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SLEAP v1.4.1a2

28 Jun 18:40
@eberrigan eberrigan
v1.4.1a2
436b177
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SLEAP v1.4.1a2 Pre-release
Pre-release

SLEAP v1.4.1a2 is a pre-release. See 1.3.3 for the latest stable release. The crucial change here is Fix zmq inference by @roomrys in #1800 since inference was not working in the pre-release v1.4.1a1 due to the addition of zmq port options for training in #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

Workflow Changes

Enhancements and Refactors

  • Set selected instance to None after removal by @roomrys in #1808
  • Add InstancesList class to handle backref to LabeledFrame by @roomrys in #1807

Full Changelog: v1.4.1a1...v1.4.1a2

Contributors

roomrys and eberrigan
Assets 2

SLEAP v1.4.1a1

03 Jun 02:53
@eberrigan eberrigan
v1.4.1a1
61dbe62
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SLEAP v1.4.1a1 Pre-release
Pre-release

SLEAP v1.4.1a1 is a pre-release. See 1.3.3 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

Refactors

Fixes

Dependency Changes

Workflow Changes

Website Changes

New Contributors

Full Changelog: v1.3.3...v1.4.1a1

Contributors

lambdaloop, talmo, and 8 other contributors
Assets 2

SLEAP v1.4.1a0

29 May 01:00
@eberrigan eberrigan
v1.4.1a0
74bada8
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SLEAP v1.4.1a0 Pre-release
Pre-release

What's Changed

New Contributors

Full Changelog: v1.3.3...v1.4.1a0

Contributors

lambdaloop, talmo, and 8 other contributors
Assets 2

SLEAP v1.4.0a0

20 May 18:11
@eberrigan eberrigan
v1.4.0a0
6a0cf9c
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SLEAP v1.4.0a0 Pre-release
Pre-release

What's Changed

New Contributors

Full Changelog: v1.3.3...v1.4.0a0

Contributors

lambdaloop, talmo, and 8 other contributors
Assets 2

SLEAP v1.3.3

15 Sep 23:54
@roomrys roomrys
v1.3.3
9eeba97
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SLEAP v1.3.3 Latest
Latest

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, 1.3.1, and 1.3.2 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 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.

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

Dependencies

Full Changelog: v1.3.2...v1.3.3

Contributors

roomrys
Assets 2

SLEAP v1.3.2

10 Sep 17:07
@roomrys roomrys
v1.3.2
e97df17
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SLEAP v1.3.2

SLEAP 1.3.2 adds some nice usability features thanks to both the community ideas and new contributors! See 1.3.0 and 1.3.1 for previous notable changes.

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 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.

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

Full Changelog

Enhancements

Fixes

Dependencies

New Contributors

Full Changelog: v1.3.1...v1.3.2

Contributors

talmo, roomrys, and 3 other contributors
Assets 2

SLEAP v1.3.1

30 Jun 20:43
@roomrys roomrys
v1.3.1
c94c755
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SLEAP v1.3.1

After the massive 1.3.0 release, SLEAP 1.3.1 underwent a much needed dependency and build update. SLEAP 1.3.1 has conda packages for Mac OS X and Apple Silicon 🎉. In terms of features, 1.3.1 has just a few small upgrades/fixes. Be sure to check back in for bigger features still in the works! 🚧 🔨 👀

The 1.3.1 dependency update requires Mamba for faster dependency resolution. If you already have anaconda installed, then you can install Mamba in the base environment:

conda install mamba -n base -c conda-forge

Otherwise, follow the recommended installation instruction for Mamba.

Quick install

mamba (Windows/Linux/GPU):

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.1

mamba (Mac):

mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.1

pip (any OS except Apple Silicon):

pip install sleap==1.3.1

Highlights

Full Changelog

Enhancements

Fixes

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

Dependencies

New Contributors

Full Changelog: v1.3.0...v1.3.1

Contributors

talmo, calebweinreb, and 2 other contributors
Assets 2

SLEAP v1.3.0

23 Mar 22:11
@roomrys roomrys
v1.3.0
81b4342
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SLEAP v1.3.0

For 1.3.0 we want to give our users some cool new features worth upgrading for! This release includes a many enhancements we hope our users will enjoy as well as its fair share of bug fixes.

Quick install

conda (Windows/Linux/GPU):

conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.3.0

pip (any OS except Apple Silicon):

pip install sleap==1.3.0

What's Changed

Highlights

Full Changelog

Documentation

Enhancements

Fixes

New Contributors

Full Changelog: v1.2.9...v1.3.0

Contributors

jgrewe, talmo, and 8 other contributors
Assets 2

SLEAP v1.3.0a0

24 Feb 17:03
@roomrys roomrys
v1.3.0a0
d4f63b8
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SLEAP v1.3.0a0 Pre-release
Pre-release

Pre-release of SLEAP v1.3.0.

For 1.3.0 we want to give our users some cool new features worth upgrading for! This pre-release includes lots of enhancements and it's fair share of bug fixes.

Warning: This is a pre-release! Expect bugs and strange behavior when testing.

Quick install

conda (Windows/Linux/GPU):

conda create -y -n sleap -c sleap -c sleap/label/dev -c nvidia -c conda-forge sleap=1.3.0a0

pip (any OS except Apple Silicon):

pip install sleap==1.3.0a0

Highlights

Full changelog

Documentation

Enhancements

Fixes

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

New Contributors

Contributors

jgrewe, talmo, and 7 other contributors
Assets 2

SLEAP v1.2.9

11 Nov 15:02
@roomrys roomrys
v1.2.9
5093f69
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SLEAP v1.2.9

Stable release of SLEAP v1.2.9. This release has lots of bug fixes, a few GUI enhancements, and one CLI fix.

See the release notes for v1.2.0, v1.2.1, v1.2.2, v1.2.7 for previous major changes.

Quick install

conda (Windows/Linux/GPU):

conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.9

pip (any OS):

pip install sleap==1.2.9

See the Installation page 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)
Assets 2