From 34021d5139d79b7bb48cec6bd24faa3e6ac17729 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Mon, 8 May 2023 11:41:19 -0700 Subject: [PATCH 1/8] make unmaintained folder --- .../CellProfiler2}/calculatehistogram.py | 0 .../CellProfiler2}/calculatemoments.py | 0 .../CellProfiler2}/enhancedmeasuretexture.py | 0 .../CellProfiler2}/identifylinearobjects.py | 0 .../CellProfiler2}/transform.py | 0 {CellProfiler3 => unmaintained_plugins/CellProfiler3}/DoGNet.py | 0 .../CellProfiler3}/activecontourmodel.py | 0 .../CellProfiler3}/blobdetection.py | 0 .../CellProfiler3}/calculatehistogram.py | 0 .../CellProfiler3}/calculatemoments.py | 0 .../CellProfiler3}/callbarcodes.py | 0 .../CellProfiler3}/classifypixelsunet.py | 0 .../CellProfiler3}/compensatecolors.py | 0 .../CellProfiler3}/constrainobjects.py | 0 .../CellProfiler3}/convertoutlinestoobjects.py | 0 {CellProfiler3 => unmaintained_plugins/CellProfiler3}/declump.py | 0 .../CellProfiler3}/edgedetection.py | 0 .../CellProfiler3}/enhancedmeasuretexture.py | 0 .../CellProfiler3}/exporttocellh5.py | 0 .../CellProfiler3}/gammacorrection.py | 0 .../CellProfiler3}/histogramequalization.py | 0 .../CellProfiler3}/identifylinearobjects.py | 0 .../CellProfiler3}/identifyyeastcells.py | 0 .../CellProfiler3}/imagegradient.py | 0 .../CellProfiler3}/laplacianofgaussian.py | 0 .../CellProfiler3}/measure_population_context.py | 0 .../CellProfiler3}/measureimagefocus.py | 0 .../CellProfiler3}/measureradialentropy.py | 0 .../CellProfiler3}/measuretrackquality.py | 0 .../CellProfiler3}/mergeobjects.py | 0 .../CellProfiler3}/nucleaizer.py | 0 {CellProfiler3 => unmaintained_plugins/CellProfiler3}/predict.py | 0 .../CellProfiler3}/randomwalkeralgorithm.py | 0 .../CellProfiler3}/rescale_mean_sd.py | 0 .../CellProfiler3}/rescale_mode_percentile.py | 0 .../CellProfiler3}/runimagej.py | 0 .../CellProfiler3}/save_16bit_pngs.py | 0 .../CellProfiler3}/seedobjects.py | 0 .../CellProfiler3}/shollanalysis.py | 0 .../CellProfiler3}/spectralanalysis.py | 0 .../CellProfiler3}/tests/conftest.py | 0 .../CellProfiler3}/thresh_all.py | 0 .../CellProfiler3}/tophattransform.py | 0 .../CellProfiler3}/transform.py | 0 .../CellProfiler3}/transformfilters.py | 0 .../CellProfiler4}/DoGNet.py | 0 .../CellProfiler4}/activecontourmodel.py | 0 .../CellProfiler4}/blobdetection.py | 0 .../CellProfiler4}/calculatehistogram.py | 0 .../CellProfiler4}/calculatemoments.py | 0 .../CellProfiler4}/classifypixelsunet.py | 0 .../CellProfiler4}/constrainobjects.py | 0 .../CellProfiler4}/convertoutlinestoobjects.py | 0 .../CellProfiler4}/edgedetection.py | 0 .../CellProfiler4}/exporttocellh5.py | 0 .../CellProfiler4}/gammacorrection.py | 0 .../CellProfiler4}/histogramequalization.py | 0 .../CellProfiler4}/identifylinearobjects.py | 0 .../CellProfiler4}/identifyyeastcells.py | 0 .../CellProfiler4}/imagegradient.py | 0 .../CellProfiler4}/laplacianofgaussian.py | 0 .../CellProfiler4}/measureimagefocus.py | 0 .../CellProfiler4}/measurepopulationcontext.py | 0 .../CellProfiler4}/measureradialentropy.py | 0 .../CellProfiler4}/measuretrackquality.py | 0 .../CellProfiler4}/mergeobjects.py | 0 .../CellProfiler4}/nucleaizer.py | 0 .../CellProfiler4}/predict.py | 0 .../CellProfiler4}/randomwalkeralgorithm.py | 0 .../CellProfiler4}/rescalemeansd.py | 0 .../CellProfiler4}/rescalemodepercentile.py | 0 .../CellProfiler4}/runimagej.py | 0 .../CellProfiler4}/save16bitpngs.py | 0 .../CellProfiler4}/seedobjects.py | 0 .../CellProfiler4}/shollanalysis.py | 0 .../CellProfiler4}/spectralanalysis.py | 0 .../CellProfiler4}/testallthresholds.py | 0 .../CellProfiler4}/tophattransform.py | 0 .../CellProfiler4}/transformfilters.py | 0 .../CellProfiler4}/transforms.py | 0 80 files changed, 0 insertions(+), 0 deletions(-) rename {CellProfiler2 => unmaintained_plugins/CellProfiler2}/calculatehistogram.py (100%) rename {CellProfiler2 => 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a/CellProfiler3/gammacorrection.py b/unmaintained_plugins/CellProfiler3/gammacorrection.py similarity index 100% rename from CellProfiler3/gammacorrection.py rename to unmaintained_plugins/CellProfiler3/gammacorrection.py diff --git a/CellProfiler3/histogramequalization.py b/unmaintained_plugins/CellProfiler3/histogramequalization.py similarity index 100% rename from CellProfiler3/histogramequalization.py rename to unmaintained_plugins/CellProfiler3/histogramequalization.py diff --git a/CellProfiler3/identifylinearobjects.py b/unmaintained_plugins/CellProfiler3/identifylinearobjects.py similarity index 100% rename from CellProfiler3/identifylinearobjects.py rename to unmaintained_plugins/CellProfiler3/identifylinearobjects.py diff --git a/CellProfiler3/identifyyeastcells.py b/unmaintained_plugins/CellProfiler3/identifyyeastcells.py similarity index 100% rename from CellProfiler3/identifyyeastcells.py rename to unmaintained_plugins/CellProfiler3/identifyyeastcells.py diff --git a/CellProfiler3/imagegradient.py b/unmaintained_plugins/CellProfiler3/imagegradient.py similarity index 100% rename from CellProfiler3/imagegradient.py rename to unmaintained_plugins/CellProfiler3/imagegradient.py diff --git a/CellProfiler3/laplacianofgaussian.py b/unmaintained_plugins/CellProfiler3/laplacianofgaussian.py similarity index 100% rename from CellProfiler3/laplacianofgaussian.py rename to unmaintained_plugins/CellProfiler3/laplacianofgaussian.py diff --git a/CellProfiler3/measure_population_context.py b/unmaintained_plugins/CellProfiler3/measure_population_context.py similarity index 100% rename from CellProfiler3/measure_population_context.py rename to unmaintained_plugins/CellProfiler3/measure_population_context.py