Use Ruff and pyproject.toml (#191)

* Use Ruff and pyproject.toml

Replace isort and Flake8 with ruff, and move black and pytest config to pyproject.toml.

* Add a pre-commit action

* Use pre-commit.ci but disable fixes

* Use pre-commit to format pyproject.toml

* Ruff fixes

.binder/test.py

@@ -8,10 +8,10 @@
     print(client.cluster)
     print(client.cluster.dashboard_link)
 
-    ds = xr.tutorial.open_dataset('air_temperature', chunks=dict(lat=5, lon=5), decode_cf=False)
+    ds = xr.tutorial.open_dataset('air_temperature', chunks={'lat': 5, 'lon': 5}, decode_cf=False)
     print(ds)
 
-    for k, da in ds.variables.items():
+    for _k, da in ds.variables.items():
         da.encoding['compressor'] = None
 
     app = ds.rest.app

.pre-commit-config.yaml

@@ -9,6 +9,12 @@ repos:
       - id: check-yaml
       - id: double-quote-string-fixer
 
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.265"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
   - repo: https://github.com/executablebooks/mdformat
     rev: 0.7.16
     hooks:
@@ -27,20 +33,6 @@ repos:
     rev: 23.3.0
     hooks:
       - id: black
-        args: ["--line-length", "100", "--skip-string-normalization"]
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-  - repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
-    hooks:
-      - id: seed-isort-config
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
 
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v3.0.0-alpha.6
@@ -49,3 +41,11 @@ repos:
         language_version: system
         exclude_types:
           - markdown # managed by mdformat
+
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "0.9.0"
+    hooks:
+      - id: pyproject-fmt
+
+ci:
+  autofix_prs: false

README.rst

@@ -18,6 +18,10 @@ Publish Xarray Datasets via a REST API.
 .. image:: https://codecov.io/gh/xarray-contrib/xpublish/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/xarray-contrib/xpublish
 
+.. image:: https://results.pre-commit.ci/badge/github/xpublish-community/xpublish/main.svg
+   :target: https://results.pre-commit.ci/latest/github/xpublish-community/xpublish/main
+   :alt: pre-commit.ci status
+
 **Serverside: Publish a Xarray Dataset through a rest API**
 
 .. code-block:: python

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

@@ -29,7 +29,7 @@ def get_mean(var_name: str, dataset=Depends(deps.dataset)):
 
 ds = xr.tutorial.open_dataset(
     'air_temperature',
-    chunks=dict(lat=5, lon=5),
+    chunks={'lat': 5, 'lon': 5},
 )
 
 rest = SingleDatasetRest(ds)

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

@@ -5,7 +5,7 @@
 
 ds = xr.tutorial.open_dataset(
     'air_temperature',
-    chunks=dict(lat=5, lon=5),
+    chunks={'lat': 5, 'lon': 5},
 )
 
 myrouter = APIRouter()

pyproject.toml

@@ -0,0 +1,61 @@
+
+[tool.black]
+line-length = 100
+skip-string-normalization = true
+
+[tool.pytest.ini_options]
+log_cli = true
+log_level = "INFO"
+addopts = "--cov=./ --cov-report=xml --verbose"
+
+[tool.ruff]
+select = [
+    "B", # flake8-bugbear
+    "C",
+    "E", # pycodestyle
+    "F", # Pyflakes
+    "I", # isort
+    "W", # pycodestyle
+    # "T4",
+    "B9",
+]
+ignore = [
+    # "E203",
+    # "E266",
+    "E501",
+    # "W503",
+    "E722",
+    "E402",
+    "C901",
+]
+line-length = 100
+
+[tool.ruff.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 18
+
+[tool.ruff.isort]
+combine-as-imports = true
+known-first-party = ["xpublish"]
+known-third-party = [
+    "cachey",
+    "dask",
+    "fastapi",
+    "numcodecs",
+    "numpy",
+    "pandas",
+    "pkg_resources",
+    "pluggy",
+    "pydantic",
+    "pytest",
+    "setuptools",
+    "sphinx_autosummary_accessors",
+    "starlette",
+    "uvicorn",
+    "xarray",
+    "zarr",
+]
+
+[tool.ruff.flake8-bugbear]
+# Allow fastapi.Depends and other dependency injection style function arguments
+extend-immutable-calls = ["fastapi.Depends", "fastapi.Query"]

tests/test_rest_api.py

@@ -14,13 +14,13 @@
 
 @pytest.fixture(scope='function')
 def airtemp_rest(airtemp_ds):
-    app_kws = dict(
-        title='My Dataset',
-        description='Dataset Description',
-        version='1.0.0',
-        openapi_url='/dataset.json',
-        docs_url='/data-docs',
-    )
+    app_kws = {
+        'title': 'My Dataset',
+        'description': 'Dataset Description',
+        'version': '1.0.0',
+        'openapi_url': '/dataset.json',
+        'docs_url': '/data-docs',
+    }
 
     return SingleDatasetRest(airtemp_ds, app_kws=app_kws)
 
