Trouble installing sleap

[GabiGreggo]

# Bug description

I've installed sleap in new environment with GPU support using: conda create --name sleap pip python=3.7.12 cudatoolkit=11.3 cudnn=8.2
These are the environments I have:

conda environments:

base C:\ProgramData\Anaconda3
DEEPLABCUT C:\ProgramData\Anaconda3\envs\DEEPLABCUT
DLC C:\ProgramData\Anaconda3\envs\DLC
minian C:\ProgramData\Anaconda3\envs\minian
napari-env C:\ProgramData\Anaconda3\envs\napari-env
sleap * C:\ProgramData\Anaconda3\envs\sleap
caiman C:\Users\Andrew.conda\envs\caiman
caiman_new C:\Users\Andrew.conda\envs\caiman_new
C:\Users\Andrew\miniforge3

And these are the packages in sleap:

packages in environment at C:\ProgramData\Anaconda3\envs\sleap:

Name Version Build Channel

absl-py 0.15.0 pypi_0 pypi
astunparse 1.6.3 pypi_0 pypi
attrs 21.4.0 pypi_0 pypi
backports-zoneinfo 0.2.1 pypi_0 pypi
ca-certificates 2024.3.11 haa95532_0
cachetools 4.2.4 pypi_0 pypi
cattrs 1.1.1 pypi_0 pypi
certifi 2022.12.7 py37haa95532_0
charset-normalizer 3.3.2 pypi_0 pypi
clang 5.0 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
commonmark 0.9.1 pypi_0 pypi
cudatoolkit 11.3.1 h59b6b97_2
cudnn 8.2.1 cuda11.3_0
efficientnet 1.0.0 pypi_0 pypi
flatbuffers 1.12 pypi_0 pypi
fonttools 4.38.0 pypi_0 pypi
gast 0.4.0 pypi_0 pypi
google-auth 1.35.0 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
grpcio 1.62.2 pypi_0 pypi
h5py 3.1.0 pypi_0 pypi
hdmf 3.6.1 pypi_0 pypi
idna 3.7 pypi_0 pypi
image-classifiers 1.0.0 pypi_0 pypi
imgstore 0.2.9 pypi_0 pypi
importlib-metadata 4.2.0 pypi_0 pypi
importlib-resources 5.12.0 pypi_0 pypi
jsmin 3.0.1 pypi_0 pypi
jsonpickle 1.2 pypi_0 pypi
jsonschema 4.17.3 pypi_0 pypi
keras 2.6.0 pypi_0 pypi
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pypi_0 pypi
libclang 18.1.1 pypi_0 pypi
markdown 3.3.4 pypi_0 pypi
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.5.3 pypi_0 pypi
ndx-pose 0.1.1 pypi_0 pypi
nixio 1.5.3 pypi_0 pypi
numpy 1.19.5 pypi_0 pypi
oauthlib 3.2.2 pypi_0 pypi
opencv-python 4.5.5.64 pypi_0 pypi
openssl 1.1.1w h2bbff1b_0
opt-einsum 3.3.0 pypi_0 pypi
packaging 24.0 pypi_0 pypi
pillow 8.4.0 pypi_0 pypi
pip 22.3.1 py37haa95532_0
pkgutil-resolve-name 1.3.10 pypi_0 pypi
protobuf 3.19.6 pypi_0 pypi
pyasn1 0.5.1 pypi_0 pypi
pyasn1-modules 0.3.0 pypi_0 pypi
pygments 2.17.2 pypi_0 pypi
pykalman 0.9.5 pypi_0 pypi
pynwb 2.3.3 pypi_0 pypi
pyparsing 3.1.2 pypi_0 pypi
pyrsistent 0.19.3 pypi_0 pypi
pyside2 5.14.1 pypi_0 pypi
python 3.7.16 h6244533_0
python-dateutil 2.9.0.post0 pypi_0 pypi
python-rapidjson 1.10 pypi_0 pypi
pyzmq 26.0.3 pypi_0 pypi
qimage2ndarray 1.10.0 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
requests 2.31.0 pypi_0 pypi
requests-oauthlib 2.0.0 pypi_0 pypi
rich 10.16.1 pypi_0 pypi
rsa 4.9 pypi_0 pypi
scikit-learn 1.0.2 pypi_0 pypi
scikit-video 1.1.11 pypi_0 pypi
seaborn 0.12.2 pypi_0 pypi
segmentation-models 1.0.1 pypi_0 pypi
setuptools 65.6.3 py37haa95532_0
shiboken2 5.14.1 pypi_0 pypi
sleap 1.3.3 pypi_0 pypi
sqlite 3.45.3 h2bbff1b_0
tensorboard 2.6.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorflow 2.6.3 pypi_0 pypi
tensorflow-estimator 2.6.0 pypi_0 pypi
tensorflow-hub 0.14.0 pypi_0 pypi
tensorflow-io-gcs-filesystem 0.31.0 pypi_0 pypi
typing-extensions 3.10.0.2 pypi_0 pypi
tzdata 2024.1 pypi_0 pypi
tzlocal 5.1 pypi_0 pypi
urllib3 1.26.19 pypi_0 pypi
vc 14.2 h2eaa2aa_4
vs2015_runtime 14.29.30133 h43f2093_4
werkzeug 2.2.3 pypi_0 pypi
wheel 0.38.4 py37haa95532_0
wincertstore 0.2 py37haa95532_2
wrapt 1.12.1 pypi_0 pypi
zipp 3.15.0 pypi_0 pypi

