Sleap

From 1.3.2+, to install SLEAP through PyPI use `pip install sleap[pypi]` to ensure all dependencies are gathered.

As a reminder:

> The 1.3.1 dependency update requires [Mamba](https://mamba.readthedocs.io/en/latest/index.html) for faster dependency resolution. If you already have anaconda installed, then you _can_ set the solver to libmamba in the base environment:
>
>conda update -n base conda
>conda install -n base conda-libmamba-solver
>conda config --set solver libmamba
>
>Any subsequent `mamba` commands in the docs will need to be replaced with `conda` if you choose to use your existing Anaconda installation.
>
>Otherwise, follow the [recommended installation instruction for Mamba](https://mamba.readthedocs.io/en/latest/installation.html).

Quick install
**`mamba` (Windows/Linux/GPU)**:

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2


**`mamba` (Mac)**:

mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.2


**`pip` (any OS except Apple Silicon)**:

pip install sleap[pypi]==1.3.2


Highlights
* Limit max tracks via track-local queues by shrivaths16 and talmo in https://github.com/talmolab/sleap/pull/1447
* Add option to remove videos in batch by gitttt-1234 in https://github.com/talmolab/sleap/pull/1382 and https://github.com/talmolab/sleap/pull/1406
* Add shortcut to export analysis for current video by KevinZ0217 in https://github.com/talmolab/sleap/pull/1414 and https://github.com/talmolab/sleap/pull/1444
* Add video path and frame indices to metrics by roomrys in https://github.com/talmolab/sleap/pull/1396
* Add a button for copying model config to clipboard by KevinZ0217 in https://github.com/talmolab/sleap/pull/1433
* Add Option to Export CSV by gitttt-1234 in https://github.com/talmolab/sleap/pull/1438

Full Changelog

Enhancements
* Add option to remove videos in batch by gitttt-1234 in https://github.com/talmolab/sleap/pull/1382 and https://github.com/talmolab/sleap/pull/1406
* Add `Track` when add `Instance` by roomrys in https://github.com/talmolab/sleap/pull/1408
* Add `Video` to cache when adding `Track` by roomrys in https://github.com/talmolab/sleap/pull/1407
* Add shortcut to export analysis for current video by KevinZ0217 in https://github.com/talmolab/sleap/pull/1414 and https://github.com/talmolab/sleap/pull/1444
* Add video path and frame indices to metrics by roomrys in https://github.com/talmolab/sleap/pull/1396
* Improve error message for detecting video backend by roomrys in https://github.com/talmolab/sleap/pull/1441
* Add a button for copying model config to clipboard by KevinZ0217 in https://github.com/talmolab/sleap/pull/1433
* Add Option to Export CSV by gitttt-1234 in https://github.com/talmolab/sleap/pull/1438
* Limit max tracks via track-local queues by shrivaths16 and talmo in https://github.com/talmolab/sleap/pull/1447

Fixes
* Minor fix in computation of OKS by shrivaths16 in https://github.com/talmolab/sleap/pull/1383 and https://github.com/talmolab/sleap/pull/1399
* Fix `Filedialog` to work across (mac)OS by roomrys in https://github.com/talmolab/sleap/pull/1393
* Fix panning bounding box by gitttt-1234 in https://github.com/talmolab/sleap/pull/1398
* Fix skeleton templates by roomrys in https://github.com/talmolab/sleap/pull/1404
* Fix labels export for json by roomrys in https://github.com/talmolab/sleap/pull/1410
* Correct GUI state emulation by roomrys in https://github.com/talmolab/sleap/pull/1422
* Update status message on status bar by shrivaths16 in https://github.com/talmolab/sleap/pull/1411
* Fix error thrown when last video is deleted by shrivaths16 in https://github.com/talmolab/sleap/pull/1421
* Add model folder to the unzip path by roomrys in https://github.com/talmolab/sleap/pull/1445
* Fix drag and drop by talmo in https://github.com/talmolab/sleap/pull/1449

