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

.github/workflows/main.yaml

@@ -8,11 +8,12 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.python-version }}-build
+    name: ${{ matrix.python-version }}-pydantic${{ matrix.pydantic-version }}-build
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
+        pydantic-version: ["<2", ">=2"]
     steps:
       - uses: actions/checkout@v3
 
@@ -26,8 +27,9 @@ jobs:
         uses: actions/cache@v3.3.1
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/dev-requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-pydantic${{ matrix.pydantic-version }}-${{ hashFiles('**/dev-requirements.txt') }}
           restore-keys: |
+            ${{ runner.os }}-pip-${{ matrix.python-version }}-pydantic${{ matrix.pydantic-version }}
             ${{ runner.os }}-pip-${{ matrix.python-version }}
             ${{ runner.os }}-pip
             ${{ runner.os }}-pip-dev
@@ -36,6 +38,7 @@ jobs:
         run: |
           python -m pip install -r dev-requirements.txt
           python -m pip install --no-deps -e .
+          python -m pip install "pydantic${{ matrix.pydantic-version }}"
           python -m pip list
 
       - name: Running Tests
@@ -44,7 +47,6 @@ jobs:
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3.1.4
-        if: ${{ matrix.python-version }} == 3.9
         with:
           file: ./coverage.xml
           fail_ci_if_error: false

.readthedocs.yml

@@ -20,6 +20,6 @@ build:
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: docs/requirements.txt
     - method: pip
       path: .
+    - requirements: docs/requirements.txt

dev-requirements.txt

@@ -1,11 +1,20 @@
+cachey
+dask
+fastapi>=0.78.0
 fsspec
 httpx
 importlib-metadata
 netcdf4
+numcodecs
+numpy
+pluggy
 pooch
 pytest
 pytest-mock
 pytest-sugar
 pytest-cov
 requests
--r requirements.txt
+toolz
+uvicorn
+xarray
+zarr

docs/requirements.txt

@@ -1,4 +1,5 @@
 sphinx>=3.1
+pydantic<2.0
 sphinx-autosummary-accessors
 pydata-sphinx-theme
 sphinx-autodoc-typehints

docs/source/getting-started/tutorial/dataset-provider-plugin.py

@@ -5,7 +5,7 @@
 
 
 class TutorialDataset(Plugin):
-    name = 'xarray-tutorial-dataset'
+    name: str = 'xarray-tutorial-dataset'
 
     @hookimpl
     def get_datasets(self):

docs/source/getting-started/tutorial/dataset-router-plugin.py

@@ -1,14 +1,16 @@
+from typing import Sequence
+
 import xarray as xr
 from fastapi import APIRouter, Depends, HTTPException
 
 from xpublish import Dependencies, Plugin, SingleDatasetRest, hookimpl
 
 
 class MeanPlugin(Plugin):
-    name = 'mean'
+    name: str = 'mean'
 
-    dataset_router_prefix = ''
-    dataset_router_tags = ['mean']
+    dataset_router_prefix: str = ''
+    dataset_router_tags: Sequence[str] = ['mean']
 
     @hookimpl
     def dataset_router(self, deps: Dependencies):

