KeyError issue training single instance using google colab

[mjin1812]

Bug description

For some reason, a "nodes" KeyError pops up whenever I try to run training on colab using a single animal pipeline.

I've been following the online tutorial for training and inference on my own
data. I labelled only ~40 frames to test the ability to train on colab. When try to train using the command !sleap-train single_instance.json colabDemo.slp I get a KeyError. I've attached the full error in a text file.

Expected behaviour

Training

Actual behaviour

KeyError: 'nodes'

Your personal set up

Error was from using the demo colab notebook.

But here is my local computer setup in case it's relevant.
Software versions:
SLEAP: 1.3.0a0
TensorFlow: 2.8.4
Numpy: 1.21.5
Python: 3.7.16
OS: Windows-10-10.0.19041-SP0

Installation was from miniconda

Environment packages

# paste output of `pip freeze` or `conda list` here

Again this is for my local setup. Not sure if it's relevant.

Name Version Build Channel

absl-py 1.4.0 pypi_0 pypi
accessible-pygments 0.0.3 pypi_0 pypi
alabaster 0.7.13 pypi_0 pypi
anyio 3.6.2 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
argon2-cffi 21.3.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
astunparse 1.6.3 pypi_0 pypi
attrs 21.4.0 pypi_0 pypi
babel 2.12.1 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
backports-zoneinfo 0.2.1 pypi_0 pypi
beautifulsoup4 4.11.2 pypi_0 pypi
black 21.6b0 pypi_0 pypi
bleach 6.0.0 pypi_0 pypi
ca-certificates 2023.01.10 haa95532_0
cached-property 1.5.2 py_0
cachetools 5.3.0 pypi_0 pypi
cattrs 1.1.1 pypi_0 pypi
certifi 2021.10.8 pypi_0 pypi
cffi 1.15.1 pypi_0 pypi
cfgv 3.3.1 pypi_0 pypi
charset-normalizer 3.1.0 pypi_0 pypi
click 8.0.4 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
commonmark 0.9.1 pypi_0 pypi
coverage 7.2.1 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
debugpy 1.6.6 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
deprecated 1.2.13 pypi_0 pypi
distlib 0.3.6 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
efficientnet 1.0.0 pypi_0 pypi
entrypoints 0.4 pypi_0 pypi
exceptiongroup 1.1.0 pypi_0 pypi
ffmpeg 4.2.2 he774522_0
filelock 3.9.0 pypi_0 pypi
flatbuffers 23.3.3 pypi_0 pypi
fonttools 4.38.0 pypi_0 pypi
freetype 2.10.4 hd328e21_0
gast 0.5.3 pypi_0 pypi
geos 3.8.0 h33f27b4_0
gitdb 4.0.10 pypi_0 pypi
gitpython 3.1.31 pypi_0 pypi
google-auth 2.16.2 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
greenlet 2.0.2 pypi_0 pypi
grpcio 1.51.3 pypi_0 pypi
h5py 3.1.0 nompi_py37h19fda09_100 conda-forge
hdf5 1.10.6 h1756f20_1
hdmf 3.5.1 pypi_0 pypi
icc_rt 2022.1.0 h6049295_2
icu 69.1 h0e60522_0 conda-forge
identify 2.5.19 pypi_0 pypi
idna 3.4 pypi_0 pypi
image-classifiers 1.0.0 pypi_0 pypi
imageio 2.15.0 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
imgaug 0.4.0 pypi_0 pypi
imgstore 0.2.9 pypi_0 pypi
importlib-metadata 6.0.0 pypi_0 pypi
importlib-resources 5.12.0 pypi_0 pypi
iniconfig 2.0.0 pypi_0 pypi
intel-openmp 2023.0.0 h59b6b97_25923
ipykernel 6.16.2 pypi_0 pypi
ipython 7.34.0 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
ipywidgets 7.7.3 pypi_0 pypi
jaraco-classes 3.2.3 pypi_0 pypi
jbig 2.1 h8d14728_2003 conda-forge
jedi 0.17.2 pypi_0 pypi
jinja2 3.1.2 pypi_0 pypi
joblib 1.2.0 pypi_0 pypi
jpeg 9e h2bbff1b_1
jsmin 3.0.1 pypi_0 pypi
json5 0.9.11 pypi_0 pypi
