medpy 0.4.0

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  a426126

• Update PULL_REQUEST_TEMPLATE.md

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• Update projective_transformation_points tool

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  a8a046c

• Update PULL_REQUEST_TEMPLATE.md

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  b429c40

• Update bioformats2raw

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  ea016d5

• Merge branch 'overhaul/dev' of github.com:kostrykin/galaxy-image-analysis into overhaul/dev

  kostrykin

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  7a1c096

• Update projective_transformation tool

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  47fb8ff

• Update bfconvert tool (tests failing)

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  aa43c16

Commits on Mar 19, 2024

• Update CONTRIBUTING.md

  kostrykin

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  1f482e9

• Fix bfconvert tests

  kostrykin

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  cb05359

• Fix test data size

  kostrykin

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  afc8190

• Update projective_transformation_points tool

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  279d936

• Remove spurious files

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  54853f3

• Update requirements using @TOOL_VERSION@ macro

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  d3a8997

• Update segmetrics tool

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• Remove spurious sym links

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  6c02b60

• Update superdsm tool

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  affd76b

• Update scale_image tool (not finished yet)

  kostrykin

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  493adf4

• Fix tests

  kostrykin

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  9165189

• Fix scale_image tool

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  aaff8b9

• Refactor

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  75453a5

• Fix linting issues

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  f749a35

Commits on Mar 20, 2024

• Update tests and help of 2d_simple_filter tool

  kostrykin

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  a074b7d

• Update scale_image help

  kostrykin

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  58052d7

• Update CI to use latest version of galaxy fork

  kostrykin

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  a4faa4e

• Fix tests for float TIFF in scale_image tool

  kostrykin

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  acd17d1

• Add tifffile to CI workflows

  kostrykin

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  ad14c4a

• Fix tests of bfconvert tool

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  9c48179

• Update 2d_filter_segmentation_by_features tool

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  f33eee4

• Update image_math tool

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  830af8d

• Update orientationpy tool

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• Update morphological_operations tool

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• Update split_labelmap tool

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Commits on Mar 21, 2024

• Add float TIFF test for 2d_simple_filter

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  a06833f

• Update slice_image tool

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• Add missing macros

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  dd3e6d4

• Update help of 2d_filter_segmentation_by_features tool

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  80df3aa

• Update concat_images tool

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  69f59ba

• Fix linting issues

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  7fc8c41

• Fix file sizes

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  df87279

• Fix missing profile

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  a4852b6