diff --git a/CellProfiler3/measureimagefocus.py b/unmaintained_plugins/CellProfiler3/measureimagefocus.py similarity index 100% rename from CellProfiler3/measureimagefocus.py rename to unmaintained_plugins/CellProfiler3/measureimagefocus.py diff --git a/CellProfiler3/measureradialentropy.py b/unmaintained_plugins/CellProfiler3/measureradialentropy.py similarity index 100% rename from CellProfiler3/measureradialentropy.py rename to unmaintained_plugins/CellProfiler3/measureradialentropy.py diff --git a/CellProfiler3/measuretrackquality.py b/unmaintained_plugins/CellProfiler3/measuretrackquality.py similarity index 100% rename from CellProfiler3/measuretrackquality.py rename to unmaintained_plugins/CellProfiler3/measuretrackquality.py diff --git a/CellProfiler3/mergeobjects.py b/unmaintained_plugins/CellProfiler3/mergeobjects.py similarity index 100% rename from CellProfiler3/mergeobjects.py rename to unmaintained_plugins/CellProfiler3/mergeobjects.py diff --git a/CellProfiler3/nucleaizer.py b/unmaintained_plugins/CellProfiler3/nucleaizer.py similarity index 100% rename from CellProfiler3/nucleaizer.py rename to unmaintained_plugins/CellProfiler3/nucleaizer.py diff --git a/CellProfiler3/predict.py 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a/CellProfiler4_AutoConvert/calculatehistogram.py b/unmaintained_plugins/CellProfiler4/calculatehistogram.py similarity index 100% rename from CellProfiler4_AutoConvert/calculatehistogram.py rename to unmaintained_plugins/CellProfiler4/calculatehistogram.py diff --git a/CellProfiler4_AutoConvert/calculatemoments.py b/unmaintained_plugins/CellProfiler4/calculatemoments.py similarity index 100% rename from CellProfiler4_AutoConvert/calculatemoments.py rename to unmaintained_plugins/CellProfiler4/calculatemoments.py diff --git a/CellProfiler4_AutoConvert/classifypixelsunet.py b/unmaintained_plugins/CellProfiler4/classifypixelsunet.py similarity index 100% rename from CellProfiler4_AutoConvert/classifypixelsunet.py rename to unmaintained_plugins/CellProfiler4/classifypixelsunet.py diff --git a/CellProfiler4_AutoConvert/constrainobjects.py b/unmaintained_plugins/CellProfiler4/constrainobjects.py similarity index 100% rename from CellProfiler4_AutoConvert/constrainobjects.py rename to 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CellProfiler4_AutoConvert/gammacorrection.py rename to unmaintained_plugins/CellProfiler4/gammacorrection.py diff --git a/CellProfiler4_AutoConvert/histogramequalization.py b/unmaintained_plugins/CellProfiler4/histogramequalization.py similarity index 100% rename from CellProfiler4_AutoConvert/histogramequalization.py rename to unmaintained_plugins/CellProfiler4/histogramequalization.py diff --git a/CellProfiler4_AutoConvert/identifylinearobjects.py b/unmaintained_plugins/CellProfiler4/identifylinearobjects.py similarity index 100% rename from CellProfiler4_AutoConvert/identifylinearobjects.py rename to unmaintained_plugins/CellProfiler4/identifylinearobjects.py diff --git a/CellProfiler4_AutoConvert/identifyyeastcells.py b/unmaintained_plugins/CellProfiler4/identifyyeastcells.py similarity index 100% rename from CellProfiler4_AutoConvert/identifyyeastcells.py rename to unmaintained_plugins/CellProfiler4/identifyyeastcells.py diff --git a/CellProfiler4_AutoConvert/imagegradient.py 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unmaintained_plugins/CellProfiler4/measurepopulationcontext.py diff --git a/CellProfiler4_AutoConvert/measureradialentropy.py b/unmaintained_plugins/CellProfiler4/measureradialentropy.py similarity index 100% rename from CellProfiler4_AutoConvert/measureradialentropy.py rename to unmaintained_plugins/CellProfiler4/measureradialentropy.py diff --git a/CellProfiler4_AutoConvert/measuretrackquality.py b/unmaintained_plugins/CellProfiler4/measuretrackquality.py similarity index 100% rename from CellProfiler4_AutoConvert/measuretrackquality.py rename to unmaintained_plugins/CellProfiler4/measuretrackquality.py diff --git a/CellProfiler4_AutoConvert/mergeobjects.py b/unmaintained_plugins/CellProfiler4/mergeobjects.py similarity index 100% rename from CellProfiler4_AutoConvert/mergeobjects.py rename to unmaintained_plugins/CellProfiler4/mergeobjects.py diff --git a/CellProfiler4_AutoConvert/nucleaizer.py b/unmaintained_plugins/CellProfiler4/nucleaizer.py similarity index 100% rename from CellProfiler4_AutoConvert/nucleaizer.py rename to unmaintained_plugins/CellProfiler4/nucleaizer.py diff --git a/CellProfiler4_AutoConvert/predict.py b/unmaintained_plugins/CellProfiler4/predict.py similarity index 100% rename from CellProfiler4_AutoConvert/predict.py rename to unmaintained_plugins/CellProfiler4/predict.py diff --git a/CellProfiler4_AutoConvert/randomwalkeralgorithm.py b/unmaintained_plugins/CellProfiler4/randomwalkeralgorithm.py similarity index 100% rename from CellProfiler4_AutoConvert/randomwalkeralgorithm.py rename to unmaintained_plugins/CellProfiler4/randomwalkeralgorithm.py diff --git a/CellProfiler4_AutoConvert/rescalemeansd.py b/unmaintained_plugins/CellProfiler4/rescalemeansd.py similarity index 100% rename from CellProfiler4_AutoConvert/rescalemeansd.py rename to unmaintained_plugins/CellProfiler4/rescalemeansd.py diff --git a/CellProfiler4_AutoConvert/rescalemodepercentile.py b/unmaintained_plugins/CellProfiler4/rescalemodepercentile.py similarity index 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from CellProfiler4_AutoConvert/shollanalysis.py rename to unmaintained_plugins/CellProfiler4/shollanalysis.py diff --git a/CellProfiler4_AutoConvert/spectralanalysis.py