Testing and minor updates

- Run tests on ubuntu
- Updated tests
- Added Log test and Log init update

Author: C-Achard

.github/workflows/preview_metadata.yml

@@ -1,21 +1,21 @@
-#name: napari hub Preview Page # we use this name to find your preview page artifact, so don't change it!
-## For more info on this action, see https://github.com/chanzuckerberg/napari-hub-preview-action/blob/main/action.yml
-#
-#on:
-#  pull_request:
-#    branches:
-#      - 'test' # '**' for all
-#
-#jobs:
-#  preview-page:
-#    name: Preview Page Deploy
-#    runs-on: ubuntu-latest
-#
-#    steps:
-#      - name: Checkout repo
-#        uses: actions/checkout@v2
-#
-#      - name: napari hub Preview Page Builder
-#        uses: chanzuckerberg/[email protected].5
-#        with:
-#          hub-ref: main
+name: napari hub Preview Page # we use this name to find your preview page artifact, so don't change it!
+# For more info on this action, see https://github.com/chanzuckerberg/napari-hub-preview-action/blob/main/action.yml
+
+on:
+  pull_request:
+    branches:
+      - 'test' # '**' for all
+
+jobs:
+  preview-page:
+    name: Preview Page Deploy
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: napari hub Preview Page Builder
+        uses: chanzuckerberg/[email protected].6
+        with:
+          hub-ref: main

.github/workflows/test_and_deploy.yml

@@ -24,8 +24,8 @@ jobs:
     strategy:
       matrix:
 # platform: [ubuntu-latest, windows-latest, macos-latest]
-        platform: [windows-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        platform: [ubuntu-latest]
+        python-version: [3.8, 3.9, 3.10]
 
     steps:
       - uses: actions/checkout@v2

napari_cellseg3d/_tests/test_interface.py

@@ -0,0 +1,13 @@
+from napari_cellseg3d.interface import Log
+
+def test_log(qtbot):
+    log = Log()
+    log.print_and_log("test")
+
+    assert log.toPlainText() == "\ntest"
+
+    log.replace_last_line("test2")
+
+    assert log.toPlainText() == "\ntest2"
+
+    qtbot.add_widget(log)

napari_cellseg3d/_tests/test_plugin_inference.py

@@ -26,10 +26,10 @@ def test_inference(make_napari_viewer, qtbot):
 
     assert widget.check_ready()
 
-    # widget.start()  # takes too long on Github Actions (~30min)
-    # assert widget.worker is not None
-    #
-    # with qtbot.waitSignal(signal=widget.worker.finished) as blocker:
-    #     blocker.connect(widget.worker.errored)
-    #
+    widget.start()  # takes too long on Github Actions (~30min)
+    assert widget.worker is not None
+
+    with qtbot.waitSignal(signal=widget.worker.finished, timeout=60000, raising=False) as blocker:
+        blocker.connect(widget.worker.errored)
+
     # assert len(viewer.layers) == 2

napari_cellseg3d/_tests/test_training.py

@@ -22,18 +22,19 @@ def test_training(make_napari_viewer, qtbot):
 
     widget.images_filepaths = [im_path]
     widget.labels_filepaths = [im_path]
+    widget.epoch_choice.setValue(1)
 
     assert widget.check_ready()
 
     #################
     # Training is too long to test properly this way. Do not use on Github
     #################
 
-    # widget.start()
-    # assert widget.worker is not None
-    #
-    # with qtbot.waitSignal(signal=widget.worker.finished, timeout=60000) as blocker:  # wait only for 60 seconds.
-    #     blocker.connect(widget.worker.errored)
+    widget.start()
+    assert widget.worker is not None
+
+    with qtbot.waitSignal(signal=widget.worker.finished, timeout=60000, raising=False) as blocker:  # wait only for 60 seconds.
+        blocker.connect(widget.worker.errored)
 
 
 def test_update_loss_plot(make_napari_viewer):

napari_cellseg3d/interface.py

@@ -208,7 +208,7 @@ def show_utils_menu(self, widget, event):
 class Log(QTextEdit):
     """Class to implement a log for important user info. Should be thread-safe."""
 
-    def __init__(self, parent):
+    def __init__(self, parent=None):
         """Creates a log with a lock for multithreading
 
         Args:
@@ -223,31 +223,31 @@ def __init__(self, parent):
 
     # def receive_log(self, text):
     #     self.print_and_log(text)
-    def write(self, message):
-        """
-        Write message to log in a thread-safe manner
-        Args:
-            message: string to be printed
-        """
-        self.lock.acquire()
-        try:
-            if not hasattr(self, "flag"):
-                self.flag = False
-            message = message.replace("\r", "").rstrip()
-            if message:
-                method = "replace_last_line" if self.flag else "append"
-                QtCore.QMetaObject.invokeMethod(
-                    self,
-                    method,
-                    QtCore.Qt.QueuedConnection,
-                    QtCore.Q_ARG(str, message),
-                )
-                self.flag = True
-            else:
-                self.flag = False
-
-        finally:
-            self.lock.release()
+    # def write(self, message):
+    #     """
+    #     Write message to log in a thread-safe manner
+    #     Args:
+    #         message: string to be printed
+    #     """
+    #     self.lock.acquire()
+    #     try:
+    #         if not hasattr(self, "flag"):
+    #             self.flag = False
+    #         message = message.replace("\r", "").rstrip()
+    #         if message:
+    #             method = "replace_last_line" if self.flag else "append"
+    #             QtCore.QMetaObject.invokeMethod(
+    #                 self,
+    #                 method,
+    #                 QtCore.Qt.QueuedConnection,
+    #                 QtCore.Q_ARG(str, message),
+    #             )
+    #             self.flag = True
+    #         else:
+    #             self.flag = False
+    #
+    #     finally:
+    #         self.lock.release()
 
     @QtCore.Slot(str)
     def replace_last_line(self, text):

setup.cfg

@@ -50,7 +50,7 @@ install_requires =
     tifffile>=2022.2.9
     imageio-ffmpeg>=0.4.5
     torch>=1.11
-    monai[nibabel,scikit-image,itk,einops]>=0.9.0
+    monai[nibabel,itk,einops]>=0.9.0
     tqdm
     nibabel
     scikit-image

tox.ini

@@ -9,15 +9,15 @@ python =
 
 [gh-actions:env]
 PLATFORM =
-;    ubuntu-latest: linux
+    ubuntu-latest: linux
 ;    macos-latest: macos
-    windows-latest: windows
+;    windows-latest: windows
 
 [testenv]
 platform = 
+    linux: linux
 ;    macos: darwin
-;    linux: linux
-    windows: win32
+;    windows: win32
 passenv = 
     CI
     PYTHONPATH