Add cellpose v4 support; migrate to npe2 and pyproject.toml

.github/workflows/test_and_deploy.yml

@@ -29,13 +29,13 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -60,19 +60,43 @@ jobs:
           PLATFORM: ${{ matrix.platform }}
 
       - name: Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v6
+
+  test-cellpose3:
+    name: cellpose v3 compat (ubuntu, py3.11)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - uses: tlambert03/setup-qt-libs@v1
+
+      - name: Install dependencies (cellpose v3 pinned)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[testing]" "cellpose>=3,<4"
+
+      - name: Test with pytest
+        uses: aganders3/headless-gui@v2
+        with:
+          run: pytest -v --color=yes
+        env:
+          CI: true
 
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
-    # and requires that you have put your twine API key in your 
+    # and requires that you have put your twine API key in your
     # github secrets (see readme for details)
-    needs: [test]
+    needs: [test, test-cellpose3]
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
       - name: Install dependencies

cellpose_napari/__init__.py

@@ -2,6 +2,3 @@
     from ._version import version as __version__
 except ImportError:
     __version__ = "unknown"
-
-from ._dock_widget import napari_experimental_provide_dock_widget
-from ._sample_data import napari_provide_sample_data

cellpose_napari/_sample_data.py

@@ -1,48 +1,36 @@
-import os
 import pathlib
-from functools import partial
 
-from napari.utils.translations import trans
-from napari_plugin_engine import napari_hook_implementation
+def extract_zip(cached_file, url, data_path):
+    import zipfile
+    from cellpose import utils
 
-CELLPOSE_DATA = [
-    ('rgb_3D.tif', trans._('Cells (3D+2Ch)')),
-    ('rgb_2D.png', trans._('Cells 2D')),
-]
-
-def _load_cellpose_data(image_name, dname):
-    # Import when users select one of sample data
-    import numpy as np
-    from cellpose.io import imread
-    from cellpose.utils import download_url_to_file
+    if not cached_file.exists():
+        utils.download_url_to_file(url, cached_file)        
+        with zipfile.ZipFile(cached_file,"r") as zip_ref:
+            zip_ref.extractall(data_path)
 
+def _get_data_dir():
     cp_dir = pathlib.Path.home().joinpath('.cellpose')
     cp_dir.mkdir(exist_ok=True)
+    zip_path = cp_dir.joinpath('data.zip')
     data_dir = cp_dir.joinpath('data')
-    data_dir.mkdir(exist_ok=True)
-    data_dir_2D = data_dir.joinpath('2D')
-    data_dir_2D.mkdir(exist_ok=True)
-    data_dir_3D = data_dir.joinpath('3D')
-    data_dir_3D.mkdir(exist_ok=True)
-
-    url = 'http://www.cellpose.org/static/data/' + image_name
-    if '2D' in image_name:
-        cached_file = str(data_dir_2D.joinpath(image_name))
-    else:
-        cached_file = str(data_dir_3D.joinpath(image_name))
-    if not os.path.exists(cached_file):
-        download_url_to_file(url, cached_file, progress=True)
-    data = imread(cached_file)
-    if '3D' in image_name:
-        data = np.moveaxis(data, 0, 1)
-    return [(data, {'name': dname})]
-
-_DATA = {
-    key: {'data': partial(_load_cellpose_data, key, dname), 'display_name': dname}
-    for (key, dname) in CELLPOSE_DATA
-}
-globals().update({k: v['data'] for k, v in _DATA.items()})
-
-@napari_hook_implementation
-def napari_provide_sample_data():
-    return _DATA
+    extract_zip(zip_path, 'https://osf.io/download/s52q3/', cp_dir)
+    return data_dir
+
+
+def make_rgb_2d_sample():
+    from cellpose.io import imread
+
+    data_dir = _get_data_dir()
+    data = imread(str(data_dir / '2D' / 'rgb_2D_tif.tif'))
+    return [(data, {'name': 'Cells (2D+2Ch)'})]
+
+
+def make_rgb_3d_sample():
+    from cellpose.io import imread
+
+    data_dir = _get_data_dir()
+    data = imread(str(data_dir / '3D' / 'rgb_3D.tif')) # shape (Z, C, Y, X)
+    # to get display in napari with channels, use channel_axis=1
+
+    return [(data, {'name': 'Cells (3D+2Ch)', "axis_labels": ("z", "c", "y", "x")})]