b/unmaintained_plugins/CellProfiler4/spectralanalysis.py similarity index 100% rename from CellProfiler4_AutoConvert/spectralanalysis.py rename to unmaintained_plugins/CellProfiler4/spectralanalysis.py diff --git a/CellProfiler4_AutoConvert/testallthresholds.py b/unmaintained_plugins/CellProfiler4/testallthresholds.py similarity index 100% rename from CellProfiler4_AutoConvert/testallthresholds.py rename to unmaintained_plugins/CellProfiler4/testallthresholds.py diff --git a/CellProfiler4_AutoConvert/tophattransform.py b/unmaintained_plugins/CellProfiler4/tophattransform.py similarity index 100% rename from CellProfiler4_AutoConvert/tophattransform.py rename to unmaintained_plugins/CellProfiler4/tophattransform.py diff --git a/CellProfiler4_AutoConvert/transformfilters.py b/unmaintained_plugins/CellProfiler4/transformfilters.py similarity index 100% rename from CellProfiler4_AutoConvert/transformfilters.py rename to unmaintained_plugins/CellProfiler4/transformfilters.py diff --git a/CellProfiler4_AutoConvert/transforms.py b/unmaintained_plugins/CellProfiler4/transforms.py similarity index 100% rename from CellProfiler4_AutoConvert/transforms.py rename to unmaintained_plugins/CellProfiler4/transforms.py From 39afe3a67a1d681f1cde090103ba8ce3a73ab43d Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 9 May 2023 12:14:20 -0700 Subject: [PATCH 2/8] move to unmaintained --- .../Simple_Anisotropic_4_11_2_prism17.t7 | Bin .../CellProfiler3/cellstar}/__init__.py | 0 .../CellProfiler3/cellstar}/core/__init__.py | 0 .../CellProfiler3/cellstar}/core/config.py | 0 .../CellProfiler3/cellstar}/core/image_repo.py | 0 .../cellstar}/core/parallel/__init__.py | 0 .../cellstar}/core/parallel/snake_grow.py | 0 .../CellProfiler3/cellstar}/core/point.py | 0 .../CellProfiler3/cellstar}/core/polar_transform.py | 0 .../CellProfiler3/cellstar}/core/seed.py | 0 .../CellProfiler3/cellstar}/core/seeder.py | 0 .../CellProfiler3/cellstar}/core/snake.py | 0 .../CellProfiler3/cellstar}/core/snake_filter.py | 0 .../cellstar}/parameter_fitting/__init__.py | 0 .../cellstar}/parameter_fitting/pf_auto_params.py | 0 .../cellstar}/parameter_fitting/pf_mutator.py | 0 .../cellstar}/parameter_fitting/pf_process.py | 0 .../cellstar}/parameter_fitting/pf_rank_process.py | 0 .../cellstar}/parameter_fitting/pf_rank_snake.py | 0 .../cellstar}/parameter_fitting/pf_runner.py | 0 .../cellstar}/parameter_fitting/pf_snake.py | 0 .../CellProfiler3/cellstar}/segmentation.py | 0 .../CellProfiler3/cellstar}/utils/__init__.py | 0 .../CellProfiler3/cellstar}/utils/calc_util.py | 0 .../CellProfiler3/cellstar}/utils/debug_util.py | 0 .../CellProfiler3/cellstar}/utils/image_util.py | 0 .../CellProfiler3/cellstar}/utils/index.py | 0 .../CellProfiler3/cellstar}/utils/params_util.py | 0 28 files changed, 0 insertions(+), 0 deletions(-) rename {DoGNetWeights => unmaintained_plugins/CellProfiler3/DoGNetWeights}/Simple_Anisotropic_4_11_2_prism17.t7 (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/__init__.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/__init__.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/config.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/image_repo.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/parallel/__init__.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/parallel/snake_grow.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/point.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/polar_transform.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/seed.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/seeder.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/snake.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/core/snake_filter.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/__init__.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_auto_params.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_mutator.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_process.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_rank_process.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_rank_snake.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_runner.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/parameter_fitting/pf_snake.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/segmentation.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/utils/__init__.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/utils/calc_util.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/utils/debug_util.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/utils/image_util.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/utils/index.py (100%) rename {cellstar => unmaintained_plugins/CellProfiler3/cellstar}/utils/params_util.py (100%) diff --git a/DoGNetWeights/Simple_Anisotropic_4_11_2_prism17.t7 b/unmaintained_plugins/CellProfiler3/DoGNetWeights/Simple_Anisotropic_4_11_2_prism17.t7 similarity index 100% rename from DoGNetWeights/Simple_Anisotropic_4_11_2_prism17.t7 rename to unmaintained_plugins/CellProfiler3/DoGNetWeights/Simple_Anisotropic_4_11_2_prism17.t7 diff --git a/cellstar/__init__.py b/unmaintained_plugins/CellProfiler3/cellstar/__init__.py similarity index 100% rename from cellstar/__init__.py rename to unmaintained_plugins/CellProfiler3/cellstar/__init__.py diff --git a/cellstar/core/__init__.py b/unmaintained_plugins/CellProfiler3/cellstar/core/__init__.py similarity index 100% rename from cellstar/core/__init__.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/__init__.py diff --git a/cellstar/core/config.py b/unmaintained_plugins/CellProfiler3/cellstar/core/config.py similarity index 100% rename from cellstar/core/config.