Complete LabData migration in behavior_analyses

.github/copilot-instructions.md

@@ -0,0 +1,4 @@
+# Copilot Instructions
+
+Read `AGENTS.md` and `README.md`. Repository code, tests, and the current
+working tree are authoritative for implementation state.

.github/workflows/ci.yml

@@ -34,3 +34,6 @@ jobs:
 
       - name: Check formatting
         run: uvx ruff format --check .
+
+      - name: Test
+        run: uv run python -m unittest discover -s tests -v

.gitignore

@@ -1,7 +1,4 @@
 .DS_Store
-AGENTS.md
-CLAUDE.md
-.github/copilot-instructions.md
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

AGENTS.md

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+# Project Instructions
+
+Behavioral-only analysis code for Churchland Lab thesis work.
+
+- Start from the actual branch, working tree, notebooks, scripts, and tests.
+- Read `README.md` and `docs/MIGRATION.md` before changing the data-access or
+  package surface.
+- Keep behavioral analysis here; electrophysiology work belongs in the
+  `ephys` repository.
+- Maintained reusable work uses `labdata`, `labdata_plugin/`, and
+  `src/behavior_analyses/`. Archived `djchurchland` notebooks live under
+  `archive/djchurchland/`.
+- Do not reintroduce `/Users/gabriel` paths or machine-local dependency paths.
+- Use Notion for current priorities and decisions, not as a copy of repository
+  state.
+
+Run the narrowest relevant checks, then `uvx ruff check .`,
+`uvx ruff format --check .`, and
+`uv run python -m unittest discover -s tests -v` when the full migration
+surface is affected.

CLAUDE.md

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+# Project Instructions
+
+Read `AGENTS.md` and `README.md`.

README.md

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+# behavior_analyses
+
+Behavioral-only analysis code for thesis work in the Churchland Lab.
+
+## Setup and checks
+
+```bash
+uv sync
+uvx ruff check .
+uvx ruff format --check .
+uv run python -m unittest discover -s tests -v
+```
+
+`fit-psychometric` is vendored under `third_party/fit_psychometric` (no sibling
+checkout or machine-local path required). Optional Chipmunk plugin fallback:
+
+```bash
+export CHIPMUNK_PLUGIN_PATH=/path/to/labdata/plugins/chipmunk
+```
+
+## Layout
+
+- `src/behavior_analyses/` — reusable analysis modules
+- `scripts/analyses/` — maintained scripts and migration entry points
+- `labdata_plugin/` — local analysis-schema plugin under development
+- `tests/` — migration-focused tests
+- `docs/MIGRATION.md` — inventory, portability notes, live-validation gates
+- `behavioral_metrics/`, `psychometric_curves/`,
+  `psychophysical_kernels/` — maintained labdata notebooks + helpers
+- `archive/djchurchland/` — preserved pre-migration notebooks
+- `archive/labdata_migration/` — preserved superseded migration smoke notebooks
+- `notebooks/` — ingestion and exploratory work
+- `oft/` — open-field analyses (archived notebooks relocated)
+
+## Data access
+
+Maintained analysis paths use `labdata` and the local plugin in
+`labdata_plugin/`. Prefer `from chipmunk import Chipmunk` for trial-level
+Chipmunk data. Archived `djchurchland` notebooks are under
+`archive/djchurchland/` and are not active entry points.
+
+## Migration CLIs
+
+```bash
+uv run python scripts/analyses/seed_behavior_analysis_set.py --help
+uv run python scripts/analyses/migrate_behavior_analysis_schema.py --help
+uv run python scripts/analyses/populate_behavior_tables.py --help
+uv run python scripts/analyses/plot_psychometrics.py --help
+```
+
+Use `--dry-run` on seed/populate before any database writes.

archive/djchurchland/README.md

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+# Archived djchurchland notebooks
+
+These notebooks are preserved as provenance for the pre-labdata analysis workflows.
+They are **not** maintained entry points.
+
+| Path | Classification |
+| --- | --- |
+| `psychometric_curves/` | archived |
+| `behavioral_metrics/` | archived |
+| `psychophysical_kernels/` | archived |
+| `root/sess.ipynb` | archived |
+| `oft/` | archived (absolute desktop paths; not part of the Chipmunk LabData migration) |
+
+Maintained replacements:
+
+- `src/behavior_analyses/` — reusable analysis functions
+- `labdata_plugin/analysisschema.py` — DataJoint computed/manual tables
+- `scripts/analyses/` — seed, populate, and plot CLIs
+- `psychometric_curves/utils.py` — labdata-backed plotting helpers
+- `psychometric_curves/plot_psychometric_fits.ipynb`
+- `behavioral_metrics/plot_learning_curves.ipynb`
+- `psychophysical_kernels/plot_kernels.ipynb`
+- `sess.ipynb`

archive/djchurchland/root/sess.ipynb

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+{
+ "cells": [
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+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "9ad1f58e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from djchurchland.schema import Chipmunk\n",
+    "\n",
+    "import pandas as pd\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib as mpl\n",
+    "\n",
+    "new_rc_params = {\"text.usetex\": False, \"svg.fonttype\": \"none\"}\n",
+    "mpl.rcParams.update(new_rc_params)\n",
+    "plt.rcParams[\"font.sans-serif\"] = [\"Arial\"]\n",
+    "plt.rcParams[\"font.size\"] = 12\n",
+    "\n",
+    "%matplotlib widget\n",
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "fd46321d",
+   "metadata": {},
+   "outputs": [
+    {
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+       "columns": [
+        {
+         "name": "index",
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+         "type": "integer"
+        },
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+         "name": "subject_name",
+         "rawType": "object",
+         "type": "string"
+        },
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+         "name": "session_datetime",
+         "rawType": "datetime64[ns]",
+         "type": "datetime"
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+         "rawType": "int64",
+         "type": "integer"
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+         "type": "datetime"
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+        {
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+         "rawType": "float64",
+         "type": "float"
+        },
+        {
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+         "rawType": "object",
+         "type": "string"
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+         "type": "float"
+        },
+        {
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+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "setting_prob_audio",
+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "setting_prob_vision",
+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "setting_high_rate_side",
+         "rawType": "object",
+         "type": "string"
+        }
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+       "      <th>session_datetime</th>\n",
+       "      <th>session_num</th>\n",
+       "      <th>starttime</th>\n",
+       "      <th>duration</th>\n",
+       "      <th>setting_task_type</th>\n",
+       "      <th>setting_modalities</th>\n",
+       "      <th>setting_left_reward_volume</th>\n",
+       "      <th>setting_right_reward_volume</th>\n",
+       "      <th>setting_prob_audio</th>\n",
+       "      <th>setting_prob_vision</th>\n",
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+       "  <tbody>\n",
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+       "      <td>2024-08-26 11:33:07</td>\n",
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+       "  subject_name    session_datetime  ...  setting_prob_vision setting_high_rate_side\n",
+       "0       GRB006 2024-08-26 11:33:07  ...                  0.0                  right\n",
+       "\n",
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+      ]
+     },
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+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "01b67aa5",
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+    "auditory = [\"20240826_113307\", \"20240827_130938\", \"20240828_115206\"]\n",
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