cellpose_napari/napari.yaml

@@ -5,20 +5,19 @@ contributions:
     - id: cellpose-napari.widget_wrapper
       title: Create cellpose
       python_name: cellpose_napari._dock_widget:widget_wrapper
-    # samples
     - id: cellpose-napari.data.rgb_3D
       title: Generate RGB 3D sample
-      python_name: cellpose_napari._sample_data:rgb_3D.tif
+      python_name: cellpose_napari._sample_data:make_rgb_3d_sample
     - id: cellpose-napari.data.rgb_2D
       title: Generate RGB 2D sample
-      python_name: cellpose_napari._sample_data:rgb_2D.png
+      python_name: cellpose_napari._sample_data:make_rgb_2d_sample
   widgets:
     - command: cellpose-napari.widget_wrapper
       display_name: cellpose
   sample_data:
+    - display_name: Cells (2D+2Ch)
+      key: rgb_2D
+      command: cellpose-napari.data.rgb_2D
     - display_name: Cells (3D+2Ch)
       key: rgb_3D
       command: cellpose-napari.data.rgb_3D
-    - display_name: Cells 2D
-      key: rgb_2D
-      command: cellpose-napari.data.rgb_2D

pyproject.toml

@@ -1,6 +1,98 @@
 [build-system]
-requires = ["setuptools", "wheel", "setuptools_scm"]
+requires = ["setuptools>=64", "setuptools_scm>=7"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "cellpose-napari"
+description = "a generalist algorithm for anatomical segmentation"
+readme = "README.md"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "Carsen Stringer", email = "stringerc@janelia.hhmi.org" }]
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: BSD License",
+    "Framework :: napari",
+]
+dependencies = [
+    "napari>=0.6",
+    "magicgui",
+    "cellpose>=3",
+    "imagecodecs",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/Mouseland/cellpose-napari"
+
+[project.optional-dependencies]
+docs = [
+    "sphinx>=3.0",
+    "sphinxcontrib-apidoc",
+    "sphinx_rtd_theme",
+    "sphinx-prompt",
+    "sphinx-autodoc-typehints",
+]
+testing = [
+    "tox",
+    "pytest",
+    "pytest-cov",
+    "pytest-qt",
+    "napari",
+    "pyqt5",
+]
+
+[project.entry-points."napari.manifest"]
+cellpose-napari = "cellpose_napari:napari.yaml"
+
 [tool.setuptools_scm]
-write_to = "cellpose_napari/_version.py"
+version_file = "cellpose_napari/_version.py"
+
+[tool.setuptools.packages.find]
+exclude = ["tests", "tests.*"]
+
+[tool.setuptools.package-data]
+cellpose_napari = ["napari.yaml"]
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{310,311,312}-{linux,macos,windows}
+isolated_build = true
+toxworkdir = /tmp/.tox
+
+[gh-actions]
+python =
+    3.10: py310
+    3.11: py311
+    3.12: py312
+
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    macos-latest: macos
+    windows-latest: windows
+
+[testenv]
+platform =
+    macos: darwin
+    linux: linux
+    windows: win32
+passenv =
+    CI
+    GITHUB_ACTIONS
+    DISPLAY
+    XAUTHORITY
+    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
+    PYVISTA_OFF_SCREEN
+setenv =
+    TORCHINDUCTOR_CACHE_DIR = {envtmpdir}/torchinductor
+extras =
+    testing
+commands = pytest -v --color=yes --cov=cellpose_napari --cov-report=xml
+"""

tests/conftest.py

@@ -0,0 +1,3 @@
+# torch must be imported before PyQt on Windows to avoid DLL init failure
+# https://github.com/pytorch/pytorch/issues/166628
+import torch  # noqa: F401