Merge branch 'main' into pre-commit-ci-update-config

CHANGELOG.md

@@ -1,5 +1,31 @@
 # Changelog
 
+## [v0.7.1](https://github.com/napari/npe2/tree/v0.7.1) (2023-07-16)
+
+[Full Changelog](https://github.com/napari/npe2/compare/v0.7.0...v0.7.1)
+
+**Implemented enhancements:**
+
+- feat: support python3.11 [\#293](https://github.com/napari/npe2/pull/293) ([tlambert03](https://github.com/tlambert03))
+- add graph layer  [\#292](https://github.com/napari/npe2/pull/292) ([JoOkuma](https://github.com/JoOkuma))
+
+**Fixed bugs:**
+
+- fix: use constraints in napari tests [\#298](https://github.com/napari/npe2/pull/298) ([Czaki](https://github.com/Czaki))
+- Use full `plugin_name` when finding chosen `reader` rather than `startswith` [\#297](https://github.com/napari/npe2/pull/297) ([DragaDoncila](https://github.com/DragaDoncila))
+- Change ArrayLike type to use read only properties [\#289](https://github.com/napari/npe2/pull/289) ([andy-sweet](https://github.com/andy-sweet))
+- Bugfix: use .lower\(\) to make paths & pattern fnmatch case  insensitive [\#275](https://github.com/napari/npe2/pull/275) ([psobolewskiPhD](https://github.com/psobolewskiPhD))
+
+**Documentation:**
+
+- Fix typo in `DynamicPlugin` [\#304](https://github.com/napari/npe2/pull/304) ([lucyleeow](https://github.com/lucyleeow))
+- DOCS: Widget guide should consistently use parent=None kwarg in examples [\#302](https://github.com/napari/npe2/pull/302) ([GenevieveBuckley](https://github.com/GenevieveBuckley))
+
+**Merged pull requests:**
+
+- remove tomlpp [\#294](https://github.com/napari/npe2/pull/294) ([tlambert03](https://github.com/tlambert03))
+- Use hatchling as build backend [\#282](https://github.com/napari/npe2/pull/282) ([tlambert03](https://github.com/tlambert03))
+
 ## [v0.7.0](https://github.com/napari/npe2/tree/v0.7.0) (2023-04-14)
 
 [Full Changelog](https://github.com/napari/npe2/compare/v0.6.2...v0.7.0)
@@ -26,6 +52,7 @@
 
 **Merged pull requests:**
 
+- chore: changelog v0.7.0 [\#286](https://github.com/napari/npe2/pull/286) ([tlambert03](https://github.com/tlambert03))
 - ci\(dependabot\): bump peter-evans/create-pull-request from 4 to 5 [\#284](https://github.com/napari/npe2/pull/284) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Pin pydantic bellow 2.0 [\#279](https://github.com/napari/npe2/pull/279) ([Czaki](https://github.com/Czaki))
 
@@ -187,7 +214,7 @@
 
 ## [v0.4.0](https://github.com/napari/npe2/tree/v0.4.0) (2022-06-13)
 
-[Full Changelog](https://github.com/napari/npe2/compare/v0.3.0...v0.4.0)
+[Full Changelog](https://github.com/napari/npe2/compare/v0.3.0.rc0...v0.4.0)
 
 **Implemented enhancements:**
 
@@ -217,13 +244,13 @@
 - Add doc links to README [\#158](https://github.com/napari/npe2/pull/158) ([nclack](https://github.com/nclack))
 - Fix codeblock directive in docstring [\#156](https://github.com/napari/npe2/pull/156) ([melissawm](https://github.com/melissawm))
 
-## [v0.3.0](https://github.com/napari/npe2/tree/v0.3.0) (2022-04-05)
+## [v0.3.0.rc0](https://github.com/napari/npe2/tree/v0.3.0.rc0) (2022-04-05)
 
-[Full Changelog](https://github.com/napari/npe2/compare/v0.3.0.rc0...v0.3.0)
+[Full Changelog](https://github.com/napari/npe2/compare/v0.3.0...v0.3.0.rc0)
 
-## [v0.3.0.rc0](https://github.com/napari/npe2/tree/v0.3.0.rc0) (2022-04-05)
+## [v0.3.0](https://github.com/napari/npe2/tree/v0.3.0) (2022-04-05)
 
-[Full Changelog](https://github.com/napari/npe2/compare/v0.2.2...v0.3.0.rc0)
+[Full Changelog](https://github.com/napari/npe2/compare/v0.2.2...v0.3.0)
 
 **Implemented enhancements:**
 

_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]]
    ```

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/io_utils.py

@@ -154,9 +154,16 @@ def _read(
     if _pm is None:
         _pm = PluginManager.instance()
 
-    for rdr in _pm.iter_compatible_readers(paths):
-        if plugin_name and rdr.plugin_name != plugin_name:
-            continue
+    # get readers compatible with paths and chosen plugin - raise errors if
+    # choices are invalid or there's nothing to try
+    chosen_compatible_readers = _get_compatible_readers_by_choice(
+        plugin_name, paths, _pm
+    )
+    assert (
+        chosen_compatible_readers
+    ), "No readers to try. Expected an exception before this point."
+
+    for rdr in chosen_compatible_readers:
         read_func = rdr.exec(
             kwargs={"path": paths, "stack": stack, "_registry": _pm.commands}
         )
@@ -167,12 +174,94 @@ def _read(
 
     if plugin_name:
         raise ValueError(
-            f"Plugin {plugin_name!r} was selected to open "
+            f"Reader {plugin_name!r} was selected to open "
             + f"{paths!r}, but returned no data."
         )
     raise ValueError(f"No readers returned data for {paths!r}")
 
 
+def _get_compatible_readers_by_choice(
+    plugin_name: Union[str, None], paths: Union[str, Sequence[str]], pm: PluginManager
+):
+    """Returns compatible readers filtered by validated plugin choice.
+
+    Checks that plugin_name is an existing plugin (and command if
+    a specific contribution was passed), and that it is compatible
+    with paths. Raises ValueError if given plugin doesn't exist,
+    it is not compatible with the given paths, or no compatible
+    readers can be found for paths (if no plugin was chosen).
+
+    Parameters
+    ----------
+    plugin_name: Union[str, None]
+        name of chosen plugin, or None
+    paths: Union[str, Sequence[str]]
+        paths to read
+    pm: PluginManager
+        plugin manager instance to check for readers
+
+    Raises
+    ------
+    ValueError
+        If the given reader doesn't exist
+    ValueError
+        If there are no compatible readers
+    ValueError
+        If the given reader is not compatible
+
+    Returns
+    -------
+    compat_readers : List[ReaderContribution]
+        Compatible readers for plugin choice
+    """
+    passed_contrib = plugin_name and ("." in plugin_name)
+    compat_readers = list(pm.iter_compatible_readers(paths))
+    compat_reader_names = sorted(
+        {(rdr.command if passed_contrib else rdr.plugin_name) for rdr in compat_readers}
+    )
+    helper_error_message = (
+        f"Available readers for {paths!r} are: {compat_reader_names!r}."
+        if compat_reader_names
+        else f"No compatible readers are available for {paths!r}."
+    )
+
+    # check whether plugin even exists.
+    if plugin_name:
+        try:
+            # note that get_manifest works with a full command e.g. my-plugin.my-reader
+            pm.get_manifest(plugin_name)
+            if passed_contrib:
+                pm.get_command(plugin_name)
+        except KeyError:
+            raise ValueError(
+                f"Given reader {plugin_name!r} does not exist. {helper_error_message}"
+            ) from None
+
+    # no choice was made and there's no readers to try
+    if not plugin_name and not len(compat_reader_names):
+        raise ValueError(helper_error_message)
+
+    # user didn't make a choice and we have some readers to try, return them
+    if not plugin_name:
+        return compat_readers
+
+    # user made a choice and it exists, but it may not be a compatible reader
+    plugin, _, _ = plugin_name.partition(".")
+    chosen_compatible_readers = [
+        rdr
+        for rdr in compat_readers
+        if rdr.plugin_name == plugin
+        and (not passed_contrib or rdr.command == plugin_name)
+    ]
+    # the user's choice is not compatible with the paths. let them know what is
+    if not chosen_compatible_readers:
+        raise ValueError(
+            f"Given reader {plugin_name!r} is not a compatible reader for {paths!r}. "
+            + helper_error_message
+        )
+    return chosen_compatible_readers
+
+
 @overload
 def _write(
     path: str,

src/npe2/manifest/contributions/_themes.py

@@ -1,3 +1,4 @@
+import sys
 from typing import Literal, Optional, Union
 
 from pydantic import BaseModel, color
@@ -64,3 +65,7 @@ class ThemeContribution(BaseModel):
         '   - RGB/RGBA strings: `"rgb(255, 255, 255)"`, `"rgba(255, 255, 255, 0.5)`"\n'
         '   - HSL strings: "`hsl(270, 60%, 70%)"`, `"hsl(270, 60%, 70%, .5)`"\n'
     )
+    font_size: str = Field(
+        default="12pt" if sys.platform == "darwin" else "9pt",
+        description="Font size (in points, pt) used in the application.",
+    )

