From f9a9579a611ad7df2c0eac126e812bd8cd0f1102 Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter Date: Wed, 22 Apr 2026 10:04:48 +0200 Subject: [PATCH 1/8] update pyproject.toml and uv.lock TF-extras - revise tf extra - add tf-cu11, tf-cu12, tf-latest This brings in line the CI testing with the actual extras provided, simplifies the installation, and allows for targeted installs for different users. --- .github/workflows/python-package.yml | 17 +- pyproject.toml | 71 +- uv.lock | 4922 +++++++++++++++----------- 3 files changed, 2948 insertions(+), 2062 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index f1b01d9a3..fad38dd1b 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -96,23 +96,12 @@ jobs: channel-priority: strict python-version: ${{ matrix.python-version }} - - name: Install TensorFlow - if: runner.os != 'macOS' - shell: bash -el {0} # Important to enable conda env - run: | - pip install --no-cache-dir tensorflow tensorpack==0.11 tf_slim==1.1.0 tf-keras - - - name: Install TensorFlow on macOS - if: runner.os == 'macOS' - shell: bash -el {0} - run: | - pip install --no-cache-dir tensorflow-macos tensorpack==0.11 tf_slim==1.1.0 tf-keras - - name: Install dependencies - shell: bash -el {0} + shell: bash -el {0} # Important to enable conda env run: | python -m pip install --upgrade pip setuptools wheel - pip install --no-cache-dir -e . --group dev + # Must match optional-dependencies [tf] in pyproject.toml (not bare tensorflow) + pip install --no-cache-dir -e ".[tf]" --group dev - name: Install ffmpeg (Linux/macOS) if: runner.os != 'Windows' diff --git a/pyproject.toml b/pyproject.toml index fb72a1b54..d044ede62 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -80,23 +80,55 @@ docs = [ "sphinxcontrib-mermaid", ] fmpose3d = [ "fmpose3d>=0.0.8" ] +# Use only one of [tf, tf-cu11, tf-cu12, tf-latest]. Do not combine extras. tf = [ "protobuf<7", - # !!! TensorFlow is not supported on Windows with Python >= 3.11 - "tensorflow>=2,<=2.10; platform_system=='Windows' and python_version<'3.11'", - "tensorflow>=2,<2.12; platform_system=='Linux' and python_version<'3.11'", - "tensorflow>=2.12; platform_system=='Linux' and python_version>='3.11'", - "tensorflow-io-gcs-filesystem==0.31; platform_system=='Windows' and python_version<'3.11'", - "tensorflow-io-gcs-filesystem>0.31; platform_system!='Windows'", - "tensorflow-macos>=2,<2.12; platform_system=='Darwin' and python_version<'3.11'", - "tensorflow-macos>=2.12; platform_system=='Darwin' and python_version>='3.11'", + "tensorflow>=2.12,<2.16; python_version<'3.12'", + "tensorflow>=2.16.1,<2.18; python_version>='3.12'", + "tensorflow-io-gcs-filesystem==0.31; platform_system=='Windows' and python_version<'3.12'", + "tensorflow-metal==1.2; platform_system=='Darwin' and python_version<'3.12'", + "tensorflow-metal>=1.2; platform_system=='Darwin' and python_version>='3.12'", "tensorpack>=0.11", - "tf-keras; platform_system!='Windows'", + "tf-keras<2.15; python_version<'3.12'", + "tf-keras>=2.15,<2.18; python_version>='3.12'", "tf-slim>=1.1", ] +tf-cu11 = [ + "protobuf<7", + "tensorflow==2.14", + "tensorflow-io-gcs-filesystem==0.31; platform_system=='Windows'", + "tensorflow-metal==1.2; platform_system=='Darwin'", + "tensorpack==0.11", + "tf-keras==2.14.1", + "tf-slim==1.1", + "torch<2.1", + "torchvision<0.16", +] +tf-cu12 = [ + "protobuf<7", + "tensorflow==2.18", + "tensorflow-metal==1.2; platform_system=='Darwin'", + "tensorpack==0.11", + "tf-keras==2.18", + "tf-slim==1.1", + "torch<2.11", + "torchvision<0.26", +] +tf-latest = [ + "protobuf<7", + "tensorflow>=2.18", + "tensorflow-metal>=1.2; platform_system=='Darwin'", + "tensorpack>=0.11", + "tf-keras", + "tf-slim>=1.1", +] +# apple_mchips