sleap-nn 0.1.0__tar.gz → 0.1.0a0__tar.gz

{sleap_nn-0.1.0 → sleap_nn-0.1.0a0}/.github/workflows/ci.yml

@@ -82,11 +82,6 @@ jobs:
         if: matrix.os != 'self-hosted-gpu'
         run: uv sync --extra torch-cpu
 
-      - name: Install graphics dependencies (Ubuntu)
-        if: matrix.os == 'ubuntu'
-        run: |
-          sudo apt-get update && sudo apt-get install -y libglapi-mesa libegl-mesa0 libegl1 libopengl0 libgl1 libglx-mesa0
-
       - name: Print environment info
         run: |
           echo "=== UV Environment ==="
@@ -108,7 +103,7 @@ jobs:
               print('CUDA is not available')
           " || echo "CUDA check failed"
           echo "=== Import Test ==="
-          uv run --frozen --extra torch-cpu python -c "import torch; import lightning; import skia; print('All imports successful')" || echo "Import test failed"
+          uv run --frozen --extra torch-cpu python -c "import torch; import lightning; import kornia; print('All imports successful')" || echo "Import test failed"
 
       - name: Check MPS backend (macOS only)
         if: runner.os == 'macOS'
@@ -131,7 +126,7 @@ jobs:
       - name: Run pytest
         run: |
           echo "=== Final environment check before tests ==="
-          uv run --frozen --extra torch-cpu python -c "import numpy, torch, lightning, skia; print(f'All packages available: numpy={numpy.__version__}, torch={torch.__version__}')"
+          uv run --frozen --extra torch-cpu python -c "import numpy, torch, lightning, kornia; print(f'All packages available: numpy={numpy.__version__}, torch={torch.__version__}')"
           echo "=== Running pytest ==="
           uv run --frozen --extra torch-cpu pytest --cov=sleap_nn --cov-report=xml --durations=-1 tests/
 

{sleap_nn-0.1.0 → sleap_nn-0.1.0a0}/.github/workflows/docs.yml

@@ -57,7 +57,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-            uv run mike deploy --update-aliases --allow-empty --push "${{ github.event.release.tag_name }}" prerelease
+            uv run mike deploy --allow-empty --push "${{ github.event.release.tag_name }}"
 
       - name: Build and upload docs (dev)
         if: ${{ github.event_name == 'push' }}

{sleap_nn-0.1.0 → sleap_nn-0.1.0a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sleap-nn
-Version: 0.1.0
+Version: 0.1.0a0
 Summary: Neural network backend for training and inference for animal pose estimation.
 Author-email: Divya Seshadri Murali <dimurali@salk.edu>, Elizabeth Berrigan <eberrigan@salk.edu>, Vincent Tu <vitu@ucsd.edu>, Liezl Maree <lmaree@salk.edu>, David Samy <davidasamy@gmail.com>, Talmo Pereira <talmo@salk.edu>
 License: BSD-3-Clause
@@ -13,10 +13,10 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: <3.14,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: sleap-io<0.7.0,>=0.6.2
+Requires-Dist: sleap-io<0.7.0,>=0.6.0
 Requires-Dist: numpy
 Requires-Dist: lightning
-Requires-Dist: skia-python>=87.0
+Requires-Dist: kornia
 Requires-Dist: jsonpickle
 Requires-Dist: scipy
 Requires-Dist: attrs
@@ -32,7 +32,6 @@ Requires-Dist: hydra-core
 Requires-Dist: jupyter
 Requires-Dist: jupyterlab
 Requires-Dist: pyzmq
-Requires-Dist: rich-click>=1.9.5
 Provides-Extra: torch
 Requires-Dist: torch; extra == "torch"
 Requires-Dist: torchvision>=0.20.0; extra == "torch"
@@ -48,17 +47,6 @@ Requires-Dist: torchvision>=0.20.0; extra == "torch-cuda128"
 Provides-Extra: torch-cuda130
 Requires-Dist: torch; extra == "torch-cuda130"
 Requires-Dist: torchvision>=0.20.0; extra == "torch-cuda130"
-Provides-Extra: export
-Requires-Dist: onnx>=1.15.0; extra == "export"
-Requires-Dist: onnxruntime>=1.16.0; extra == "export"
-Requires-Dist: onnxscript>=0.1.0; extra == "export"
-Provides-Extra: export-gpu
-Requires-Dist: onnx>=1.15.0; extra == "export-gpu"
-Requires-Dist: onnxruntime-gpu>=1.16.0; extra == "export-gpu"
-Requires-Dist: onnxscript>=0.1.0; extra == "export-gpu"
-Provides-Extra: tensorrt
-Requires-Dist: tensorrt>=10.13.0; (sys_platform == "linux" or sys_platform == "win32") and extra == "tensorrt"
-Requires-Dist: torch-tensorrt>=2.5.0; (sys_platform == "linux" or sys_platform == "win32") and extra == "tensorrt"
 Dynamic: license-file
 
