npe2 0.7.7rc0__tar.gz → 0.7.8rc0__tar.gz

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/.github/workflows/ci.yml

@@ -53,11 +53,12 @@ jobs:
           coverage run --source=npe2 -m pytest --color yes
 
       - name: Upload coverage as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: coverage reports
+          name: coverage reports ${{ matrix.platform }} py ${{ matrix.python-version }} ${{ (matrix.pydantic == 'pydantic<2' && 'pydantic_lt_2') || 'pydantic_gt_2' }}
           path: |
             ./.coverage.*
+          include-hidden-files: true
 
   test_napari:
     name: napari tests
@@ -124,10 +125,11 @@ jobs:
           pip install codecov
 
       - name: Download coverage data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: coverage reports
+          pattern: coverage reports*
           path: coverage
+          merge-multiple: true
 
       - name: combine coverage data
         run: |
@@ -138,7 +140,7 @@ jobs:
           python -Im coverage report --format=markdown --skip-empty --skip-covered >> $GITHUB_STEP_SUMMARY
 
       - name: Upload coverage data
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/.github/workflows/test_all_plugins.yml

@@ -1,6 +1,7 @@
 name: Test all plugins
 
 on:
+  # To run this workflow, trigger it manually, or add the label 'test-all-plugins' to a pull request
   pull_request:
     types: [ labeled ]
   workflow_dispatch:
@@ -15,7 +16,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - id: plugin_names
-        run: echo "::set-output name=plugins::$(curl -s https://api.napari-hub.org/plugins | jq -c 'keys')"
+        # Query npe2api for index of all plugins, select the keys, turn them into an array, select 10 random
+        # names from that array, convert the "one per line" output back into a string array
+        # save the string array of 10 plugins into the output from this step
+        run: |
+          set -eux
+          DATA=$(echo $(curl -s https://npe2api.vercel.app/api/plugins | jq -c 'keys' | jq -r '.[]' | shuf -n 10 | jq -R -s 'split("\n") | map(select(. != ""))'))
+          echo "plugins=$DATA" >> "$GITHUB_OUTPUT"
     outputs:
       plugins: ${{ steps.plugin_names.outputs.plugins }}
 
@@ -38,8 +45,9 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: 3.9
-          miniforge-variant: Mambaforge
+          python-version: '3.10'
+          miniforge-variant: Miniforge3
+          conda-remove-defaults: "true"
           miniforge-version: latest
           use-mamba: true
 

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/.github/workflows/update_changelog.yml

@@ -13,13 +13,13 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
       - name: "✏️ Generate release changelog"
-        uses: heinrichreimer/github-changelog-generator-action@v2.3
+        uses: heinrichreimer/github-changelog-generator-action@v2.4
         with:
           futureRelease: ${{ github.event.inputs.next_tag }}
           token: ${{ secrets.GITHUB_TOKEN }}
           repo: napari/npe2
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Automatic changelog update

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/.pre-commit-config.yaml

@@ -7,24 +7,24 @@ exclude: _docs/example_plugin/some_module.py
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 25.1.0
     hooks:
       - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.282
+    rev: v0.9.4
     hooks:
       - id: ruff
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.14.1
     hooks:
       - id: mypy
         additional_dependencies:

