Merge pull request populse#350 from DimitriPapadopoulos/ruff

flake8 → ruff

.pre-commit-config.yaml

@@ -22,16 +22,8 @@ repos:
     -   id: trailing-whitespace
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.3.0
     hooks:
-    #-   id: ruff
+    -   id: ruff
     -   id: ruff-format
         exclude: '^doc/'
-
--   repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
-    hooks:
-    -   id: flake8
-        name: flake8
-        args:
-        - --ignore=F722,F821

capsul/__init__.py

@@ -5,10 +5,11 @@
 
 def _init_doc_path():
     global _doc_path
-    import capsul
     import os
-    from .info import version_major
-    from .info import version_minor
+
+    import capsul
+
+    from .info import version_major, version_minor
 
     p = os.path.dirname(os.path.dirname(capsul.__file__))
     doc_path = os.path.join(p, "doc/build/html")

capsul/__main__.py

@@ -1,12 +1,13 @@
 import argparse
-from datetime import datetime
 import json
 import re
 import sys
+from datetime import datetime
+
+from soma.controller import undefined
 
 from .api import Capsul
 from .config.configuration import ApplicationConfiguration
-from soma.controller import undefined
 
 
 def executable_parser(executable):
@@ -112,7 +113,8 @@ def set_executable_cmd_args(executable, args):
 
 if options.subcommand == "configure":
     # Other commands must be able to work without PyQt installed
-    from soma.qt_gui.qt_backend import QtGui, Qt
+    from soma.qt_gui.qt_backend import Qt, QtGui
+
     from .qt_gui.widgets.settings_editor import SettingsEditor
 
     app_config = ApplicationConfiguration("global_config")
@@ -155,6 +157,7 @@ def set_executable_cmd_args(executable, args):
 elif options.subcommand == "view":
     # Other commands must be able to work without PyQt installed
     from soma.qt_gui.qt_backend import Qt
+
     from capsul.qt_gui.widgets import PipelineDeveloperView
 
     # WARNING: QApplication should always be instantiated before aims PluginLoader

capsul/api.py

@@ -21,15 +21,13 @@
 
 """
 
+from .application import Capsul, executable
 from .debug import debug
+from .execution_context import CapsulWorkflow
+from .pipeline.pipeline import Pipeline
+from .pipeline.pipeline_nodes import Node, Plug, Switch
 from .process.process import (
-    Process,
-    NipypeProcess,
     FileCopyProcess,
+    NipypeProcess,
+    Process,
 )
-from .pipeline.pipeline import Pipeline
-from .pipeline.pipeline_nodes import Plug
-from .pipeline.pipeline_nodes import Node
-from .pipeline.pipeline_nodes import Switch
-from .application import Capsul, executable
-from .execution_context import CapsulWorkflow

capsul/application.py

@@ -4,19 +4,19 @@
 import inspect
 import json
 import os
-from pathlib import Path
-import types
 import sys
+import types
+from pathlib import Path
 
-from soma.controller import field, Controller
-from soma.undefined import undefined
+from soma.controller import Controller, field
 from soma.singleton import Singleton
+from soma.undefined import undefined
 
 from .config.configuration import ApplicationConfiguration
 from .dataset import Dataset
-from .pipeline.pipeline import Pipeline, CustomPipeline
+from .pipeline.pipeline import CustomPipeline, Pipeline
 from .pipeline.process_iteration import ProcessIteration
-from .process.process import Process, Node
+from .process.process import Node, Process
 
 # note: nipype and related imports are not done here to avoid several seconds
 # of import time when we don't use them.

capsul/config/afni.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, field
 
 
 class AfniConfiguration(ModuleConfiguration):

capsul/config/ants.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, field
 
 
 class AntsConfiguration(ModuleConfiguration):

capsul/config/axon.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, File, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, File, field
 
 
 def axon_default_shared_dir():

capsul/config/configuration.py

@@ -4,12 +4,11 @@
 import os
 import sys
 
-from soma.controller import Controller, field, OpenKeyDictController, File
+from soma.controller import Controller, File, OpenKeyDictController, field
 from soma.undefined import undefined
 
 from ..dataset import Dataset
 
-
 default_builtin_database = {
     "type": "sqlite",
     "path": "$HOME/.config/{app_name}/database.sqlite",

capsul/config/freesurfer.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, File, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, File, field
 
 
 class FreesurferConfiguration(ModuleConfiguration):

capsul/config/fsl.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, File, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, File, field
 
 
 class FSLConfiguration(ModuleConfiguration):

capsul/config/matlab.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, File, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, File, field
 
 
 class MatlabConfiguration(ModuleConfiguration):

capsul/config/mrtrix.py

@@ -1,5 +1,6 @@
+from soma.controller import Directory, field, undefined
+
 from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, field
 
 
 class MRTrixConfiguration(ModuleConfiguration):

capsul/config/nipype.py

@@ -1,8 +1,9 @@
-from .configuration import ModuleConfiguration
 import os
 import os.path as osp
 import tempfile
 
+from .configuration import ModuleConfiguration
+
 
 class NipypeConfiguration(ModuleConfiguration):
     """Nipype configuration module"""

capsul/config/python.py

@@ -1,7 +1,9 @@
-from .configuration import ModuleConfiguration
-from soma.controller import Directory, undefined, File, field
 import sys
 
+from soma.controller import Directory, File, field, undefined
+
+from .configuration import ModuleConfiguration
+
 
 class PythonConfiguration(ModuleConfiguration):
     """Python configuration module"""

capsul/config/spm.py

@@ -1,6 +1,7 @@
-from .configuration import ModuleConfiguration
 from soma.controller import Directory, undefined
 
