Merge pull request #28 from kostrykin/develop

Refactor for v1.0.0-beta3

repype/stage.py

@@ -45,10 +45,18 @@ def suggest_stage_id(class_name: str) -> str:
     """
     Suggests a stage identifier based on a class name.
 
-    This function validates the class name, then finds and groups tokens in the class name.
+    This function validates the `class_name`, then tokenizes it.
     Tokens are grouped if they are consecutive and alphanumeric, but do not start with numbers.
     The function then converts the tokens to lowercase, removes underscores, and joins them with hyphens.
 
+    Example:
+
+        .. runblock:: pycon
+
+            >>> from repype.stage import suggest_stage_id
+            >>> print(suggest_stage_id('TheGreatMapperStage'))
+            >>> print(suggest_stage_id('TheGreat123PCMapper'))
+
     Arguments:
         class_name: The name of the class to suggest a configuration namespace for.
 
@@ -59,7 +67,11 @@ def suggest_stage_id(class_name: str) -> str:
         AssertionError: If the class name is not valid.
     """
     assert class_name != '_' and re.match('[a-zA-Z]', class_name) and re.match('^[a-zA-Z_](?:[a-zA-Z0-9_])*$', class_name), f'not a valid class name: "{class_name}"'
-    tokens1 = re.findall('[A-Z0-9][^A-Z0-9_]*', class_name)
+
+    # Find all tokens in the class name (letters or numbers, followed by lowercase letters until the next underscore)
+    tokens1 = re.findall('[a-zA-Z0-9][^A-Z0-9_]*', class_name)
+
+    # Join tokens that are alphanumeric and consecutive
     tokens2 = list()
     i1 = 0
     while i1 < len(tokens1):
@@ -73,7 +85,12 @@ def suggest_stage_id(class_name: str) -> str:
                 else:
                     break
         tokens2.append(token.lower().replace('_', ''))
-    if len(tokens2) >= 2 and tokens2[-1] == 'stage': tokens2 = tokens2[:-1]
+
+    # Remove the last token if it is "stage"
+    if len(tokens2) >= 2 and tokens2[-1] == 'stage':
+        tokens2 = tokens2[:-1]
+
+    # Join the tokens
     return '-'.join(tokens2)
 
 

repype/task.py

@@ -160,17 +160,27 @@ def root(self) -> Self:
         return self.parent.root if self.parent else self
 
     @property
-    def marginal_stages(self) -> List[str]:
+    def marginal_stages(self) -> Iterator[str]:
         """
         The stages which are considered marginal.
 
         Outputs of marginal stages are removed from the *pipeline data objects* when storing the results of the task.
         The default implementation reads the list of marginal stages from the ``marginal_stages`` field in the task specification.
 
-        Returns:
-            List of the stage identifiers corresponding to the marginal stages.
+        Yields:
+            Stage identifiers corresponding to the marginal stages.
         """
-        return self.full_spec.get('marginal_stages', [])
+        for stage_spec in self.full_spec.get('marginal_stages', []):
+            assert isinstance(stage_spec, str), f'Stage identifier must be a string (f{type(stage_spec)}).'
+
+            # Load the stage from a module
+            if '.' in stage_spec:
+                stage_cls = load_from_module(stage_spec)
+                yield stage_cls().id
+
+            # Use the stage identifier directly
+            else:
+                yield stage_spec
 
     @property
     def data_filepath(self) -> pathlib.Path:
@@ -352,7 +362,7 @@ def get_marginal_fields(self, pipeline: repype.pipeline.Pipeline) -> FrozenSet[s
         Returns:
             Set of marginal fields.
         """
-        marginal_fields = sum((list(stage.outputs) for stage in pipeline.stages if stage.id in self.marginal_stages), list())
+        marginal_fields = sum((list(stage.outputs) for stage in pipeline.stages if stage.id in set(self.marginal_stages)), list())
         return frozenset(marginal_fields)
 
     def load(self, pipeline: Optional[repype.pipeline.Pipeline] = None) -> TaskData:

repype/version.py

@@ -1,6 +1,6 @@
 VERSION_MAJOR = 1
 VERSION_MINOR = 0
 VERSION_PATCH = 0
-VERSION_SUFFIX = 'beta2'
+VERSION_SUFFIX = 'beta3'
 
 VERSION = '%d.%d.%s%s' % (VERSION_MAJOR, VERSION_MINOR, VERSION_PATCH, '-%s' % VERSION_SUFFIX if VERSION_SUFFIX else '')

tests/test_stage.py

@@ -23,6 +23,7 @@ def test(self):
         self.assertEqual(repype.stage.suggest_stage_id('TheGreat123PCMapper'  ), 'the-great-123-pc-mapper')
         self.assertEqual(repype.stage.suggest_stage_id('TheGreatMapperStage'  ), 'the-great-mapper'       )
         self.assertEqual(repype.stage.suggest_stage_id('Stage'                ), 'stage'                  )
+        self.assertEqual(repype.stage.suggest_stage_id('stage1_abc_cls'       ), 'stage-1-abc-cls'        )
 
     def test_illegal(self):
         self.assertRaises(AssertionError, lambda: repype.stage.suggest_stage_id(''))

tests/test_task.py

@@ -540,7 +540,7 @@ def test_with_changed_pipeline(self, path):
         self.assertTrue(task.is_pending(self.pipeline, config))
 
 
-class Task__marginal_states(unittest.TestCase):
+class Task__marginal_stages(unittest.TestCase):
 
     @testsuite.with_temporary_paths(1)
     def test_from_spec_missing(self, path):
@@ -549,7 +549,7 @@ def test_from_spec_missing(self, path):
             parent = None,
             spec = dict(),
         )
-        self.assertEqual(task.marginal_stages, [])
+        self.assertEqual(list(task.marginal_stages), [])
 
     @testsuite.with_temporary_paths(1)
     def test_from_spec(self, path):
@@ -563,7 +563,21 @@ def test_from_spec(self, path):
                 ],
             ),
         )
-        self.assertEqual(task.marginal_stages, ['stage1', 'stage2'])
+        self.assertEqual(list(task.marginal_stages), ['stage1', 'stage2'])
+
+    @testsuite.with_temporary_paths(1)
+    def test_from_spec_class_names(self, path):
+        task = repype.task.Task(
+            path = path,
+            parent = None,
+            spec = dict(
+                marginal_stages = [
+                    'tests.test_task.Task__create_pipeline.stage1_cls',
+                    'tests.test_task.Task__create_pipeline.stage2_cls',
+                ],
+            ),
+        )
+        self.assertEqual(list(task.marginal_stages), ['stage1', 'stage2'])
 
     @testsuite.with_temporary_paths(1)
     def test_override(self, path):
@@ -579,7 +593,7 @@ class DerivedTask(repype.task.Task):
             parent = None,
             spec = dict(),
         )
-        self.assertEqual(task.marginal_stages, ['stage1', 'stage2'])
+        self.assertEqual(list(task.marginal_stages), ['stage1', 'stage2'])
 
 
 class Task__get_marginal_fields(unittest.TestCase):