Merge pull request #367 from DimitriPapadopoulos/pre-commit

pre-commit autoupdate

Author: denisri

.github/workflows/test-v3.yml

@@ -51,12 +51,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    
+
     - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
         python-version: "3.10"
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.gitignore

@@ -15,4 +15,4 @@
 build/
 /doc/source/*/generated/
 /doc/source/tutorial/capsul_tutorial.ipynb
-*.egg-info/
+*.egg-info/

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ exclude: |
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
     -   id: check-added-large-files
     -   id: check-case-conflict
@@ -30,7 +30,7 @@ repos:
     -   id: trailing-whitespace
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.0
+    rev: v0.9.1
     hooks:
     -   id: ruff
     -   id: ruff-format

capsul/application.py

@@ -247,8 +247,7 @@ def executable(definition, **kwargs):
     elif isinstance(definition, Process):
         if kwargs:
             raise ValueError(
-                "executable() do not allow to modify parameters "
-                "of an existing process"
+                "executable() do not allow to modify parameters of an existing process"
             )
         return definition
     elif isinstance(definition, type) and issubclass(definition, Process):

capsul/config/configuration.py

@@ -121,12 +121,12 @@ def is_valid_config(self, requirements, explain=False):
             other requirements. The implementation is free to interpret it as
             it needs. Thus modules implementations should document how they
             define and check their requirements.
-        
+
         explain: bool
-            bool value to specify that an explanation is required when a module 
-            configuration is not valid. When :param:`explain` is true and the 
-            configuration module is invalid, the returned value is a 
-            :type:`str` containing the reason why the module is not valid. 
+            bool value to specify that an explanation is required when a module
+            configuration is not valid. When :param:`explain` is true and the
+            configuration module is invalid, the returned value is a
+            :type:`str` containing the reason why the module is not valid.
 
         Returns
         -------
@@ -140,7 +140,7 @@ def is_valid_config(self, requirements, explain=False):
             instance a SPM module may return ``{'matlab': {'mcr': True'}}``
         """
         raise NotImplementedError(
-            "A subclass of ModuleConfiguration must " "define is_valid_config()"
+            "A subclass of ModuleConfiguration must define is_valid_config()"
         )
 
 

capsul/database/__init__.py

@@ -84,7 +84,7 @@ class ConnectionError(Exception):
 def engine_database(config):
     class_string = database_classes.get(config["type"])
     if class_string is None:
-        raise ValueError(f'Invalid database type: {config["type"]}')
+        raise ValueError(f"Invalid database type: {config['type']}")
     module_name, class_name = class_string.rsplit(":", 1)
     module = importlib.import_module(module_name)
     database_class = getattr(module, class_name)
@@ -274,7 +274,7 @@ def failed_node_paths(self, engine_id, execution_id):
 
     def print_execution_report(self, report, file=sys.stdout):
         print(
-            "====================\n" "| Execution report |\n" "====================\n",
+            "====================\n| Execution report |\n====================\n",
             file=file,
         )
         print("label:", report["label"], file=file)
@@ -290,7 +290,7 @@ def print_execution_report(self, report, file=sys.stdout):
             print("-" * 50, file=file)
             print(report["error_detail"], file=file)
             print("-" * 50, file=file)
-        print("\n---------------\n" "| Jobs status |\n" "---------------\n", file=file)
+        print("\n---------------\n| Jobs status |\n---------------\n", file=file)
         print("waiting:", report["waiting"])
         print("ready:", report["ready"])
         print("ongoing:", report["ongoing"])
@@ -348,7 +348,7 @@ def print_execution_report(self, report, file=sys.stdout):
 
         if report["engine_debug"]:
             print(
-                "\n----------------\n" "| Engine debug |\n" "----------------\n",
+                "\n----------------\n| Engine debug |\n----------------\n",
                 file=file,
             )
             for k, v in report["engine_debug"].items():