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/config.py diff --git a/cellstar/core/image_repo.py b/unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py similarity index 100% rename from cellstar/core/image_repo.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py diff --git a/cellstar/core/parallel/__init__.py b/unmaintained_plugins/CellProfiler3/cellstar/core/parallel/__init__.py similarity index 100% rename from cellstar/core/parallel/__init__.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/parallel/__init__.py diff --git a/cellstar/core/parallel/snake_grow.py b/unmaintained_plugins/CellProfiler3/cellstar/core/parallel/snake_grow.py similarity index 100% rename from cellstar/core/parallel/snake_grow.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/parallel/snake_grow.py diff --git a/cellstar/core/point.py b/unmaintained_plugins/CellProfiler3/cellstar/core/point.py similarity index 100% rename from cellstar/core/point.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/point.py diff --git a/cellstar/core/polar_transform.py b/unmaintained_plugins/CellProfiler3/cellstar/core/polar_transform.py similarity index 100% rename from cellstar/core/polar_transform.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/polar_transform.py diff --git a/cellstar/core/seed.py b/unmaintained_plugins/CellProfiler3/cellstar/core/seed.py similarity index 100% rename from cellstar/core/seed.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/seed.py diff --git a/cellstar/core/seeder.py b/unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py similarity index 100% rename from cellstar/core/seeder.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py diff --git a/cellstar/core/snake.py b/unmaintained_plugins/CellProfiler3/cellstar/core/snake.py similarity index 100% rename from cellstar/core/snake.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/snake.py diff --git a/cellstar/core/snake_filter.py b/unmaintained_plugins/CellProfiler3/cellstar/core/snake_filter.py similarity index 100% rename from cellstar/core/snake_filter.py rename to unmaintained_plugins/CellProfiler3/cellstar/core/snake_filter.py diff --git a/cellstar/parameter_fitting/__init__.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/__init__.py similarity index 100% rename from cellstar/parameter_fitting/__init__.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/__init__.py diff --git a/cellstar/parameter_fitting/pf_auto_params.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_auto_params.py similarity index 100% rename from cellstar/parameter_fitting/pf_auto_params.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_auto_params.py diff --git a/cellstar/parameter_fitting/pf_mutator.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_mutator.py similarity index 100% rename from cellstar/parameter_fitting/pf_mutator.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_mutator.py diff --git a/cellstar/parameter_fitting/pf_process.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py similarity index 100% rename from cellstar/parameter_fitting/pf_process.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py diff --git a/cellstar/parameter_fitting/pf_rank_process.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py similarity index 100% rename from cellstar/parameter_fitting/pf_rank_process.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py diff --git a/cellstar/parameter_fitting/pf_rank_snake.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_snake.py similarity index 100% rename from cellstar/parameter_fitting/pf_rank_snake.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_snake.py diff --git a/cellstar/parameter_fitting/pf_runner.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_runner.py similarity index 100% rename from cellstar/parameter_fitting/pf_runner.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_runner.py diff --git a/cellstar/parameter_fitting/pf_snake.py b/unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py similarity index 100% rename from cellstar/parameter_fitting/pf_snake.py rename to unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py diff --git a/cellstar/segmentation.py b/unmaintained_plugins/CellProfiler3/cellstar/segmentation.py similarity index 100% rename from cellstar/segmentation.py rename to unmaintained_plugins/CellProfiler3/cellstar/segmentation.py diff --git a/cellstar/utils/__init__.py b/unmaintained_plugins/CellProfiler3/cellstar/utils/__init__.py similarity index 100% rename from cellstar/utils/__init__.py rename to unmaintained_plugins/CellProfiler3/cellstar/utils/__init__.py diff --git a/cellstar/utils/calc_util.py b/unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py similarity index 100% rename from cellstar/utils/calc_util.py rename to unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py diff --git a/cellstar/utils/debug_util.py b/unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py similarity index 100% rename from cellstar/utils/debug_util.py rename to unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py diff --git a/cellstar/utils/image_util.py b/unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py similarity index 100% rename from cellstar/utils/image_util.py rename to unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py diff --git a/cellstar/utils/index.py b/unmaintained_plugins/CellProfiler3/cellstar/utils/index.py similarity index 100% rename from cellstar/utils/index.py rename to unmaintained_plugins/CellProfiler3/cellstar/utils/index.py diff --git