Merge tag '1.0.0' into develop

Version 1.0.0

.gitlab-ci.yml

@@ -20,7 +20,8 @@ releaseTest:
   script:
     - . "/builds/miniconda3/etc/profile.d/conda.sh"
     - conda activate base
-    - mamba env update -f conda/env.yaml
+    - conda env remove -n gnomon_package_tissueimagemesh
+    - mamba env create -f conda/env.yaml
     - conda activate gnomon_package_tissueimagemesh
     - python -m pip install .
     - nose2 -v
@@ -37,7 +38,8 @@ test_MR_linux:
   script:
     - . "/builds/miniconda3/etc/profile.d/conda.sh"
     - conda activate base
-    - mamba env update -f conda/env.yaml
+    - conda env remove -n gnomon_package_tissueimagemesh
+    - mamba env create -f conda/env.yaml
     - conda activate gnomon_package_tissueimagemesh
     - python -m pip install .
     - nose2 -v
@@ -72,7 +74,8 @@ test_MR_macos:
   script:
     - source /Users/ci/miniconda3/etc/profile.d/conda.sh
     - conda activate base
-    - mamba env update -f conda/env.yaml
+    - conda env remove -n gnomon_package_tissueimagemesh
+    - mamba env create -f conda/env.yaml
     - conda activate gnomon_package_tissueimagemesh
     - pip install .
     - nose2 -v
@@ -124,9 +127,7 @@ anaconda:
   script:
     - . "/builds/miniconda3/etc/profile.d/conda.sh"
     - conda activate base
-    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/linux-64/gnomon_package_tissueimagemesh-* --user gnomon --force
-    - conda convert -p osx-64 conda-bld/linux-64/gnomon_package_tissueimagemesh-* --output-dir conda-bld/
-    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/osx-64/gnomon_package_tissueimagemesh-* --user gnomon --force
+    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/noarch/gnomon_package_tissueimagemesh-* --user gnomon --force
   only:
     - master
 
@@ -138,9 +139,7 @@ anaconda_develop:
   script:
     - . "/builds/miniconda3/etc/profile.d/conda.sh"
     - conda activate base
-    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/linux-64/gnomon_package_tissueimagemesh-* --user gnomon --force
-    - conda convert -p osx-64 conda-bld/linux-64/gnomon_package_tissueimagemesh-* --output-dir conda-bld/
-    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/osx-64/gnomon_package_tissueimagemesh-* --user gnomon --force
+    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/noarch/gnomon_package_tissueimagemesh-* --user gnomon --force
   when: manual
   only:
     - develop

CHANGES.md

 # ChangeLog
 
+## version 1.0.0 - 2024-03-27
+* gnomon 1.0.0
+* progress bar + message
+* more operation on mesh
+
+
 ## version 0.3.0 - 2023-07-10
 * gnomon 0.81.0
 * new cell layer/curvature plugin

README.md

-# Gnomon plugin package : `Tissue Image Mesk`
+# Gnomon plugin package : `Tissue Image Mesh`
 
 This package contains Python plugins for the [Gnomon computational platform](https://gnomon.gitlabpages.inria.fr/gnomon/) to convert 3D images into topological representations.
\ No newline at end of file

conda/env.yaml

@@ -4,12 +4,13 @@ channels:
   - mosaic
   - morpheme
   - gnomon
-  - dtk-forge-staging
+  - dtk-forge6
   - conda-forge
 dependencies:
   - python=3.9
-  - libgnomon>=0.72.0
+  - gnomon=1.0
   - gnomon_package_tissueimage
+  - gnomon_package_tissuemesh
   - ipython
   - nose2
   - coverage

conda/meta.yaml

@@ -6,6 +6,7 @@ source:
   path: ../
 
 build:
+  noarch: python
   number: {{ GIT_DESCRIBE_NUMBER }}
   preserve_egg_dir: True
 
@@ -13,14 +14,13 @@ requirements:
   build:
     - setuptools
     - python=3.9
-    - libgnomon>=0.81.0
   host:
     - python=3.9
-    - libgnomon>=0.81.0
   run:
     - python=3.9
-    - libgnomon>=0.81.0
+    - gnomon=1.0
     - gnomon_package_tissueimage
+    - gnomon_package_tissuemesh
     - ipython
     - nose2
     - coverage
@@ -31,6 +31,7 @@ requirements:
 
 about:
   home: https://gnomon.gitlabpages.inria.fr/gnomon/
-  license: LGPL-3.0
+  dev_url: https://gitlab.inria.fr/gnomon/gnomon-packages/gnomon-package-tissueimagemesh
+  license: LGPL-3.0-or-later
   license_file: LICENSE
   summary: Gnomon python plugins to convert 3D images into topological representations

setup.py

@@ -12,7 +12,7 @@ pkgs = find_packages('src')
 
 setup_kwds = dict(
     name='gnomon_package_tissueimagemesh',
-    version="0.3.0",
+    version="1.0.0",
     description=short_descr,
     long_description=readme + '\n\n' + history,
     author="moi",

src/gnomon_package_tissueimagemesh/algorithm/cellComplexFromCellImage/cellReconstructionDracoStem.py