npe2-0.7.8rc0/PKG-INFO

@@ -0,0 +1,196 @@
+Metadata-Version: 2.4
+Name: npe2
+Version: 0.7.8rc0
+Summary: napari plugin engine v2
+Project-URL: homepage, https://github.com/napari/npe2
+Project-URL: repository, https://github.com/napari/npe2
+Author: Nathan Clack
+Author-email: Talley Lambert <talley.lambert@gmail.com>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Requires-Dist: appdirs
+Requires-Dist: build>=1
+Requires-Dist: psygnal>=0.3.0
+Requires-Dist: pydantic
+Requires-Dist: pyyaml
+Requires-Dist: rich
+Requires-Dist: tomli-w
+Requires-Dist: tomli; python_version < '3.11'
+Requires-Dist: typer
+Provides-Extra: dev
+Requires-Dist: black; extra == 'dev'
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: isort; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: jinja2; extra == 'docs'
+Requires-Dist: magicgui>=0.3.3; extra == 'docs'
+Provides-Extra: json
+Requires-Dist: jsonschema; extra == 'json'
+Provides-Extra: testing
+Requires-Dist: jsonschema; extra == 'testing'
+Requires-Dist: magicgui; extra == 'testing'
+Requires-Dist: napari-plugin-engine; extra == 'testing'
+Requires-Dist: napari-svg==0.1.5; extra == 'testing'
+Requires-Dist: numpy; extra == 'testing'
+Requires-Dist: pytest; extra == 'testing'
+Requires-Dist: pytest-cov; extra == 'testing'
+Requires-Dist: pytest-pretty; extra == 'testing'
+Description-Content-Type: text/markdown
+
+# npe2 - napari plugin engine version 2
+
+[![CI](https://github.com/napari/npe2/actions/workflows/ci.yml/badge.svg)](https://github.com/napari/npe2/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/napari/npe2/branch/main/graph/badge.svg?token=FTH635x542)](https://codecov.io/gh/napari/npe2)
+
+## Project description
+
+The **napari plugin engine version 2**, **npe2** extends the functionality of
+[napari's core](https://github.com/napari/napari).
+The plugin ecosystem offers user additional functionality for napari as well
+as specific support for different scientific domains.
+
+This repo contains all source code and documentation required for defining, validating and managing plugins for napari.
+
+## Getting started
+
+The [napari plugin docs landing page](https://napari.org/stable/plugins/index.html)
+offers comprehensive information for **plugin users** and for **plugin developers**.
+
+### Plugin users
+
+For plugin users, the docs include information about:
+- [Starting to use plugins](https://napari.org/stable/plugins/start_using_plugins/index.html#plugins-getting-started)
+- [Finding and installing plugins](https://napari.org/stable/plugins/start_using_plugins/finding_and_installing_plugins.html#find-and-install-plugins)
+
+### Plugin developers
+
+For plugin developers, the docs cover topics like:
+- [Building a plugin](https://napari.org/stable/plugins/building_a_plugin/index.html)
+- [Guides to different plugin contributions](https://napari.org/stable/plugins/building_a_plugin/guides.html)
+- [Technical references such as the plugin manifest](https://napari.org/stable/plugins/technical_references/manifest.html)
+
+Try the [**napari plugin template**](https://github.com/napari/napari-plugin-template)
+to streamline development of a new plugin.
+
+## Installation
+
+The `npe2` command line tool can be installed with `pip` or `conda`, but will already be installed as a dependency if you have napari installed.
+
+### Using pip
+
+1. Create and activate a virtual environment.
+
+*If you are new to using virtual environments, visit our [virtual environments guide](https://napari.org/stable/plugins/virtual_environment_docs/1-virtual-environments.html)*.
+
+    ```bash
+    python3 -m venv .venv
+    source .venv/bin/activate
+    ```
+
+2. Install npe2.
+
+    ```bash
+    pip install npe2
+    ```
+
+3. Test your installation.
+
+    ```bash
+    npe2 --help
+    ```
+
+### Using conda
+
+1. Create and activate a virtual environment.
+
+    ```bash
+    conda create -n npe-test -c conda-forge python=3.12
+    conda activate npe-test
+    ```
+
+2. Install npe2.
+
+    ```bash
+    conda install npe2
+    ```
+
+3. Test your installation.
+
+    ```bash
+    npe2 --help
+    ```
+
+## Usage
+
+The command line tool `npe2` offers the following commands:
+
+```bash
+cache      Cache utils
+compile    Compile @npe2.implements contributions to generate a manifest.
+convert    Convert first generation napari plugin to new (manifest) format.
+fetch      Fetch manifest from remote package.
+list       List currently installed plugins.
+parse      Show parsed manifest as yaml.
+validate   Validate manifest for a distribution name or manifest filepath.
+```
+
+### Examples
+
+List currently installed plugins:
+
+```bash
+npe2 list
+```
+
+Compile a source directory to create a plugin manifest:
+
+```bash
+npe2 compile PATH_TO_SOURCE_DIRECTORY
+```
+
+Convert current directory to an npe2-ready plugin
+(note: the repo must also be installed and importable in the current environment.):
+
+```bash
+npe2 convert .
+```
+
+Validate a plugin package. For example, a plugin named `your-plugin-package`:
+
+```bash
+npe2 validate your-plugin-package
+```
+
+Show a parsed manifest of your plugin:
+
+```bash
+npe2 parse your-plugin-package
+```
+
+## License
+
+npe2 uses the [BSD License](./LICENSE).
+
+## History
+
+This repo replaces the initial napari plugin engine v1.
+See also https://github.com/napari/napari/issues/3115 for
+motivation and technical discussion about the creation of v2.
+
+## Contact us
+
+Visit [our community documentation](https://napari.org/stable/community/index.html)
+or [open a new issue on this repo](https://github.com/napari/npe2/issues/new).