a/cellstar/utils/params_util.py b/unmaintained_plugins/CellProfiler3/cellstar/utils/params_util.py similarity index 100% rename from cellstar/utils/params_util.py rename to unmaintained_plugins/CellProfiler3/cellstar/utils/params_util.py From 662bef04ae3904799f88ee71fa357cd6fee1e891 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 9 May 2023 12:15:19 -0700 Subject: [PATCH 3/8] delete unnecessary folder --- cellprofiler_plugins/__init__.py | 0 cellprofiler_plugins/setting.py | 33 -------------------------------- 2 files changed, 33 deletions(-) delete mode 100644 cellprofiler_plugins/__init__.py delete mode 100644 cellprofiler_plugins/setting.py diff --git a/cellprofiler_plugins/__init__.py b/cellprofiler_plugins/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/cellprofiler_plugins/setting.py b/cellprofiler_plugins/setting.py deleted file mode 100644 index 16da7509..00000000 --- a/cellprofiler_plugins/setting.py +++ /dev/null @@ -1,33 +0,0 @@ -""" Settings.py - GUIs for module settings -""" - -import cellprofiler.setting - -class MeasurementMultiChoiceForCategory(cellprofiler.setting.MeasurementMultiChoice): - '''A multi-choice setting for selecting multiple measurements within a given category''' - - def __init__(self, text, category_chooser, value='', *args, **kwargs): - '''Initialize the measurement multi-choice - - At initialization, the choices are empty because the measurements - can't be fetched here. It's done (bit of a hack) in test_valid. - ''' - super(cellprofiler.setting.MeasurementMultiChoice, self).__init__(text, [], value, *args, **kwargs) - self.category_chooser = category_chooser - - def populate_choices(self, pipeline): - # - # Find our module - # - for module in pipeline.modules(): - for setting in module.visible_settings(): - if id(setting) == id(self): - break - columns = pipeline.get_measurement_columns(module) - - def valid_mc(c): - '''Disallow any measurement column with "," or "|" in its names. Must be from specified category.''' - return not any([any([bad in f for f in c[:2]]) for bad in (",", "|")]) and c[0] == self.category_chooser.get_value() - - self.set_choices([self.make_measurement_choice(c[0], c[1]) - for c in columns if valid_mc(c)]) From 035a3585680360a8a44e51de284e217cfb87ae26 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 9 May 2023 12:30:57 -0700 Subject: [PATCH 4/8] rename folder for clarity --- .../{CellProfiler4 => CellProfiler4_autoconverted}/DoGNet.py | 0 .../activecontourmodel.py | 0 .../blobdetection.py | 0 .../calculatehistogram.py | 0 .../calculatemoments.py | 0 .../classifypixelsunet.py | 0 .../constrainobjects.py | 0 .../convertoutlinestoobjects.py | 0 .../edgedetection.py | 0 .../exporttocellh5.py | 0 .../gammacorrection.py | 0 .../histogramequalization.py | 0 .../identifylinearobjects.py | 0 .../identifyyeastcells.py | 0 .../imagegradient.py | 0 .../laplacianofgaussian.py | 0 .../measureimagefocus.py | 0 .../measurepopulationcontext.py | 0 .../measureradialentropy.py | 0 .../measuretrackquality.py | 0 .../mergeobjects.py | 0 .../{CellProfiler4 => CellProfiler4_autoconverted}/nucleaizer.py | 0 .../{CellProfiler4 => CellProfiler4_autoconverted}/predict.py | 0 .../randomwalkeralgorithm.py | 0 .../rescalemeansd.py | 0 .../rescalemodepercentile.py | 0 .../{CellProfiler4 => CellProfiler4_autoconverted}/runimagej.py | 0 .../save16bitpngs.py | 0 .../{CellProfiler4 => CellProfiler4_autoconverted}/seedobjects.py | 0 .../shollanalysis.py | 0 .../spectralanalysis.py | 0 .../testallthresholds.py | 0 .../tophattransform.py | 0 .../transformfilters.py | 0 .../{CellProfiler4 => CellProfiler4_autoconverted}/transforms.py | 0 35 files changed, 0 insertions(+), 0 deletions(-) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/DoGNet.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/activecontourmodel.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/blobdetection.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/calculatehistogram.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/calculatemoments.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/classifypixelsunet.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/constrainobjects.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/convertoutlinestoobjects.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/edgedetection.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/exporttocellh5.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/gammacorrection.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/histogramequalization.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/identifylinearobjects.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/identifyyeastcells.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/imagegradient.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/laplacianofgaussian.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/measureimagefocus.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/measurepopulationcontext.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/measureradialentropy.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/measuretrackquality.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/mergeobjects.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/nucleaizer.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/predict.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/randomwalkeralgorithm.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/rescalemeansd.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/rescalemodepercentile.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/runimagej.