Sleap

SLEAP v1.4.1a2 is a pre-release. See [1.3.3](https://github.com/talmolab/sleap/releases/tag/v1.3.3) for the latest stable release. The crucial change here is _Fix zmq inference by roomrys in https://github.com/talmolab/sleap/pull/1800_ since inference was not working in the pre-release v1.4.1a1 due to the addition of zmq port options for training in https://github.com/talmolab/sleap/pull/1780 that were not being used for inference.

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

mamba create -y -n sleap_v1.4.1a2 -c conda-forge -c nvidia -c sleap/label/dev -c anaconda sleap=1.4.1a2


**`mamba` (Mac)**:

mamba create -y -n sleap_v1.4.1a2 -c conda-forge -c anaconda -c sleap/label/dev sleap=1.4.1a2


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

pip install sleap[pypi]==1.4.1a2


What's Changed

Fixes
* Fix zmq inference by roomrys in https://github.com/talmolab/sleap/pull/1800

Workflow Changes
* Fix windows conda package upload and build ci by eberrigan in https://github.com/talmolab/sleap/pull/1792
* Bump to v1.4.1a2 by eberrigan in https://github.com/talmolab/sleap/pull/1835

Enhancements and Refactors
* Set selected instance to None after removal by roomrys in https://github.com/talmolab/sleap/pull/1808
* Add `InstancesList` class to handle backref to `LabeledFrame` by roomrys in https://github.com/talmolab/sleap/pull/1807

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.4.1a1...v1.4.1a2

SLEAP v1.4.1a1 is a pre-release. See [1.3.3](https://github.com/talmolab/sleap/releases/tag/v1.3.3) for the latest stable release. There are many changes to dependencies in this pre-release: if you are having installation issues with v1.3.3, you should try this version instead.

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

mamba create -y -n sleap_v1.4.1a1 -c conda-forge -c nvidia -c sleap/label/dev -c anaconda sleap=1.4.1a1


**`mamba` (Mac)**:

mamba create -y -n sleap_v1.4.1a1 -c conda-forge -c anaconda -c sleap/label/dev sleap=1.4.1a1


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

pip install sleap[pypi]==1.4.1a1


What's Changed

Enhancements
* Add options to set background color when exporting video by scott-yj-yang in https://github.com/talmolab/sleap/pull/1328
* Increase range on batch size by roomrys in https://github.com/talmolab/sleap/pull/1513
* Add resize/scroll to training GUI by KevinZ0217 in https://github.com/talmolab/sleap/pull/1565
* support loading slp files with non-compound types and str in metadata by lambdaloop in https://github.com/talmolab/sleap/pull/1566
* change inference pipeline option to tracking-only by shrivaths16 in https://github.com/talmolab/sleap/pull/1666
* Only propagate Transpose Tracks when propagate is checked by vaibhavtrip29 in https://github.com/talmolab/sleap/pull/1748
* Add batch size to GUI for inference by shrivaths16 in https://github.com/talmolab/sleap/pull/1771
* Add ZMQ support via GUI and CLI by shrivaths16 in https://github.com/talmolab/sleap/pull/1780
* Change menu name to match deleting predictions beyond max instance by shrivaths16 in https://github.com/talmolab/sleap/pull/1790
* Adding ragged metadata to `info.json` by shrivaths16 in https://github.com/talmolab/sleap/pull/1765
* Add option to export to CSV via sleap-convert and API by eberrigan in https://github.com/talmolab/sleap/pull/1730

Refactors
* Set default callable for `match_lists_function` by roomrys in https://github.com/talmolab/sleap/pull/1520
* Allow passing in `Labels` to `app.main` by roomrys in https://github.com/talmolab/sleap/pull/1524
* Replace (broken) `--unrag` with `--ragged` by roomrys in https://github.com/talmolab/sleap/pull/1539
* Add function to create app by roomrys in https://github.com/talmolab/sleap/pull/1546
* Refactor `AddInstance` command by roomrys in https://github.com/talmolab/sleap/pull/1561


Fixes
* Graceful failing with seeking errors by talmo in https://github.com/talmolab/sleap/pull/1712
* Fix IndexError for hdf5 file import for single instance analysis files by shrivaths16 in https://github.com/talmolab/sleap/pull/1695
* Import DLC with uniquebodyparts, add Tracks by getzze in https://github.com/talmolab/sleap/pull/1562
* Make the hdf5 videos store as int8 format by lambdaloop in https://github.com/talmolab/sleap/pull/1559
* Scale new instances to new frame size by ssrinath22 in https://github.com/talmolab/sleap/pull/1568
* Fix package export by talmo in https://github.com/talmolab/sleap/pull/1619
* View Hyperparameter nonetype fix by shrivaths16 in https://github.com/talmolab/sleap/pull/1766