npe2-0.7.8rc0/README.md

@@ -0,0 +1,144 @@
+# npe2 - napari plugin engine version 2
+
+[![CI](https://github.com/napari/npe2/actions/workflows/ci.yml/badge.svg)](https://github.com/napari/npe2/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/napari/npe2/branch/main/graph/badge.svg?token=FTH635x542)](https://codecov.io/gh/napari/npe2)
+
+## Project description
+
+The **napari plugin engine version 2**, **npe2** extends the functionality of
+[napari's core](https://github.com/napari/napari).
+The plugin ecosystem offers user additional functionality for napari as well
+as specific support for different scientific domains.
+
+This repo contains all source code and documentation required for defining, validating and managing plugins for napari.
+
+## Getting started
+
+The [napari plugin docs landing page](https://napari.org/stable/plugins/index.html)
+offers comprehensive information for **plugin users** and for **plugin developers**.
+
+### Plugin users
+
+For plugin users, the docs include information about:
+- [Starting to use plugins](https://napari.org/stable/plugins/start_using_plugins/index.html#plugins-getting-started)
+- [Finding and installing plugins](https://napari.org/stable/plugins/start_using_plugins/finding_and_installing_plugins.html#find-and-install-plugins)
+
+### Plugin developers
+
+For plugin developers, the docs cover topics like:
+- [Building a plugin](https://napari.org/stable/plugins/building_a_plugin/index.html)
+- [Guides to different plugin contributions](https://napari.org/stable/plugins/building_a_plugin/guides.html)
+- [Technical references such as the plugin manifest](https://napari.org/stable/plugins/technical_references/manifest.html)
+
+Try the [**napari plugin template**](https://github.com/napari/napari-plugin-template)
+to streamline development of a new plugin.
+
+## Installation
+
+The `npe2` command line tool can be installed with `pip` or `conda`, but will already be installed as a dependency if you have napari installed.
+
+### Using pip
+
+1. Create and activate a virtual environment.
+
+*If you are new to using virtual environments, visit our [virtual environments guide](https://napari.org/stable/plugins/virtual_environment_docs/1-virtual-environments.html)*.
+
+    ```bash
+    python3 -m venv .venv
+    source .venv/bin/activate
+    ```
+
+2. Install npe2.
+
+    ```bash
+    pip install npe2
+    ```
+
+3. Test your installation.
+
+    ```bash
+    npe2 --help
+    ```
+
+### Using conda
+
+1. Create and activate a virtual environment.
+
+    ```bash
+    conda create -n npe-test -c conda-forge python=3.12
+    conda activate npe-test
+    ```
+
+2. Install npe2.
+
+    ```bash
+    conda install npe2
+    ```
+
+3. Test your installation.
+
+    ```bash
+    npe2 --help
+    ```
+
+## Usage
+
+The command line tool `npe2` offers the following commands:
+
+```bash
+cache      Cache utils
+compile    Compile @npe2.implements contributions to generate a manifest.
+convert    Convert first generation napari plugin to new (manifest) format.
+fetch      Fetch manifest from remote package.
+list       List currently installed plugins.
+parse      Show parsed manifest as yaml.
+validate   Validate manifest for a distribution name or manifest filepath.
+```
+
+### Examples
+
+List currently installed plugins:
+
+```bash
+npe2 list
+```
+
+Compile a source directory to create a plugin manifest:
+
+```bash
+npe2 compile PATH_TO_SOURCE_DIRECTORY
+```
+
+Convert current directory to an npe2-ready plugin
+(note: the repo must also be installed and importable in the current environment.):
+
+```bash
+npe2 convert .
+```
+
+Validate a plugin package. For example, a plugin named `your-plugin-package`:
+
+```bash
+npe2 validate your-plugin-package
+```
+
+Show a parsed manifest of your plugin:
+
+```bash
+npe2 parse your-plugin-package
+```
+
+## License
+
+npe2 uses the [BSD License](./LICENSE).
+
+## History
+
+This repo replaces the initial napari plugin engine v1.
+See also https://github.com/napari/napari/issues/3115 for
+motivation and technical discussion about the creation of v2.
+
+## Contact us
+
+Visit [our community documentation](https://napari.org/stable/community/index.html)
+or [open a new issue on this repo](https://github.com/napari/npe2/issues/new).