capsul/database/populse_db.py

@@ -107,7 +107,7 @@ def _enter(self):
                 self.storage = Storage(self.path)
         else:
             raise NotImplementedError(
-                f'Invalid populse-db connection type: {self.config["type"]}'
+                f"Invalid populse-db connection type: {self.config['type']}"
             )
         with self.storage.schema() as schema:
             schema.add_schema("capsul.database.populse_db")
@@ -397,9 +397,9 @@ def job_finished_json(
                         waiting_job["return_code"] = (
                             "Not started because de dependent job failed"
                         )
-                        db.capsul_job[engine_id, execution_id, waiting_id].job = (
-                            waiting_job
-                        )
+                        db.capsul_job[
+                            engine_id, execution_id, waiting_id
+                        ].job = waiting_job
                         waiting.remove(waiting_id)
                         failed.append(waiting_id)
                     stack.update(waiting_job.get("waited_by", []))
@@ -429,9 +429,9 @@ def job_finished_json(
 
             if not ongoing and not ready:
                 if failed:
-                    db.capsul_execution[engine_id, execution_id].error = (
-                        "Some jobs failed"
-                    )
+                    db.capsul_execution[
+                        engine_id, execution_id
+                    ].error = "Some jobs failed"
                 db.capsul_execution[engine_id, execution_id].update(
                     {
                         "status": "finalization",
@@ -485,12 +485,12 @@ def set_job_output_parameters(
             indices = job.get("parameters_index", {})
             for name, value in output_parameters.items():
                 values[indices[name]] = value
-            db.capsul_job[engine_id, execution_id, job_id].job.output_parameters = (
-                output_parameters
-            )
-            db.capsul_execution[engine_id, execution_id].workflow_parameters_values = (
-                values
-            )
+            db.capsul_job[
+                engine_id, execution_id, job_id
+            ].job.output_parameters = output_parameters
+            db.capsul_execution[
+                engine_id, execution_id
+            ].workflow_parameters_values = values
 
     def job_json(self, engine_id, execution_id, job_id):
         if os.path.exists(self.path):

capsul/database/redis.py

@@ -113,7 +113,7 @@ def _enter(self):
             self.redis = self._connect(decode_responses=True)
         else:
             raise NotImplementedError(
-                f'Invalid Redis connection type: {self.config["type"]}'
+                f"Invalid Redis connection type: {self.config['type']}"
             )
         if self.redis.get("capsul:shutting_down"):
             raise RuntimeError(

capsul/dataset.py

@@ -236,7 +236,7 @@ def _path_list(self, unused_meta=None):
             path_list.append(self.data_type)
         elif not self.process:
             raise ValueError(
-                "BIDS schema requires a value for either " "data_type or process"
+                "BIDS schema requires a value for either data_type or process"
             )
 
         filename = [f"sub-{self.sub}", f"ses-{self.ses}"]
@@ -1247,7 +1247,8 @@ def path_for_parameters(self, executable, parameters=None):
 
         if parameters is None:
             parameters = [
-                field.name for field in executable.user_fields()  # if field.path_type
+                field.name
+                for field in executable.user_fields()  # if field.path_type
             ]
         if self.debug:
             if self._current_iteration is not None:

capsul/engine/__init__.py

@@ -62,24 +62,30 @@ def execution_context(engine_label, engine_config, executable):
                     req_to_check.update(added_req)
             else:
                 if module_name in needed_modules:
-                   # Keep the invalid config in order to be able to display explanation
-                   # later
-                   invalid_needed_configs.setdefault(module_name, {})[module_field] = module_config
+                    # Keep the invalid config in order to be able to display explanation
+                    # later
+                    invalid_needed_configs.setdefault(module_name, {})[module_field] = (
+                        module_config
+                    )
 
     # now check we have only one module for each
     for module_name in needed_modules:
         valid_module_configs = valid_configs.get(module_name)
         if valid_module_configs is None:
-            message = f'Execution environment "{engine_label}" has no ' \
-                      f"valid configuration for module {module_name}."
-            
-            for module_field, module_config in invalid_needed_configs.get(module_name, {}).items():
+            message = (
+                f'Execution environment "{engine_label}" has no '
+                f"valid configuration for module {module_name}."
+            )
+
+            for module_field, module_config in invalid_needed_configs.get(
+                module_name, {}
+            ).items():
                 # Get explanation about invalid config rejection
                 explaination = module_config.is_valid_config(requirements, explain=True)
                 message += f"\n  - {module_field.name} is not valid for requirements: {explaination}"
 
             raise RuntimeError(message)
-        
+
         if len(valid_module_configs) > 1:
             # print(f"several {module_name} valid condfigs:")
             # for field, v in valid_module_configs.items():
@@ -211,7 +217,7 @@ def quote(x):
                         return f"'{x}'"
 
                     raise RuntimeError(
-                        f'Command failed: {" ".join(quote(i) for i in workers_command)}'
+                        f"Command failed: {' '.join(quote(i) for i in workers_command)}"
                     ) from e
 
     def kill_workers(self, worker_ids=None):
@@ -232,7 +238,7 @@ def quote(x):
                     return f"'{x}'"
 
                 raise RuntimeError(
-                    f'Command failed: {" ".join(quote(i) for i in cmd)}'
+                    f"Command failed: {' '.join(quote(i) for i in cmd)}"
                 ) from e
             self.database.worker_ended(self.engine_id, worker_id)
 
@@ -261,7 +267,7 @@ def assess_ready_to_start(self, executable):
                 missing.append(field.name)
         if missing:
             raise ValueError(
-                f'Value missing for the following parameters: {", ".join(missing)}'
+                f"Value missing for the following parameters: {', '.join(missing)}"
             )
 
     def start(self, executable, debug=False):

capsul/execution_context.py

@@ -760,9 +760,9 @@ def find_temporary_to_generate(executable):
             else:
                 field.generate_temporary = True
             if isinstance(node, ProcessIteration):
-                node.process.field(field.name).generate_temporary = (
-                    field.generate_temporary
-                )
+                node.process.field(
+                    field.name
+                ).generate_temporary = field.generate_temporary
             # print('!temporaries!  ', field.name, '=', field.generate_temporary)
 
     stack = [(executable, field) for field in executable.user_fields()]

capsul/in_context/spm.py

@@ -55,7 +55,7 @@ def spm_command(spm_batch_filename, execution_context=None):
         if spm_batch_filename is not None:
             cmd += ["batch", spm_batch_filename]
     else:
-        raise NotImplementedError("Running SPM with matlab is not " "implemented yet")
+        raise NotImplementedError("Running SPM with matlab is not implemented yet")
     return cmd
 
 

capsul/pipeline/custom_nodes/reduce_node.py

@@ -75,8 +75,7 @@ def __init__(
             bool,
             default=False,
             output=False,
-            doc="remove empty (Undefined, None, empty strings) "
-            "from the output lists",
+            doc="remove empty (Undefined, None, empty strings) from the output lists",
         )
         self.input_names = input_names
         self.output_names = output_names

capsul/pipeline/pipeline.py

@@ -1122,7 +1122,7 @@ def export_parameter(
         # Check if the plug name is valid
         if source_field is None:
             raise ValueError(
-                f"Node {node_name} ({node.name}) has no parameter " f"{plug_name}"
+                f"Node {node_name} ({node.name}) has no parameter {plug_name}"
             )
 