is kept for older systems, prefer [tf] in new projects. apple_mchips = [ - "tensorflow-macos; platform_system=='Darwin'", - "tensorflow-metal; platform_system=='Darwin'", + "protobuf<7; platform_system=='Darwin'", + "tensorflow>=2.12,<2.15; platform_system=='Darwin' and python_version<'3.12'", + "tensorflow>=2.15,<2.18; platform_system=='Darwin' and python_version>='3.12'", + "tensorflow-metal==1.2; platform_system=='Darwin' and python_version<'3.12'", + "tensorflow-metal>=1.2; platform_system=='Darwin' and python_version>='3.12'", "tensorpack>=0.11; platform_system=='Darwin'", "tf-keras; platform_system=='Darwin'", "tf-slim>=1.1; platform_system=='Darwin'", @@ -128,6 +160,23 @@ include-package-data = false include = [ "deeplabcut*" ] exclude = [ "tests*", "docs*", "examples*" ] +[tool.uv] +# One of tf / tf-cu12 / tf-latest. apple_mchips matches [tf] on macOS but conflicts with +# [tf-cu12] and [tf-latest] (overlapping tensorflow pins cannot be unified with uv's lock). +conflicts = [ + [ + { extra = "tf" }, + { extra = "tf-cu11" }, + { extra = "tf-cu12" }, + { extra = "tf-latest" }, + { extra = "apple_mchips" }, + ], + [ + { extra = "tf-cu11" }, + { extra = "tf-cu12" }, + { extra = "fmpose3d" }, + ], +] [[tool.uv.dependency-metadata]] name = "openvino-dev" version = "2022.1.0" diff --git a/uv.lock b/uv.lock index 4c11f8619..5925becbc 100644 --- a/uv.lock +++ b/uv.lock @@ -6,27 +6,30 @@ resolution-markers = [ "python_full_version == '3.12.*' and platform_machine == 'x86_64' and sys_platform == 'linux'", "python_full_version == '3.11.*' and platform_machine == 'x86_64' and sys_platform == 'linux'", "python_full_version < '3.11' and platform_machine == 'x86_64' and sys_platform == 'linux'", - "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "python_full_version >= '3.13' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux'", - "python_full_version == '3.12.*' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux'", - "python_full_version == '3.11.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "python_full_version == '3.11.*' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux'", "python_full_version >= '3.13' and sys_platform == 'darwin'", "python_full_version == '3.12.*' and sys_platform == 'darwin'", + "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version >= '3.13' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux')", + "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux')", "python_full_version == '3.11.*' and sys_platform == 'darwin'", - "python_full_version >= '3.13' and sys_platform == 'win32'", - "python_full_version == '3.12.*' and sys_platform == 'win32'", - "python_full_version == '3.11.*' and sys_platform == 'win32'", - "python_full_version < '3.11' and sys_platform == 'win32'", - "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "python_full_version < '3.11' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux'", + "python_full_version == '3.11.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version == '3.11.*' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'linux')", "python_full_version < '3.11' and sys_platform == 'darwin'", - "python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32'", - "python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32'", - "python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32'", - "python_full_version < '3.11' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32'", -] + "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version < '3.11' and platform_machine != 'aarch64' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version < '3.11' and sys_platform != 'darwin' and sys_platform != 'linux')", +] +conflicts = [[ + { package = "deeplabcut", extra = "apple-mchips" }, + { package = "deeplabcut", extra = "tf" }, + { package = "deeplabcut", extra = "tf-cu11" }, + { package = "deeplabcut", extra = "tf-cu12" }, + { package = "deeplabcut", extra = "tf-latest" }, +], [ + { package = "deeplabcut", extra = "fmpose3d" }, + { package = "deeplabcut", extra = "tf-cu11" }, + { package = "deeplabcut", extra = "tf-cu12" }, +]] [manifest] @@ -72,12 +75,12 @@ dependencies = [ { name = "numpy" }, { name = "opencv-python-headless" }, { name = "pyyaml" }, - { name = "scikit-image", version = "0.25.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, - { name = "scikit-image", version = "0.26.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, - { name = "scikit-learn", version = "1.7.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, - { name = "scikit-learn", version = "1.8.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, - { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, - { name = "scipy", version = "1.17.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "scikit-image", version = "0.25.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11' or (extra == 'extra-10-deeplabcut-apple-mchips' and extra == 'extra-10-deeplabcut-tf') or (extra == 'extra-10-deeplabcut-apple-mchips' and extra == 'extra-10-deeplabcut-tf-cu11') or (extra == 'extra-10-deeplabcut-apple-mchips' and extra == 'extra-10-deeplabcut-tf-cu12') or (extra == 'extra-10-deeplabcut-apple-mchips' and extra == 'extra-10-deeplabcut-tf-latest') or (extra == 'extra-10-deeplabcut-fmpose3d' and extra == 'extra-10-deeplabcut-tf-cu11') or (extra == 'extra-10-deeplabcut-fmpose3d' and extra == 'extra-10-deeplabcut-tf-cu12') or (extra == 'extra-10-deeplabcut-tf' and extra == 'extra-10-deeplabcut-tf-cu11') or (extra == 'extra-10-deeplabcut-tf' and extra == 'extra-10-deeplabcut-tf-cu12') or (extra == 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specifier = "==1.2" }, + { name = "tensorflow-metal", marker = "sys_platform == 'darwin' and extra == 'tf-cu11'", specifier = "==1.2" }, + { name = "tensorflow-metal", marker = "sys_platform == 'darwin' and extra == 'tf-cu12'", specifier = "==1.2" }, + { name = "tensorflow-metal", marker = "sys_platform == 'darwin' and extra == 'tf-latest'", specifier = ">=1.2" }, { name = "tensorpack", marker = "sys_platform == 'darwin' and extra == 'apple-mchips'", specifier = ">=0.11" }, { name = "tensorpack", marker = "extra == 'tf'", specifier = ">=0.11" }, + { name = "tensorpack", marker = "extra == 'tf-cu11'", specifier = "==0.11" }, + { name = "tensorpack", marker = "extra == 'tf-cu12'", specifier = "==0.11" }, + { name = "tensorpack", marker = "extra == 'tf-latest'", specifier = ">=0.11" }, + { name = "tf-keras", marker = "python_full_version >= '3.12' and extra == 'tf'", specifier = ">=2.15,<2.18" }, + { name = "tf-keras", marker = "python_full_version < '3.12' and extra == 'tf'", specifier = 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Mathis Labs +# https://github.com/DeepLabCut/DeepLabCut +# +# Please see AUTHORS for contributors. +# https://github.com/DeepLabCut/DeepLabCut/blob/main/AUTHORS +# +# Licensed under GNU Lesser General Public License v3.0 +# + +"""Smoke test for TensorFlow when optional TF extras are installed.""" + +import pytest + +tf = pytest.importorskip( + "tensorflow", + reason="TensorFlow not installed (use a project extra such as .[tf])", +) + + +def test_tensorflow_imports_and_has_matmul() -> None: + assert tf.