Dependency Changes
* Replace imgaug with albumentations by talmo in https://github.com/talmolab/sleap/pull/1623
* Fix out of bounds albumentations issues and update dependencies by eberrigan in https://github.com/talmolab/sleap/pull/1724
* Update to new TensorFlow conda package by eberrigan in https://github.com/talmolab/sleap/pull/1726
* Fix conda builds by eberrigan in https://github.com/talmolab/sleap/pull/1776

Workflow Changes
* Fix CI on macosx-arm64 by talmo in https://github.com/talmolab/sleap/pull/1734
* Upgrade build actions for release by eberrigan in https://github.com/talmolab/sleap/pull/1779
* Fix website build and remove build cache across workflows by eberrigan in https://github.com/talmolab/sleap/pull/1786
* Bump to 1.4.1a1 by eberrigan in https://github.com/talmolab/sleap/pull/1791

Website Changes
* Add ABL:AOC 2023 Workshop link by roomrys in https://github.com/talmolab/sleap/pull/1673

New Contributors
* scott-yj-yang made their first contribution in https://github.com/talmolab/sleap/pull/1328
* lambdaloop made their first contribution in https://github.com/talmolab/sleap/pull/1559
* ssrinath22 made their first contribution in https://github.com/talmolab/sleap/pull/1568

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.3.3...v1.4.1a1

What's Changed
* Add options to set background color when exporting video by scott-yj-yang in https://github.com/talmolab/sleap/pull/1328
* Increase range on batch size by roomrys in https://github.com/talmolab/sleap/pull/1513
* Set default callable for `match_lists_function` by roomrys in https://github.com/talmolab/sleap/pull/1520
* Allow passing in `Labels` to `app.main` by roomrys in https://github.com/talmolab/sleap/pull/1524
* Replace (broken) `--unrag` with `--ragged` by roomrys in https://github.com/talmolab/sleap/pull/1539
* Add function to create app by roomrys in https://github.com/talmolab/sleap/pull/1546
* Refactor `AddInstance` command by roomrys in https://github.com/talmolab/sleap/pull/1561
* Import DLC with uniquebodyparts, add Tracks by getzze in https://github.com/talmolab/sleap/pull/1562
* Make the hdf5 videos store as int8 format by lambdaloop in https://github.com/talmolab/sleap/pull/1559
* Scale new instances to new frame size by ssrinath22 in https://github.com/talmolab/sleap/pull/1568
* Fix package export by talmo in https://github.com/talmolab/sleap/pull/1619
* Add resize/scroll to training GUI by KevinZ0217 in https://github.com/talmolab/sleap/pull/1565
* support loading slp files with non-compound types and str in metadata by lambdaloop in https://github.com/talmolab/sleap/pull/1566
* change inference pipeline option to tracking-only by shrivaths16 in https://github.com/talmolab/sleap/pull/1666
* Add ABL:AOC 2023 Workshop link by roomrys in https://github.com/talmolab/sleap/pull/1673
* Graceful failing with seeking errors by talmo in https://github.com/talmolab/sleap/pull/1712
* Fix IndexError for hdf5 file import for single instance analysis files by shrivaths16 in https://github.com/talmolab/sleap/pull/1695
* Replace imgaug with albumentations by talmo in https://github.com/talmolab/sleap/pull/1623
* Fix out of bounds albumentations issues and update dependencies by eberrigan in https://github.com/talmolab/sleap/pull/1724
* Update to new TensorFlow conda package by eberrigan in https://github.com/talmolab/sleap/pull/1726
* Fix CI on macosx-arm64 by talmo in https://github.com/talmolab/sleap/pull/1734
* Add option to export to CSV via sleap-convert and API by eberrigan in https://github.com/talmolab/sleap/pull/1730
* Only propagate Transpose Tracks when propagate is checked by vaibhavtrip29 in https://github.com/talmolab/sleap/pull/1748
* View Hyperparameter nonetype fix by shrivaths16 in https://github.com/talmolab/sleap/pull/1766
* Adding ragged metadata to `info.json` by shrivaths16 in https://github.com/talmolab/sleap/pull/1765
* Add batch size to GUI for inference by shrivaths16 in https://github.com/talmolab/sleap/pull/1771
* Fix conda builds by eberrigan in https://github.com/talmolab/sleap/pull/1776
* Upgrade build actions for release by eberrigan in https://github.com/talmolab/sleap/pull/1779

New Contributors
* scott-yj-yang made their first contribution in https://github.com/talmolab/sleap/pull/1328
* lambdaloop made their first contribution in https://github.com/talmolab/sleap/pull/1559
* ssrinath22 made their first contribution in https://github.com/talmolab/sleap/pull/1568