         # Check the pipeline parameter name is not already used

capsul/pipeline/pipeline_nodes.py

@@ -125,7 +125,7 @@ def __init__(
                 raise ValueError("output_types parameter should be a list or tuple")
             if len(output_types) != len(outputs):
                 raise ValueError(
-                    "output_types should have the same number of " "elements as outputs"
+                    "output_types should have the same number of elements as outputs"
                 )
         else:
             output_types = [typing.Any] * len(outputs)
@@ -385,7 +385,9 @@ def configure_controller(cls):
     def configured_controller(self):
         c = self.configure_controller()
         c.outputs = [
-            field.name for field in self.fields() if field.is_output()  # noqa: F811
+            field.name
+            for field in self.fields()
+            if field.is_output()  # noqa: F811
         ]
         c.inputs = self.get_switch_inputs()
         c.output_types = [self.field(p).type_str() for p in self.outputs]

capsul/pipeline/test/fake_morphologist/brainorientation.py

@@ -399,9 +399,7 @@ def pipeline_definition(self):
         self.Normalization_NormalizeFSL_allow_retry_initialization = True
         self.Normalization_NormalizeFSL_NormalizeFSL_cost_function = "corratio"
         self.Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = "corratio"
-        self.Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
-            0
-        )
+        self.Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
         self.Normalization_NormalizeSPM_allow_retry_initialization = True
         self.Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.Normalization_NormalizeSPM_cutoff_option = 25

capsul/pipeline/test/fake_morphologist/morphologist.py

@@ -1875,30 +1875,18 @@ def pipeline_definition(self):
         self.PrepareSubject_Normalization_NormalizeFSL_alignment = (
             "Not Aligned but Same Orientation"
         )
-        self.PrepareSubject_Normalization_NormalizeFSL_set_transformation_in_source_volume = (
-            True
-        )
+        self.PrepareSubject_Normalization_NormalizeFSL_set_transformation_in_source_volume = True
         self.PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_cost_function = (
             "corratio"
         )
-        self.PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = (
-            "corratio"
-        )
-        self.PrepareSubject_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
-            0
-        )
+        self.PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = "corratio"
+        self.PrepareSubject_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
         self.PrepareSubject_Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.PrepareSubject_Normalization_NormalizeSPM_cutoff_option = 25
         self.PrepareSubject_Normalization_NormalizeSPM_nbiteration = 16
-        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target = (
-            "MNI template"
-        )
-        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = (
-            False
-        )
-        self.PrepareSubject_Normalization_NormalizeBaladin_set_transformation_in_source_volume = (
-            True
-        )
+        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target = "MNI template"
+        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = False
+        self.PrepareSubject_Normalization_NormalizeBaladin_set_transformation_in_source_volume = True
         self.PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template = "/casa/host/build/share/brainvisa-share-5.2/anatomical_templates/MNI152_T1_2mm.nii.gz"
         self.PrepareSubject_Normalization_Normalization_AimsMIRegister_mni_to_acpc = "/casa/host/build/share/brainvisa-share-5.2/transformation/talairach_TO_spm_template_novoxels.trm"
         self.PrepareSubject_Normalization_Normalization_AimsMIRegister_smoothing = 1.0
@@ -1941,21 +1929,15 @@ def pipeline_definition(self):
         self.Renorm_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = (
             "corratio"
         )
-        self.Renorm_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
-            0
-        )
+        self.Renorm_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
         self.Renorm_Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.Renorm_Normalization_NormalizeSPM_cutoff_option = 25
         self.Renorm_Normalization_NormalizeSPM_nbiteration = 16
         self.Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target = (
             "MNI template"
         )
-        self.Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = (
-            False
-        )
-        self.Renorm_Normalization_NormalizeBaladin_set_transformation_in_source_volume = (
-            True
-        )
+        self.Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = False
+        self.Renorm_Normalization_NormalizeBaladin_set_transformation_in_source_volume = True
         self.Renorm_Normalization_Normalization_AimsMIRegister_mni_to_acpc = "/casa/host/build/share/brainvisa-share-5.2/transformation/talairach_TO_spm_template_novoxels.trm"
         self.Renorm_Normalization_Normalization_AimsMIRegister_smoothing = 1.0
         self.SplitBrain_use_ridges = True