 # sleap-nn

sleap_nn-0.1.0a0/docs/cli.md

@@ -0,0 +1,312 @@
+# CLI Reference
+
+This page provides a quick reference for all `sleap-nn` command-line interface (CLI) commands. For detailed usage and examples, see the linked guides.
+
+## Commands Overview
+
+| Command | Description | Guide |
+|---------|-------------|-------|
+| [`sleap-nn train`](#sleap-nn-train) | Train pose estimation models | [Training Guide](training.md) |
+| [`sleap-nn track`](#sleap-nn-track) | Run inference and/or tracking | [Inference Guide](inference.md) |
+| [`sleap-nn eval`](#sleap-nn-eval) | Evaluate predictions against ground truth | [Inference Guide](inference.md#evaluation-metrics) |
+| [`sleap-nn system`](#sleap-nn-system) | Display system info and GPU diagnostics | - |
+
+## Global Options
+
+| Option | Short | Description |
+|--------|-------|-------------|
+| `--version` | `-v` | Show sleap-nn version and exit |
+
+```bash
+sleap-nn --version
+# Output: sleap-nn 0.1.0a0
+```
+
+---
+
+## `sleap-nn train`
+
+Train SLEAP models using a configuration file.
+
+```bash
+sleap-nn train --config-dir <dir> --config-name <name> [options] [overrides]
+```
+
+### Options
+
+| Option | Short | Description |
+|--------|-------|-------------|
+| `--config-name` | `-c` | Name of the config file (without `.yaml` extension) |
+| `--config-dir` | `-d` | Path to the directory containing the config file |
+| `--video-paths` | `-v` | Video paths to replace existing paths in labels (can be specified multiple times) |
+| `--video-path-map` | | Map old video path to new path (takes two arguments: OLD NEW) |
+| `--prefix-map` | | Map old path prefix to new prefix (takes two arguments: OLD NEW) |
+
+### Config Overrides
+
+Override any configuration value directly from the command line:
+
+```bash
+# Change max epochs
+sleap-nn train -c config -d /path/to/dir trainer_config.max_epochs=100
+
+# Change batch size
+sleap-nn train -c config -d /path/to/dir trainer_config.train_data_loader.batch_size=8
+
+# Set training data path
+sleap-nn train -c config -d /path/to/dir "data_config.train_labels_path=[train.slp]"
+
+# Resume from checkpoint
+sleap-nn train -c config -d /path/to/dir trainer_config.resume_ckpt_path=/path/to/best.ckpt
+```
+
+### Video Path Remapping
+
+When training on a different machine than where labels were created:
+
+```bash
+# Replace paths by order
+sleap-nn train -c config -d /path/to/dir \
+    --video-paths /new/path/video1.mp4 \
+    --video-paths /new/path/video2.mp4
+
+# Map specific paths
+sleap-nn train -c config -d /path/to/dir \
+    --video-path-map /old/video.mp4 /new/video.mp4
+
+# Replace path prefixes (updates all matching videos)
+sleap-nn train -c config -d /path/to/dir \
+    --prefix-map /old/server/data /new/local/data
+```
+
+See [Remapping Video Paths](training.md#remapping-video-paths) for more details.
+
+---
+
+## `sleap-nn track`
+
+Run inference on videos or labels files, with optional tracking.
+
+```bash
+sleap-nn track --data_path <input> --model_paths <model_dir> [options]
+```
+
+### Essential Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--data_path` | `-i` | Path to video (`.mp4`) or labels (`.slp`) file | Required |
+| `--model_paths` | `-m` | Path to model checkpoint directory (can be specified multiple times for top-down) | Required* |
+| `--output_path` | `-o` | Output path for predictions | `<input>.predictions.slp` |
+| `--device` | `-d` | Device to use (`cpu`, `cuda`, `cuda:0`, `mps`, `auto`) | `auto` |
+| `--batch_size` | `-b` | Frames per batch (higher = faster but more memory). Note: `--queue_maxsize` should be at least 2x batch size. | `4` |
+| `--queue_maxsize` | | Maximum size of the frame buffer queue (should be at least 2x batch size) | `8` |