I was trying to open the interface after installing and it wasn't working and I originally had TensorFlow 2.7+ so I tried downgrading the TensorFlow 2.6 but this didn't fix the issue...

When I try : sleap-label...

Expected behaviour: see the SLEAP labeling interface pop up within a few moments, but instead I get this:

Actual behaviour:

(sleap) C:\Users\Andrew>sleap-label
Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\envs\sleap\lib\runpy.py", line 193, in run_module_as_main
"main", mod_spec)
File "C:\ProgramData\Anaconda3\envs\sleap\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\ProgramData\Anaconda3\envs\sleap\Scripts\sleap-label.exe_main.py", line 4, in
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap_init.py", line 14, in
import sleap.nn
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn_init_.py", line 1, in
import sleap.nn.architectures
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\architectures_init_.py", line 4, in
from sleap.nn.architectures import resnet
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\architectures\resnet.py", line 56, in
) -> Tuple[tf.keras.Model, List[IntermediateFeature]]:
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\tensorflow\python\util\lazy_loader.py", line 62, in getattr
module = self._load()
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\tensorflow\python\util\lazy_loader.py", line 45, in load
module = importlib.import_module(self.name)
File "C:\ProgramData\Anaconda3\envs\sleap\lib\importlib_init.py", line 127, in import_module
return bootstrap.gcd_import(name[level:], package, level)
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras_init.py", line 25, in
from keras import models
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\models.py", line 20, in
from keras import metrics as metrics_module
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\metrics.py", line 27, in
from keras import activations
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\activations.py", line 20, in
from keras.layers import advanced_activations
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\layers_init.py", line 24, in
from keras.engine.input_layer import Input
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\engine\input_layer.py", line 21, in
from keras.engine import base_layer
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\engine\base_layer.py", line 41, in
from keras.mixed_precision import loss_scale_optimizer
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\mixed_precision\loss_scale_optimizer.py", line 1180, in
mixed_precision._register_wrapper_optimizer_cls(optimizer_v2.OptimizerV2,
AttributeError: module 'tensorflow.python.training.experimental.mixed_precision' has no attribute '_register_wrapper_optimizer_cls'

I get essentially the same error when I try
python -c "import sleap; sleap.system_summary()"
python -c "import sleap; sleap.versions()"
sleap-diagnostic

Your personal set up

• OS:

• Version(s):

• SLEAP installation method (listed here):
  • Conda from package
  • Conda from source
  • pip package
  • Apple Silicon Macs

Environment packages

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

Logs

(sleap) C:\Users\Andrew>sleap-diagnostic
Traceback (most recent call last):
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\envs\sleap\Scripts\sleap-diagnostic.exe\__main__.py", line 4, in <module>
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\__init__.py", line 14, in <module>
    import sleap.nn
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\__init__.py", line 1, in <module>
    import sleap.nn.architectures
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\architectures\__init__.py", line 4, in <module>
    from sleap.nn.architectures import resnet
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\architectures\resnet.py", line 56, in <module>
    ) -> Tuple[tf.keras.Model, List[IntermediateFeature]]:
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\tensorflow\python\util\lazy_loader.py", line 62, in __getattr__
    module = self._load()
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\tensorflow\python\util\lazy_loader.py", line 45, in _load
    module = importlib.import_module(self.__name__)
  File "C:\ProgramData\Anaconda3\envs\sleap\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\__init__.py", line 25, in <module>
    from keras import models
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\models.py", line 20, in <module>
    from keras import metrics as metrics_module
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\metrics.py", line 27, in <module>
    from keras import activations
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\activations.py", line 20, in <module>
    from keras.layers import advanced_activations
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\layers\__init__.py", line 24, in <module>
    from keras.engine.input_layer import Input
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\engine\input_layer.py", line 21, in <module>
    from keras.engine import base_layer
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\engine\base_layer.py", line 41, in <module>
    from keras.mixed_precision import loss_scale_optimizer
  File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\mixed_precision\loss_scale_optimizer.py", line 1180, in <module>
    mixed_precision._register_wrapper_optimizer_cls(optimizer_v2.OptimizerV2,
AttributeError: module 'tensorflow.python.training.experimental.mixed_precision' has no attribute '_register_wrapper_optimizer_cls'

Screenshots

How to reproduce

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

[talmo]

Hi @GabiGreggo,

Apologies for the delay. Have you tried the conda installation command from the Installation docs?

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

Cheers,

Talmo

[GabiGreggo]

Hi Talmo,

Thanks for replying!
Yes - I tried this command.
However, I already had Anaconda on your computer, so I set the solver to libmamba in the base environment using this:

conda update -n base conda
conda install -n base conda-libmamba-solver
conda config --set solver libmamba

And then instead of putting the command in as you wrote above, I replaced all subsequent mamba commands in the docs with conda... could this be the issue?

So, I used: conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.3

Everything seemed to install fine I just can't seem to open the interface and I keep getting errors that I think are to do with dependencies. I have tried uninstalling and reinstalling sleap, tensorflow, python, pretty much everything in versions that should be compatible. You can see all the packages that are in my sleap environment in my post above...

Any additional advice?

[talmo]

I see -- do you mind sharing the error that you get when opening the GUI after you first install it (with conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.3)?

[GabiGreggo]

No worries!

I don't get any errors when installing until I try opening the GUI with the command sleap-label

The error I get is:

(sleap) C:\Users\Andrew>sleap-label
Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\envs\sleap\lib\runpy.py", line 193, in run_module_as_main
"main", mod_spec)
File "C:\ProgramData\Anaconda3\envs\sleap\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\ProgramData\Anaconda3\envs\sleap\Scripts\sleap-label.exe_main.py", line 4, in
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap_init.py", line 14, in
import sleap.nn
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn_init_.py", line 1, in
import sleap.nn.architectures
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\architectures_init_.py", line 4, in
from sleap.nn.architectures import resnet
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\sleap\nn\architectures\resnet.py", line 56, in
) -> Tuple[tf.keras.Model, List[IntermediateFeature]]:
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\tensorflow\python\util\lazy_loader.py", line 62, in getattr
module = self._load()
File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\tensorflow\python\util\lazy_loader.py", line 45, in load
module = importlib.import_module(self.name)
File "C:\ProgramData\Anaconda3\envs\sleap\lib\importlib_init.py", line 127, in import_module
return bootstrap.gcd_import(name[level:], package, level)
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras_init.py", line 25, in
from keras import models
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\models.py", line 20, in
from keras import metrics as metrics_module
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\metrics.py", line 27, in
from keras import activations
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\activations.py", line 20, in
from keras.layers import advanced_activations
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\layers_init.py", line 24, in
from keras.engine.input_layer import Input
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\engine\input_layer.py", line 21, in
from keras.engine import base_layer
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\engine\base_layer.py", line 41, in
from keras.mixed_precision import loss_scale_optimizer
File "C:\Users\Andrew\AppData\Roaming\Python\Python37\site-packages\keras\mixed_precision\loss_scale_optimizer.py", line 1180, in
mixed_precision._register_wrapper_optimizer_cls(optimizer_v2.OptimizerV2,
AttributeError: module 'tensorflow.python.training.experimental.mixed_precision' has no attribute '_register_wrapper_optimizer_cls'