8000 SLEAP v1.2.6 by talmo · Pull Request #862 · talmolab/sleap · GitHub
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SLEAP v1.2.6 #862

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Merged
merged 65 commits into from
Jul 26, 2022
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1c57287
Add support for new maDLC labels format (#678)
talmo Mar 17, 2022
a2738ec
Supervised Identity Prediction (#460) (#679)
roomrys Mar 19, 2022
c1878dd
Merge branch 'main' into develop
talmo Mar 21, 2022
d02d7b5
Merge branch 'main' into develop
talmo Mar 21, 2022
fba45fe
Bump minor version (#684)
talmo Mar 21, 2022
e32e7e3
Fix numpy conversion in inference (#687)
sheridana Mar 24, 2022
19f3bfe
Fix topological sorting to always start with root node (#688)
talmo Mar 25, 2022
3c743ef
Create unique default shortcuts (#686) (#690)
roomrys Mar 25, 2022
b0f4780
Training monitor enhancements (#691)
talmo Mar 30, 2022
251df12
add hide instance menu item and hotkey (#692)
roomrys Mar 30, 2022
219bd80
Fix formatting to read and save tracking scores (#693)
sheridana Apr 1, 2022
a3a1742
Hide predicted instances with hotkey (#694)
roomrys Apr 3, 2022
608c7fd
Talmo/pre v1.2.2 (#696)
talmo Apr 3, 2022
f04d95c
Merge branch 'main' into develop
talmo Apr 3, 2022
1e6f1d7
Merge branch 'main' into develop
talmo Apr 3, 2022
24e4a9a
Add more notebooks to docs (#698)
talmo Apr 4, 2022
64299c4
Merge branch 'main' into develop
talmo Apr 4, 2022
e7b78a5
Add troubleshooting guide
talmo Apr 4, 2022
e25a11e
Datasets and paper link update
talmo Apr 4, 2022
13ba3f6
Add support for new single animal DLC format (#704)
roomrys Apr 14, 2022
487b3dd
Add edges to analysis h5 (#707)
roomrys Apr 15, 2022
6da8f0d
Speed-up labeling suggestions look-up (#709)
roomrys Apr 25, 2022
aa1da06
Add support for AlphaTracker import (#716)
roomrys May 10, 2022
e343b8e
Update links from murthylab to talmolab (#724)
sheridana May 10, 2022
ea1dc0a
SLEAP v1.2.3 (#726)
talmo May 10, 2022
20903cb
Merge branch 'main' into develop
talmo May 10, 2022
f9702b0
Test CI
talmo May 10, 2022
391bc04
Fix Imports in test_format.py (#732)
roomrys May 12, 2022
beed238
Add links to discussion (#748)
roomrys May 17, 2022
279cabb
Update codecov badge token
talmo May 17, 2022
c75fdbf
Add option to predict on all videos (#749)
roomrys May 18, 2022
6340f0d
Contributing Guide, Code of Conduct, and Issues Template (#746)
sheridana May 24, 2022
f907cad
Update bug_report.md
roomrys May 25, 2022
19266b0
Create codecov.yml
roomrys May 27, 2022
8b3bba7
Update codecov.yml
roomrys May 28, 2022
2931262
Update codecov.yml
roomrys May 29, 2022
7efb8fb
Create multiple analysis files for multi-video projects (#768)
roomrys May 31, 2022
67b4b3e
Update tracking docs (#761)
sheridana Jun 3, 2022
e02cee0
Generate suggestions for videos with less frames than samples per vid…
davidasamy Jun 7, 2022
2962d64
Add support for videos that have less frames than the desired (random…
davidasamy Jun 9, 2022
5d71030
Add button to toggle grayscale
roomrys Jun 11, 2022
adcc56e
Revert "Add button to toggle grayscale"
roomrys Jun 11, 2022
7b9d854
Add button to toggle grayscale of current video (#788)
roomrys Jun 13, 2022
e430283
Analysis HDF5 should prefer user-labeled instance over predicted inst…
roomrys Jun 13, 2022
9f85239
Choose video to generate suggestions (#786)
davidasamy Jun 14, 2022
5e27751
Add CLI sleap-render command to render videos (#796)
davidasamy Jun 15, 2022
37f1423
Allow user to set grayscale when replacing videos (mp4/avi only) (#787)
roomrys Jun 24, 2022
663c4d1
Support grayscale for SingleImageVideo backend (#789)
roomrys Jun 27, 2022
7af4132
Fix h5py dependency (#815)
roomrys Jun 28, 2022
085da16
Remove low-scoring predictions before merging inference results (#817)
roomrys Jun 28, 2022
51de3b9
SLEAP v1.2.4
roomrys Jun 28, 2022
12b5c2f
SLEAP v1.2.4
roomrys Jun 28, 2022
5be75b1
Merge branch 'develop' of https://github.com/talmolab/sleap into develop
roomrys Jun 28, 2022
a25e093
Manual merge of main into develop
roomrys Jun 28, 2022
8fbaa30
Remove cli.rst (back from the dead)
roomrys Jun 28, 2022
a03b05c
Manual merge main into develop
roomrys Jun 29, 2022
69c1ef0
Add read/write adaptor for ndx-pose (#835)
roomrys Jul 15, 2022
5bf218e
Change existing skeleton to match skeleton loaded via "Load Skeleton"…
roomrys Jul 15, 2022
254759d
Fix Save As bug (#845)
roomrys Jul 19, 2022
fefd2b5
Update installation and labeling docs and no cuda yml (#847)
roomrys Jul 19, 2022
d522f1d
Recalculate crop size if user-specified crop size indivisible by max …
roomrys Jul 19, 2022
7e833a2
Expose attributes of NWBFile and create Labels API for exporting to N…
roomrys Jul 23, 2022
ee45c4d
SLEAP v1.2.5 (develop) (#856)
roomrys Jul 24, 2022
e2ec3b3
Merge branch 'main' of https://github.com/talmolab/sleap into develop
roomrys Jul 24, 2022
5447a6f
Fix NWB conda packaging (#860)
talmo Jul 26, 2022
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2 changes: 2 additions & 0 deletions .conda/bld.bat
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,8 @@ pip install pykalman==0.9.5
pip install segmentation-models==1.0.1
pip install rich==10.16.1
pip install certifi==2021.10.8
pip install pynwb
pip install ndx-pose