@@ -13,7 +13,7 @@ from gnomon.utils import algorithmPlugin
 from gnomon.utils.decorators import cellImageInput, cellComplexOutput
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="DRACO Reconstruction")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="DRACO Reconstruction")
 @cellImageInput('tissue', data_plugin="gnomonCellImageDataTissueImage")
 @cellComplexOutput('topomesh', data_plugin="gnomonCellComplexDataPropertyTopomesh")
 class cellReconstructionDracoStem(gnomonAbstractCellComplexFromCellImage):

src/gnomon_package_tissueimagemesh/algorithm/cellComplexFromCellImage/cellReconstructionGrifone.py

@@ -14,7 +14,7 @@ from gnomon.utils import algorithmPlugin
 from gnomon.utils.decorators import cellImageInput, cellComplexOutput
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="GRIFONE Reconstruction")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="GRIFONE Reconstruction")
 @cellImageInput('seg_img', data_plugin="gnomonCellImageDataTissueImage")
 @cellComplexOutput('element_topomesh', data_plugin="gnomonCellComplexDataPropertyTopomesh")
 class cellReconstructionGrifone(gnomonAbstractCellComplexFromCellImage):

src/gnomon_package_tissueimagemesh/algorithm/cellImageQuantification/surfaceMeshCellCurvature.py

@@ -17,7 +17,7 @@ from timagetk_geometry.image_surface.tissue_image_mesh import tissue_image_surfa
 from timagetk_geometry.features.tissue_mesh import compute_cell_curvature_features
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Surface Mesh Curvature")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Surface Mesh Curvature")
 @meshInput('surface_topomesh', data_plugin="gnomonMeshDataPropertyTopomesh")
 @cellImageInput("tissue", data_plugin="gnomonCellImageDataTissueImage")
 @cellImageOutput("out_tissue", data_plugin="gnomonCellImageDataTissueImage")

src/gnomon_package_tissueimagemesh/algorithm/cellImageQuantification/surfaceMeshCellLayer.py

@@ -17,7 +17,7 @@ from timagetk_geometry.image_surface.tissue_image_mesh import tissue_image_surfa
 from timagetk_geometry.features.tissue_mesh import compute_cell_layer_feature
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Surface Mesh Layer")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Surface Mesh Layer")
 @meshInput('surface_topomesh', data_plugin="gnomonMeshDataPropertyTopomesh")
 @cellImageInput("tissue", data_plugin="gnomonCellImageDataTissueImage")
 @cellImageOutput("out_tissue", data_plugin="gnomonCellImageDataTissueImage")

src/gnomon_package_tissueimagemesh/algorithm/cellImageQuantification/surfaceMeshCellProperty.py

@@ -16,7 +16,7 @@ from timagetk.features.pandas_tools import cells_to_dataframe
 
 from timagetk_geometry.features.cells import compute_cell_surface_center_feature
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Surface Mesh Property")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Surface Mesh Property")
 @meshInput('surface_topomesh', data_plugin="gnomonMeshDataPropertyTopomesh")
 @cellImageInput("tissue", data_plugin="gnomonCellImageDataTissueImage")
 @cellImageOutput('out_tissue', data_plugin="gnomonCellImageDataTissueImage")

src/gnomon_package_tissueimagemesh/algorithm/cellImageQuantification/wallMeshImageSignal.py

@@ -16,7 +16,7 @@ from timagetk.features.pandas_tools import cells_to_dataframe
 from timagetk_geometry.signal_quantification.wall_mesh import quantify_wall_topomesh_signal_intensity
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Wall Mesh Signal")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Wall Mesh Signal")
 @meshInput('wall_topomesh', data_plugin="gnomonMeshDataPropertyTopomesh")
 @imageInput('img', data_plugin='gnomonImageDataMultiChannelImage')
 @cellImageInput("tissue", data_plugin="gnomonCellImageDataTissueImage")

src/gnomon_package_tissueimagemesh/algorithm/cellImageQuantification/wallMeshSignalPolarities.py

@@ -16,7 +16,7 @@ from timagetk.features.pandas_tools import cell_walls_to_dataframe
 from timagetk_geometry.signal_quantification.wall_mesh import quantify_wall_topomesh_membrane_signal_intensity, compute_wall_property
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Wall Signal Polarities")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Wall Signal Polarities")
 @meshInput('wall_topomesh', data_plugin="gnomonMeshDataPropertyTopomesh")
 @imageInput('img', data_plugin='gnomonImageDataMultiChannelImage')
 @cellImageInput("tissue", data_plugin="gnomonCellImageDataTissueImage")

src/gnomon_package_tissueimagemesh/algorithm/meshFilter/surfaceCellMeshDecimation.py

