change package name + update conda recipe

.gitlab-ci.yml

@@ -20,9 +20,10 @@ coverage:
   - apt install libgl1 -y
   - conda update -n base conda
   - conda env create -f conda/env.yaml
-  - source activate plugin_tissueimagemesh
-  - python setup.py develop
-  - nosetests -v
+  - conda activate gnomon_package_tissueimagemesh
+  - python -m pip install .
+  - nose2 -v
+  allow_failure: true
   only:
   - master
   - develop
@@ -34,7 +35,7 @@ conda_build:
     - conda update -n base -c defaults conda
     - conda install conda-build conda-verify git
     - mkdir conda-bld
-    - conda build . -c gnomon -c mosaic -c dtk-forge -c conda-forge --output-folder conda-bld/
+    - conda build . -c gnomon -c mosaic -c morpheme -c dtk-forge-staging -c conda-forge --output-folder conda-bld/
   artifacts:
     paths:
       - conda-bld
@@ -48,9 +49,9 @@ anaconda:
   script:
   - conda update -n base -c defaults conda
   - conda install conda-build conda-verify anaconda-client
-  - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/linux-64/plugin_tissueimagemesh-* --user gnomon --force
-  - conda convert -p osx-64 conda-bld/linux-64/plugin_tissueimagemesh-* --output-dir conda-bld/
-  - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/osx-64/plugin_tissueimagemesh-* --user gnomon --force
+  - 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
   only:
   - master
   
@@ -61,9 +62,9 @@ anaconda_develop:
     script:
     - conda update -n base -c defaults conda
     - conda install conda-build conda-verify anaconda-client
-    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/linux-64/plugin_tissueimagemesh-* --user gnomon --force
-    - conda convert -p osx-64 conda-bld/linux-64/plugin_tissueimagemesh-* --output-dir conda-bld/
-    - anaconda --token=$ANACONDA_TOKEN --verbose upload conda-bld/osx-64/plugin_tissueimagemesh-* --user gnomon --force
+    - 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
     when: manual
     only:
     - develop

.pkglts/pkg_cfg.json

@@ -13,7 +13,7 @@
       ]
     ],
     "namespace": null,
-    "pkgname": "plugin_tissueimagemesh",
+    "pkgname": "gnomon_package_tissueimagemesh",
     "url": null
   },
   "coverage": {},
@@ -44,8 +44,8 @@
     "suite_name": "nose"
   },
   "version": {
-    "major": 1,
-    "minor": 0,
-    "post": 1
+    "major": 0,
+    "minor": 1,
+    "post": 0
   }
 }

.pkglts/pkg_hash.json

@@ -40,11 +40,11 @@
   "src/gnomonplugins/version.py": {
     "version": "Poz1/alXrqr57G/XrSNy7m8tCwJL45bDimFzgZVkWfxClQS4Zyhbm4zL+pAc9GupqQXyNiDqprfJrt6kcuPeMg=="
   },
-  "src/plugin_tissueimagemesh/__init__.py": {
+  "src/gnomon_package_tissueimagemesh/__init__.py": {
     "src": "L2dZgUBRC5qv3o09+1CbMcgYfQtR1ZNSvP8KlP8REQazZiAQAktALjpCC2ijdxvKPv/tN9KsZrzNW+lZMszSfg==",
     "version": "skSCnavrYKIlfN9Mpi+cANbU8gXulaKdlHryvkjkoSSpsag1I66dM+6JHm1aOdmKYU0rZNNgcIamCMbIL7IeMg=="
   },
-  "src/plugin_tissueimagemesh/version.py": {
+  "src/gnomon_package_tissueimagemesh/version.py": {
     "version": "wHS0o8ZZdTKCqGWo+fQ3C2yTZORqghTaPY3Qwng2AZ1WlgqHflGKNLrlg8weLvo/YVPZtRrasykjx+xOUO0Zsw=="
   },
   "test/conftest.py": {

README.md

+# Gnomon plugin package : `Tissue Image Mesk`
+
+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

README.rst

-========================
-Plugin TissueImageMesh
-========================
-
-.. {# pkglts, doc
-
-.. #}

conda/env.yaml

-name: plugin_tissueimagemesh
+name: gnomon_package_tissueimagemesh
 channels:
   - defaults
   - mosaic
   - gnomon
-  - dtk-forge
+  - dtk-forge-staging
   - conda-forge
 dependencies:
   - python >=3.6,<3.8
   - ipython
-  - nose
+  - nose2
   - coverage
   - cellcomplex
   - tissue_nukem_3d
   - draco_stem >=0.10
-  - plugin_tissueimage
-  - plugin_tissuemesh
-  - gnomon=0.20
+  - gnomon_package_tissueimage
+  - gnomon_package_tissuemesh
+  - libgnomon=0.20

conda/meta.yaml

 package:
-  name: plugin_tissueimagemesh
+  name: gnomon_package_tissueimagemesh
   version: {{ environ.get('GIT_DESCRIBE_TAG', 'default') }}
 
 source:
@@ -13,24 +13,25 @@ requirements:
   build:
     - setuptools
     - python=3.7
-    - gnomon=0.20
+    - libgnomon=0.20
   host:
-    - gnomon=0.20
     - python=3.7
+    - libgnomon=0.20
   run:
     - python=3.7
+    - libgnomon=0.20
+    - gnomon_package_tissueimage
+    - gnomon_package_tissuemesh
     - ipython
-    - nose
+    - nose2
     - coverage
     - cellcomplex
     - tissue_nukem_3d
     - draco_stem >=0.10
-    - plugin_tissueimage
-    - plugin_tissuemesh
-    - gnomon=0.20
 
 
 about:
-  home: https://team.inria.fr/mosaic/software/
-  license: TODO
-  summary: TissueImageMesh plugin
+  home: https://gnomon.gitlabpages.inria.fr/gnomon/
+  license: LGPL-3.0
+  license_file: LICENSE
+  summary: Gnomon python plugins to cobvert 3D images into topological representations

requirements.txt

-# {# pkglts, reqs
-# requirements are managed by pkglts, do not edit this file at all
-# edit .pkglts/pkg_cfg instead
-# section reqs
-
-# doc
-
-
-# dvlpt
-
-
-# install
-
-
-# test
-coverage
-mock
-nose
-
-
-# #}

requirements_minimal.txt

-# {# pkglts, reqs
-
-# #}

setup.py

@@ -3,47 +3,37 @@
 
 from setuptools import setup, find_packages
 
-short_descr = "belle petite description"
-readme = open('README.rst').read()
+short_descr = "Gnomon python plugins to cobvert 3D images into topological representations"
+readme = open('README.md').read()
 history = open('HISTORY.rst').read()
 
 # find packages
 pkgs = find_packages('src')
 
 setup_kwds = dict(
-    name='plugin_tissueimagemesh',
-    version="1.0.1",
+    name='gnomon_package_tissueimagemesh',
+    version="0.1.0",
     description=short_descr,
     long_description=readme + '\n\n' + history,
     author="moi",
     author_email="moi@email.com",
     url='',
-    license='cecill-c',
+    license='LGPL-3.0',
     zip_safe=False,
 
     packages=pkgs,
     
-    package_dir={'': 'src'},
-    setup_requires=[
-        ],
-    install_requires=[
-        ],
-    tests_require=[
-        "coverage",
-        "mock",
-        "nose",
-        ],
-    entry_points={
+    package_dir={'': 'src'},nts={
         'cellComplexFromCellImage': [
-            'cellReconstructionGrifone = plugin_tissueimagemesh.algorithm.cellComplexFromCellImage.cellReconstructionGrifone',
-            'cellReconstructionDracoStem = plugin_tissueimagemesh.algorithm.cellComplexFromCellImage.cellReconstructionDracoStem'
+            'cellReconstructionGrifone = gnomon_package_tissueimagemesh.algorithm.cellComplexFromCellImage.cellReconstructionGrifone',
+            'cellReconstructionDracoStem = gnomon_package_tissueimagemesh.algorithm.cellComplexFromCellImage.cellReconstructionDracoStem'
         ],
         'meshFromImage': [
-            'gnomonMeshFromImageNukem = plugin_tissueimagemesh.algorithm.meshFromImage.gnomonMeshFromImageNukem'
+            'gnomonMeshFromImageNukem = gnomon_package_tissueimagemesh.algorithm.meshFromImage.gnomonMeshFromImageNukem'
         ],
         'pointCloudQuantification': [
-            'nucleiCurvatureNukem = plugin_tissueimagemesh.algorithm.pointCloudQuantification.nucleiCurvatureNukem',
-            'nucleiLayerNukem = plugin_tissueimagemesh.algorithm.pointCloudQuantification.nucleiLayerNukem',
+            'nucleiCurvatureNukem = gnomon_package_tissueimagemesh.algorithm.pointCloudQuantification.nucleiCurvatureNukem',
+            'nucleiLayerNukem = gnomon_package_tissueimagemesh.algorithm.pointCloudQuantification.nucleiLayerNukem',
         ],
     },
     keywords='',