Merge pull request #37 from AdaptiveMotorControlLab/cy/docs-action

Updated docs building action + 0.0.2rc2

Author: C-Achard

.github/workflows/build_docs.yml

@@ -1,27 +1,19 @@
-name: CI
+name: Deploy Sphinx documentation to Pages
 
 on:
   push:
-    branches:
+    branches: # branch to trigger deployment
       - main
 
 jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
+  pages:
+    runs-on: ubuntu-20.04
     steps:
-    - run: sudo apt-get update && sudo apt-get install libgl1
-    - run: /usr/local/bin/python -m pip install --upgrade pip
-    - uses: actions/checkout@v1
-    # Standard drop-in approach that should work for most people.
-    - uses: ammaraskar/sphinx-action@master
+    - id: deployment
+      uses: sphinx-notes/pages@v3
       with:
-        pre-build-command: "pip install -r requirements.txt napari-cellseg3d opencv-python-headless"
-        docs-folder: "docs/"
-
-    - name: GitHub Pages action
-      uses: peaceiris/[email protected]
+        publish: false
+    - uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs/_build/html
+        publish_dir: ${{ steps.deployment.outputs.artifact }}

napari_cellseg3d/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.2rc1"
+__version__ = "0.0.2rc2"

napari_cellseg3d/code_plugins/plugin_helper.py

@@ -37,7 +37,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.logo_label.setToolTip("Open Github page")
 
         self.info_label = ui.make_label(
-            f"You are using napari-cellseg3d v.{'0.0.2rc1'}\n\n"
+            f"You are using napari-cellseg3d v.{'0.0.2rc2'}\n\n"
             f"Plugin for cell segmentation developed\n"
             f"by the Mathis Lab of Adaptive Motor Control\n\n"
             f"Code by :\nCyril Achard\nMaxime Vidal\nJessy Lauer\nMackenzie Mathis\n"

napari_cellseg3d/interface.py

@@ -581,7 +581,7 @@ def slider_value(self, value: int):
                 f"The value for the slider ({value}) cannot be out of ({self.minimum()};{self.maximum()}) "
             )
 
-        self.setValue(value)
+        self.setValue(int(value))
 
         divided = value / self._divide_factor
         if self._divide_factor == 1.0:

napari_cellseg3d/utils.py

@@ -14,8 +14,8 @@
 LOGGER = logging.getLogger(__name__)
 ###############
 # Global logging level setting
-LOGGER.setLevel(logging.DEBUG)
-# LOGGER.setLevel(logging.INFO)
+# LOGGER.setLevel(logging.DEBUG)
+LOGGER.setLevel(logging.INFO)
 ###############
 
 """
@@ -161,7 +161,7 @@ def align_array_sizes(array_shape, target_shape):
     for i in range(len(targets)):
         targets[i] = reverse_mapping[targets[i]]
     infos = np.unique(origins, return_index=True, return_counts=True)
-    info_dict = {"origins": infos[0], "index": infos[1], "counts": infos[2]}
+    {"origins": infos[0], "index": infos[1], "counts": infos[2]}
     # print(info_dict)
 
     final_orig = []

pyproject.toml

@@ -1,12 +1,65 @@
+[project]
+name = "napari_cellseg3d"
+version = "0.0.2rc2"
+authors = [
+    {name = "Cyril Achard", email = "[email protected]"},
+    {name = "Maxime Vidal", email = "[email protected]"},
+    {name = "Mackenzie Mathis", email = "[email protected]"},
+]
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "napari[all]>=0.4.14",
+    "QtPy",
+    "opencv-python>=4.5.5",
+    "dask-image>=0.6.0",
+    "scikit-image>=0.19.2",
+    "matplotlib>=3.4.1",
+    "tifffile>=2022.2.9",
+    "imageio-ffmpeg>=0.4.5",
+    "torch>=1.11",
+    "monai[nibabel,einops]>=0.9.0",
+    "itk",
+    "tqdm",
+    "nibabel",
+    "scikit-image",
+    "pillow",
+    "tqdm",
+    "matplotlib",
+    "vispy>=0.9.6",
+]
+
 [build-system]
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
-
+[tool.ruff]
+# Never enforce `E501` (line length violations).
+ignore = ["E501", "E741"]
 
 [tool.black]
 line-length = 79
 
 [tool.isort]
 profile = "black"
 line_length = 79
+
+[project.optional-dependencies]
+dev = [
+    "isort",
+    "black",
+    "ruff",
+]
+docs = [
+    "sphinx",
+    "sphinx_autodoc_typehints",
+    "sphinx_rtd_theme",
+    "twine",
+]
+test = [
+    "pytest",
+    "pytest_qt",
+    "coverage",
+    "tox",
+    "twine",
+]

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-cellseg3d
-version = 0.0.2rc1
+version = 0.0.2rc2
 author = Cyril Achard, Maxime Vidal, Jessy Lauer, Mackenzie Mathis
 author_email = [email protected], [email protected], [email protected]
 

tox.ini

@@ -29,6 +29,7 @@ passenv =
 deps =
     pytest  # https://docs.pytest.org/en/latest/contents.html
     pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    dask-image
 ;    # you can remove these if you don't use them
     napari
     PyQt5