__version__ + a = tf.constant([[1.0, 2.0]]) + b = tf.constant([[3.0], [4.0]]) + c = tf.matmul(a, b) + + if tf.executing_eagerly(): + result = c.numpy() + else: + with tf.compat.v1.Session() as sess: + result = sess.run(c) + + assert (result == [[11.0]]).all() + + +def test_tf_slim_imports_and_has_conv2d() -> None: + try: + import tf_slim as slim + except ImportError as e: + raise AssertionError("tf_slim is not installed or not importable") from e + + assert slim.conv2d(tf.constant([[[[1.0]]]]), 1, kernel_size=[1, 1], stride=1).shape == (1, 1, 1, 1) + + +def test_tf_keras_imports_and_has_regularizers() -> None: + try: + import tf_keras as keras + except ImportError as e: + raise AssertionError("tf_keras is not installed or not importable") from e + import numpy as np + + assert keras.regularizers.l2(0.01).l2 == np.array(0.01, dtype="float32") From 9a78331bad67630db29b742cf7b1fa2e66d3d720 Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter Date: Wed, 22 Apr 2026 17:40:20 +0200 Subject: [PATCH 3/8] update CI: add "extras" field to matrix_json --- .github/workflows/intelligent-testing.yml | 20 ++++++++++---------- .github/workflows/python-package.yml | 3 +-- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/.github/workflows/intelligent-testing.yml b/.github/workflows/intelligent-testing.yml index e612beaba..b882d2030 100644 --- a/.github/workflows/intelligent-testing.yml +++ b/.github/workflows/intelligent-testing.yml @@ -95,7 +95,7 @@ jobs: with: concurrency_key: ${{ github.event.pull_request.number && format('pr-{0}', github.event.pull_request.number) || '' }} matrix_json: >- - {"include":[{"os":"ubuntu-latest","python-version":"3.12"}]} + {"include":[{"os":"ubuntu-latest","python-version":"3.12", "extras": "[tf]"}]} pytest_paths_json: ${{ needs.intelligent-test-selection.outputs.pytest_paths }} functional_scripts_json: ${{ needs.intelligent-test-selection.outputs.functional_scripts }} full_suite: false @@ -110,15 +110,15 @@ jobs: matrix_json: >- { "include": [ - {"os":"ubuntu-latest","python-version":"3.10"}, - {"os":"ubuntu-latest","python-version":"3.11"}, - {"os":"ubuntu-latest","python-version":"3.12"}, - {"os":"macos-latest","python-version":"3.10"}, - {"os":"macos-latest","python-version":"3.11"}, - {"os":"macos-latest","python-version":"3.12"}, - {"os":"windows-latest","python-version":"3.10"}, - {"os":"windows-latest","python-version":"3.11"}, - {"os":"windows-latest","python-version":"3.12"} + {"os":"ubuntu-latest","python-version":"3.10", "extras": "[tf]"}, + {"os":"ubuntu-latest","python-version":"3.11", "extras": "[tf]"}, + {"os":"ubuntu-latest","python-version":"3.12", "extras": "[tf]"}, + {"os":"macos-latest","python-version":"3.10", "extras": "[tf]"}, + {"os":"macos-latest","python-version":"3.11", "extras": "[tf]"}, + {"os":"macos-latest","python-version":"3.12", "extras": "[tf]"}, + {"os":"windows-latest","python-version":"3.10", "extras": "[tf]"}, + {"os":"windows-latest","python-version":"3.11", "extras": "[tf]"}, + {"os":"windows-latest","python-version":"3.12", "extras": "[tf]"} ] } full_suite: true diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index fad38dd1b..2b45e3ccd 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -100,8 +100,7 @@ jobs: shell: bash -el {0} # Important to enable conda env run: | python -m pip install --upgrade pip setuptools wheel - # Must match optional-dependencies [tf] in pyproject.toml (not bare tensorflow) - pip install --no-cache-dir -e ".[tf]" --group dev + pip install --no-cache-dir -e ".${{ matrix.extras }}" --group dev - name: Install ffmpeg (Linux/macOS) if: runner.os != 'Windows' From 77085d76846abf09744bb7fd988be58ddf858b76 Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter Date: Wed, 22 Apr 2026 17:41:49 +0200 Subject: [PATCH 4/8] update CI: add TF install smoke test (runs on full test lane) --- .github/workflows/intelligent-testing.yml | 41 +++++++++++++++++++++++ .github/workflows/python-package.yml | 2 +- 2 files changed, 42 insertions(+), 1 deletion(-) diff --git a/.github/workflows/intelligent-testing.yml b/.github/workflows/intelligent-testing.yml index b882d2030..18ff9c378 100644 --- a/.github/workflows/intelligent-testing.yml +++ b/.github/workflows/intelligent-testing.yml @@ -122,3 +122,44 @@ jobs: ] } full_suite: true + + tf-install-smoke-test: + name: TensorFlow install smoke test + needs: intelligent-test-selection + if: needs.intelligent-test-selection.outputs.run_full == 'true' + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + python-version: ['3.10', '3.11', '3.12'] + # Run smoke test on the extras that are not tested in the full matrix tests + extras: ["[tf-cu11]", "[tf-cu12]"] + exclude: + - os: windows-latest + python-version: '3.11' + - os: windows-latest + python-version: '3.12' + - extras: "[tf-cu11]" + python-version: '3.12' + + steps: + - name: Checkout code + uses: actions/checkout@v6 + + - name: Set up Python + uses: conda-incubator/setup-miniconda@v3 + with: + channels: conda-forge + channel-priority: strict + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + shell: bash -el {0} + run: | + python -m pip install --upgrade pip setuptools wheel + pip install --no-cache-dir -e ".${{ matrix.extras }}" --group dev + + - name: Run TensorFlow install smoke test + shell: bash -el {0} + run: | + pytest tests/test_tf_install_smoke.py diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2b45e3ccd..d6ea4b92a 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -33,7 +33,7 @@ on: description: "JSON matrix definition" required: true type: string - default: '{"include":[{"os":"ubuntu-latest","python-version":"3.12"}]}' + default: '{"include":[{"os":"ubuntu-latest","python-version":"3.12","extras": ""}]}' pytest_paths_json: description: "JSON array of pytest paths" required: false From b5662c4e05be593877587e30b0125e6fefe5338c Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter Date: Wed, 22 Apr 2026 18:58:30 +0200 Subject: [PATCH 5/8] skip functional tests for tensorflow and windows with python >=3.11 --- .github/workflows/python-package.yml | 28 +++++++++------------------- 1 file changed, 9 insertions(+), 19 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index d6ea4b92a..347915087 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -209,8 +209,6 @@ jobs: env: FULL_SUITE: ${{ inputs.full_suite }} FUNCTIONAL_SCRIPTS_JSON: ${{ inputs.functional_scripts_json }} - RUNNER_OS: ${{ runner.os }} - PYTHON_VERSION: ${{ matrix.python-version }} run: | python - << 'PY' import json @@ -218,10 +216,11 @@ jobs: import subprocess import sys - full_suite = os.environ["FULL_SUITE"].lower() == "true" - runner_os = os.environ["RUNNER_OS"] - python_version = os.environ["PYTHON_VERSION"] + def is_windows_python_3_11_or_greater() -> bool: + """Aligned with pyproject: .[tf*] omits TensorFlow on Windows for Python 3.11+.""" + return sys.platform == "win32" and sys.version_info >= (3, 11) + full_suite = os.environ["FULL_SUITE"].lower() == "true" if full_suite: scripts = [ "examples/testscript_tensorflow_single_animal.py", @@ -235,22 +234,13 @@ jobs: print("No functional scripts selected; skipping functional tests.") raise SystemExit(0) - # Respect current TensorFlow support expectations on Windows - tf_allowed = not (runner_os == "Windows" and python_version in {"3.11", "3.12"}) - - filtered = [] for script in scripts: - is_tf = "tensorflow" in script - if is_tf and not tf_allowed: - print(f"Skipping unsupported TensorFlow script on {runner_os} Python {python_version}: {script}") + if "tensorflow" in script and is_windows_python_3_11_or_greater(): + ver = f"{sys.version_info.major}.