Merge pull request #58 from bcdev/forman-0.5.0

Release 0.5.0

Author: forman

CHANGES.md

@@ -1,6 +1,6 @@
 # XRLint Change History
 
-## Version 0.5.0 (in development)
+## Version 0.5.0 (from 2025-02-13)
 
 ### Adjustments and Enhancements
 

docs/rule-ref.md

@@ -20,15 +20,15 @@ A dataset should provide information about where the data came from and what has
 - `no_vars`: do not check variables at all. Defaults to `False`.
 - `ignored_vars`: list of ignored variables (regex patterns). Defaults to `['crs', 'spatial_ref']`.
 
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#description-of-file-contents)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#description-of-file-contents)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
 ### :material-lightbulb: `conventions`
 
 Datasets should identify the applicable conventions using the `Conventions` attribute.
  The rule has an optional configuration parameter `match` which is a regex pattern that the value of the `Conventions` attribute must match, if any. If not provided, the rule just verifies that the attribute exists and whether it is a character string.
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#identification-of-conventions)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#identification-of-conventions)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
@@ -41,20 +41,21 @@ Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning
 ### :material-bug: `grid-mappings`
 
 Grid mappings, if any, shall have valid grid mapping coordinate variables.
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#grid-mappings-and-projections)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-bug: `lat-coordinate`
 
 Latitude coordinate should have standard units and standard names.
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#latitude-coordinate)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#latitude-coordinate)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-bug: `lon-coordinate`
 
 Longitude coordinate should have standard units and standard names.
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#longitude-coordinate)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#longitude-coordinate)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
@@ -67,35 +68,42 @@ Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 ### :material-lightbulb: `no-empty-chunks`
 
 Empty chunks should not be encoded and written. The rule currently applies to Zarr format only.
-[:material-information-variant:](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.to_zarr.html#xarray-dataset-to-zarr)
+[More...](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.to_zarr.html#xarray-dataset-to-zarr)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-circle-off-outline:
 
 ### :material-bug: `time-coordinate`
 
 Time coordinates should have valid and unambiguous time units encoding.
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#time-coordinate)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#time-coordinate)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-lightbulb: `var-desc`
 
 Check that each data variable provides an identification and description of the content. The rule can be configured by parameter `attrs` which is a list of names of attributes that provides descriptive information. It defaults to `['standard_name', 'long_name']`.
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#standard-name)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#standard-name)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
 ### :material-lightbulb: `var-flags`
 
 Validate attributes 'flag_values', 'flag_masks' and 'flag_meanings' that make variables that contain flag values self describing. 
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#flags)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#flags)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
+### :material-lightbulb: `var-missing-data`
+
+Checks the recommended use of missing data, i.e., coordinate variables should not define missing data, but packed data should. Notifies about the use of valid ranges to indicate missing data, which is currently not supported by xarray.
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#units)
+
+Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
+
 ### :material-lightbulb: `var-units`
 
 Every variable should provide a description of its units.
-[:material-information-variant:](https://cfconventions.org/cf-conventions/cf-conventions.html#units)
+[More...](https://cfconventions.org/cf-conventions/cf-conventions.html#units)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
@@ -104,70 +112,70 @@ Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 ### :material-bug: `any-spatial-data-var`
 
 A datacube should have spatial data variables.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#data-model-and-format)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#data-model-and-format)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-bug: `cube-dims-order`
 
 Order of dimensions in spatio-temporal datacube variables should be [time, ..., y, x].
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#data-model-and-format)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#data-model-and-format)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-lightbulb: `data-var-colors`
 
 Spatial data variables should encode xcube color mappings in their metadata.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#encoding-of-colors)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#encoding-of-colors)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
 ### :material-bug: `dataset-title`
 
 Datasets should be given a non-empty title.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#metadata)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#metadata)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-lightbulb: `grid-mapping-naming`
 
 Grid mapping variables should be called 'spatial_ref' or 'crs' for compatibility with rioxarray and other packages.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#spatial-reference)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#spatial-reference)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
 ### :material-bug: `increasing-time`
 
 Time coordinate labels should be monotonically increasing.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#temporal-reference)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#temporal-reference)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-bug: `lat-lon-naming`
 
 Latitude and longitude coordinates and dimensions should be called 'lat' and 'lon'.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#spatial-reference)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#spatial-reference)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-lightbulb: `ml-dataset-meta`
 
 Multi-level datasets should provide a '.zlevels' meta-info file, and if so, it should be consistent. Without the meta-info file the multi-level dataset cannot be reliably extended by new time slices as the aggregation method used for each variable must be specified.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/mldatasets.html#the-xcube-levels-format)
+[More...](https://xcube.readthedocs.io/en/latest/mldatasets.html#the-xcube-levels-format)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-bug: `ml-dataset-time`
 