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/save16bitpngs.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/seedobjects.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/shollanalysis.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/spectralanalysis.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/testallthresholds.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/tophattransform.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/transformfilters.py (100%) rename unmaintained_plugins/{CellProfiler4 => CellProfiler4_autoconverted}/transforms.py (100%) diff --git a/unmaintained_plugins/CellProfiler4/DoGNet.py b/unmaintained_plugins/CellProfiler4_autoconverted/DoGNet.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/DoGNet.py rename to unmaintained_plugins/CellProfiler4_autoconverted/DoGNet.py diff --git a/unmaintained_plugins/CellProfiler4/activecontourmodel.py b/unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/activecontourmodel.py rename to unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py diff --git a/unmaintained_plugins/CellProfiler4/blobdetection.py b/unmaintained_plugins/CellProfiler4_autoconverted/blobdetection.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/blobdetection.py rename to unmaintained_plugins/CellProfiler4_autoconverted/blobdetection.py diff --git a/unmaintained_plugins/CellProfiler4/calculatehistogram.py b/unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/calculatehistogram.py rename to unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py diff --git a/unmaintained_plugins/CellProfiler4/calculatemoments.py b/unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/calculatemoments.py rename to unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py diff --git a/unmaintained_plugins/CellProfiler4/classifypixelsunet.py b/unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/classifypixelsunet.py rename to unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py diff --git a/unmaintained_plugins/CellProfiler4/constrainobjects.py b/unmaintained_plugins/CellProfiler4_autoconverted/constrainobjects.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/constrainobjects.py rename to unmaintained_plugins/CellProfiler4_autoconverted/constrainobjects.py diff --git a/unmaintained_plugins/CellProfiler4/convertoutlinestoobjects.py b/unmaintained_plugins/CellProfiler4_autoconverted/convertoutlinestoobjects.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/convertoutlinestoobjects.py rename to unmaintained_plugins/CellProfiler4_autoconverted/convertoutlinestoobjects.py diff --git a/unmaintained_plugins/CellProfiler4/edgedetection.py b/unmaintained_plugins/CellProfiler4_autoconverted/edgedetection.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/edgedetection.py rename to unmaintained_plugins/CellProfiler4_autoconverted/edgedetection.py diff --git a/unmaintained_plugins/CellProfiler4/exporttocellh5.py b/unmaintained_plugins/CellProfiler4_autoconverted/exporttocellh5.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/exporttocellh5.py rename to unmaintained_plugins/CellProfiler4_autoconverted/exporttocellh5.py diff --git a/unmaintained_plugins/CellProfiler4/gammacorrection.py b/unmaintained_plugins/CellProfiler4_autoconverted/gammacorrection.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/gammacorrection.py rename to unmaintained_plugins/CellProfiler4_autoconverted/gammacorrection.py diff --git a/unmaintained_plugins/CellProfiler4/histogramequalization.py b/unmaintained_plugins/CellProfiler4_autoconverted/histogramequalization.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/histogramequalization.py rename to unmaintained_plugins/CellProfiler4_autoconverted/histogramequalization.py diff --git a/unmaintained_plugins/CellProfiler4/identifylinearobjects.py b/unmaintained_plugins/CellProfiler4_autoconverted/identifylinearobjects.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/identifylinearobjects.py rename to unmaintained_plugins/CellProfiler4_autoconverted/identifylinearobjects.py diff --git a/unmaintained_plugins/CellProfiler4/identifyyeastcells.py b/unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/identifyyeastcells.py rename to unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py diff --git a/unmaintained_plugins/CellProfiler4/imagegradient.py b/unmaintained_plugins/CellProfiler4_autoconverted/imagegradient.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/imagegradient.py rename to unmaintained_plugins/CellProfiler4_autoconverted/imagegradient.py diff --git a/unmaintained_plugins/CellProfiler4/laplacianofgaussian.py b/unmaintained_plugins/CellProfiler4_autoconverted/laplacianofgaussian.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/laplacianofgaussian.py rename to unmaintained_plugins/CellProfiler4_autoconverted/laplacianofgaussian.py diff --git a/unmaintained_plugins/CellProfiler4/measureimagefocus.py b/unmaintained_plugins/CellProfiler4_autoconverted/measureimagefocus.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/measureimagefocus.py rename to unmaintained_plugins/CellProfiler4_autoconverted/measureimagefocus.py diff --git a/unmaintained_plugins/CellProfiler4/measurepopulationcontext.py b/unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/measurepopulationcontext.py rename to unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py diff --git a/unmaintained_plugins/CellProfiler4/measureradialentropy.py b/unmaintained_plugins/CellProfiler4_autoconverted/measureradialentropy.