Merge pull request #55 from bcdev/forman-54-data_tree

Added support for `xarray.DataTree`

Author: forman

CHANGES.md

@@ -4,6 +4,11 @@
 
 ### Adjustments and Enhancements
 
+- Added support for validating Zarr and HDF-5 groups and their items. 
+  Rules can now validate `xarray.DataTree` objects originating 
+  from `xarray.open_datatree()` by implementing
+  rule operation method `RuleOp.validate_datatree(ctx, node)`. (#54)
+
 - Added a new core rule `var-missing-data` that checks for the recommended 
   use of a variable's missing data.
 
@@ -48,6 +53,8 @@
   - added class method `from_config()` to `ConfigList`.
   - removed function `xrlint.config.merge_configs` as it was no longer used.
 
+- Removed class method `Result.new()` as it was no longer used.
+
 ### Other changes
 
 - XRLint now works with zarr >=2,<3 and zarr >=3.0.2

docs/api.md

@@ -26,7 +26,7 @@ This chapter provides a plain reference for the XRLint Python API.
 - The `node` module defines the nodes passed to [RuleOp][xrlint.rule.RuleOp]:
   base classes [None][xrlint.node.Node], [XarrayNode][xrlint.node.XarrayNode],
   and the specific [DatasetNode][xrlint.node.DatasetNode],
-  [DataArray][xrlint.node.DataArrayNode], [AttrsNode][xrlint.node.AttrsNode], 
+  [VariableNode][xrlint.node.VariableNode], [AttrsNode][xrlint.node.AttrsNode], 
   and [AttrNode][xrlint.node.AttrNode] nodes.
 - The `processor` module provides processor related classes and functions:
   [Processor][xrlint.processor.Processor] comprising processor metadata
@@ -84,7 +84,7 @@ Note:
 
 ::: xrlint.node.DatasetNode
 
-::: xrlint.node.DataArrayNode
+::: xrlint.node.VariableNode
 
 ::: xrlint.node.AttrsNode
 

pyproject.toml

@@ -10,7 +10,7 @@ authors = [
 ]
 description = "A linter for xarray datasets."
 keywords = [
-  "xarray"
+  "xarray", "data-science", "cf", "metadata"
 ]
 license = {text = "MIT"}
 requires-python = ">=3.10"

tests/_linter/test_rulectx.py

@@ -9,7 +9,7 @@
 # noinspection PyProtectedMember
 from xrlint._linter.rulectx import RuleContextImpl
 from xrlint.config import ConfigObject
-from xrlint.constants import NODE_ROOT_NAME
+from xrlint.constants import DATASET_ROOT_NAME
 from xrlint.result import Message, Suggestion
 
 
@@ -39,7 +39,7 @@ def test_report(self):
             [
                 Message(
                     message="What the heck do you mean?",
-                    node_path=NODE_ROOT_NAME,
+                    node_path=DATASET_ROOT_NAME,
                     rule_id="no-xxx",
                     severity=2,
                     suggestions=[
@@ -48,7 +48,7 @@ def test_report(self):
                 ),
                 Message(
                     message="You said it.",
-                    node_path=NODE_ROOT_NAME,
+                    node_path=DATASET_ROOT_NAME,
                     rule_id="no-xxx",
                     severity=2,
                     fatal=True,

tests/cli/test_main.py

@@ -66,6 +66,9 @@ def xrlint(self, *args: tuple[str, ...]) -> click.testing.Result:
         runner = CliRunner()
         result = runner.invoke(main, args)
         if not isinstance(result.exception, SystemExit):
+            import traceback
+
+            traceback.print_exception(result.exception)
             self.assertIsNone(result.exception)
         return result
 

tests/formatters/helpers.py

@@ -45,9 +45,9 @@ class Rule2(RuleOp):
     config_obj = ConfigObject(plugins={"test": plugin})
 
     return [
-        Result.new(
-            config_object=config_obj,
+        Result(
             file_path="test.nc",
+            config_object=config_obj,
             messages=[
                 Message(
                     message="message-1",
@@ -64,9 +64,9 @@ class Rule2(RuleOp):
                 Message(message="message-3", fatal=True),
             ],
         ),
-        Result.new(
+        Result(
+            file_path="test.nc",
             config_object=config_obj,
-            file_path="test-2.nc",
             messages=[
                 Message(message="message-1", rule_id="test/rule-1", severity=1),
                 Message(message="message-2", rule_id="test/rule-2", severity=2),

tests/formatters/test_simple.py

@@ -12,9 +12,9 @@
 
 class SimpleTest(TestCase):
     errors_and_warnings = [
-        Result.new(
-            config_object=ConfigObject(),
+        Result(
             file_path="test1.nc",
+            config_object=ConfigObject(),
             messages=[
                 Message(message="what", rule_id="rule-1", severity=2),
                 Message(message="is", fatal=True),
@@ -24,9 +24,9 @@ class SimpleTest(TestCase):
     ]
 
     warnings_only = [
-        Result.new(
-            ConfigObject(),
+        Result(
             file_path="test2.nc",
+            config_object=ConfigObject(),
             messages=[
                 Message(message="what", rule_id="rule-1", severity=1),
                 Message(message="happened?", rule_id="rule-2", severity=1),

tests/plugins/core/rules/test_access_latency.py

@@ -10,6 +10,7 @@
 # noinspection PyProtectedMember
 from xrlint._linter.rulectx import RuleContextImpl
 from xrlint.config import ConfigObject
+from xrlint.constants import DATASET_ROOT_NAME
 from xrlint.node import DatasetNode
 from xrlint.plugins.core.rules.access_latency import AccessLatency
 from xrlint.result import Message
@@ -33,8 +34,9 @@ def invoke_op(
             access_latency=access_latency,
         )
         node = DatasetNode(
-            path="dataset",
             parent=None,
+            path=DATASET_ROOT_NAME,
+            name=DATASET_ROOT_NAME,
             dataset=ctx.dataset,
         )
         rule_op = (
@@ -59,7 +61,7 @@ def test_invalid(self):
             [
                 Message(
                     message="Access latency exceeds threshold: 3.2 > 2.5 seconds.",
-                    node_path="dataset",
+                    node_path=DATASET_ROOT_NAME,
                     severity=2,
                 )
             ],
@@ -71,7 +73,7 @@ def test_invalid(self):
             [
                 Message(
                     message="Access latency exceeds threshold: 0.2 > 0.1 seconds.",
-                    node_path="dataset",
+                    node_path=DATASET_ROOT_NAME,
                     severity=2,
                 )
             ],