+| `--max_instances` | `-n` | Maximum instances per frame | `None` |
+| `--tracking` | `-t` | Enable tracking | `False` |
+
+*Not required for track-only workflow on labeled data.
+
+### Common Examples
+
+```bash
+# Basic inference
+sleap-nn track -i video.mp4 -m models/bottomup/
+
+# Top-down inference (two models)
+sleap-nn track -i video.mp4 \
+    -m models/centroid/ \
+    -m models/centered_instance/
+
+# Inference with tracking
+sleap-nn track -i video.mp4 -m models/bottomup/ -t
+
+# Specific frames only
+sleap-nn track -i video.mp4 -m models/bottomup/ --frames 0-100,200-300
+
+# Track-only (no inference, just assign tracks to existing labels)
+sleap-nn track -i labels.slp -t
+```
+
+### All Options by Category
+
+#### Model Configuration
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--backbone_ckpt_path` | Path to alternative backbone weights | `None` |
+| `--head_ckpt_path` | Path to alternative head weights | `None` |
+
+#### Image Pre-processing
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--max_height` | Pad image to this height | From training config |
+| `--max_width` | Pad image to this width | From training config |
+| `--input_scale` | Scale factor for input image | From training config |
+| `--crop_size` | Crop size for centered-instance models | From training config |
+| `--ensure_rgb` | Convert to RGB (3 channels) | `False` |
+| `--ensure_grayscale` | Convert to grayscale (1 channel) | `False` |
+| `--anchor_part` | Node name for centroid anchor | From training config |
+
+#### Data Selection
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--frames` | Frame indices (e.g., `0-100,200-300`) | All frames |
+| `--video_index` | Video index in `.slp` file | `None` |
+| `--video_dataset` | Dataset name for HDF5 videos | `None` |
+| `--video_input_format` | Input format for HDF5 videos | `channels_last` |
+| `--only_labeled_frames` | Only run on labeled frames | `False` |
+| `--only_suggested_frames` | Only run on suggested frames | `False` |
+| `--exclude_user_labeled` | Skip frames with user-labeled instances | `False` |
+| `--only_predicted_frames` | Only run on frames with existing predictions | `False` |
+| `--no_empty_frames` | Remove empty frames from output | `False` |
+
+#### Peak Detection
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--peak_threshold` | Minimum confidence for valid peaks | `0.2` |
+| `--integral_refinement` | Refinement method (`integral` or `None`) | `integral` |
+| `--integral_patch_size` | Patch size for integral refinement | `5` |
+
+#### Tracking Options
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--tracking` / `-t` | Enable tracking | `False` |
+| `--tracking_window_size` | Frames to look back for candidates | `5` |
+| `--candidates_method` | `fixed_window` or `local_queues` | `fixed_window` |
+| `--features` | Feature type: `keypoints`, `centroids`, `bboxes`, `image` | `keypoints` |
+| `--scoring_method` | Matching score: `oks`, `cosine_sim`, `iou`, `euclidean_dist` | `oks` |
+| `--scoring_reduction` | Score reduction: `mean`, `max`, `robust_quantile` | `mean` |
+| `--robust_best_instance` | Quantile for robust similarity (0-1, or 1 for max) | `1.0` |
+| `--track_matching_method` | Matching algorithm: `hungarian`, `greedy` | `hungarian` |
+| `--max_tracks` | Maximum number of tracks (local queues only) | `None` |
+| `--min_new_track_points` | Minimum points to spawn new track | `0` |
+| `--min_match_points` | Minimum points for match candidates | `0` |
+| `--post_connect_single_breaks` | Connect single track breaks (local queues only) | `False` |
+
+#### Optical Flow Tracking
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--use_flow` | Use optical flow for tracking | `False` |