jsonpickle 1.2 pypi_0 pypi
jsonschema 4.17.3 pypi_0 pypi
jupyter-cache 0.4.3 pypi_0 pypi
jupyter-client 7.4.9 pypi_0 pypi
jupyter-core 4.12.0 pypi_0 pypi
jupyter-server 1.13.5 pypi_0 pypi
jupyter-server-mathjax 0.2.6 pypi_0 pypi
jupyter-sphinx 0.3.2 pypi_0 pypi
jupyterlab 3.3.4 pypi_0 pypi
jupyterlab-pygments 0.2.2 pypi_0 pypi
jupyterlab-server 2.16.3 pypi_0 pypi
jupyterlab-widgets 1.1.2 pypi_0 pypi
keras 2.8.0 pypi_0 pypi
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pypi_0 pypi
keyring 23.13.1 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
lcms2 2.12 h83e58a3_0
lerc 3.0 hd77b12b_0
libblas 3.8.0 20_mkl conda-forge
libcblas 3.8.0 20_mkl conda-forge
libclang 15.0.6.1 pypi_0 pypi
libdeflate 1.8 h2bbff1b_5
libiconv 1.16 h2bbff1b_2
liblapack 3.8.0 20_mkl conda-forge
libpng 1.6.37 h2a8f88b_0
libtiff 4.3.0 hd413186_2 conda-forge
libxml2 2.9.14 h0ad7f3c_0
libxslt 1.1.35 h2bbff1b_0
libzlib 1.2.12 h8ffe710_2 conda-forge
linkify-it-py 2.0.0 pypi_0 pypi
livereload 2.6.3 pypi_0 pypi
lxml 4.9.2 pypi_0 pypi
lz4-c 1.9.4 h2bbff1b_0
m2w64-gcc-libgfortran 5.3.0 6
m2w64-gcc-libs 5.3.0 7
m2w64-gcc-libs-core 5.3.0 7
m2w64-gmp 6.1.0 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
markdown 3.4.1 pypi_0 pypi
markdown-it-py 1.1.0 pypi_0 pypi
markupsafe 2.1.2 pypi_0 pypi
matplotlib 3.5.3 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
mdit-py-plugins 0.2.8 pypi_0 pypi
mistune 0.8.4 pypi_0 pypi
mkl 2020.2 256
more-itertools 9.1.0 pypi_0 pypi
msys2-conda-epoch 20160418 1
mypy-extensions 1.0.0 pypi_0 pypi
myst-nb 0.13.2 pypi_0 pypi
myst-parser 0.15.2 pypi_0 pypi
nbclassic 0.5.3 pypi_0 pypi
nbclient 0.5.13 pypi_0 pypi
nbconvert 6.5.4 pypi_0 pypi
nbdime 3.1.1 pypi_0 pypi
nbformat 5.1.3 pypi_0 pypi
ndx-pose 0.1.1 pypi_0 pypi
nest-asyncio 1.5.6 pypi_0 pypi
networkx 2.6.3 pypi_0 pypi
nixio 1.5.3 pypi_0 pypi
nodeenv 1.7.0 pypi_0 pypi
notebook 6.5.3 pypi_0 pypi
notebook-shim 0.2.2 pypi_0 pypi
numpy 1.21.5 py37h2830a78_1 conda-forge
oauthlib 3.2.2 pypi_0 pypi
olefile 0.46 py37_0
opencv-python 4.5.5.64 pypi_0 pypi
openjpeg 2.4.0 h4fc8c34_0
openssl 1.1.1t h2bbff1b_0
opt-einsum 3.3.0 pypi_0 pypi
packaging 22.0 py37haa95532_0
pandas 1.3.5 py37h9386db6_0 conda-forge
pandocfilters 1.5.0 pypi_0 pypi
parso 0.7.1 pypi_0 pypi
pathspec 0.11.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 8.4.0 py37hd7d9ad0_0 conda-forge
pip 23.0.1 pyhd8ed1ab_0 conda-forge
pkginfo 1.9.6 pypi_0 pypi
pkgutil-resolve-name 1.3.10 pypi_0 pypi
platformdirs 3.1.0 pypi_0 pypi
pluggy 1.0.0 pypi_0 pypi
pre-commit 2.21.0 pypi_0 pypi
prometheus-client 0.16.0 pypi_0 pypi
prompt-toolkit 3.0.38 pypi_0 pypi
protobuf 3.19.6 pypi_0 pypi
psutil 5.9.4 pypi_0 pypi
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pycparser 2.21 pypi_0 pypi
pydata-sphinx-theme 0.13.1 pypi_0 pypi
pygithub 1.58.0 pypi_0 pypi
pygments 2.14.0 pypi_0 pypi
pyjwt 2.6.0 pypi_0 pypi
pykalman 0.9.5 pypi_0 pypi
pynacl 1.5.0 pypi_0 pypi
pynwb 2.3.1 pypi_0 pypi
pyparsing 3.0.9 pypi_0 pypi
pyreadline 2.1 py37_1
pyrsistent 0.19.3 pypi_0 pypi
pyside2 5.14.1 pypi_0 pypi
pytest 7.2.2 pypi_0 pypi
pytest-cov 3.0.0 pypi_0 pypi
pytest-qt 4.2.0 pypi_0 pypi
pytest-xvfb 2.0.0 pypi_0 pypi
python 3.7.16 h6244533_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-rapidjson 1.9 pypi_0 pypi
python_abi 3.7 2_cp37m conda-forge
pytz 2022.7 py37haa95532_0
pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi
pyvirtualdisplay 3.0 pypi_0 pypi
pywavelets 1.3.0 pypi_0 pypi
pywin32 305 pypi_0 pypi
pywin32-ctypes 0.2.0 pypi_0 pypi
pywinpty 1.1.6 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 25.0.0 pypi_0 pypi
qimage2ndarray 1.10.0 pypi_0 pypi
qt 5.12.9 h556501e_6 conda-forge
qtpy 2.2.0 py37haa95532_0
readme-renderer 37.3 pypi_0 pypi
regex 2022.10.31 pypi_0 pypi
requests 2.28.2 pypi_0 pypi
requests-oauthlib 1.3.1 pypi_0 pypi
requests-toolbelt 0.10.1 pypi_0 pypi
rfc3986 2.0.0 pypi_0 pypi
rich 10.16.1 pypi_0 pypi
rsa 4.9 pypi_0 pypi
ruamel-yaml 0.17.21 pypi_0 pypi
ruamel-yaml-clib 0.2.7 pypi_0 pypi
scikit-image 0.19.3 pypi_0 pypi
scikit-learn 1.0.2 pypi_0 pypi
scikit-video 1.1.11 pypi_0 pypi
scipy 1.7.3 py37hb6553fb_0 conda-forge
seaborn 0.12.2 pypi_0 pypi
segmentation-models 1.0.1 pypi_0 pypi
send2trash 1.8.0 pypi_0 pypi
setuptools 58.0.4 py37haa95532_0
shapely 1.7.1 py37h06580b3_0
shiboken2 5.14.1 pypi_0 pypi
six 1.16.0 pyhd3eb1b0_1
sleap 1.3.0a0 dev_0
smmap 5.0.0 pypi_0 pypi
sniffio 1.3.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
soupsieve 2.4 pypi_0 pypi
sphinx 4.5.0 pypi_0 pypi
sphinx-autobuild 2021.3.14 pypi_0 pypi
sphinx-book-theme 1.0.0 pypi_0 pypi
sphinx-copybutton 0.5.1 pypi_0 pypi
sphinx-togglebutton 0.3.2 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlalchemy 1.4.46 pypi_0 pypi
sqlite 3.40.1 h2bbff1b_0
tensorboard 2.8.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorflow 2.8.4 pypi_0 pypi
tensorflow-estimator 2.8.0 pypi_0 pypi
tensorflow-hub 0.12.0 pypi_0 pypi
tensorflow-io-gcs-filesystem 0.31.0 pypi_0 pypi
termcolor 2.2.0 pypi_0 pypi
terminado 0.17.1 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tifffile 2021.11.2 pypi_0 pypi
tinycss2 1.2.1 pypi_0 pypi
tk 8.6.12 h2bbff1b_0
toml 0.10.2 pypi_0 pypi
tomli 2.0.1 pypi_0 pypi
tornado 6.2 pypi_0 pypi
tqdm 4.65.0 pypi_0 pypi
traitlets 5.9.0 pypi_0 pypi
twine 3.3.0 pypi_0 pypi
typed-ast 1.5.4 pypi_0 pypi
typing-extensions 4.5.0 pypi_0 pypi
tzdata 2022.7 pypi_0 pypi
tzlocal 4.2 pypi_0 pypi
uc-micro-py 1.0.1 pypi_0 pypi
urllib3 1.26.14 pypi_0 pypi
vc 14.2 h21ff451_1
virtualenv 20.20.0 pypi_0 pypi
vs2015_runtime 14.27.29016 h5e58377_2
wcwidth 0.2.6 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.5.1 pypi_0 pypi
werkzeug 2.2.3 pypi_0 pypi
wheel 0.38.4 py37haa95532_0
widgetsnbextension 3.6.2 pypi_0 pypi
wincertstore 0.2 py37haa95532_2
wrapt 1.15.0 pypi_0 pypi
xz 5.2.10 h8cc25b3_1
zipp 3.15.0 pypi_0 pypi
zlib 1.2.12 h8cc25b3_2
zstd 1.5.2 h19a0ad4_0

Logs

# paste relevant logs here, if any

Screenshots

How to reproduce

1. Following the example colab notebook.
2. Running on the demo labelled .slp file and training package I generated (should be linked)

SleapDemoColabError.txt

[aereimer]

Maybe related with this, I am trying the version 1.3.0a0 and after opening (and saving) a slp file with the new version, I am unable to open it with previous versions (1.2.9, 1.2.6, 1.2.2). It still opens with 1.3.0a0, but with other versions I get the KeyError: 'nodes' too.

[mjin1812]

The previous comment helped me solve this issue! I checked the version of sleap automatically downloaded on colab and it was 1.2.8. I forced an installation of the same version as my local computer with `!pip install -v 'sleap==1.3.0a0' and now I can train!

[roomrys]

Related issue: #1217
Related PR: #1222