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/_docs/templates/_npe2_readers_guide.md.jinja

@@ -12,7 +12,8 @@ that accepts a path (`str`) or a list of paths and:
 * returns a *new function* (a `ReaderFunction`) that is capable of doing the reading.
 
 The `ReaderFunction` will be passed the same path (or list of paths) and
-is expected to return a list of {ref}`LayerData tuples <layer-data-tuples>`.
+is expected to return a list containing {ref}`LayerData tuples <layer-data-tuples>` or
+a fully instantiated napari `Layer` objects like `Image` or `Labels`.
 
 In the rare case that a reader plugin would like to "claim" a file, but *not*
 actually add any data to the viewer, the `ReaderFunction` may return

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/_docs/templates/_npe2_widgets_guide.md.jinja

@@ -64,7 +64,7 @@ specification:
 For more examples see [](creating-widgets) and
 [GUI gallery examples](https://napari.org/stable/_tags/gui.html) (only a subset
 involve widgets). Additionally,
-[cookiecutter-napari-plugin](https://github.com/napari/cookiecutter-napari-plugin)
+[napari-plugin-template](https://github.com/napari/napari-plugin-template)
 has more robust widget examples that you can adapt to your needs.
 
 ```{note}

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/pyproject.toml

@@ -98,7 +98,7 @@ line-length = 88
 target-version = "py38"
 fix = true
 src = ["src/npe2", "tests"]
-select = [
+lint.select = [
     "E",
     "F",
     "W",   #flake8
@@ -110,14 +110,15 @@ select = [
     "RUF", # ruff-specific rules
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "src/npe2/cli.py" = ["B008", "A00"]
+"**/test_*.py" = ["RUF018"]
 
-[tool.ruff.pyupgrade]
+[tool.ruff.lint.pyupgrade]
 # Preserve types, even if a file imports `from __future__ import annotations`.
 keep-runtime-typing = true
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ['npe2']
 
 # https://mypy.readthedocs.io/en/stable/config_file.html

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/src/npe2/_dynamic_plugin.py

@@ -203,14 +203,12 @@ class ContributionDecorator(Generic[C]):
         self._contrib_name = CONTRIB_NAMES[self.contrib_type]
 
     @overload
-    def __call__(self, func: T, **kwargs) -> T:
-        ...
+    def __call__(self, func: T, **kwargs) -> T: ...
 
     @overload
     def __call__(
         self, func: Optional[Literal[None]] = None, **kwargs
-    ) -> Callable[[T], T]:
-        ...
+    ) -> Callable[[T], T]: ...
 
     def __call__(
         self, func: Optional[T] = None, **kwargs

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/src/npe2/_inspection/_fetch.py

@@ -3,10 +3,8 @@ from __future__ import annotations
 import io
 import json
 import os
-import re
 import subprocess
 import tempfile
-from concurrent.futures import ProcessPoolExecutor
 from contextlib import contextmanager
 from functools import lru_cache
 from importlib import metadata
@@ -20,11 +18,10 @@ from typing import (
     Iterator,
     List,
     Optional,
-    Tuple,
     Union,
 )
 from unittest.mock import patch
-from urllib import error, parse, request
+from urllib import error, request
 from zipfile import ZipFile
 
 from npe2.manifest import PackageMetadata
@@ -39,9 +36,8 @@ NPE1_ENTRY_POINT = "napari.plugin"
 NPE2_ENTRY_POINT = "napari.manifest"
 __all__ = [
     "fetch_manifest",
-    "get_pypi_url",
     "get_hub_plugin",
-    "get_pypi_plugins",
+    "get_pypi_url",
 ]
 
 
@@ -59,7 +55,7 @@ def _manifest_from_npe2_dist(
     module: str = match.groupdict()["module"]
     attr: str = match.groupdict()["attr"]
 
-    mf_file = Path(dist.locate_file(Path(module.replace(".", os.sep)) / attr))
+    mf_file = Path(dist.locate_file(Path(module.replace(".", os.sep)) / attr))  # type: ignore[arg-type]
     if not mf_file.exists():
         raise ValueError(  # pragma: no cover
             f"manifest {mf_file.name!r} does not exist in distribution "
@@ -264,7 +260,7 @@ def fetch_manifest(
                 return _manifest_from_extracted_wheel(td)
         except metadata.PackageNotFoundError:
             return _manifest_from_pypi_sdist(package_or_url, version)