rem # Use and update environment.yml call to install pip dependencies. This is slick.
rem # While environment.yml contains the non pip dependencies, the only thing left
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2 changes: 2 additions & 0 deletions .conda/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,8 @@ pip install pykalman==0.9.5
pip install segmentation-models==1.0.1
pip install rich==10.16.1
pip install certifi==2021.10.8
pip install pynwb
pip install ndx-pose

pip install setuptools-scm

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4 changes: 2 additions & 2 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -28,15 +28,15 @@
copyright = f"2019–{date.today().year}, Talmo Lab"

# The short X.Y version
version = "1.2.5"
version = "1.2.6"

# Get the sleap version
# with open("../sleap/version.py") as f:
# version_file = f.read()
# version = re.search("\d.+(?=['\"])", version_file).group(0)

# Release should be the full branch name
release = "v1.2.5"
release = "v1.2.6"

html_title = f"SLEAP ({release})"
html_short_title = "SLEAP"
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4 changes: 2 additions & 2 deletions docs/installation.md
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ On Windows, our personal preference is to use alternative terminal apps like [Cm
### `conda` package

```bash
conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.5
conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.6
```

**This is the recommended installation method**. Works on **Windows** and **Linux**.
Expand Down Expand Up @@ -113,7 +113,7 @@ conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.5
### `pip` package

```bash
pip install sleap==1.2.5
pip install sleap==1.2.6
```

This works on **any OS** and on **Google Colab**.
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2 changes: 1 addition & 1 deletion sleap/version.py
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
"""


__version__ = "1.2.5"
__version__ = "1.2.6"


def versions():
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0