Merge pull request #12 from haesleinhuepf/delayed_imports

delayed_imports
haesleinhuepf · Nov 12, 2023 · fbe2a63 · fbe2a63
2 parents 90797a7 + f2cb78e
commit fbe2a63
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Showing 3 changed files with 45 additions and 19 deletions.
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -53,16 +53,38 @@ jobs:
       # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
       # and
       # tox-conda: https://github.com/tox-dev/tox-conda
+      - name: Set up conda ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2.2.0
+        with:
+          auto-update-conda: true
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Install pocl
+        if: runner.os == 'Linux'
+        shell: bash -l {0}
+        run: conda install -y pocl
       - name: Install dependencies
+        shell: bash -l {0}
         run: |
-          python -m pip install --upgrade pip
-          pip install setuptools tox tox-gh-actions
+          python --version
+          conda install -y pip setuptools wheel pytest pytest-cov pytest-benchmark pytest-qt pyqt pytest-xvfb 
+          # pip install setuptools tox tox-gh-actions
 
+          pip install -e .
       # this runs the platform-specific tests declared in tox.ini
-      - name: Test with tox
-        run: tox
-        env:
-          PLATFORM: ${{ matrix.platform }}
+      #- name: Install tox-conda
+      #  run: pip install tox-conda
+      #- name: Test with tox
+      #  run: tox
+      #  env:
+      #    PLATFORM: ${{ matrix.platform }}
+      - name: Test
+        shell: bash -l {0}
+        run: pytest -v --cov=./ --cov-report=xml
 
       - name: Coverage
         uses: codecov/codecov-action@v1

diff --git a/src/napari_time_slicer/_function.py b/src/napari_time_slicer/_function.py
@@ -4,19 +4,15 @@
 import numpy as np
 from typing_extensions import Annotated
 from napari_plugin_engine import napari_hook_implementation
-from napari.layers import Image, Labels, Layer
 from napari_tools_menu import register_function, register_action
-import napari
-import tempfile
-
-LayerInput = Annotated[Layer, {"label": "Image"}]
 
 @napari_hook_implementation
 def napari_experimental_provide_function():
     return [convert_to_2d_timelapse]
 
 @register_function(menu="Utilities > Convert 3D stack to 2D timelapse (time-slicer)")
-def convert_to_2d_timelapse(layer : LayerInput, viewer:napari.Viewer = None) -> Layer:
+def convert_to_2d_timelapse(layer : "napari.layers.Layer", viewer:"napari.Viewer" = None) -> "napari.layers.Layer":
+    from napari.layers import Image, Labels, Layer
     if isinstance(layer, Labels):
         result = Labels(layer.data[:,np.newaxis,:,:], name="2d+t " + layer.name)
     else:
@@ -29,11 +25,13 @@ def convert_to_2d_timelapse(layer : LayerInput, viewer:napari.Viewer = None) ->
     return result
 
 @register_function(menu="Utilities > Convert on-the-fly processed timelapse to 4D stack (time-slicer)")
-def convert_to_stack4d(layer : LayerInput, viewer: napari.Viewer) -> Layer:
+def convert_to_stack4d(layer : "napari.layers.Layer", viewer: "napari.Viewer") -> "napari.layers.Layer":
     """
     Go through time (by moving the time-slider in napari) and copy 3D frames of a given layer
     and store them in a new 4D layer in napari.
     """
+    from napari.layers import Image, Labels, Layer
+
     # in case of 4D-data (timelapse) crop out the current 3D timepoint
     if len(viewer.dims.current_step) != 4:
         raise NotImplementedError("Processing all frames only supports 4D-data")
@@ -77,17 +75,20 @@ def convert_to_stack4d(layer : LayerInput, viewer: napari.Viewer) -> Layer:
 
 @register_function(menu="Utilities > Convert to file-backed timelapse data (time-slicer)",
                       folder_name = dict(widget_type='FileEdit', mode='d'))
-def convert_to_file_backed_timelapse(layer : LayerInput,
+def convert_to_file_backed_timelapse(layer : "napari.layers.Layer",
                                      folder_name: "magicgui.types.PathLike" = "",
-                                     viewer: napari.Viewer = None) -> Layer:
+                                     viewer: "napari.Viewer" = None) -> "napari.layers.Layer":
     """
     Save a 4D stack to disk and create a new layer that reads only the current timepoint from disk
     """
+    from napari.layers import Image, Labels, Layer
+    from skimage.io import imsave
+    import os
+    import tempfile
+
     if len(viewer.dims.current_step) != 4:
         raise NotImplementedError("Convert to file-backed timelapse data only supports 4D-data")
 
-    from skimage.io import imsave
-    import os
 
     folder_name = str(folder_name)
     if len(folder_name) == 0 or folder_name == ".":
@@ -143,10 +144,12 @@ def convert_to_file_backed_timelapse(layer : LayerInput,
 def load_file_backed_timelapse(folder_name: "magicgui.types.PathLike" = "",
                                 is_labels:bool = False,
                                 name:str = "",
-                                viewer: napari.Viewer = None) -> Layer:
+                                viewer: "napari.Viewer" = None) -> "napari.layers.Layer":
     """
     Load a folder of tif-images where every tif-file corresponds to a frame in a 4D stack.
     """
+    from napari.layers import Image, Labels, Layer
+
     import os
     from skimage.io import imsave
     from functools import partial

diff --git a/tox.ini b/tox.ini
@@ -22,7 +22,8 @@ platform =
 passenv = 
     CI
     GITHUB_ACTIONS
-    DISPLAY XAUTHORITY
+    DISPLAY
+    XAUTHORITY
     NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
     PYVISTA_OFF_SCREEN
 deps =