Fix formatting

Author: edeno

PLAN.md

@@ -5,6 +5,7 @@ This document tracks the plan to fix the remaining 56 ruff issues (excluding not
 ## 🔴 Priority 1: Critical Fixes (7 issues) - ✅ COMPLETED
 
 ### Immediate Action Required
+
 - [x] **Mutable Default Argument** (`convert_ephys.py:42`)
   - Change `nwb_hw_channel_order=[]` to `nwb_hw_channel_order=None`
   - Add `if nwb_hw_channel_order is None: nwb_hw_channel_order = []` inside function
@@ -21,6 +22,7 @@ This document tracks the plan to fix the remaining 56 ruff issues (excluding not
 ## 🟡 Priority 2: Code Quality (25 issues) - ✅ COMPLETED
 
 ### Quick Wins - Auto-fixable patterns
+
 - [x] **Dictionary/List Inefficiencies** (11 issues)
   - Replace `key in dict.keys()` with `key in dict` (8 instances)
   - Replace `dict()` with `{}` literals (2 instances)
@@ -41,6 +43,7 @@ This document tracks the plan to fix the remaining 56 ruff issues (excluding not
 ## 🟠 Priority 3: Style & Performance (9 issues remaining) - PARTIALLY COMPLETED
 
 ### Consider for future refactoring
+
 - [ ] **Magic Numbers** (`convert_position.py` - 4 instances)
   - Extract constants: `MIN_TIMESTAMPS = 2`, `DEFAULT_TIMEOUT = 2000`, `MIN_TICKS = 100`
   - **Note**: These are context-specific values that may be better left as literals
@@ -60,14 +63,16 @@ This document tracks the plan to fix the remaining 56 ruff issues (excluding not
 ## Progress Tracking
 
 **Total Issues**: 56 (excluding notebooks)
+
 - **Fixed**: 47 (7 Priority 1 + 37 Priority 2 + 3 Priority 3)
 - **Remaining**: 9 (4 magic numbers + 4 memory optimizations + 1 unused import)
 
 **Estimated Timeline**:
+
 - Phase 1 (Critical): 30 minutes
 - Phase 2 (Quality): 45 minutes
 - Phase 3 (Style): As needed during regular development
 
 ## Commit Strategy
 
-Each priority level will be committed separately with detailed commit messages explaining the fixes applied.
+Each priority level will be committed separately with detailed commit messages explaining the fixes applied.

pyproject.toml

@@ -83,7 +83,10 @@ extend-exclude = '''
 '''
 
 [tool.pytest.ini_options]
-testpaths = ["src/trodes_to_nwb/tests", "src/trodes_to_nwb/tests/integration-tests"]
+testpaths = [
+    "src/trodes_to_nwb/tests",
+    "src/trodes_to_nwb/tests/integration-tests",
+]
 python_files = ["test_*.py"]
 python_classes = ["Test*"]
 python_functions = ["test_*"]
@@ -99,7 +102,7 @@ warn_return_any = true
 warn_unused_configs = true
 warn_redundant_casts = true
 warn_unused_ignores = true
-disallow_untyped_defs = false  # Set to true gradually
+disallow_untyped_defs = false      # Set to true gradually
 disallow_incomplete_defs = true
 check_untyped_defs = true
 disallow_untyped_decorators = true
@@ -125,26 +128,26 @@ line-length = 88
 
 [tool.ruff.lint]
 select = [
-    "E",  # pycodestyle errors
-    "W",  # pycodestyle warnings
-    "F",  # pyflakes
-    "B",  # flake8-bugbear
-    "I",  # isort
-    "UP", # pyupgrade
-    "C4", # flake8-comprehensions
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # pyflakes
+    "B",   # flake8-bugbear
+    "I",   # isort
+    "UP",  # pyupgrade
+    "C4",  # flake8-comprehensions
     "SIM", # flake8-simplify
-    "PL", # pylint
+    "PL",  # pylint
 ]
 ignore = [
-    "E501",  # line too long, handled by black
+    "E501",    # line too long, handled by black
     "PLR0913", # too many arguments to function call
     "PLR0912", # too many branches
     "PLR0915", # too many statements
     "PLW2901", # redefined loop variable
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"tests/**/*.py" = ["PLR2004"]  # magic value used in comparison
+"tests/**/*.py" = ["PLR2004"]                   # magic value used in comparison
 "src/trodes_to_nwb/tests/**/*.py" = ["PLR2004"]
 "notebooks/**/*.py" = ["E402", "F401", "F821"]  # notebook-specific ignores
 

src/trodes_to_nwb/convert.py

@@ -8,9 +8,9 @@
 import logging
 from pathlib import Path
 
-from dask.distributed import Client
 import nwbinspector
 import pandas as pd
+from dask.distributed import Client
 from pynwb import NWBHDF5IO
 
 from trodes_to_nwb.convert_analog import add_analog_data

src/trodes_to_nwb/convert_analog.py

@@ -2,9 +2,9 @@
 
 from xml.etree import ElementTree
 
-from hdmf.backends.hdf5 import H5DataIO
 import numpy as np
 import pynwb
+from hdmf.backends.hdf5 import H5DataIO
 from pynwb import NWBFile
 
 from trodes_to_nwb import convert_rec_header

src/trodes_to_nwb/convert_dios.py

@@ -31,9 +31,7 @@ def _get_channel_name_map(metadata: dict) -> dict[str, str]:
             )
         channel_name_map[dio_event["description"]] = {
             "name": dio_event["name"],
-            "comments": (
-                dio_event.get("comments", "no comments")
-            ),
+            "comments": (dio_event.get("comments", "no comments")),
         }
     return channel_name_map
 

src/trodes_to_nwb/convert_ephys.py

@@ -5,9 +5,9 @@
 import logging
 from warnings import warn
 
+import numpy as np
 from hdmf.backends.hdf5 import H5DataIO
 from hdmf.data_utils import GenericDataChunkIterator
-import numpy as np
 from pynwb import NWBFile
 from pynwb.ecephys import ElectricalSeries
 
@@ -97,8 +97,7 @@ def __init__(
         assert all(neo_io.block_count() == 1 for neo_io in self.neo_io)
         assert all(neo_io.segment_count(0) == 1 for neo_io in self.neo_io)
         assert all(
-            neo_io.signal_streams_count() == 4 - behavior_only
-                for neo_io in self.neo_io
+            neo_io.signal_streams_count() == 4 - behavior_only for neo_io in self.neo_io
         ), (
             "Unexpected number of signal streams. "
             + "Confirm whether behavior_only is set correctly for this recording"
@@ -132,10 +131,8 @@ def __init__(
         if (
             len(
                 {
-
-                        neo_io.signal_channels_count(stream_index=self.stream_index)
-                        for neo_io in self.neo_io
-
+                    neo_io.signal_channels_count(stream_index=self.stream_index)
+                    for neo_io in self.neo_io
                 }
             )
             > 1
@@ -222,7 +219,8 @@ def __init__(
         is_timestamps_sequential = np.all(np.diff(self.timestamps))
         if not is_timestamps_sequential:
             warn(
-                "Timestamps are not sequential. This may cause problems with some software or data analysis.", stacklevel=2
+                "Timestamps are not sequential. This may cause problems with some software or data analysis.",
+                stacklevel=2,
             )
 
         self.n_time = [
@@ -265,22 +263,20 @@ def _get_data(self, selection: tuple[slice]) -> np.ndarray:
             io_stream = np.argmin(i >= file_start_ind) - 1
             # get the data from that stream
             data.append(
-
-                    self.neo_io[io_stream].get_analogsignal_chunk(
-                        block_index=self.block_index,
-                        seg_index=self.seg_index,
-                        i_start=int(i - file_start_ind[io_stream]),
-                        i_stop=int(
-                            min(
-                                time_index[-1] - file_start_ind[io_stream],
-                                self.n_time[io_stream],
-                            )
+                self.neo_io[io_stream].get_analogsignal_chunk(
+                    block_index=self.block_index,
+                    seg_index=self.seg_index,
+                    i_start=int(i - file_start_ind[io_stream]),
+                    i_stop=int(
+                        min(
+                            time_index[-1] - file_start_ind[io_stream],
+                            self.n_time[io_stream],
                         )
-                        + 1,
-                        stream_index=self.stream_index,
-                        channel_ids=channel_ids,
                     )
-
+                    + 1,
+                    stream_index=self.stream_index,
+                    channel_ids=channel_ids,
+                )
             )
             i += min(
                 self.n_time[io_stream]

src/trodes_to_nwb/convert_optogenetics.py

@@ -2,6 +2,8 @@
 import os
 from pathlib import Path
 
+import numpy as np
+import yaml
 from ndx_franklab_novela import FrankLabOptogeneticEpochsTable
 from ndx_optogenetics import (
     ExcitationSource,
@@ -15,9 +17,7 @@
     OptogeneticVirusInjection,
     OptogeneticVirusInjections,
 )
-import numpy as np
 from pynwb import NWBFile
-import yaml
 
 from trodes_to_nwb.tests.utils import data_path
 

src/trodes_to_nwb/convert_position.py

@@ -5,9 +5,9 @@
 
 import datetime
 import logging
-from pathlib import Path
 import re
 import subprocess
+from pathlib import Path
 from typing import Any
 
 import numpy as np

src/trodes_to_nwb/convert_rec_header.py

@@ -120,9 +120,7 @@ def validate_yaml_header_electrode_map(
         # find appropriate channel map metadata
         channel_map = None
         map_number = None
-        for _, test_meta in enumerate(
-            metadata["ntrode_electrode_group_channel_map"]
-        ):
+        for _, test_meta in enumerate(metadata["ntrode_electrode_group_channel_map"]):
             if str(test_meta["ntrode_id"]) == ntrode_id:
                 channel_map = test_meta
                 break

src/trodes_to_nwb/convert_yaml.py

@@ -3,12 +3,15 @@
 initial NWB file setup, subject info, device entries, electrode tables, etc.
 """
 
-from copy import deepcopy
-from datetime import datetime
 import logging
 import uuid
+from copy import deepcopy
+from datetime import datetime
 from xml.etree import ElementTree
 
+import pandas as pd
+import pytz
+import yaml
 from hdmf.common.table import DynamicTable, VectorData
 from ndx_franklab_novela import (
     AssociatedFiles,
@@ -19,14 +22,11 @@
     Shank,
     ShanksElectrode,
 )
-import pandas as pd
 from pynwb import NWBFile
 from pynwb.file import ProcessingModule, Subject
-import pytz
-import yaml
 
-from trodes_to_nwb import __version__
 import trodes_to_nwb.metadata_validation
+from trodes_to_nwb import __version__
 
 
 def load_metadata(