Update Python version requirement to 3.10+ and auto-fix ruff issues

- Increase minimum Python version from 3.8 to 3.10
- Update all tool configurations to target Python 3.10
- Auto-fix 124 code style issues with ruff --fix including:
  - Import sorting and organization
  - Remove unused imports and variables
  - Simplify code patterns (list comprehensions, conditionals)
  - Fix whitespace and formatting issues

61 issues remain that require manual review, mostly in notebooks
and complex logic patterns that need careful consideration.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edeno

CLAUDE.md

@@ -0,0 +1,97 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+This is a Python package that converts SpikeGadgets .rec files (electrophysiology data) to NWB 2.0+ format. The conversion includes ephys data, position tracking, video files, DIO events, and behavioral metadata, with validation for DANDI archive compatibility.
+
+## Development Setup Commands
+
+**Environment Setup:**
+
+```bash
+mamba env create -f environment.yml
+mamba activate trodes_to_nwb
+pip install -e .
+```
+
+**Testing:**
+
+```bash
+pytest --cov=src --cov-report=xml --doctest-modules -v --pyargs trodes_to_nwb
+```
+
+**Linting:**
+
+```bash
+black .
+```
+
+**Build Package:**
+
+```bash
+python -m build
+twine check dist/*
+```
+
+## Architecture
+
+### Core Conversion Pipeline
+
+The main conversion happens in `src/trodes_to_nwb/convert.py` with the `create_nwbs()` function which orchestrates:
+
+1. **File Discovery** (`data_scanner.py`): Scans directories for .rec files and associated data files
+2. **Metadata Loading** (`convert_yaml.py`): Loads and validates YAML metadata files
+3. **Header Processing** (`convert_rec_header.py`): Extracts device configuration from .rec file headers
+4. **Data Conversion**: Modular converters for different data types:
+   - `convert_ephys.py`: Raw electrophysiology data
+   - `convert_position.py`: Position tracking and video
+   - `convert_dios.py`: Digital I/O events
+   - `convert_analog.py`: Analog signals
+   - `convert_intervals.py`: Epoch and behavioral intervals
+   - `convert_optogenetics.py`: Optogenetic stimulation data
+
+### File Structure Requirements
+
+Input files must follow naming convention: `{YYYYMMDD}_{animal}_{epoch}_{tag}.{extension}`
+
+Required files per session:
+
+- `.rec`: Main recording file
+- `{date}_{animal}.metadata.yml`: Session metadata
+- Optional: `.h264`, `.videoPositionTracking`, `.cameraHWSync`, `.stateScriptLog`
+
+### Metadata System
+
+- Uses YAML metadata files validated against JSON schema (`nwb_schema.json`)
+- Probe configurations stored in `device_metadata/probe_metadata/`
+- Virus metadata in `device_metadata/virus_metadata/`
+- See `docs/yaml_mapping.md` for complete metadata field mapping
+
+### Key Data Processing
+
+- Uses Neo library (`spike_gadgets_raw_io.py`) for .rec file I/O
+- Implements chunked data loading (`RecFileDataChunkIterator`) for memory efficiency
+- Parallel processing support via Dask for batch conversions
+- NWB validation using nwbinspector after conversion
+
+## Testing
+
+- Unit tests in `src/trodes_to_nwb/tests/`
+- Integration tests in `tests/integration-tests/`
+- Test data downloaded from secure UCSF Box in CI
+- Coverage reports uploaded to Codecov
+
+## Release Process
+
+1. Tag release commit (e.g. `v0.1.0`)
+2. Push tag to GitHub (triggers PyPI upload)
+3. Create GitHub release
+
+## Important Notes
+
+- Package supports Python >=3.8
+- Requires `ffmpeg` for video conversion
+- Uses hatch for build system with VCS-based versioning
+- Main branch protected, requires PR reviews

notebooks/explore_rec_file_neo.ipynb

@@ -118,7 +118,7 @@
     "# The raw data block consists of N packets.\n",
     "# Each packet consists of:\n",
     "# First byte is 0x55\n",
-    "# Some number of bytes for each device (e.g., Controller_DIO has 1 byte, \n",
+    "# Some number of bytes for each device (e.g., Controller_DIO has 1 byte,\n",
     "# ECU has 32 bytes, Multiplexed has 8 bytes, SysClock has 8 bytes)\n",
     "# Timestamp (uint32) which has 4 bytes\n",
     "# Ephys data (int16) which has 2 * num_ephy_channels bytes\n",
@@ -182,6 +182,7 @@
    "source": [
     "# read the binary part lazily\n",
     "import numpy as np\n",
+    "\n",
     "raw_memmap = np.memmap(rec_file_path, mode='r', offset=header_size, dtype='<u1')\n",
     "\n",
     "num_packet = raw_memmap.size // packet_size\n",
@@ -325,10 +326,10 @@
     "for device in hconf:\n",
     "    stream_id = device.attrib['name']\n",
     "    print(stream_id)\n",
-    "    \n",
+    "\n",
     "    for channel in device:\n",
     "        print(channel.attrib)\n",
-    "        \n",
+    "\n",
     "        if 'interleavedDataIDByte' in channel.attrib:\n",
     "            # TODO LATER: deal with \"headstageSensor\" which have interleaved\n",
     "            continue\n",