Dependencies
* Pin micromamba version by roomrys in https://github.com/talmolab/sleap/pull/1376
* Add pip extras by roomrys in https://github.com/talmolab/sleap/pull/1481

New Contributors
* shrivaths16 made their first contribution in https://github.com/talmolab/sleap/pull/1383
* gitttt-1234 made their first contribution in https://github.com/talmolab/sleap/pull/1382
* KevinZ0217 made their first contribution in https://github.com/talmolab/sleap/pull/1414

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.3.1...v1.3.2

Highlights
* Update environment creation by roomrys in 1366
* Add `--max_instances` to `sleap-track` and GUI by roomrys in https://github.com/talmolab/sleap/pull/1305
* Increase GUI crop size range from 512 to 832 by roomrys in https://github.com/talmolab/sleap/pull/1295
* Allow returning PAF graph during low level inference by calebweinreb in https://github.com/talmolab/sleap/pull/1329
* Fix GUI resume training by roomrys in https://github.com/talmolab/sleap/pull/1314
* Fixes GPU memory polling using environment variable filtering by ericleonardis in https://github.com/talmolab/sleap/pull/1272

Full Changelog

Enhancements
* Centralize video extensions by talmo in https://github.com/talmolab/sleap/pull/1244
* Organize docks by roomrys in https://github.com/talmolab/sleap/pull/1265
* Increase GUI crop size range from 512 to 832 by roomrys in https://github.com/talmolab/sleap/pull/1295
* Add `--max_instances` to `sleap-track` and GUI by roomrys in https://github.com/talmolab/sleap/pull/1305
* Allow returning PAF graph during low level inference by calebweinreb in https://github.com/talmolab/sleap/pull/1329

Fixes
* Disable data caching by default for SingleImageVideos by talmo in https://github.com/talmolab/sleap/pull/1243
* Fix single frame GUI increment by roomrys in https://github.com/talmolab/sleap/pull/1254
* Fix conversion to numpy array when last frame(s) do not have labels by talmo in https://github.com/talmolab/sleap/pull/1307
* Ensure frames to predict list is unique by roomrys in https://github.com/talmolab/sleap/pull/1293
* Fix GUI resume training by roomrys in https://github.com/talmolab/sleap/pull/1314
* Do not choose `top_k` instances if `max_instances` < num centroids by roomrys in https://github.com/talmolab/sleap/pull/1313
* Remove `--labels` and redundant `data_path` by roomrys in https://github.com/talmolab/sleap/pull/1326
* Create copy of config info to modify (gui) by roomrys in https://github.com/talmolab/sleap/pull/1325
* Fixes GPU memory polling using environment variable filtering by ericleonardis in https://github.com/talmolab/sleap/pull/1272
* Set `split_by_inds`, `test_labels`, and `validation_labels` to default (GUI) by roomrys in https://github.com/talmolab/sleap/pull/1331
* Fix (remove) `SingleImageVideo` caching by roomrys in https://github.com/talmolab/sleap/pull/1330

Dependencies
* Update environment creation by roomrys in 1366

New Contributors
* ericleonardis made their first contribution in https://github.com/talmolab/sleap/pull/1272
* calebweinreb made their first contribution in https://github.com/talmolab/sleap/pull/1329

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.3.0...v1.3.1

What's Changed

Highlights
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068
* Expose MoveNet to the Inference GUI by sheridana in https://github.com/talmolab/sleap/pull/1190
* Add option to "Add Videos..." from single image files by eberrigan in https://github.com/talmolab/sleap/pull/1183
* Add GUI and API option to remove unused tracks by roomrys in https://github.com/talmolab/sleap/pull/1210
* Add instance and track copy/pasting by talmo in https://github.com/talmolab/sleap/pull/1206
* Expose supervised ID models to GUI by sheridana in https://github.com/talmolab/sleap/pull/1213
* Ensure data format compatibility by roomrys in https://github.com/talmolab/sleap/pull/1222