-        except error.HTTPError:
+        except error.HTTPError:  # pragma: no cover
             pass  # pragma: no cover
     raise ValueError(  # pragma: no cover
         f"Could not interpret {package_or_url!r} as a PYPI package name or URL to a "
@@ -377,75 +373,8 @@ def _tmp_pypi_sdist_download(
     return _tmp_targz_download(url)
 
 
-@lru_cache
-def _get_packages_by_classifier(classifier: str) -> Dict[str, str]:
-    """Search for packages declaring ``classifier`` on PyPI.
-
-    Returns
-    -------
-    packages : List[str]
-        name of all packages at pypi that declare ``classifier``
-    """
-    PACKAGE_NAME_PATTERN = re.compile('class="package-snippet__name">(.+)</span>')
-    PACKAGE_VERSION_PATTERN = re.compile('class="package-snippet__version">(.+)</span>')
-
-    packages = {}
-    page = 1
-    url = f"https://pypi.org/search/?c={parse.quote_plus(classifier)}&page="
-    while True:
-        try:
-            with request.urlopen(f"{url}{page}") as response:
-                html = response.read().decode()
-            names = PACKAGE_NAME_PATTERN.findall(html)
-            versions = PACKAGE_VERSION_PATTERN.findall(html)
-            packages.update(dict(zip(names, versions)))
-            page += 1
-        except error.HTTPError:
-            break
-
-    return dict(sorted(packages.items()))
-
-
-def get_pypi_plugins() -> Dict[str, str]:
-    """Return {name: latest_version} for all plugins found on pypi."""
-    NAPARI_CLASSIFIER = "Framework :: napari"
-    return _get_packages_by_classifier(NAPARI_CLASSIFIER)
-
-
 @lru_cache
 def get_hub_plugin(plugin_name: str) -> Dict[str, Any]:
     """Return hub information for a specific plugin."""
     with request.urlopen(f"https://api.napari-hub.org/plugins/{plugin_name}") as r:
         return json.load(r)
-
-
-def _try_fetch_and_write_manifest(args: Tuple[str, str, Path, int]):
-    name, version, dest, indent = args
-    FORMAT = "json"
-
-    try:  # pragma: no cover
-        mf = fetch_manifest(name, version=version)
-        manifest_string = getattr(mf, FORMAT)(exclude=set(), indent=indent)
-
-        (dest / f"{name}.{FORMAT}").write_text(manifest_string)
-        print(f"✅ {name}")
-    except Exception as e:
-        print(f"❌ {name}")
-        return name, {"version": version, "error": str(e)}
-
-
-def fetch_all_manifests(dest: str = "manifests", indent: int = 2) -> None:
-    """Fetch all manifests for plugins on PyPI and write to ``dest`` directory."""
-    _dest = Path(dest)
-    _dest.mkdir(exist_ok=True, parents=True)
-
-    args = [
-        (name, ver, _dest, indent) for name, ver in sorted(get_pypi_plugins().items())
-    ]
-
-    # use processes instead of threads, because many of the subroutines in build
-    # and setuptools use `os.chdir()`, which is not thread-safe
-    with ProcessPoolExecutor() as executor:
-        errors = list(executor.map(_try_fetch_and_write_manifest, args))
-    _errors = {tup[0]: tup[1] for tup in errors if tup}
-    (_dest / "errors.json").write_text(json.dumps(_errors, indent=indent))

{npe2-0.7.7rc0 → npe2-0.7.8rc0}/src/npe2/_inspection/_from_npe1.py

@@ -404,11 +404,11 @@ class HookImplParser:
         )
 
     def add_command(self, impl: HookImplementation, py_name: str = "") -> str:
-        name = impl.specname.replace("napari_", "")
-        id = f"{self.package}.{name}"
-        title = " ".join(name.split("_")).title()
         if not py_name:
             py_name = _python_name(impl.function)
+        name = impl.function.__name__
+        id = f"{self.package}.{name}"
+        title = " ".join(name.split("_")).title()
         c = CommandContribution(id=id, python_name=py_name, title=title)
         self.contributions["commands"].append(c)
         return id
@@ -516,7 +516,7 @@ def get_top_module_path(package_name, top_module: Optional[str] = None) -> Path:
             )
         top_module = top_mods[0]
 
-    path = Path(dist.locate_file(top_module))
+    path = Path(dist.locate_file(top_module))  # type: ignore[arg-type]
     if not path.is_dir() and dist.files:
         for f_path in dist.files:
             if "__editable__" in f_path.name: