SLEAP in Colab : Dependency incompatibility errors

[ValeriePineauNoel]

I am trying to use Colab to train a model with SLEAP and I have a lot of errors relating dependencies, preventing me from installing sleap correctly in Colab. Is there a simple way to solve this easily?

Install sleap in colab.

I followed the instructions here.

My Colab is in a folder in my GoogleDrive called sleap. Here is a screenshot of what is in my repo.

My first cell in my Colab is this

!pip uninstall -qqq -y opencv-python opencv-contrib-python
!pip install -qqq "sleap[pypi]>=1.3.3"

It returns a lot of dependency incompatibility errors (pasted bellow). I am not able to run anything after this.

     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 28.8/28.8 MB 17.4 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
  Preparing metadata (setup.py) ... done
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 228.9/228.9 kB 13.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.1/50.1 kB 3.3 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 42.4 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 214.3/214.3 kB 14.6 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 26.5/26.5 MB 53.4 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 5.2 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 904.1/904.1 kB 40.7 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.8/16.8 MB 71.7 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.5/60.5 MB 12.9 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 64.8 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 50.9 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 45.7 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 156.1/156.1 MB 6.6 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 832.9/832.9 kB 35.2 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 95.2/95.2 kB 8.5 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.9/13.9 MB 54.4 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 MB 12.2 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 498.1/498.1 MB 3.4 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.3/90.3 kB 6.5 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 144.2/144.2 kB 10.9 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 54.5 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 61.7 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 4.8 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 338.5/338.5 kB 23.6 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 55.6 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.7/50.7 kB 4.1 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.6/42.6 kB 3.8 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 75.8 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.8/5.8 MB 76.1 MB/s eta 0:00:00
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 462.3/462.3 kB 22.6 MB/s eta 0:00:00
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   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 78.2 MB/s eta 0:00:00
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  Building wheel for pykalman (setup.py) ... done
  Building wheel for nixio (setup.py) ... done
  Building wheel for jsmin (setup.py) ... done
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
albucore 0.0.19 requires numpy>=1.24.4, but you have numpy 1.22.4 which is incompatible.
albumentations 1.4.20 requires numpy>=1.24.4, but you have numpy 1.22.4 which is incompatible.
albumentations 1.4.20 requires scipy>=1.10.0, but you have scipy 1.9.0 which is incompatible.
arviz 0.20.0 requires numpy>=1.23.0, but you have numpy 1.22.4 which is incompatible.
astropy 6.1.5 requires numpy>=1.23, but you have numpy 1.22.4 which is incompatible.
bigframes 1.25.0 requires numpy>=1.24.0, but you have numpy 1.22.4 which is incompatible.
bigframes 1.25.0 requires scikit-learn>=1.2.2, but you have scikit-learn 1.0.2 which is incompatible.
chex 0.1.87 requires numpy>=1.24.1, but you have numpy 1.22.4 which is incompatible.
cudf-cu12 24.10.1 requires numpy<3.0a0,>=1.23, but you have numpy 1.22.4 which is incompatible.
fastai 2.7.18 requires pillow>=9.0.0, but you have pillow 8.4.0 which is incompatible.
flax 0.8.5 requires rich>=11.1, but you have rich 10.16.1 which is incompatible.
google-ai-generativelanguage 0.6.10 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-aiplatform 1.71.1 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-bigquery-connection 1.16.1 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-bigquery-storage 2.27.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-bigtable 2.26.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-datastore 2.20.1 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-firestore 2.19.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-functions 1.18.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-iam 2.16.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-language 2.15.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-pubsub 2.26.1 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-resource-manager 1.13.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
google-cloud-translate 3.17.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
googleapis-common-protos 1.65.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0.dev0,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
grpc-google-iam-v1 0.13.1 requires protobuf!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.2, but you have protobuf 3.19.6 which is incompatible.
grpcio-status 1.62.3 requires protobuf>=4.21.6, but you have protobuf 3.19.6 which is incompatible.
ibis-framework 9.2.0 requires numpy<3,>=1.23.2, but you have numpy 1.22.4 which is incompatible.
ibis-framework 9.2.0 requires rich<14,>=12.4.4, but you have rich 10.16.1 which is incompatible.
jax 0.4.33 requires numpy>=1.24, but you have numpy 1.22.4 which is incompatible.
jax 0.4.33 requires scipy>=1.10, but you have scipy 1.9.0 which is incompatible.
jaxlib 0.4.33 requires numpy>=1.24, but you have numpy 1.22.4 which is incompatible.
jaxlib 0.4.33 requires scipy>=1.10, but you have scipy 1.9.0 which is incompatible.
mizani 0.13.0 requires numpy>=1.23.5, but you have numpy 1.22.4 which is incompatible.
mlxtend 0.23.2 requires scikit-learn>=1.3.1, but you have scikit-learn 1.0.2 which is incompatible.
numexpr 2.10.1 requires numpy>=1.23.0, but you have numpy 1.22.4 which is incompatible.
nx-cugraph-cu12 24.10.0 requires numpy<3.0a0,>=1.23, but you have numpy 1.22.4 which is incompatible.
pandas-gbq 0.24.0 requires google-auth-oauthlib>=0.7.0, but you have google-auth-oauthlib 0.4.6 which is incompatible.
pandas-stubs 2.2.2.240909 requires numpy>=1.23.5, but you have numpy 1.22.4 which is incompatible.
plotnine 0.14.1 requires numpy>=1.23.5, but you have numpy 1.22.4 which is incompatible.
pylibraft-cu12 24.10.0 requires numpy<3.0a0,>=1.23, but you have numpy 1.22.4 which is incompatible.
pymc 5.18.0 requires rich>=13.7.1, but you have rich 10.16.1 which is incompatible.
referencing 0.35.1 requires attrs>=22.2.0, but you have attrs 21.4.0 which is incompatible.
rmm-cu12 24.10.0 requires numpy<3.0a0,>=1.23, but you have numpy 1.22.4 which is incompatible.
tensorflow-datasets 4.9.7 requires protobuf>=3.20, but you have protobuf 3.19.6 which is incompatible.
tensorflow-metadata 1.13.1 requires protobuf<5,>=3.20.3, but you have protobuf 3.19.6 which is incompatible.
tf-keras 2.17.0 requires tensorflow<2.18,>=2.17, but you have tensorflow 2.8.4 which is incompatible.
xarray 2024.10.0 requires numpy>=1.24, but you have numpy 1.22.4 which is incompatible.
xarray-einstats 0.8.0 requires numpy>=1.23, but you have numpy 1.22.4 which is incompatible.

• OS:

• Version(s):

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

Environment packages

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