Full Changelog

Documentation
* Change 'M1' to 'Apple Silicon' by roomrys in https://github.com/talmolab/sleap/pull/1188
* Update the Documentation badge by roomrys in https://github.com/talmolab/sleap/pull/1211

Enhancements
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Add optional unragging arg to model export by sheridana in https://github.com/talmolab/sleap/pull/1054
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* Add Option to Make Trail Shade Darker/Lighter by roomrys in https://github.com/talmolab/sleap/pull/1103
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121
* Add central padding to SizeMatcher by jiayinghsu in https://github.com/talmolab/sleap/pull/1129
* Added MoveNet as an external model reference by jiayinghsu in https://github.com/talmolab/sleap/pull/1141
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* GenericTableModel/View improvements by jgrewe in https://github.com/talmolab/sleap/pull/1163
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121
* Add option of 2 for marker size by roomrys in https://github.com/talmolab/sleap/pull/1205
* Support new DLC multi-animal configs by roomrys in https://github.com/talmolab/sleap/pull/1204
* Expose MoveNet to the Inference GUI by sheridana in https://github.com/talmolab/sleap/pull/1190
* Add option to "Add Videos..." from single image files by eberrigan in https://github.com/talmolab/sleap/pull/1183
* Add GUI and API option to remove unused tracks by roomrys in https://github.com/talmolab/sleap/pull/1210
* Add instance and track copy/pasting by talmo in https://github.com/talmolab/sleap/pull/1206
* Expose supervised ID models to GUI by sheridana in https://github.com/talmolab/sleap/pull/1213
* Toggle grayscale of all videos using "Toggle Grayscale" button by roomrys in https://github.com/talmolab/sleap/pull/1215

Fixes
* Fix config option to `split_by_inds` by roomrys in https://github.com/talmolab/sleap/pull/1060
* Don't create instances during inference if no points were found by talmo in https://github.com/talmolab/sleap/pull/1073
* Add one-line fix to VideoWriterSkyvideo by roomrys in https://github.com/talmolab/sleap/pull/1082
* Fix parser for sleap-export by roomrys in https://github.com/talmolab/sleap/pull/1085
* Refactor commands to load project as `AppCommand`s by roomrys in https://github.com/talmolab/sleap/pull/1098
* Create signal that updates plot instead of removing and replotting items by roomrys in https://github.com/talmolab/sleap/pull/1134
* Fix symmetric skeletons (via table input) by roomrys in https://github.com/talmolab/sleap/pull/1136
* Fix body vs symmetry subgraph filtering by talmo in https://github.com/talmolab/sleap/pull/1142
* Handle changing backbones in training editor GUI by talmo in https://github.com/talmolab/sleap/pull/1140
* Hotfix for video save 1098 by roomrys in https://github.com/talmolab/sleap/pull/1148
* Update no-cuda-env to fix pillow errors by roomrys in https://github.com/talmolab/sleap/pull/1201
* Fix environment.yml by talmo in https://github.com/talmolab/sleap/pull/1202
* Fix typo in `Skeleton.__repr__` by roomrys in https://github.com/talmolab/sleap/pull/1200
* Split trainer cli function into two functions by roomrys in https://github.com/talmolab/sleap/pull/1197
* Threaded inference by talmo in https://github.com/talmolab/sleap/pull/1203
* Emit the signals to reset table views when data is empty by talmo in https://github.com/talmolab/sleap/pull/1207
* Ensure data format compatibility by roomrys in https://github.com/talmolab/sleap/pull/1222

New Contributors
* jgrewe made their first contribution in https://github.com/talmolab/sleap/pull/1068
* sean-afshar made their first contribution in https://github.com/talmolab/sleap/pull/1133
* eberrigan made their first contribution in https://github.com/talmolab/sleap/pull/1183

