Add pytests, adjust pin bounds

.github/workflows/test.yml

@@ -0,0 +1,158 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, dev ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 0 * * 0'  # Run weekly on Sundays at midnight UTC
+  workflow_dispatch:  # Allow manual triggering
+
+jobs:
+  quick-tests:
+    name: Quick Tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache pip packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run quick tests
+        run: |
+          pytest tests/ -m "quick" -v --tb=short
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: quick-test-results-py${{ matrix.python-version }}
+          path: |
+            .pytest_cache
+            test-results.xml
+          retention-days: 7
+
+  full-tests:
+    name: Full Test Suite
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request' || github.ref == 'refs/heads/main'
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Cache pip packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Cache test data
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/keypoint_moseq_tests
+          key: ${{ runner.os }}-test-data-v1
+          restore-keys: |
+            ${{ runner.os }}-test-data-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run full test suite (exclude slow)
+        run: |
+          pytest tests/ \
+            --cov=keypoint_moseq \
+            --cov-report=xml \
+            --cov-report=term \
+            -m "not slow" \
+            -v \
+            --tb=short \
+            --junitxml=test-results.xml
+
+      - name: Check coverage threshold
+        run: |
+          coverage report --fail-under=40
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+          verbose: true
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: full-test-results
+          path: |
+            coverage.xml
+            test-results.xml
+            htmlcov/
+          retention-days: 30
+
+      - name: Comment PR with coverage
+        if: github.event_name == 'pull_request'
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+          MINIMUM_GREEN: 50
+          MINIMUM_ORANGE: 40
+
+  slow-tests:
+    name: Slow Tests (Weekly)
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' || github.event_name == 'schedule'
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run all tests including slow
+        run: |
+          pytest tests/ -v --tb=short --timeout=7200
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: slow-test-results
+          path: test-results.xml
+          retention-days: 30

.gitignore

@@ -1,6 +1,10 @@
 **/.DS_Store
 testing
 update_pypi.sh
+docs/source/dlc*
+docs/source/demo*
+tests/dlc*
+temp*
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -1,4 +1,8 @@
-# Keypoint MoSeq 
+# Keypoint MoSeq
+
+![Tests](https://github.com/dattalab/keypoint-moseq/actions/workflows/test.yml/badge.svg)
+[![codecov](https://codecov.io/gh/dattalab/keypoint-moseq/branch/main/graph/badge.svg)](https://codecov.io/gh/dattalab/keypoint-moseq)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 
 ![logo](docs/source/_static/logo.jpg)
 

keypoint_moseq/analysis.py

@@ -16,10 +16,29 @@
 from glob import glob
 import panel as pn
 from jax_moseq.utils import get_durations, get_frequencies
+from packaging import version
 
 pn.extension("plotly", "tabulator")
 na = np.newaxis
 
+# seaborn version compatibility: evaluate once at import time
+_SEABORN_VERSION = version.parse(sns.__version__)
+_USE_NATIVE_SCALE = _SEABORN_VERSION >= version.parse("0.14")
+
+
+def _get_pointplot_errorbar_kwargs():
+    """Get the appropriate errorbar kwargs for seaborn pointplot based on version.
+
+    seaborn 0.14.0 changed the errorbar API from errorbar=("ci", 68)
+    to using native_scale parameter and errorbar="se".
+    """
+    if _USE_NATIVE_SCALE:
+        # seaborn >= 0.14
+        return {"errorbar": "se", "native_scale": True}
+    else:
+        # seaborn < 0.14
+        return {"errorbar": ("ci", 68)}
+
 
 def get_syllable_names(project_dir, model_name, syllable_ixs):
     """Get syllable names from syll_info.csv file. Labels consist of the
@@ -1151,16 +1170,17 @@ def plot_syll_stats_with_sem(
 
     # plot each group's stat data separately, computes groupwise SEM, and orders data based on the stat/ordering parameters
     hue = "group" if groups is not None else None
+    errorbar_kwargs = _get_pointplot_errorbar_kwargs()
     ax = sns.pointplot(
         data=stats_df,
         x="syllable",
         y=stat,
         hue=hue,
         order=ordering,
-        errorbar=("ci", 68),
         ax=ax,
         hue_order=groups,
         palette=colors,
+        **errorbar_kwargs,
     )
 
     # where some data has already been plotted to ax

keypoint_moseq/io.py

@@ -860,7 +860,7 @@ def save_keypoints(
         bodyparts = [f"bodypart{i}" for i in range(num_keypoints)]
 
     # create column names
-    suffixes = ["x", "y", "z"][:num_keypoints]
+    suffixes = ["x", "y", "z"][:num_dims]
     if confidences is not None:
         suffixes += ["conf"]
     columns = [f"{bp}_{suffix}" for bp in bodyparts for suffix in suffixes]

keypoint_moseq/viz.py

@@ -7,6 +7,7 @@
 import h5py
 import numpy as np
 import plotly
+import matplotlib
 import matplotlib.pyplot as plt
 from scipy.ndimage import gaussian_filter1d
 from vidio.read import OpenCVReader
@@ -22,6 +23,7 @@
 
 from plotly.subplots import make_subplots
 import plotly.io as pio
+from packaging import version
 
 pio.renderers.default = "iframe"
 
@@ -31,6 +33,10 @@
 # suppress warnings from imageio
 logging.getLogger().setLevel(logging.ERROR)
 
+# matplotlib version compatibility: evaluate once at import time
+_MATPLOTLIB_VERSION = version.parse(matplotlib.__version__)
+_USE_BUFFER_RGBA = _MATPLOTLIB_VERSION >= version.parse("3.10")
+
 
 def crop_image(image, centroid, crop_size):
     """Crop an image around a centroid.
@@ -1428,12 +1434,39 @@ def get_limits(
     return lims.astype(int)
 
 
+def _get_canvas_buffer_method(canvas):
+    """Get the appropriate canvas buffer method based on matplotlib version.
+
+    matplotlib 3.10 removed tostring_rgb() in favor of buffer_rgba().
+    This function returns the correct method to call.
+    """
+    if _USE_BUFFER_RGBA:
+        return canvas.buffer_rgba
+    else:
+        return canvas.tostring_rgb
+
+
+def _reshape_canvas_buffer(raster_flat, height, width):
+    """Reshape and convert canvas buffer to RGB format.
+
+    For matplotlib >= 3.10, drops the alpha channel from RGBA.
+    For matplotlib < 3.10, returns RGB directly.
+    """
+    if _USE_BUFFER_RGBA:
+        # matplotlib >= 3.10: RGBA buffer, drop alpha channel
+        return raster_flat.reshape((height, width, 4))[:, :, :3]
+    else:
+        # matplotlib < 3.10: RGB buffer
+        return raster_flat.reshape((height, width, 3))
+
+
 def rasterize_figure(fig):
     canvas = fig.canvas
     canvas.draw()
     width, height = canvas.get_width_height()
-    raster_flat = np.frombuffer(canvas.tostring_rgb(), dtype="uint8")
-    raster = raster_flat.reshape((height, width, 3))
+    buffer_method = _get_canvas_buffer_method(canvas)
+    raster_flat = np.frombuffer(buffer_method(), dtype="uint8")
+    raster = _reshape_canvas_buffer(raster_flat, height, width)
     return raster