@@ -115,13 +115,13 @@ def test_init_cache_kws(airtemp_ds):
 def test_init_app_kws(airtemp_ds):
     rest = Rest(
         {'airtemp': airtemp_ds},
-        app_kws=dict(
-            title='My Dataset',
-            description='Dataset Description',
-            version='1.0.0',
-            openapi_url='/dataset.json',
-            docs_url='/data-docs',
-        ),
+        app_kws={
+            'title': 'My Dataset',
+            'description': 'Dataset Description',
+            'version': '1.0.0',
+            'openapi_url': '/dataset.json',
+            'docs_url': '/data-docs',
+        },
     )
 
     assert rest.app.title == 'My Dataset'
@@ -353,8 +353,8 @@ def test_rest_accessor(airtemp_ds):
 
 def test_rest_accessor_kws(airtemp_ds):
     airtemp_ds.rest(
-        app_kws=dict(docs_url='/data-docs'),
-        cache_kws=dict(available_bytes=1e9),
+        app_kws={'docs_url': '/data-docs'},
+        cache_kws={'available_bytes': 1e9},
     )
 
     assert airtemp_ds.rest.cache.available_bytes == 1e9
@@ -414,14 +414,14 @@ def test_single_dataset_openapi_override(airtemp_rest):
 
 
 def test_serve(airtemp_rest, mocker):
-    kwargs = dict(host='0.0.0.0', log_level='debug', port=9000)
+    kwargs = {'host': '0.0.0.0', 'log_level': 'debug', 'port': 9000}
     mocker.patch('uvicorn.run')
     airtemp_rest.serve(**kwargs)
     uvicorn.run.assert_called_once_with(airtemp_rest.app, **kwargs)
 
 
 def test_accessor_serve(airtemp_ds, mocker):
-    kwargs = dict(host='0.0.0.0', log_level='debug', port=9000)
+    kwargs = {'host': '0.0.0.0', 'log_level': 'debug', 'port': 9000}
     mocker.patch('uvicorn.run')
     airtemp_ds.rest.serve(**kwargs)
     uvicorn.run.assert_called_once_with(airtemp_ds.rest.app, **kwargs)

xpublish/routers/__init__.py

@@ -1 +1 @@
-from .common import dataset_collection_router
+from .common import dataset_collection_router  # noqa: F401

xpublish/utils/api.py

@@ -25,7 +25,7 @@ def normalize_datasets(datasets) -> Dict[str, xr.Dataset]:
     if isinstance(datasets, xr.Dataset):
         return {}
     elif isinstance(datasets, Mapping):
-        if not all([isinstance(obj, xr.Dataset) for obj in datasets.values()]):
+        if not all(isinstance(obj, xr.Dataset) for obj in datasets.values()):
             raise TypeError(error_msg)
         return {str(k): ds.assign_attrs({DATASET_ID_ATTR_KEY: k}) for k, ds in datasets.items()}
     else:
@@ -97,14 +97,14 @@ def openapi(self):
         if self._app.openapi_schema:
             return self._app.openapi_schema
 
-        kwargs = dict(
-            title=self._app.title,
-            version=self._app.version,
-            description=self._app.description,
-            routes=self._app.routes,
-            tags=self._app.openapi_tags,
-            servers=self._app.servers,
-        )
+        kwargs = {
+            'title': self._app.title,
+            'version': self._app.version,
+            'description': self._app.description,
+            'routes': self._app.routes,
+            'tags': self._app.openapi_tags,
+            'servers': self._app.servers,
+        }
 
         openapi_schema = get_openapi(**kwargs)
 
@@ -124,9 +124,12 @@ def openapi(self):
 
 class JSONResponse(StarletteJSONResponse):
     def __init__(self, *args, **kwargs):
-        self._render_kwargs = dict(
-            ensure_ascii=True, allow_nan=True, indent=None, separators=(',', ':')
-        )
+        self._render_kwargs = {
+            'ensure_ascii': True,
+            'allow_nan': True,
+            'indent': None,
+            'separators': (',', ':'),
+        }
         self._render_kwargs.update(kwargs.pop('render_kwargs', {}))
         super().__init__(*args, **kwargs)
 

xpublish/utils/zarr.py

@@ -58,7 +58,7 @@ def _extract_dataarray_coords(da, zattrs):
         nondim_coords = set(da.coords) - set(da.dims)
 
         if len(nondim_coords) > 0 and da.name not in nondim_coords:
-            coords = ' '.join(sorted(list(nondim_coords)))
+            coords = ' '.join(sorted(nondim_coords))
             zattrs['coordinates'] = encode_zarr_attr_value(coords)
     return zattrs