{sys.version_info.minor}" + print( + f"Skipping TensorFlow example on Windows {ver} (no TF in .[tf*] for 3.11+): {script}" + ) continue - filtered.append(script) - - if not filtered: - print("No functional scripts remain after platform filtering; skipping.") - raise SystemExit(0) - - for script in filtered: print("Running:", script) rc = subprocess.call([sys.executable, script]) if rc != 0: From 9e7ed5867021cb145053a0f9a61183ecacd6ab12 Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter Date: Thu, 23 Apr 2026 12:14:27 +0200 Subject: [PATCH 6/8] Update tests that rely on TF: add import-or-skip. --- tests/test_dataset_augmentation.py | 5 +++++ tests/test_evaluate.py | 5 +++++ tests/test_pose_multianimal_imgaug.py | 5 +++++ tests/test_predict_multianimal.py | 7 ++++++- 4 files changed, 21 insertions(+), 1 deletion(-) diff --git a/tests/test_dataset_augmentation.py b/tests/test_dataset_augmentation.py index 57d33ca90..9e935c725 100644 --- a/tests/test_dataset_augmentation.py +++ b/tests/test_dataset_augmentation.py @@ -14,6 +14,11 @@ from deeplabcut.pose_estimation_tensorflow.datasets import augmentation +tf = pytest.importorskip( + "tensorflow", + reason="TensorFlow not installed (use a project extra such as .[tf])", +) + @pytest.mark.parametrize( "width, height", diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py index fd4405bb6..69ea13d7c 100644 --- a/tests/test_evaluate.py +++ b/tests/test_evaluate.py @@ -18,6 +18,11 @@ get_snapshots_by_index, ) +tf = pytest.importorskip( + "tensorflow", + reason="TensorFlow not installed (use a project extra such as .[tf])", +) + def make_single_animal_rmse_df( bodyparts, diff --git a/tests/test_pose_multianimal_imgaug.py b/tests/test_pose_multianimal_imgaug.py index 381681f36..d0f1debab 100644 --- a/tests/test_pose_multianimal_imgaug.py +++ b/tests/test_pose_multianimal_imgaug.py @@ -21,6 +21,11 @@ ) from deeplabcut.utils import read_plainconfig +tf = pytest.importorskip( + "tensorflow", + reason="TensorFlow not installed (use a project extra such as .[tf])", +) + def mock_imread(path, mode): return (np.random.rand(400, 400, 3) * 255).astype(np.uint8) diff --git a/tests/test_predict_multianimal.py b/tests/test_predict_multianimal.py index 9f7b342d5..4646a6ca9 100644 --- a/tests/test_predict_multianimal.py +++ b/tests/test_predict_multianimal.py @@ -9,10 +9,15 @@ # Licensed under GNU Lesser General Public License v3.0 # import numpy as np -import tensorflow as tf +import pytest from deeplabcut.pose_estimation_tensorflow.core import predict_multianimal +tf = pytest.importorskip( + "tensorflow", + reason="TensorFlow not installed (use a project extra such as .[tf])", +) + RADIUS = 5 THRESHOLD = 0.01 STRIDE = 8 From f7b4e378171b6c45909a8ccfe029819c2a3a36a0 Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter van Steveninck <32810691+deruyter92@users.noreply.github.com> Date: Thu, 7 May 2026 11:12:33 +0200 Subject: [PATCH 7/8] Update CI: ensure pip with `dev` dependency groups --- .github/workflows/intelligent-testing.yml | 4 +++- .github/workflows/python-package.yml | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/intelligent-testing.yml b/.github/workflows/intelligent-testing.yml index 18ff9c378..ae85292c7 100644 --- a/.github/workflows/intelligent-testing.yml +++ b/.github/workflows/intelligent-testing.yml @@ -156,8 +156,10 @@ jobs: - name: Install dependencies shell: bash -el {0} run: | + python -m ensurepip --upgrade python -m pip install --upgrade pip setuptools wheel - pip install --no-cache-dir -e ".${{ matrix.extras }}" --group dev + python -m pip install dependency-groups + python -m pip install --no-cache-dir -e ".${{ matrix.extras }}" --group dev - name: Run TensorFlow install smoke test shell: bash -el {0} diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 347915087..db2a30a1f 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -99,8 +99,10 @@ jobs: - name: Install dependencies shell: bash -el {0} # Important to enable conda env run: | + python -m ensurepip --upgrade python -m pip install --upgrade pip setuptools wheel - pip install --no-cache-dir -e ".${{ matrix.extras }}" --group dev + python -m pip install dependency-groups + python -m pip install --no-cache-dir -e ".${{ matrix.extras }}" --group dev - name: Install ffmpeg (Linux/macOS) if: runner.os != 'Windows' From a9f3d51451a728898868dbe93d9d4a4bc7a7bb69 Mon Sep 17 00:00:00 2001 From: Jaap de Ruyter van Steveninck <32810691+deruyter92@users.noreply.github.com> Date: Thu, 7 May 2026 10:47:12 +0200 Subject: [PATCH 8/8] CircleCI: disable hugginface xet MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Xet is Hugging Face’s new storage backend designed to replace the aging Git LFS (Large File Storage). While Git LFS treats every file as a single "blob," Xet breaks files into small "chunks." In restricted CI environments (like CircleCI, GCP, or Kaggle), the Xet "chunked" download often stalls. Because Xet opens many simultaneous connections to different data chunks, CI firewalls or NAT gateways sometimes flag this as suspicious activity or simply drop the connections when they hit a certain threshold. --- .circleci/config.yml | 34 +++++++++++++++++++++++++++++----- 1 file changed, 29 insertions(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d224a721d..ed9ee61a3 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -8,43 +8,67 @@ jobs: executor: name: python/default tag: '3.10' # or '3.12' + environment: + # HuggingFace: disable xet and use cache directory + # NOTE @deruyter92 2026-05-07: "xet" opens many simultaneous connections + # to different data chunks. Currently doesn't work well with CircleCI. + # See: https://github.com/huggingface/xet-core/issues/800 + HF_HUB_DISABLE_XET: 1 + HF_HOME: ~/.cache/huggingface + steps: - checkout - # 1) Restore uv cache + # Restore uv cache - restore_cache: name: Restore uv cache keys: - v2-uv-pip-{{ checksum "pyproject.toml" }} - v2-uv-pip- - # 2) Install uv + + # Restore HuggingFace weights cache + - restore_cache: + name: Restore Hugging Face cache + keys: + - hf-weights-v1-{{ checksum "pyproject.toml" }} + - hf-weights-v1- + + # Install uv - run: name: Install uv command: | pip install uv + # Install DeepLabCut runtime deps only - run: name: Install DeepLabCut runtime deps only command: | uv pip install --system -e . - # 3) (Optional) Trim the cache for CI so uploads stay small and fast + # (Optional) Trim the cache for CI so uploads stay small and fast - run: name: Prune uv cache for CI command: uv cache prune --ci || true - # 4) Save the cache for next runs + # Save the uv cache for next runs - save_cache: name: Save uv cache key: v2-uv-pip-{{ checksum "pyproject.toml" }} paths: - ~/.cache/uv + # Test DLC - run: name: TestDLC - # uv handles the installation of the dependencies command: python testscript_cli.py + # Save the HF weights cache for next runs + - save_cache: + name: Save huggingface cache + key: hf-weights-v1-{{ checksum "pyproject.toml" }} + paths: + - ~/.cache/huggingface + workflows: main: jobs: