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Update TensorFlow backend for Python 3.12 compatibility (Keras 2 via `tf-keras`) by maximpavliv · Pull Request #3087 · DeepLabCut/DeepLabCut · GitHub
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Update TensorFlow backend for Python 3.12 compatibility (Keras 2 via tf-keras) #3087

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Merged
AlexEMG merged 27 commits into from
Oct 1, 2025
Merged

Update TensorFlow backend for Python 3.12 compatibility (Keras 2 via tf-keras) #3087

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aa1cafe
Relax pyside6
maximpavliv Sep 4, 2025
ae989b1
Relax tensorflow non-Windows
maximpavliv Sep 4, 2025
a7a8a86
Add higher python releases to CI/CD
maximpavliv Sep 4, 2025
05cf09a
Relax tensorflow in CI/CD
maximpavliv Sep 4, 2025
17c4e13
Relax pytables in CI/CD
maximpavliv Sep 4, 2025
0f7c454
Remove pytables from CI/CD installation
maximpavliv Sep 4, 2025
79e54a9
Install tf-keras for tensorflow>=2.16 support
maximpavliv Sep 4, 2025
40d159a
Add TF_USE_LEGACY_KERAS env var to CI/CD
maximpavliv Sep 6, 2025
2a1de93
TMP Add tables to requirements?
maximpavliv Sep 6, 2025
bf51dbc
Add _tf_legacy.py
maximpavliv Sep 8, 2025
57ca3f6
TMP try install specific wrapt version?
maximpavliv Sep 8, 2025
b4aca6e
Set WRAPT_DISABLE_EXTENSIONS env var
maximpavliv Sep 8, 2025
74b48a0
Exclude Windows & python=3.13 from CI/CD
maximpavliv Sep 8, 2025
01c3008
TMP tf macos pin
maximpavliv Sep 8, 2025
d597152
Remove python 3.12 from cicd
maximpavliv Sep 8, 2025
d08878e
Try pin tensorflow-macos==2.15.0
maximpavliv Sep 8, 2025
e6655f7
TMP try unpin tensorflow-macos and add tf-keras
maximpavliv Sep 8, 2025
a6fd9a9
Replace macos-14 by macos-latest
maximpavliv Sep 9, 2025
8b8ec8c
Set dataloader_workers to 0
maximpavliv Sep 9, 2025
f1ccf01
Add tables to setup.py
maximpavliv Sep 9, 2025
db39c94
Relax tensorflow-macos
maximpavliv Sep 9, 2025
fb8bd4e
Update 3mice colab installation
maximpavliv Sep 9, 2025
23d4bc3
Update modelzoo reid colab installations
maximpavliv Sep 9, 2025
6fe5238
Merge branch 'main' into maxim/relax_dependencies
maximpavliv Sep 12, 2025
4cc497d
Merge branch 'main' into maxim/relax_dependencies
maximpavliv Sep 16, 2025
1f3806e
Merge branch 'main' into maxim/relax_dependencies
maximpavliv Sep 22, 2025
8c8dbf6
Merge branch 'main' into maxim/relax_dependencies
maximpavliv Oct 1, 2025
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Update modelzoo reid colab installations
  • Loading branch information
@maximpavliv
maximpavliv committed Sep 9, 2025
commit 23d4bc3e99d41a11d2ff3cc4bb031ae6ff69f665
38 changes: 2 additions & 36 deletions examples/COLAB/COLAB_DLC_ModelZoo.ipynb
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Expand Up @@ -45,30 +45,7 @@
"\n",
"## **Let's get going: install DeepLabCut into COLAB:**\n",
"\n",
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n"
]
},
{
Expand All @@ -78,18 +55,7 @@
"outputs": [],
"source": [
"# Install the latest version of DeepLabCut\n",
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git#egg=deeplabcut[modelzoo]\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
"!pip install --pre \"deeplabcut[tf,modelzoo]\""
]
},
{
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108 changes: 3 additions & 105 deletions examples/COLAB/COLAB_transformer_reID.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -32,91 +32,18 @@
"- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
"\n",
"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
]
},
{
"cell_type": "markdown",
"source": [
"‼️ **Attention: this demo is for maDLC, which is version 2.2**\n",
"- the installation is very slow on Colab due to the several steps needed to use older versions of `torch` and `dlc`."
"‼️ **Attention: this demo is for maDLC, which is version 2.2**\n"
],
"metadata": {
"id": "xOe2hvy85EVP"
}
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "6_Q4_GKM45Oe"
},
"outputs": [],
"source": [
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
]
},
{
"cell_type": "code",
"source": [
"import torch\n",
"print(torch.cuda.is_available())\n",
"print(torch.cuda.get_device_name(0))\n",
"!nvcc --version # sometimes not available"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "3HLeBRGL9jYJ",
"outputId": "b8e49307-f51c-4f12-8dec-d2c2929928e2"
},
"execution_count": 3,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"True\n",
"NVIDIA A100-SXM4-40GB\n",
"nvcc: NVIDIA (R) Cuda compiler driver\n",
"Copyright (c) 2005-2024 NVIDIA Corporation\n",
"Built on Thu_Jun__6_02:18:23_PDT_2024\n",
"Cuda compilation tools, release 12.5, V12.5.82\n",
"Build cuda_12.5.r12.5/compiler.34385749_0\n"
]
}
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "Vz3B6Zyf45Od"
},
"outputs": [],
"source": [
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "UUpac75T45Of"
},
"outputs": [],
"source": [
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions,\n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -126,15 +53,13 @@
"outputs": [],
"source": [
"# Install DLC version 2.2-2.3 (pre DLC3):\n",
"!pip install deeplabcut==2.3.11"
"!pip install \"deeplabcut[tf]\""
]
},
{
"cell_type": "code",
"source": [
"import tensorflow\n",
"import deeplabcut\n",
"import torch\n",
"import os"
],
"metadata": {
Expand All @@ -143,33 +68,6 @@
"execution_count": 3,
"outputs": []
},
{
"cell_type": "code",
"source": [
"print(\"DLC version: \", deeplabcut.__version__)\n",
"print(\"torch version: \",torch.__version__)\n",
"print(\"tensorflow version: \",tensorflow.__version__)\n"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "wRojzQO98X2H",
"outputId": "fad889d6-15da-4888-8138-283f1f13cf99"
},
"execution_count": 4,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"DLC version: 2.3.11\n",
"torch version: 2.3.1+cu118\n",
"tensorflow version: 2.12.1\n"
]
}
]
},
{
"cell_type": "markdown",
"metadata": {
Expand Down