@@ -17,7 +17,7 @@ from cellcomplex.property_topomesh.extraction import contiguous_wisps_topomesh
 
 # {# gnomon, plugin.class
 # do not modify, any code after the gnomon tag will be overwritten
-@algorithmPlugin(version='0.1.0', coreversion='0.81.0', name="Surface cell mesh decimation")
+@algorithmPlugin(version='1.0.0', coreversion='1.0.0', name="Surface cell mesh decimation")
 @meshInput(attr='in_surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')
 @meshOutput(attr='surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')
 class surfaceCellMeshDecimation(gnomon.core.gnomonAbstractMeshFilter):

src/gnomon_package_tissueimagemesh/algorithm/meshFilter/surfaceCellMeshFlipOptimization.py

@@ -18,7 +18,7 @@ from timagetk_geometry.image_surface.tissue_image_mesh import surface_tissue_mes
 
 # {# gnomon, plugin.class
 # do not modify, any code after the gnomon tag will be overwritten
-@algorithmPlugin(version='0.1.0', coreversion='0.72.0', name="Cell Mesh Flip Optimization")
+@algorithmPlugin(version='1.0.0', coreversion='0.72.0', name="Cell Mesh Flip Optimization")
 @cellImageInput("seg_img", data_plugin="gnomonCellImageDataTissueImage")
 @meshInput(attr='in_surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')
 @meshOutput(attr='surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')

src/gnomon_package_tissueimagemesh/algorithm/meshFilter/surfaceMeshCellProjection.py

@@ -16,7 +16,7 @@ from timagetk_geometry.image_surface.tissue_image_mesh import surface_vertex_nor
 
 # {# gnomon, plugin.class
 # do not modify, any code after the gnomon tag will be overwritten
-@algorithmPlugin(version='0.1.0', coreversion='0.72.0', name="Surface Cell Projection")
+@algorithmPlugin(version='1.0.0', coreversion='0.72.0', name="Surface Cell Projection")
 @cellImageInput("seg_img", data_plugin="gnomonCellImageDataTissueImage")
 @meshInput(attr='in_surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')
 @meshOutput(attr='surface_topomesh', data_plugin='gnomonMeshDataPropertyTopomesh')

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/imageSurfaceMesh.py

@@ -18,7 +18,7 @@ from cellcomplex.property_topomesh.creation import triangle_topomesh
 from cellcomplex.utils import array_dict
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Surface Mesh")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Surface Mesh")
 @imageInput("img", data_plugin='gnomonImageDataMultiChannelImage')
 @meshOutput("topomesh", data_plugin="gnomonMeshDataPropertyTopomesh")
 class imageSurfaceMesh(gnomonAbstractMeshFromImage):

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/segmentationSurfaceMesh.py

@@ -16,7 +16,7 @@ from timagetk_geometry.image_surface.tissue_image_mesh import tissue_image_surfa
 from cellcomplex.property_topomesh.analysis import compute_topomesh_property
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Segmentation Surface Mesh")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Segmentation Surface Mesh")
 @cellImageInput("seg_img", data_plugin='gnomonCellImageDataTissueImage')
 @meshOutput("topomesh", data_plugin="gnomonMeshDataPropertyTopomesh")
 class segmentationSurfaceMesh(gnomonAbstractMeshFromImage):

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/segmentationWallMesh.py

@@ -14,7 +14,7 @@ from timagetk_geometry.image_surface.wall_mesh import tissue_image_wall_topomesh
 from cellcomplex.property_topomesh.analysis import compute_topomesh_property
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Cell Wall Meshes")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Cell Wall Meshes")
 @cellImageInput("seg_img", data_plugin='gnomonCellImageDataTissueImage')
 @meshOutput("topomesh", data_plugin="gnomonMeshDataPropertyTopomesh")
 class segmentationWallMesh(gnomonAbstractMeshFromImage):

src/gnomon_package_tissueimagemesh/algorithm/pointCloudQuantification/nucleiLayerEstimation.py

@@ -13,7 +13,7 @@ from timagetk.components.spatial_image import SpatialImage
 from timagetk_geometry.features.nuclei import nuclei_layer
 
 
-@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Nuclei L1 Estimation")
+@algorithmPlugin(version="1.0.0", coreversion="1.0.0", name="Nuclei L1 Estimation")
 @imageInput('img', data_plugin='gnomonImageDataMultiChannelImage')
 @meshInput('surface_topomesh', data_plugin="gnomonMeshDataPropertyTopomesh")
 @pointCloudInput("df", data_plugin="gnomonPointCloudDataPandas")