docs/source/user-guide/plugins.md

@@ -47,10 +47,10 @@ from xpublish import Plugin
 
 
 class HelloWorldPlugin(Plugin):
-    name = "hello_world"
+    name: str = "hello_world"
 ```
 
-At the minimum, a plugin needs to specify a `name` attribute.
+At the minimum, a plugin needs to specify a `name` attribute with a type annotation. For example, `name: str = my_plugin_name`.
 
 ### Marking implementation methods
 
@@ -66,7 +66,7 @@ from xpublish import Plugin, hookimpl
 from fastapi import APIRouter
 
 class HelloWorldPlugin(Plugin):
-    name = "hello_world"
+    name: str = "hello_world"
 
     @hookimpl
     def app_router(self):
@@ -188,7 +188,7 @@ from xpublish import Plugin, Dependencies, hookimpl
 
 
 class DatasetAttrs(Plugin):
-    name = "dataset-attrs"
+    name: str = "dataset-attrs"
 
     @hookimpl
     def dataset_router(self, deps: Dependencies):
@@ -224,7 +224,7 @@ from xpublish import Plugin, Dependencies, hookimpl
 
 
 class DatasetInfoPlugin(Plugin):
-    name = "dataset-info"
+    name: str = "dataset-info"
 
     dataset_router_prefix = "/info"
     dataset_router_tags = ["info"]
@@ -257,7 +257,7 @@ from xpublish import Plugin, Dependencies, hookimpl
 
 
 class PluginInfo(Plugin):
-    name = "plugin_info"
+    name: str = "plugin_info"
 
     app_router_prefix = "/info"
     app_router_tags = ["info"]
@@ -298,7 +298,7 @@ from xpublish import Plugin, hookimpl
 
 
 class TutorialDataset(Plugin):
-    name = "xarray-tutorial-dataset"
+    name: str = "xarray-tutorial-dataset"
 
     @hookimpl
     def get_datasets(self):

tests/test_rest_api.py

@@ -64,7 +64,7 @@ def get_dims(dataset: xr.Dataset = Depends(get_dataset)):
 @pytest.fixture(scope='function')
 def dataset_plugin(airtemp_ds):
     class AirtempPlugin(Plugin):
-        name = 'airtemp'
+        name: str = 'airtemp'
 
         @hookimpl
         def get_dataset(self, dataset_id: str):
@@ -86,7 +86,7 @@ def hello(self):
             pass
 
     class HookSpecPlugin(Plugin):
-        name = 'hook_spec'
+        name: str = 'hook_spec'
 
         @hookimpl
         def register_hookspec(self):
@@ -98,7 +98,7 @@ def register_hookspec(self):
 @pytest.fixture(scope='function')
 def hook_implementation_plugin():
     class HookImplementationPlugin(Plugin):
-        name = 'hook_implementation'
+        name: str = 'hook_implementation'
 
         @hookimpl
         def hello(self):

xpublish/dependencies.py

@@ -9,7 +9,7 @@
 from fastapi import Depends
 
 from .utils.api import DATASET_ID_ATTR_KEY
-from .utils.zarr import create_zmetadata, create_zvariables, zarr_metadata_key
+from .utils.zarr import ZARR_METADATA_KEY, create_zmetadata, create_zvariables
 
 if TYPE_CHECKING:
     from .plugins import Plugin  # pragma: no cover
@@ -90,7 +90,7 @@ def get_zmetadata(
 ):
     """FastAPI dependency that returns a consolidated zmetadata dictionary."""
 
-    cache_key = dataset.attrs.get(DATASET_ID_ATTR_KEY, '') + '/' + zarr_metadata_key
+    cache_key = dataset.attrs.get(DATASET_ID_ATTR_KEY, '') + '/' + ZARR_METADATA_KEY
     zmeta = cache.get(cache_key)
 
     if zmeta is None:

xpublish/plugins/hooks.py

@@ -26,19 +26,24 @@ class Dependencies(BaseModel):
     """
 
     dataset_ids: Callable[..., List[str]] = Field(
-        get_dataset_ids, description='Returns a list of all valid dataset ids'
+        get_dataset_ids,
+        description='Returns a list of all valid dataset ids',
     )
     dataset: Callable[[str], xr.Dataset] = Field(
-        get_dataset, description='Returns a dataset using ``/<dataset_id>/`` in the path.'
+        get_dataset,
+        description='Returns a dataset using ``/<dataset_id>/`` in the path.',
     )
     cache: Callable[..., cachey.Cache] = Field(
-        get_cache, description='Provide access to :py:class:`cachey.Cache`'
+        get_cache,
+        description='Provide access to :py:class:`cachey.Cache`',
     )
     plugins: Callable[..., Dict[str, 'Plugin']] = Field(
-        get_plugins, description='A dictionary of plugins allowing direct access'
+        get_plugins,
+        description='A dictionary of plugins allowing direct access',
     )
     plugin_manager: Callable[..., pluggy.PluginManager] = Field(
-        get_plugin_manager, description='The plugin manager itself, allowing for maximum creativity'
+        get_plugin_manager,
+        description='The plugin manager itself, allowing for maximum creativity',
     )
 
     def __hash__(self):
@@ -64,7 +69,13 @@ def __hash__(self):
         """Make sure that the plugin is hashable to load with pluggy"""
         things_to_hash = []
 
-        for e in self.dict():
+        # try/except is for pydantic backwards compatibility
+        try:
+            model_dict = self.model_dump()
+        except AttributeError:
+            model_dict = self.dict()
+
+        for e in model_dict:
             if isinstance(e, list):
                 things_to_hash.append(tuple(e))  # pragma: no cover
             else:
@@ -115,7 +126,8 @@ def get_datasets(self) -> Iterable[str]:  # type: ignore
         """Return an iterable of dataset ids that the plugin can provide"""
 
     @hookspec(firstresult=True)
-    def get_dataset(self, dataset_id: str) -> Optional[xr.Dataset]:  # type: ignore
+    # type: ignore
+    def get_dataset(self, dataset_id: str) -> Optional[xr.Dataset]:
         """Return a dataset by requested dataset_id.
 
         If the plugin does not have the dataset, return None

xpublish/plugins/included/dataset_info.py

@@ -14,19 +14,22 @@
 class DatasetInfoPlugin(Plugin):
     """Dataset metadata"""
 
-    name = 'dataset_info'
+    name: str = 'dataset_info'
 
     dataset_router_prefix: str = ''
     dataset_router_tags: Sequence[str] = ['dataset_info']
 
     @hookimpl
-    def dataset_router(self, deps: Dependencies):
-        router = APIRouter(prefix=self.dataset_router_prefix, tags=list(self.dataset_router_tags))
+    def dataset_router(self, deps: Dependencies) -> APIRouter:
+        router = APIRouter(
+            prefix=self.dataset_router_prefix,
+            tags=list(self.dataset_router_tags),
+        )
 
         @router.get('/')
         def html_representation(
             dataset=Depends(deps.dataset),
-        ):
+        ) -> HTMLResponse:
             """Returns the xarray HTML representation of the dataset."""
 
             with xr.set_options(display_style='html'):
@@ -43,15 +46,15 @@ def list_keys(
         @router.get('/dict')
         def to_dict(
             dataset=Depends(deps.dataset),
-        ):
+        ) -> dict:
             """The full dataset as a dictionary"""
             return JSONResponse(dataset.to_dict(data=False))
 
         @router.get('/info')
         def info(
             dataset=Depends(deps.dataset),
             cache=Depends(deps.cache),
-        ):
+        ) -> dict:
             """Dataset schema (close to the NCO-JSON schema)."""
 
             zvariables = get_zvariables(dataset, cache)
@@ -66,6 +69,7 @@ def info(
             for name, var in zvariables.items():
                 attrs = meta[f'{name}/{attrs_key}'].copy()
                 attrs.pop('_ARRAY_DIMENSIONS')
+
                 info['variables'][name] = {
                     'type': var.data.dtype.name,
                     'dimensions': list(var.dims),

xpublish/plugins/included/module_version.py

@@ -3,7 +3,7 @@
 """
 import importlib
 import sys
-from typing import List
+from typing import Sequence
 
 from fastapi import APIRouter
 
@@ -14,17 +14,20 @@
 class ModuleVersionPlugin(Plugin):
     """Share the currently loaded versions of key libraries"""
 
-    name = 'module_version'
+    name: str = 'module_version'
 
     app_router_prefix: str = ''
-    app_router_tags: List[str] = ['module_version']
+    app_router_tags: Sequence[str] = ['module_version']
 
     @hookimpl
-    def app_router(self):
-        router = APIRouter(prefix=self.app_router_prefix, tags=self.app_router_tags)
+    def app_router(self) -> APIRouter:
+        router = APIRouter(
+            prefix=self.app_router_prefix,
+            tags=self.app_router_tags,
+        )
 
         @router.get('/versions')
-        def get_versions():
+        def get_versions() -> dict:
             """Currently loaded versions of key libraries"""
             versions = dict(get_sys_info() + netcdf_and_hdf5_versions())
             modules = [

xpublish/plugins/included/plugin_info.py

@@ -12,20 +12,23 @@
 
 class PluginInfo(BaseModel):
     path: str
-    version: Optional[str]
+    version: Optional[str] = None
 
 
 class PluginInfoPlugin(Plugin):
     """Expose plugin source and version"""
 
-    name = 'plugin_info'
+    name: str = 'plugin_info'
 
     app_router_prefix: str = ''
     app_router_tags: Sequence[str] = ['plugin_info']
 
     @hookimpl
-    def app_router(self, deps: Dependencies):
-        router = APIRouter(prefix=self.app_router_prefix, tags=list(self.app_router_tags))
+    def app_router(self, deps: Dependencies) -> APIRouter:
+        router = APIRouter(
+            prefix=self.app_router_prefix,
+            tags=list(self.app_router_tags),
+        )
 
         @router.get('/plugins')
         def get_plugins(
@@ -44,7 +47,8 @@ def get_plugins(
                     version = None  # pragma: no cover
 
                 plugin_info[name] = PluginInfo(
-                    path=f'{plugin_type.__module__}.{plugin.__repr_name__()}', version=version
+                    path=f'{plugin_type.__module__}.{plugin.__repr_name__()}',
+                    version=version,
                 )
 
             return plugin_info