Merge pull request #14 from Image-Analysis-Hub/citests

Add automatic tests when the version is changed
Fix a bug on windows loading .pkl file
Tried to fix missing setuptools on one setup (not reproduced)
test do python 3.10 and 3.12, ubuntu, mac and windows

Author: gletort

.github/workflows/cross-platform.yml

@@ -0,0 +1,54 @@
+name: Cross-Platform Tests
+
+  ## activate tests when change the version, or a test
+on:
+  push:
+    #branches: [main]
+    paths:
+      - 'pyproject.toml'
+      - 'tox.ini'
+      - 'requirements*.txt'
+      - '.github/workflows/cross-platform.yml'
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        #os: [ubuntu-latest, macos-latest]
+        #os: [debian-latest]
+        python-version: ["3.10", "3.12"]
+        #python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}      
+

pyproject.toml

@@ -53,6 +53,15 @@ pyqt5 = [
 	"PyQtWebEngine",
 ]
 
+testing = [
+    "tox",
+    "pytest",
+    "pytest-cov",
+    "pytest-qt",
+    "napari",
+    "pyqt5",
+]
+
 [project.urls]
 "Bug Tracker" = "https://github.com/Image-Analysis-Hub/Epicure/issues"
 "Documentation" = "https://image-analysis-hub.github.io/Epicure/"

src/epicure/Utils.py

@@ -1094,6 +1094,7 @@ def get_border_cells( img ):
     labels += list( np.unique( img[ :, (height-2): ] ) )   ## bottom border
     labels += list( np.unique( img[ 0:2,] ) )   ## left border
     labels += list( np.unique( img[ (width-2):,] ) )   ## right border
+    labels = list( np.unique(labels) )
     return labels
 
 def count_neighbors( label_img, label ):
@@ -1175,6 +1176,13 @@ def shortcut_click_match( shortcut, event ):
             return False
         return True
 
+def is_windows():
+    """ Is running on windows or not """
+    try:
+        return platform.lower().startswith("win")
+    except:
+        return False
+
 def is_darwin():
     """ Test if OS is MacOS or not """
     try:

src/epicure/_version.py

@@ -17,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev193+g631d088.d20260324'
-__version_tuple__ = version_tuple = (0, 1, 'dev193', 'g631d088.d20260324')
+__version__ = version = '1.5.4.dev47+g2d83614.d20260513'
+__version_tuple__ = version_tuple = (1, 5, 4, 'dev47', 'g2d83614.d20260513')

src/epicure/epicuring.py

@@ -804,6 +804,10 @@ def load_epicure_data(self, epiname):
         """Load saved infos from file"""
         infile = open(epiname, "rb")
         try:
+            if ut.is_windows():
+               import pathlib
+               pathlib.PosixPath = pathlib.WindowsPath
+               #epidata = pickle.load( infile, encoding="utf8" )
             epidata = pickle.load( infile )
             #print(epidata)
             if "EpiMetaData" in epidata.keys():
@@ -815,9 +819,10 @@ def load_epicure_data(self, epiname):
                 self.load_epicure_data_old(epidata, infile)
         except Exception as e:
             if self.verbose > 1:
-                print(f"Line 619 - {type(e)} {e} - Could not read EpiCure data file {epiname}")
+                print(f" {type(e)} {e} - Could not read EpiCure data file {epiname}")
             else:
                 ut.show_warning(f"Could not read EpiCure data file {epiname}")
+                print(f" {type(e)} {e} - Could not read EpiCure data file {epiname}")
 
     def read_epidata(self, epidata):
         """Read the dict of saved state and initialize all instances with it"""

src/epicure/inspecting.py

@@ -537,7 +537,11 @@ def add_event_type(self, ind, sid, feature):
         if self.event_types.get(feature) is None:
             self.event_types[feature] = []
         self.event_types[feature].append(sid)
-        self.events.properties["score"][ind] = self.events.properties["score"][ind] + 1
+        score = self.events.properties["score"].copy()
+        score[ind] = score[ind] + 1
+        self.events.properties["score"] = score 
+        self.events.properties["score"].flags.writeable = True
+        #self.events.properties()
 
     def first_event(self, pos, label, featurename):
         """ Addition of the first event (initialize all) """
@@ -549,6 +553,10 @@ def first_event(self, pos, label, featurename):
         features["score"] = np.array([0], dtype="uint8")
         pts = [pos]
         self.events = self.viewer.add_points( np.array(pts), properties=features, face_color="score", size = int( self.event_size.value() ), symbol="x", name="Events", scale=self.viewer.layers["Segmentation"].scale )
+        props = self.events.properties
+        props["label"].flags.writeable = True
+        props["score"].flags.writeable = True
+        props["id"].flags.writeable = True
         self.add_event_type(0, sid, featurename)
         self.events.refresh()
         self.update_nevents_display()
@@ -586,9 +594,13 @@ def add_event(self, pos, label, reason, symb="x", color="white", force=False, re
             ind = len(self.events.data)
             sid = self.new_event_id()
             self.events.add(pos)
-            self.events.properties["label"][ind] = label
-            self.events.properties["id"][ind] = sid
-            self.events.properties["score"][ind] = 0
+            props = self.events.properties
+            props["label"].flags.writeable = True
+            props["score"].flags.writeable = True
+            props["id"].flags.writeable = True
+            props["label"][ind] = label
+            props["id"][ind] = sid
+            props["score"][ind] = 0
             self.add_event_type(ind, sid, reason)
 
         self.events.symbol.flags.writeable = True
@@ -772,7 +784,9 @@ def remove_event_types(self, sid):
 
     def decrease_score(self, ind):
         """ Decrease by one score of event at index ind. Delete it if reach 0"""
-        self.events.properties["score"][ind] = self.events.properties["score"][ind] - 1
+        score = self.events.properties["score"]
+        score.flags.writeable = True
+        score[ind] = score[ind] - 1
         if self.events.properties["score"][ind] == 0:
             self.exonerate_one( ind, remove_division=False )
             self.update_nevents_display()

src/epicure/resources/pixi.toml

@@ -10,6 +10,7 @@ platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
 python = "==3.10"
 numpy = "<2"
 pip = "*"
+setuptools = ">=65.0" 
 
 [pypi-dependencies]
 napari-epyseg = "==0.0.14"

src/tests/test_basics.py

@@ -6,31 +6,34 @@
 from epicure.start_epicuring import gui_files
 
 
-def test_load_movie():
+def test_load_movie( make_napari_viewer ):
     """ Read a standard tif movie """
     test_img = os.path.join(".", "test_data", "003_crop.tif")
-    epic = epi.EpiCure()
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure(viewer)
     epic.load_movie(test_img)
     assert epic.img.shape == (11,189,212)
     return
 
-def test_load_image():
+def test_load_image( make_napari_viewer ):
     """ Read a single image and a cellpose (labels) segmentation """
     test_img = os.path.join(".", "test_data", "static_image.tif")
     test_seg = os.path.join(".", "test_data", "static_image_cellpose.tif")
-    epic = epi.EpiCure()
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure(viewer)
     epic.load_movie(test_img)
     assert epic.img.shape == (1,507,585)
     epic.load_segmentation(test_seg)
     assert epic.seg.shape == epic.img.shape
     assert np.max(epic.seg) == 706
     return
 
-def test_load_movie_with_chanel():
+def test_load_movie_with_chanel( make_napari_viewer ):
     """ Read a tif movie with 2 channels """
     test_img = os.path.join(".", "test_data", "area3_Composite.tif")
     test_seg = os.path.join(".", "test_data", "area3_Composite_epyseg.tif")
-    epic = epi.EpiCure()
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure( viewer )
     resaxis, resval = epic.load_movie(test_img)
     # check the dimensions are correctly loaded
     assert epic.img.shape == (5,2,146,228)
@@ -43,19 +46,21 @@ def test_load_movie_with_chanel():
     assert np.mean(epic.img)>100
     return
 
-def test_load_segmentation():
+def test_load_segmentation( make_napari_viewer ):
     test_seg = os.path.join(".", "test_data", "003_crop_epyseg.tif")
-    epic = epi.EpiCure()
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure( viewer )
     epic.load_segmentation(test_seg)
     assert epic.seg.shape == (11,189,212)
     assert np.max(epic.seg) == 1294
     return
 
-def test_suggest():
+def test_suggest( make_napari_viewer ):
     """ Check segmentation file name suggestion """
     ## case 1: file doesn't exists, creates it
     test_img = os.path.join(".", "test_data", "003_crop.tif")
-    epic = epi.EpiCure()
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure(viewer)
     epic.load_movie(test_img)
     segfile = epic.suggest_segfile("epics")
     assert segfile is None
@@ -68,14 +73,15 @@ def test_suggest():
     assert segfile == absp 
     return
 
-def test_init_epic():
-    epic = epi.EpiCure()
+def test_init_epic( make_napari_viewer ):
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure(viewer)
     assert epic.img is None
     return
 
-def test_load_from_layers():
+def test_load_from_layers( make_napari_viewer ):
     """ Open a new EpiCure project from opened layers """
-    viewer = napari.Viewer(show=False)
+    viewer = make_napari_viewer()
     test_img = os.path.join(".", "test_data", "003_crop.tif")
     img, _, _, _, _, _ = ut.open_image(test_img, get_metadata=False, verbose=0)
     movie_layer = viewer.add_image(img, name="TestImage")
@@ -104,6 +110,7 @@ def test_load_from_layers():
     #viewer.show() # manual check
 
 if __name__ == "__main__":
+    test_load_movie()
     test_load_from_layers()
     test_load_image()
     print("********* Test basics completed ***********")

src/tests/test_editings.py

@@ -6,11 +6,11 @@
 import napari
 from vispy import keys
 
-def test_epicuring_bindings():
+def test_epicuring_bindings( make_napari_viewer ):
     """ Test shortcuts for displaying layers """
     test_img = os.path.join(".", "test_data", "003_crop.tif")
     test_seg = os.path.join(".", "test_data", "003_crop_epyseg.tif")
-    viewer = napari.Viewer(show=False)
+    viewer = make_napari_viewer()
     epic = epi.EpiCure(viewer)
     epic.load_movie(test_img)
     epic.go_epicure("test_epics", test_seg)
@@ -31,10 +31,10 @@ def test_epicuring_bindings():
     view.canvas.events.key_press(key=keys.Key("g"), modifiers=[])
     assert "EpicGrid" in epic.viewer.layers
 
-def test_merge():
+def test_merge( make_napari_viewer ):
     test_img = os.path.join(".", "test_data", "003_crop.tif")
     test_seg = os.path.join(".", "test_data", "003_crop_epyseg.tif")
-    viewer = napari.Viewer(show=False)
+    viewer = make_napari_viewer()
     epic = epi.EpiCure(viewer)
     epic.load_movie(test_img)
     epic.load_segmentation(test_seg)
@@ -55,10 +55,10 @@ def test_merge():
     assert val == 1296 
 
 
-def test_group():
+def test_group( make_napari_viewer ):
     test_img = os.path.join(".", "test_data", "003_crop.tif")
     test_seg = os.path.join(".", "test_data", "003_crop_epyseg.tif")
-    viewer = napari.Viewer(show=False)
+    viewer = make_napari_viewer()
     epic = epi.EpiCure(viewer)
     epic.load_movie(test_img)
     epic.go_epicure("test_epics", test_seg)

src/tests/test_operations.py

@@ -4,11 +4,12 @@
 import epicure.Utils as ut
 import napari
 
-def test_get_free_label():
+def test_get_free_label( make_napari_viewer ):
     ## test from a skeletonized movie
     test_mov = os.path.join(".", "test_data", "003_crop.tif")
     test_seg = os.path.join(".", "test_data", "003_crop_epyseg.tif")
-    epic = epi.EpiCure()
+    viewer = make_napari_viewer()
+    epic = epi.EpiCure(viewer)
     epic.load_movie(test_mov)
     #epic.viewer = napari.Viewer(show=False)
     epic.go_epicure("epics", test_seg)
@@ -29,11 +30,11 @@ def test_get_free_label():
 #    epic.inspecting.first_event((0,10,20), 10, "suspect")
 #    assert "Events" in epic.viewer.layers 
 
-def utils_value():
+def utils_value(make_napari_viewer):
     """ Labels operations in Utils """
     test_mov = os.path.join(".", "test_data", "003_crop.tif")
     test_seg = os.path.join(".", "test_data", "003_crop_epyseg.tif")
-    viewer = napari.Viewer(show=False)
+    viewer = make_napari_viewer()
     epic = epi.EpiCure(viewer)
     epic.load_movie(test_mov)
     epic.go_epicure("epics", test_seg)
@@ -56,4 +57,4 @@ def utils_value():
 if __name__ == "__main__":
     test_get_free_label()
     utils_value()
-    print("********* Test operations cure completed ***********")
+    print("********* Test operations cure completed ***********")