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

@@ -1,5 +1,6 @@
 # extra underscore in name to run this first
 from pathlib import Path
+from unittest.mock import patch
 
 import pytest
 
@@ -23,14 +24,30 @@ def test_read(uses_sample_plugin):
 
 def test_read_with_unknown_plugin(uses_sample_plugin):
     # no such plugin name.... skips over the sample plugin & error is specific
-    with pytest.raises(ValueError, match="Plugin 'nope' was selected"):
-        read(["some.fzzy"], plugin_name="nope", stack=False)
+    paths = ["some.fzzy"]
+    chosen_reader = "not-a-plugin"
+    with pytest.raises(
+        ValueError, match=f"Given reader {chosen_reader!r} does not exist."
+    ) as e:
+        read(paths, plugin_name=chosen_reader, stack=False)
+    assert f"Available readers for {paths!r} are: {[SAMPLE_PLUGIN_NAME]!r}" in str(e)
+
+
+def test_read_with_unknown_plugin_no_readers(uses_sample_plugin):
+    paths = ["some.nope"]
+    chosen_reader = "not-a-plugin"
+    with pytest.raises(
+        ValueError, match=f"Given reader {chosen_reader!r} does not exist."
+    ) as e:
+        read(paths, plugin_name=chosen_reader, stack=False)
+    assert "No compatible readers are available" in str(e)
 
 
 def test_read_with_no_plugin():
     # no plugin passed and none registered
-    with pytest.raises(ValueError, match="No readers returned"):
-        read(["some.nope"], stack=False)
+    paths = ["some.nope"]
+    with pytest.raises(ValueError, match="No compatible readers are available"):
+        read(paths, stack=False)
 
 
 def test_read_uses_correct_passed_plugin(tmp_path):
@@ -40,6 +57,9 @@ def test_read_uses_correct_passed_plugin(tmp_path):
     long_name_plugin = DynamicPlugin(long_name, plugin_manager=pm)
     short_name_plugin = DynamicPlugin(short_name, plugin_manager=pm)
 
+    long_name_plugin.register()
+    short_name_plugin.register()
+
     path = "something.fzzy"
     mock_file = tmp_path / path
     mock_file.touch()
@@ -62,6 +82,82 @@ def read(paths):
     io_utils._read(["some.fzzy"], plugin_name=short_name, stack=False, _pm=pm)
 
 
+def test_read_fails():
+    pm = PluginManager()
+    plugin_name = "always-fails"
+    plugin = DynamicPlugin(plugin_name, plugin_manager=pm)
+    plugin.register()
+
+    @plugin.contribute.reader(filename_patterns=["*.fzzy"])
+    def get_read(path):
+        return None
+
+    with pytest.raises(ValueError, match=f"Reader {plugin_name!r} was selected"):
+        io_utils._read(["some.fzzy"], plugin_name=plugin_name, stack=False, _pm=pm)
+
+    with pytest.raises(ValueError, match="No readers returned data"):
+        io_utils._read(["some.fzzy"], stack=False, _pm=pm)
+
+
+def test_read_with_incompatible_reader(uses_sample_plugin):
+    paths = ["some.notfzzy"]
+    chosen_reader = f"{SAMPLE_PLUGIN_NAME}"
+    with pytest.raises(
+        ValueError, match=f"Given reader {chosen_reader!r} is not a compatible reader"
+    ):
+        read(paths, stack=False, plugin_name=chosen_reader)
+
+
+def test_read_with_no_compatible_reader():
+    paths = ["some.notfzzy"]
+    with pytest.raises(ValueError, match="No compatible readers are available"):
+        read(paths, stack=False)
+
+
+def test_read_with_reader_contribution_plugin(uses_sample_plugin):
+    paths = ["some.fzzy"]
+    chosen_reader = f"{SAMPLE_PLUGIN_NAME}.some_reader"
+    assert read(paths, stack=False, plugin_name=chosen_reader) == [(None,)]
+
+    # if the wrong contribution is passed we get useful error message
+    chosen_reader = f"{SAMPLE_PLUGIN_NAME}.not_a_reader"
+    with pytest.raises(
+        ValueError,
+        match=f"Given reader {chosen_reader!r} does not exist.",
+    ) as e:
+        read(paths, stack=False, plugin_name=chosen_reader)
+    assert "Available readers for" in str(e)
+
+
+def test_read_assertion_with_no_compatible_readers(uses_sample_plugin):
+    paths = ["some.noreader"]
+    with patch("npe2.io_utils._get_compatible_readers_by_choice", return_value=[]):
+        with pytest.raises(AssertionError, match="No readers to try."):
+            read(paths, stack=False)
+
+
+def test_available_readers_show_commands(uses_sample_plugin):
+    paths = ["some.fzzy"]
+    chosen_reader = "not-a-plugin.not-a-reader"
+    with pytest.raises(
+        ValueError,
+        match=f"Given reader {chosen_reader!r} does not exist.",
+    ) as e:
+        read(paths, stack=False, plugin_name=chosen_reader)
+    assert "Available readers " in str(e)
+    assert f"{SAMPLE_PLUGIN_NAME}.some_reader" in str(e)
+
+    chosen_reader = "not-a-plugin"
+    with pytest.raises(
+        ValueError,
+        match=f"Given reader {chosen_reader!r} does not exist.",
+    ) as e:
+        read(paths, stack=False, plugin_name=chosen_reader)
+    assert "Available readers " in str(e)
+    assert f"{SAMPLE_PLUGIN_NAME}.some_reader" not in str(e)
+    assert f"{SAMPLE_PLUGIN_NAME}" in str(e)
+
+
 def test_read_return_reader(uses_sample_plugin):
     data, reader = read_get_reader("some.fzzy")
     assert data == [(None,)]