Merge branch 'main' into fix_editable

.github/workflows/ci.yml

@@ -70,7 +70,7 @@ jobs:
       - name: Install
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e ./napari-from-github
+          python -m pip install -e ./napari-from-github -c "./napari-from-github/resources/constraints/constraints_py3.10.txt"
           python -m pip install -e .[json]
           # bare minimum required to test napari/plugins
           python -m pip install pytest scikit-image[data] zarr xarray hypothesis matplotlib

.gitignore

@@ -24,6 +24,7 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+.DS_Store
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -100,6 +101,7 @@ ENV/
 
 # mypy
 .mypy_cache/
+.ruff_cache/
 
 # IDE settings
 .vscode/

_docs/render.py

@@ -154,9 +154,9 @@ def example_contribution(
     if format == "yaml":
         return yaml.safe_dump(output, sort_keys=False)
     if format == "toml":
-        import pytomlpp as toml
+        import tomli_w
 
-        return toml.dumps(output)
+        return tomli_w.dumps(output)
     if format == "json":
         return json.dumps(output)
     raise ValueError("Invalid format: {format}.  Must be 'yaml', 'toml' or 'json'.")

_docs/templates/_npe2_widgets_guide.md.jinja

@@ -30,8 +30,8 @@ specification:
    from qtpy.QtWidgets import QWidget
 
    class MyPluginWidget(QWidget):
-       def __init__(self, viewer: 'napari.viewer.Viewer'):
-           super().__init__()
+       def __init__(self, viewer: 'napari.viewer.Viewer', parent=None):
+           super().__init__(parent)
            self._viewer = viewer
    ```
 

_docs/templates/_npe2_writers_guide.md.jinja

@@ -58,7 +58,7 @@ by the corresponding writer contribution in the manifest).
    ```python
    DataType = Any  # usually something like a numpy array, but varies by layer
    LayerAttributes = dict
-   LayerName = Literal["image", "labels", "points", "shapes", "surface", "tracks", "vectors"]
+   LayerName = Literal["graph", "image", "labels", "points", "shapes", "surface", "tracks", "vectors"]
    FullLayerData = Tuple[DataType, LayerAttributes, LayerName]
    MultiWriterFunction = Callable[[str, List[FullLayerData]], List[str]]
    ```

pyproject.toml

@@ -1,7 +1,10 @@
 # pyproject.toml
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "vcs"
 
 # https://peps.python.org/pep-0621/
 [project]
@@ -33,7 +36,8 @@ dependencies = [
     "build",
     "psygnal>=0.3.0",
     "pydantic<2",
-    "pytomlpp",
+    "tomli-w",
+    "tomli; python_version < '3.11'",
     "rich",
     "typer",
 ]
@@ -72,25 +76,9 @@ npe2 = "npe2._pytest_plugin"
 [project.entry-points."setuptools.finalize_distribution_options"]
 finalize_npe2 = "npe2._setuptools_plugin:finalize_npe2"
 
-[tool.setuptools]
-package-dir = { "" = "src" }
-include-package-data = true
-
-[tool.setuptools.packages.find]
-where = ["src"]
-
-[tool.setuptools.package-data]
-"*" = ["*.pyi", "py.typed"]
-
-[tool.setuptools_scm]
-write_to = "src/npe2/_version.py"
 
 [tool.check-manifest]
-ignore = [
-    "src/npe2/_version.py",
-    ".pre-commit-config.yaml",
-    ".github_changelog_generator",
-]
+ignore = []
 
 [tool.pytest.ini_options]
 filterwarnings = ["error:::npe2"]

src/npe2/__init__.py

@@ -1,6 +1,8 @@
+from importlib.metadata import PackageNotFoundError, version
+
 try:
-    from ._version import version as __version__
-except ImportError:
+    __version__ = version("npe2")
+except PackageNotFoundError:  # pragma: no cover
     __version__ = "unknown"
 __author__ = "Talley Lambert"
 __email__ = "talley.lambert@gmail.com"

src/npe2/_dynamic_plugin.py

@@ -90,7 +90,7 @@ def cleanup(self) -> None:
         self.plugin_manager.unregister(self.manifest.name)
 
     def register(self) -> None:
-        """Remove this plugin from its plugin manager."""
+        """Register this plugin with its plugin manager."""
         self.plugin_manager.register(self.manifest)
 
     def clear(self) -> None:

src/npe2/_inspection/_setuputils.py

@@ -86,18 +86,6 @@ def get_package_dir_info(path: Union[Path, str]) -> PackageInfo:
                         EntryPoint(name.strip(), value.strip(), group)
                     )
 
-    # # check for pyproject.toml
-    # pyproject_toml = path / "pyproject.toml"
-    # if pyproject_toml.exists():
-    #     info.pyproject_toml = pyproject_toml
-    #     with open(pyproject_toml, "r") as f:
-    #         data = pytomlpp.load(f)
-    #     if project := data.get("project"):
-    #         info.package_name = project.get("name", "")
-    #         for group, ep in project.get('entry-points', {}).items():
-    #             for name, value in ep.items():
-    #                 info.entry_points.append(EntryPoint(name, value, group))
-
     return info
 