 The `time` dimension of multi-level datasets should use a chunk size of 1. This allows for faster image tile generation for visualisation.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/mldatasets.html#definition)
+[More...](https://xcube.readthedocs.io/en/latest/mldatasets.html#definition)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 
 ### :material-bug: `ml-dataset-xy`
 
 Multi-level dataset levels should provide spatial resolutions decreasing by powers of two.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/mldatasets.html#definition)
+[More...](https://xcube.readthedocs.io/en/latest/mldatasets.html#definition)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
@@ -180,14 +188,14 @@ Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-alert:
 ### :material-bug: `single-grid-mapping`
 
 A single grid mapping shall be used for all spatial data variables of a datacube.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#spatial-reference)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#spatial-reference)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 
 ### :material-bug: `time-naming`
 
 Time coordinate and dimension should be called 'time'.
-[:material-information-variant:](https://xcube.readthedocs.io/en/latest/cubespec.html#temporal-reference)
+[More...](https://xcube.readthedocs.io/en/latest/cubespec.html#temporal-reference)
 
 Contained in:  `all`-:material-lightning-bolt: `recommended`-:material-lightning-bolt:
 

environment.yml

@@ -10,6 +10,7 @@ dependencies:
   - tabulate
   - xarray
   # Dev Dependencies
+  - isort
   - mkdocs
   - mkdocs-autorefs
   - mkdocs-material

mkruleref.py

@@ -52,7 +52,7 @@ def write_plugin_rules(stream, plugin: Plugin):
         )
         stream.write(rule_meta.description or "_No description._")
         if rule_meta.docs_url:
-            stream.write("\n" + f"[:{read_more_icon}:]({rule_meta.docs_url})")
+            stream.write(f"\n[More...]({rule_meta.docs_url})")
         stream.write("\n\n")
         # List the predefined configurations that contain the rule
         stream.write("Contained in: ")

pyproject.toml

@@ -68,6 +68,7 @@ dev = [
   # Development tools
   "build",
   "hatch",
+  "isort",
   "pytest",
   "pytest-cov",
   "ruff",

tests/test_linter.py

@@ -10,7 +10,7 @@
 from xrlint.config import Config, ConfigObject
 from xrlint.constants import CORE_PLUGIN_NAME, DATASET_ROOT_NAME
 from xrlint.linter import Linter, new_linter
-from xrlint.node import AttrNode, AttrsNode, DatasetNode, VariableNode, DataTreeNode
+from xrlint.node import AttrNode, AttrsNode, DatasetNode, DataTreeNode, VariableNode
 from xrlint.plugin import new_plugin
 from xrlint.processor import ProcessorOp
 from xrlint.result import Message, Result

xrlint/_linter/apply.py

@@ -2,7 +2,7 @@
 #  This software is distributed under the terms and conditions of the
 #  MIT license (https://mit-license.org/).
 
-from xrlint.node import AttrNode, AttrsNode, DataTreeNode, DatasetNode, VariableNode
+from xrlint.node import AttrNode, AttrsNode, DatasetNode, DataTreeNode, VariableNode
 from xrlint.rule import RuleConfig, RuleExit, RuleOp
 
 from ..constants import DATASET_ROOT_NAME, DATATREE_ROOT_NAME

xrlint/formatters/html.py

@@ -5,10 +5,7 @@
 import html
 from collections.abc import Iterable
 
-from xrlint.constants import (
-    SEVERITY_CODE_TO_COLOR,
-    SEVERITY_CODE_TO_NAME,
-)
+from xrlint.constants import SEVERITY_CODE_TO_COLOR, SEVERITY_CODE_TO_NAME
 from xrlint.formatter import FormatterContext, FormatterOp
 from xrlint.formatters import registry
 from xrlint.result import Message, Result, get_rules_meta_for_results

xrlint/formatters/simple.py

@@ -6,10 +6,7 @@
 
 from tabulate import tabulate
 
-from xrlint.constants import (
-    SEVERITY_CODE_TO_COLOR,
-    SEVERITY_CODE_TO_NAME,
-)
+from xrlint.constants import SEVERITY_CODE_TO_COLOR, SEVERITY_CODE_TO_NAME
 from xrlint.formatter import FormatterContext, FormatterOp
 from xrlint.formatters import registry
 from xrlint.result import Message, Result

xrlint/plugins/core/rules/grid_mappings.py

@@ -14,6 +14,10 @@
     description=(
         "Grid mappings, if any, shall have valid grid mapping coordinate variables."
     ),
+    docs_url=(
+        "https://cfconventions.org/cf-conventions/cf-conventions.html"
+        "#grid-mappings-and-projections"
+    ),
 )
 class GridMappings(RuleOp):
     def validate_dataset(self, ctx: RuleContext, node: DatasetNode):