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.2.9...v1.3.0

Highlights
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068

Full changelog

Documentation
* Change 'M1' to 'Apple Silicon' by roomrys in https://github.com/talmolab/sleap/pull/1188

Enhancements
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Add optional unragging arg to model export by sheridana in https://github.com/talmolab/sleap/pull/1054
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* Add Option to Make Trail Shade Darker/Lighter by roomrys in https://github.com/talmolab/sleap/pull/1103
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121
* Add central padding to SizeMatcher by jiayinghsu in https://github.com/talmolab/sleap/pull/1129
* Added MoveNet as an external model reference by jiayinghsu in https://github.com/talmolab/sleap/pull/1141
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* GenericTableModel/View improvements by jgrewe in https://github.com/talmolab/sleap/pull/1163
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121

Fixes
* Fix config option to `split_by_inds` by roomrys in https://github.com/talmolab/sleap/pull/1060
* Don't create instances during inference if no points were found by talmo in https://github.com/talmolab/sleap/pull/1073
* Add one-line fix to VideoWriterSkyvideo by roomrys in https://github.com/talmolab/sleap/pull/1082
* Fix parser for sleap-export by roomrys in https://github.com/talmolab/sleap/pull/1085
* Refactor commands to load project as `AppCommand`s by roomrys in https://github.com/talmolab/sleap/pull/1098
* Create signal that updates plot instead of removing and replotting items by roomrys in https://github.com/talmolab/sleap/pull/1134
* Fix symmetric skeletons (via table input) by roomrys in https://github.com/talmolab/sleap/pull/1136
* Fix body vs symmetry subgraph filtering by talmo in https://github.com/talmolab/sleap/pull/1142
* Handle changing backbones in training editor GUI by talmo in https://github.com/talmolab/sleap/pull/1140
* Hotfix for video save 1098 by roomrys in https://github.com/talmolab/sleap/pull/1148

New Contributors
* jgrewe made their first contribution in https://github.com/talmolab/sleap/pull/1068
* sean-afshar made their first contribution in https://github.com/talmolab/sleap/pull/1133

See the [Installation page](https://sleap.ai/installation.html) in the docs for more info.

Highlights
- Prefer user instances when calling Labels.numpy() (996)
- Add upper limit of the instance count in prediction score labeling suggestion method (981)
- Add more options to render video: wedges, palette, and distinctly color (998)
- Always draw user instances even if all nodes marked as not visible (1002)
- Add frame chunk method in labeling suggestions (1007)

Full changelog
Documentation
- Add sample movies to docs (992)
- Fix docs in Model_evaluation.ipynb (1034)

Enhancements
- Prefer user instances when calling Labels.numpy() (996)
- Add more options to render video: wedges, palette, and distinctly color (998)
- Add upper limit of the instance count in prediction score labeling suggestion method (981)
- Speed-up cache for multi-video projects (1017)
- Increase max number for target instances in simple tracker form (1037)
- Share usage data 1038
- Add frame chunk method in labeling suggestions (1007)

Fixes
- Fix printing of auto-selected GPU free memory (955)
- Fix add suggestions when target is current video (956)
- Fix `sleap-export` cli arg parsing (962)
- Fix cattr in Python 3.9 (967)
- Fix editing track name clears the old entry on double-click (980)
- Prune saved shifted instances (1001)
- Update suggestions upon video removal (1009)
- Correctly add .h5 extension to analysis files on Linux (1010)
- GUI Table: Do not set item value if same as current value (1022)
- Always draw user instances even if all nodes marked as not visible (1002)
- Shifted instances: make sure ref_instances is not empty (1029)
- Trails prefer user instances over predicted (1036)

See the [Installation page](https://sleap.ai/installation.html) in the docs for more info.

Full changelog
Fixes
- Add test and fix for GPU memory query (946, 949, 950)
- Fix sleap-export CLI and add docs (951)