 

src/npe2/_inspection/_visitors.py

@@ -235,6 +235,9 @@ def napari_get_writer(self, node: ast.FunctionDef):
         # we can't convert this to an npe2 command contribution
         pass  # pragma: no cover
 
+    def napari_write_graph(self, node: ast.FunctionDef):
+        self._parse_writer(node, "graph")  # pragma: no cover
+
     def napari_write_image(self, node: ast.FunctionDef):
         self._parse_writer(node, "image")
 

src/npe2/_setuptools_plugin.py

@@ -36,9 +36,12 @@ def trace(*k: object) -> None:
 
 
 def _lazy_tomli_load(data: str) -> dict[str, Any]:
-    from pytomlpp import loads
+    try:
+        import tomllib
+    except ImportError:
+        import tomli as tomllib  # type: ignore [no-redef]
 
-    return loads(data)
+    return tomllib.loads(data)
 
 
 def _read_dist_name_from_setup_cfg() -> str | None:

src/npe2/io_utils.py

@@ -155,7 +155,7 @@ def _read(
         _pm = PluginManager.instance()
 
     for rdr in _pm.iter_compatible_readers(paths):
-        if plugin_name and not rdr.command.startswith(plugin_name):
+        if plugin_name and rdr.plugin_name != plugin_name:
             continue
         read_func = rdr.exec(
             kwargs={"path": paths, "stack": stack, "_registry": _pm.commands}

src/npe2/manifest/_bases.py

@@ -3,7 +3,6 @@
 from pathlib import Path
 from typing import Callable, Dict, Optional, Union
 
-import pytomlpp as toml
 import yaml
 from pydantic import BaseModel, PrivateAttr
 
@@ -30,10 +29,12 @@ def toml(self, pyproject=False, **kwargs) -> str:
         **kwargs
             passed to `BaseModel.json()`
         """
+        import tomli_w
+
         d = self._serialized_data(**kwargs)
         if pyproject:
             d = {"tool": {"napari": d}}
-        return toml.dumps(d)
+        return tomli_w.dumps(d)
 
     def yaml(self, **kwargs) -> str:
         """Generate serialized `yaml` string for this model.
@@ -74,13 +75,18 @@ def from_file(cls, path: Union[Path, str]):
         if path.suffix.lower() == ".json":
             loader = json.load
         elif path.suffix.lower() == ".toml":
-            loader = toml.load
+            try:
+                import tomllib
+            except ImportError:
+                import tomli as tomllib  # type: ignore [no-redef]
+
+            loader = tomllib.load
         elif path.suffix.lower() in (".yaml", ".yml"):
             loader = yaml.safe_load
         else:
             raise ValueError(f"unrecognized file extension: {path}")  # pragma: no cover
 
-        with open(path, encoding="utf-8") as f:
+        with open(path, mode="rb") as f:
             data = loader(f) or {}
 
         if path.name == "pyproject.toml":

src/npe2/manifest/contributions/_writers.py

@@ -7,6 +7,7 @@
 
 
 class LayerType(str, Enum):
+    graph = "graph"
     image = "image"
     labels = "labels"
     points = "points"

src/npe2/types.py

@@ -46,7 +46,7 @@ def __array__(self) -> "np.ndarray":
 
 
 LayerName = Literal[
-    "image", "labels", "points", "shapes", "surface", "tracks", "vectors"
+    "graph", "image", "labels", "points", "shapes", "surface", "tracks", "vectors"
 ]
 Metadata = Dict
 DataType = Union[ArrayLike, Sequence[ArrayLike]]

tests/conftest.py

@@ -118,6 +118,7 @@ class HookSpecs:
         def napari_provide_sample_data(): ...  # type: ignore
         def napari_get_reader(path): ...
         def napari_get_writer(path, layer_types): ...
+        def napari_write_graph(path, data, meta): ...
         def napari_write_image(path, data, meta): ...
         def napari_write_labels(path, data, meta): ...
         def napari_write_points(path, data, meta): ...

tests/test__io_utils.py

@@ -33,6 +33,35 @@ def test_read_with_no_plugin():
         read(["some.nope"], stack=False)
 
 
+def test_read_uses_correct_passed_plugin(tmp_path):
+    pm = PluginManager()
+    long_name = "gooby-again"
+    short_name = "gooby"
+    long_name_plugin = DynamicPlugin(long_name, plugin_manager=pm)
+    short_name_plugin = DynamicPlugin(short_name, plugin_manager=pm)
+
+    path = "something.fzzy"
+    mock_file = tmp_path / path
+    mock_file.touch()
+
+    @long_name_plugin.contribute.reader(filename_patterns=["*.fzzy"])
+    def get_read_long(path=mock_file):
+        raise ValueError(
+            f"Uhoh, {long_name} was chosen, but given plugin was {short_name}"
+        )
+
+    @short_name_plugin.contribute.reader(filename_patterns=["*.fzzy"])
+    def get_read(path=mock_file):
+        def read(paths):
+            return [(None,)]
+
+        return read
+
+    # "gooby-again" isn't used even though given plugin starts with the same name
+    # if an error is thrown here, it means we selected the wrong plugin
+    io_utils._read(["some.fzzy"], plugin_name=short_name, stack=False, _pm=pm)
+
+
 def test_read_return_reader(uses_sample_plugin):
     data, reader = read_get_reader("some.fzzy")
     assert data == [(None,)]