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/measureradialentropy.py rename to unmaintained_plugins/CellProfiler4_autoconverted/measureradialentropy.py diff --git a/unmaintained_plugins/CellProfiler4/measuretrackquality.py b/unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/measuretrackquality.py rename to unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py diff --git a/unmaintained_plugins/CellProfiler4/mergeobjects.py b/unmaintained_plugins/CellProfiler4_autoconverted/mergeobjects.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/mergeobjects.py rename to unmaintained_plugins/CellProfiler4_autoconverted/mergeobjects.py diff --git a/unmaintained_plugins/CellProfiler4/nucleaizer.py b/unmaintained_plugins/CellProfiler4_autoconverted/nucleaizer.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/nucleaizer.py rename to unmaintained_plugins/CellProfiler4_autoconverted/nucleaizer.py diff --git a/unmaintained_plugins/CellProfiler4/predict.py b/unmaintained_plugins/CellProfiler4_autoconverted/predict.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/predict.py rename to unmaintained_plugins/CellProfiler4_autoconverted/predict.py diff --git a/unmaintained_plugins/CellProfiler4/randomwalkeralgorithm.py b/unmaintained_plugins/CellProfiler4_autoconverted/randomwalkeralgorithm.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/randomwalkeralgorithm.py rename to unmaintained_plugins/CellProfiler4_autoconverted/randomwalkeralgorithm.py diff --git a/unmaintained_plugins/CellProfiler4/rescalemeansd.py b/unmaintained_plugins/CellProfiler4_autoconverted/rescalemeansd.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/rescalemeansd.py rename to unmaintained_plugins/CellProfiler4_autoconverted/rescalemeansd.py diff --git a/unmaintained_plugins/CellProfiler4/rescalemodepercentile.py b/unmaintained_plugins/CellProfiler4_autoconverted/rescalemodepercentile.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/rescalemodepercentile.py rename to unmaintained_plugins/CellProfiler4_autoconverted/rescalemodepercentile.py diff --git a/unmaintained_plugins/CellProfiler4/runimagej.py b/unmaintained_plugins/CellProfiler4_autoconverted/runimagej.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/runimagej.py rename to unmaintained_plugins/CellProfiler4_autoconverted/runimagej.py diff --git a/unmaintained_plugins/CellProfiler4/save16bitpngs.py b/unmaintained_plugins/CellProfiler4_autoconverted/save16bitpngs.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/save16bitpngs.py rename to unmaintained_plugins/CellProfiler4_autoconverted/save16bitpngs.py diff --git a/unmaintained_plugins/CellProfiler4/seedobjects.py b/unmaintained_plugins/CellProfiler4_autoconverted/seedobjects.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/seedobjects.py rename to unmaintained_plugins/CellProfiler4_autoconverted/seedobjects.py diff --git a/unmaintained_plugins/CellProfiler4/shollanalysis.py b/unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/shollanalysis.py rename to unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py diff --git a/unmaintained_plugins/CellProfiler4/spectralanalysis.py b/unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/spectralanalysis.py rename to unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py diff --git a/unmaintained_plugins/CellProfiler4/testallthresholds.py b/unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/testallthresholds.py rename to unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py diff --git a/unmaintained_plugins/CellProfiler4/tophattransform.py b/unmaintained_plugins/CellProfiler4_autoconverted/tophattransform.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/tophattransform.py rename to unmaintained_plugins/CellProfiler4_autoconverted/tophattransform.py diff --git a/unmaintained_plugins/CellProfiler4/transformfilters.py b/unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/transformfilters.py rename to unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py diff --git a/unmaintained_plugins/CellProfiler4/transforms.py b/unmaintained_plugins/CellProfiler4_autoconverted/transforms.py similarity index 100% rename from unmaintained_plugins/CellProfiler4/transforms.py rename to unmaintained_plugins/CellProfiler4_autoconverted/transforms.py From 7dc85eef478a66f0e6a6d516cbf65d1cd9c6e0c8 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 9 May 2023 12:37:58 -0700 Subject: [PATCH 5/8] add readme to CP4_autoconverted --- unmaintained_plugins/CellProfiler4_autoconverted/README.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 unmaintained_plugins/CellProfiler4_autoconverted/README.md diff --git a/unmaintained_plugins/CellProfiler4_autoconverted/README.md b/unmaintained_plugins/CellProfiler4_autoconverted/README.md new file mode 100644 index 00000000..8c8bbff2 --- /dev/null +++ b/unmaintained_plugins/CellProfiler4_autoconverted/README.md @@ -0,0 +1,2 @@ +Plugins in the CellProfiler4_autoconverted folder were automatically converted from Python2 to Python3 in preparation for compatability with CellProfiler4, but +they have not been tested for functionality. From b06f02b8b49c40f7bc4a634065336d56f4faa451 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 23 May 2023 08:24:14 -0700 Subject: [PATCH 6/8] reorganize unmaintained tests --- {tests => unmaintained_tests}/test_blobdetection.py | 0 {tests => unmaintained_tests}/test_constrainobjects.py | 0 {tests => unmaintained_tests}/test_edgedetection.py | 0 {tests => unmaintained_tests}/test_gammacorrection.py | 0 {tests => unmaintained_tests}/test_identifyyeastcells.py | 0 {tests => unmaintained_tests}/test_imagegradient.py | 0 {tests => unmaintained_tests}/test_laplacianofgaussian.py | 0 {tests => unmaintained_tests}/test_measuretrackquality.py | 0 {tests => unmaintained_tests}/test_mergeobjects.py | 0 {tests => unmaintained_tests}/test_randomwalkeralgorithm.py | 0 {tests => unmaintained_tests}/test_seedobjects.py | 0 {tests => unmaintained_tests}/test_shollanalysis.py | 0 {tests => unmaintained_tests}/test_tophattransform.py | 0 13 files changed, 0 insertions(+), 0 deletions(-) rename {tests => unmaintained_tests}/test_blobdetection.py (100%) rename {tests => unmaintained_tests}/test_constrainobjects.py (100%) rename {tests => unmaintained_tests}/test_edgedetection.py (100%) rename {tests => unmaintained_tests}/test_gammacorrection.py (100%) rename {tests => unmaintained_tests}/test_identifyyeastcells.py (100%) rename {tests => unmaintained_tests}/test_imagegradient.py (100%) rename {tests => unmaintained_tests}/test_laplacianofgaussian.py (100%) rename {tests => unmaintained_tests}/test_measuretrackquality.py (100%) rename {tests => unmaintained_tests}/test_mergeobjects.py (100%) rename {tests => unmaintained_tests}/test_randomwalkeralgorithm.py (100%) rename {tests => unmaintained_tests}/test_seedobjects.py (100%) rename {tests => unmaintained_tests}/test_shollanalysis.py (100%) rename {tests => unmaintained_tests}/test_tophattransform.py (100%) diff --git a/tests/test_blobdetection.py b/unmaintained_tests/test_blobdetection.py similarity index 100% rename from tests/test_blobdetection.py rename to unmaintained_tests/test_blobdetection.py diff --git a/tests/test_constrainobjects.py b/unmaintained_tests/test_constrainobjects.py similarity index 100% rename from tests/test_constrainobjects.py rename to unmaintained_tests/test_constrainobjects.py diff --git a/tests/test_edgedetection.py b/unmaintained_tests/test_edgedetection.py similarity index 100% rename from tests/test_edgedetection.py rename to unmaintained_tests/test_edgedetection.py diff --git a/tests/test_gammacorrection.py b/unmaintained_tests/test_gammacorrection.py similarity index 100% rename from tests/test_gammacorrection.py rename to unmaintained_tests/test_gammacorrection.py diff --git a/tests/test_identifyyeastcells.py b/unmaintained_tests/test_identifyyeastcells.py similarity index 100% rename from tests/test_identifyyeastcells.py rename to unmaintained_tests/test_identifyyeastcells.py diff --git a/tests/test_imagegradient.py b/unmaintained_tests/test_imagegradient.py similarity index 100% rename from tests/test_imagegradient.py rename to unmaintained_tests/test_imagegradient.py diff --git a/tests/test_laplacianofgaussian.py b/unmaintained_tests/test_laplacianofgaussian.py similarity index 100% rename from tests/test_laplacianofgaussian.py rename to unmaintained_tests/test_laplacianofgaussian.py diff --git a/tests/test_measuretrackquality.py b/unmaintained_tests/test_measuretrackquality.py similarity index 100% rename from tests/test_measuretrackquality.py rename to unmaintained_tests/test_measuretrackquality.py diff --git a/tests/test_mergeobjects.py b/unmaintained_tests/test_mergeobjects.py similarity index 100% rename from tests/test_mergeobjects.py rename to unmaintained_tests/test_mergeobjects.py diff --git a/tests/test_randomwalkeralgorithm.py b/unmaintained_tests/test_randomwalkeralgorithm.py similarity index 100% rename from tests/test_randomwalkeralgorithm.py rename to unmaintained_tests/test_randomwalkeralgorithm.py diff --git a/tests/test_seedobjects.py b/unmaintained_tests/test_seedobjects.py similarity index 100% rename from tests/test_seedobjects.py rename to unmaintained_tests/test_seedobjects.py diff --git a/tests/test_shollanalysis.py b/unmaintained_tests/test_shollanalysis.py similarity index 100% rename from tests/test_shollanalysis.py rename to unmaintained_tests/test_shollanalysis.py diff --git a/tests/test_tophattransform.py b/unmaintained_tests/test_tophattransform.py similarity index 100% rename from tests/test_tophattransform.py rename to unmaintained_tests/test_tophattransform.py From 67a4b118921f17afe1ee5dc4bac70ac735e0f7f9 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 23 May 2023 15:07:26 -0700 Subject: [PATCH 7/8] reorganize --- .../dummyscript.py => runimagejscript_dummyscript.py} | 0 tests/{modules => }/test_runimagejscript.py | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename tests/resources/{modules/runimagejscript/dummyscript.py => runimagejscript_dummyscript.py} (100%) rename tests/{modules => }/test_runimagejscript.py (100%) diff --git a/tests/resources/modules/runimagejscript/dummyscript.py b/tests/resources/runimagejscript_dummyscript.py similarity index 100% rename from tests/resources/modules/runimagejscript/dummyscript.py rename to tests/resources/runimagejscript_dummyscript.py diff --git a/tests/modules/test_runimagejscript.py b/tests/test_runimagejscript.py similarity index 100% rename from tests/modules/test_runimagejscript.py rename to tests/test_runimagejscript.py From 0cb40784e1bca469f31a2c048de1026f1ddca514 Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Tue, 23 May 2023 15:36:03 -0700 Subject: [PATCH 8/8] add Barcodes.csv example for CallBarcodes --- tests/resources/callbarcodes_Barcodes.csv | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 tests/resources/callbarcodes_Barcodes.csv diff --git a/tests/resources/callbarcodes_Barcodes.csv b/tests/resources/callbarcodes_Barcodes.csv new file mode 100644 index 00000000..0f6f6e35 --- /dev/null +++ b/tests/resources/callbarcodes_Barcodes.csv @@ -0,0 +1,6 @@ +gene_symbol,sgRNA +ABCF1,GCAACACATCAATGTTGGGA +ADAR,TTCTTGTAGGGTGAACACCG +SLC25A6,CGAAGTTGAGGGCTTGAGTG +ANXA2,GGTCCTTCTCTGGTAGGCGA +nontargeting,CGCAATCCCTTAGGATAGCC \ No newline at end of file