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.3.3...v1.4.1a0

What's Changed
* Add options to set background color when exporting video by scott-yj-yang in https://github.com/talmolab/sleap/pull/1328
* Increase range on batch size by roomrys in https://github.com/talmolab/sleap/pull/1513
* Set default callable for `match_lists_function` by roomrys in https://github.com/talmolab/sleap/pull/1520
* Allow passing in `Labels` to `app.main` by roomrys in https://github.com/talmolab/sleap/pull/1524
* Replace (broken) `--unrag` with `--ragged` by roomrys in https://github.com/talmolab/sleap/pull/1539
* Add function to create app by roomrys in https://github.com/talmolab/sleap/pull/1546
* Refactor `AddInstance` command by roomrys in https://github.com/talmolab/sleap/pull/1561
* Import DLC with uniquebodyparts, add Tracks by getzze in https://github.com/talmolab/sleap/pull/1562
* Make the hdf5 videos store as int8 format by lambdaloop in https://github.com/talmolab/sleap/pull/1559
* Scale new instances to new frame size by ssrinath22 in https://github.com/talmolab/sleap/pull/1568
* Fix package export by talmo in https://github.com/talmolab/sleap/pull/1619
* Add resize/scroll to training GUI by KevinZ0217 in https://github.com/talmolab/sleap/pull/1565
* support loading slp files with non-compound types and str in metadata by lambdaloop in https://github.com/talmolab/sleap/pull/1566
* change inference pipeline option to tracking-only by shrivaths16 in https://github.com/talmolab/sleap/pull/1666
* Add ABL:AOC 2023 Workshop link by roomrys in https://github.com/talmolab/sleap/pull/1673
* Graceful failing with seeking errors by talmo in https://github.com/talmolab/sleap/pull/1712
* Fix IndexError for hdf5 file import for single instance analysis files by shrivaths16 in https://github.com/talmolab/sleap/pull/1695
* Replace imgaug with albumentations by talmo in https://github.com/talmolab/sleap/pull/1623
* Fix out of bounds albumentations issues and update dependencies by eberrigan in https://github.com/talmolab/sleap/pull/1724
* Update to new TensorFlow conda package by eberrigan in https://github.com/talmolab/sleap/pull/1726
* Fix CI on macosx-arm64 by talmo in https://github.com/talmolab/sleap/pull/1734
* Add option to export to CSV via sleap-convert and API by eberrigan in https://github.com/talmolab/sleap/pull/1730
* Only propagate Transpose Tracks when propagate is checked by vaibhavtrip29 in https://github.com/talmolab/sleap/pull/1748
* View Hyperparameter nonetype fix by shrivaths16 in https://github.com/talmolab/sleap/pull/1766
* Adding ragged metadata to `info.json` by shrivaths16 in https://github.com/talmolab/sleap/pull/1765
* Add batch size to GUI for inference by shrivaths16 in https://github.com/talmolab/sleap/pull/1771
* Fix conda builds by eberrigan in https://github.com/talmolab/sleap/pull/1776

New Contributors
* scott-yj-yang made their first contribution in https://github.com/talmolab/sleap/pull/1328
* lambdaloop made their first contribution in https://github.com/talmolab/sleap/pull/1559
* ssrinath22 made their first contribution in https://github.com/talmolab/sleap/pull/1568

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.3.3...v1.4.0a0

SLEAP 1.3.4 has no changes to the SLEAP source code, but adds constraints to the `attrs` and `opencv` versions being pulled in.

From 1.3.2+, to install SLEAP through pip 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/index.html).

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

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.4


**`mamba` (Mac)**:

mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.4


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

pip install sleap[pypi]==1.3.4


Full Changelog
- Constrain attrs (mac) and opencv (linux) in 1.3.4 1927

This is a brown-bag release following insufficient restrictions on allowable `tensorflow` versions for the "pypi" extra `sleap[pypi]` in 1.3.2. While the conda packages for 1.3.2 were not affected (since `tensorflow` is pulled in from anaconda), the PyPI only package installed via `pip install sleap[pypi]` had conflicts between the version of `tensorflow` and the version of `keras`. See [1.3.0](https://github.com/talmolab/sleap/releases/tag/v1.3.0), [1.3.1](https://github.com/talmolab/sleap/releases/tag/v1.3.1), and [1.3.2](https://github.com/talmolab/sleap/releases/tag/v1.3.2) for previous notable changes.

From 1.3.2+, to install SLEAP through pip 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=1.3.3


**`mamba` (Mac)**:

mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.3


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

pip install sleap[pypi]==1.3.3


Full Changelog

Fixes
* Do not try to remove item if already deleted by roomrys in https://github.com/talmolab/sleap/pull/1498
* Set `LD_LIBRARY_PATH` on mamba activate by roomrys in https://github.com/talmolab/sleap/pull/1496
* Reset `LD_LIBRARY_PATH` on deactivate by roomrys in 1502

Dependencies
* Add version restirctions to tensorflow for pypi by roomrys in 1485
* Remove `imageio` pin by roomrys in 1501

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.3.2...v1.3.3