+| `--of_img_scale` | Image scale for optical flow (lower = faster) | `1.0` |
+| `--of_window_size` | Window size at each pyramid level | `21` |
+| `--of_max_levels` | Number of pyramid levels | `3` |
+
+#### Bottom-Up Specific
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--max_edge_length_ratio` | Max edge length as fraction of image size | `0.25` |
+| `--dist_penalty_weight` | Distance penalty weight | `1.0` |
+| `--n_points` | Points to sample along line integral | `10` |
+| `--min_instance_peaks` | Minimum peaks for valid instance | `0` |
+| `--min_line_scores` | Minimum line score for PAF matching | `0.25` |
+
+#### Legacy Tracking Options
+
+!!! warning
+    These options are provided for backwards compatibility and may be removed in future releases. Use `--max_instances` instead.
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--tracking_target_instance_count` | Target instances per frame | `0` |
+| `--tracking_pre_cull_to_target` | Cull instances before tracking | `0` |
+| `--tracking_pre_cull_iou_threshold` | IOU threshold for pre-cull | `0` |
+| `--tracking_clean_instance_count` | Target instances after tracking | `0` |
+| `--tracking_clean_iou_threshold` | IOU threshold for post-tracking cull | `0` |
+
+See [Inference Guide](inference.md) for detailed examples and explanations.
+
+---
+
+## `sleap-nn eval`
+
+Evaluate predictions against ground truth labels.
+
+```bash
+sleap-nn eval --ground_truth_path <gt.slp> --predicted_path <pred.slp> [options]
+```
+
+### Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--ground_truth_path` | `-g` | Path to ground truth labels (`.slp`) | Required |
+| `--predicted_path` | `-p` | Path to predicted labels (`.slp`) | Required |
+| `--save_metrics` | `-s` | Path to save metrics (`.npz`) | `None` |
+| `--oks_stddev` | | Standard deviation for OKS calculation | `0.05` |
+| `--oks_scale` | | Scale factor for OKS calculation | `None` |
+| `--match_threshold` | | Threshold for instance matching | `0.0` |
+| `--user_labels_only` | | Only evaluate user-labeled frames | `False` |
+
+### Example
+
+```bash
+sleap-nn eval \
+    -g ground_truth.slp \
+    -p predictions.slp \
+    -s metrics.npz
+```
+
+See [Evaluation Metrics](inference.md#evaluation-metrics) for more details.
+
+---
+
+## `sleap-nn system`
+
+Display system information and GPU diagnostics. Useful for troubleshooting GPU issues and verifying your installation.
+
+```bash
+sleap-nn system
+```
+
+### Output Includes
+
+- Python version and platform
+- PyTorch version and build info
+- CUDA/cuDNN versions with driver compatibility check
+- GPU details (name, compute capability, memory)
+- Functional GPU tests (tensor operations, convolution)
+- Installed package versions (sleap-nn, sleap-io, torch, etc.)
+
+### Example Output
+
+```
+System Information
+==================
+Python: 3.12.8
+Platform: Linux-6.14.0-27-generic-x86_64-with-glibc2.39
+PyTorch: 2.7.0+cu130
+
+CUDA Available: Yes
+CUDA Version: 13.0
+cuDNN Version: 90800
+Driver Version: 570.133.20
+...
+```
+
+This command is particularly helpful when:
+
+- Debugging GPU detection issues
+- Verifying CUDA/cuDNN compatibility
+- Reporting issues or asking for help
+
+---
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `CUDA_VISIBLE_DEVICES` | Control which GPUs are visible (e.g., `0,1`) |
+| `WANDB_API_KEY` | Weights & Biases API key for logging |
+
+## See Also
+
+- [Installation Guide](installation.md) - Setup instructions
+- [Configuration Guide](config.md) - Full config reference
+- [Training Guide](training.md) - Detailed training documentation
+- [Inference Guide](inference.md) - Detailed inference documentation