+from .configuration import ModuleConfiguration
+
 
 class SPMConfiguration(ModuleConfiguration):
     """SPM configuration module"""

capsul/config/test/test_config.py

@@ -9,8 +9,8 @@
 
 from capsul.config import ApplicationConfiguration
 from capsul.config.configuration import (
-    default_engine_start_workers,
     default_builtin_database,
+    default_engine_start_workers,
 )
 
 expected_default_builtin_database = default_builtin_database.copy()

capsul/database/__init__.py

@@ -1,20 +1,18 @@
-from datetime import datetime
-import dateutil.parser
 import importlib
 import json
-from pprint import pprint
 import re
 import sys
 import time
+from datetime import datetime
+from pprint import pprint
 
-from populse_db.database import json_encode, json_decode
-
+import dateutil.parser
+from populse_db.database import json_decode, json_encode
 from soma.api import DictWithProxy, undefined
 
 from ..application import Capsul
 from ..execution_context import ExecutionContext
-from ..pipeline.pipeline import Process, Pipeline
-
+from ..pipeline.pipeline import Pipeline, Process
 
 database_classes = {
     "sqlite": "capsul.database.sqlite:SQliteExecutionDatabase",
@@ -61,15 +59,15 @@ def __str__(self):
         else:
             path = ""
         if self.parameters:
-            parameters = f";{parameters}"
+            parameters = f";{self.parameters}"
         else:
             parameters = ""
         if self.query:
-            query = f"?{query}"
+            query = f"?{self.query}"
         else:
             query = ""
         if self.fragment:
-            fragment = f"#{fragment}"
+            fragment = f"#{self.fragment}"
         else:
             fragment = ""
         return f"{self.scheme}://{login}{host}{path}{parameters}{query}{fragment}"

capsul/database/redis.py

@@ -1,15 +1,15 @@
-from datetime import datetime
-import shutil
-import tempfile
 import json
 import os
+import shutil
 import subprocess
+import tempfile
 import time
+from datetime import datetime
 from uuid import uuid4
 
 import redis
 
-from . import ExecutionDatabase, ResponseError, ConnectionError
+from . import ConnectionError, ExecutionDatabase, ResponseError
 
 
 class RedisExecutionDatabase(ExecutionDatabase):

capsul/database/sqlite.py

@@ -1,12 +1,11 @@
-from contextlib import contextmanager
-from datetime import datetime
 import json
 import os
 import sqlite3
 import tempfile
+from contextlib import contextmanager
+from datetime import datetime
 from uuid import uuid4
 
-
 from . import ExecutionDatabase
 
 
@@ -473,7 +472,7 @@ def job_finished_json(
 
             sql = "SELECT ready, ongoing, failed, waiting, done FROM capsul_execution WHERE engine_id=? AND execution_id=?"
             row = sqlite.execute(sql, [engine_id, execution_id]).fetchone()
-            ready, ongoing, failed, waiting, done = [json.loads(i) for i in row]
+            ready, ongoing, failed, waiting, done = (json.loads(i) for i in row)
             ongoing.remove(job_id)
             if return_code != 0:
                 failed.append(job_id)
@@ -486,9 +485,9 @@ def job_finished_json(
                         sql, [engine_id, execution_id, waiting_id]
                     ).fetchone()
                     waiting_job = json.loads(row[0])
-                    waiting_job[
-                        "return_code"
-                    ] = "Not started because de dependent job failed"
+                    waiting_job["return_code"] = (
+                        "Not started because de dependent job failed"
+                    )
                     sql = "UPDATE capsul_job SET job=? WHERE engine_id=? AND execution_id=? AND job_id=?"
                     sqlite.execute(
                         sql, [json.dumps(waiting_job), engine_id, execution_id, job_id]

capsul/dataset.py

@@ -7,24 +7,24 @@
 """
 
 import csv
-from collections import defaultdict
 import fnmatch
 import functools
+import importlib
 import itertools
 import json
 import operator
-from pathlib import Path
 import re
 import sys
-import importlib
 import weakref
+from collections import defaultdict
+from pathlib import Path
 
-from capsul.pipeline.pipeline import Process, Pipeline, Switch
-from capsul.pipeline.process_iteration import ProcessIteration
-
-from soma.controller import Controller, Literal, Directory, field
+from soma.controller import Controller, Directory, Literal, field
 from soma.undefined import undefined
 
+from capsul.pipeline.pipeline import Pipeline, Process, Switch
+from capsul.pipeline.process_iteration import ProcessIteration
+
 global_debug = False
 
 
@@ -178,7 +178,7 @@ class BIDSSchema(MetadataSchema):
 
     schema_name = "bids"
 
-    folder: Literal["sourcedata", "rawdata", "derivative"]
+    folder: Literal["sourcedata", "rawdata", "derivative"]  # noqa: F821
     process: str = None
     sub: str
     ses: str
@@ -485,7 +485,7 @@ def _path_list(self, unused_meta=None):
 class MorphologistBIDSSchema(BrainVISASchema):
     schema_name = "morphologist_bids"
 
-    folder: Literal["sourcedata", "rawdata", "derivative"]
+    folder: Literal["sourcedata", "rawdata", "derivative"]  # noqa: F821
 
     def _path_list(self, unused_meta=None):
         if unused_meta is None:

capsul/engine/__init__.py

@@ -1,14 +1,14 @@
-from datetime import datetime
 import os
 import subprocess
 import sys
+from datetime import datetime
 
 from soma.controller import Controller, undefined
 
-from ..execution_context import CapsulWorkflow, ExecutionContext
+from ..api import Pipeline
 from ..config.configuration import ModuleConfiguration
 from ..database import engine_database
-from ..api import Pipeline
+from ..execution_context import CapsulWorkflow, ExecutionContext
 
 
 def execution_context(engine_label, engine_config, executable):