diff --git a/tutorials/1-getting-started/DTGS101_intro.ipynb b/tutorials/1-getting-started/DTGS101_intro.ipynb index 80eefb936..22e736c47 100644 --- a/tutorials/1-getting-started/DTGS101_intro.ipynb +++ b/tutorials/1-getting-started/DTGS101_intro.ipynb @@ -11,10 +11,12 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ + "# Install dependencies\n", + "!pip install deeplay seaborn\n", "# !pip install deeptrack # Uncomment if running on Colab/Kaggle." ] }, @@ -972,7 +974,7 @@ ], "metadata": { "kernelspec": { - "display_name": "py_env_book", + "display_name": "deeptrack2", "language": "python", "name": "python3" }, @@ -986,7 +988,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.15" + "version": "3.13.14" } }, "nbformat": 4, diff --git a/tutorials/1-getting-started/DTGS111_datafiles.ipynb b/tutorials/1-getting-started/DTGS111_datafiles.ipynb index c68b0a1dd..da7a14a31 100644 --- a/tutorials/1-getting-started/DTGS111_datafiles.ipynb +++ b/tutorials/1-getting-started/DTGS111_datafiles.ipynb @@ -11,10 +11,12 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ + "# Install dependencies\n", + "!pip install deeplay opencv-python torch torchmetrics torchvision\n", "# !pip install deeptrack # Uncomment if running on Colab/Kaggle." ] }, diff --git a/tutorials/1-getting-started/DTGS121_tracking_particle_cnn.ipynb b/tutorials/1-getting-started/DTGS121_tracking_particle_cnn.ipynb index 9b142b55f..f4542709e 100644 --- a/tutorials/1-getting-started/DTGS121_tracking_particle_cnn.ipynb +++ b/tutorials/1-getting-started/DTGS121_tracking_particle_cnn.ipynb @@ -11,11 +11,13 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle." + "# Install dependencies\n", + "!pip install deeplay seaborn\n", + "# !pip install deeptrack # Uncomment if running on Colab/Kaggle." ] }, { diff --git a/tutorials/1-getting-started/DTGS126_characterizing_aberrations_cnn.ipynb b/tutorials/1-getting-started/DTGS126_characterizing_aberrations_cnn.ipynb index 1b82e4a71..23d217d55 100644 --- a/tutorials/1-getting-started/DTGS126_characterizing_aberrations_cnn.ipynb +++ b/tutorials/1-getting-started/DTGS126_characterizing_aberrations_cnn.ipynb @@ -6,16 +6,18 @@ "source": [ "# DTGS126. Characterizing Aberrations with a CNN\n", "\n", - "\"Open" + "\"Open" ] }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle." + "# Install dependencies\n", + "!pip install deeplay torch\n", + "# !pip install deeptrack # Uncomment if running on Colab/Kaggle." ] }, { @@ -556,7 +558,7 @@ ], "metadata": { "kernelspec": { - "display_name": "py_env_book (3.10.15)", + "display_name": "deeptrack2", "language": "python", "name": "python3" }, @@ -570,7 +572,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.15" + "version": "3.13.14" } }, "nbformat": 4, diff --git a/tutorials/1-getting-started/DTGS127_characterizing_aberrations_optuna.ipynb b/tutorials/1-getting-started/DTGS127_characterizing_aberrations_optuna.ipynb index f2be112e1..efe072e15 100644 --- a/tutorials/1-getting-started/DTGS127_characterizing_aberrations_optuna.ipynb +++ b/tutorials/1-getting-started/DTGS127_characterizing_aberrations_optuna.ipynb @@ -7,16 +7,18 @@ "source": [ "# Characterizing Aberrations with Optuna\n", "\n", - "\"Open" + "\"Open" ] }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "1d3be940", "metadata": {}, "outputs": [], "source": [ + "# Install dependencies\n", + "!pip install optuna\n", "# !pip install deeptrack optuna # Uncomment if running on Colab/Kaggle." ] }, @@ -932,7 +934,7 @@ ], "metadata": { "kernelspec": { - "display_name": "py_env_book", + "display_name": "deeptrack2", "language": "python", "name": "python3" }, @@ -946,7 +948,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.15" + "version": "3.13.14" } }, "nbformat": 4, diff --git a/tutorials/1-getting-started/DTGS151_unsupervised_object_detection_with_lodestar.ipynb b/tutorials/1-getting-started/DTGS151_unsupervised_object_detection_with_lodestar.ipynb index 2d1e2fdc8..5acca3316 100644 --- a/tutorials/1-getting-started/DTGS151_unsupervised_object_detection_with_lodestar.ipynb +++ b/tutorials/1-getting-started/DTGS151_unsupervised_object_detection_with_lodestar.ipynb @@ -12,7 +12,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "98c6d466", "metadata": { "execution": { @@ -24,7 +24,9 @@ }, "outputs": [], "source": [ - "# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle." + "# Install dependencies\n", + "!pip install deeplay torch torchvision\n", + "# !pip install deeptrack # Uncomment if running on Colab/Kaggle." ] }, { @@ -607,7 +609,7 @@ ], "metadata": { "kernelspec": { - "display_name": "py_env_book (3.10.15)", + "display_name": "deeptrack2", "language": "python", "name": "python3" }, @@ -621,7 +623,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.15" + "version": "3.13.14" } }, "nbformat": 4, diff --git a/tutorials/1-getting-started/DTGS161_torch_fitting.ipynb b/tutorials/1-getting-started/DTGS161_torch_fitting.ipynb index 09f903726..f9c279560 100644 --- a/tutorials/1-getting-started/DTGS161_torch_fitting.ipynb +++ b/tutorials/1-getting-started/DTGS161_torch_fitting.ipynb @@ -11,10 +11,12 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ + "# Install dependencies\n", + "!pip install torch\n", "# !pip install deeptrack # Uncomment if running on Colab/Kaggle." ] }, diff --git a/tutorials/test_notebooks.py b/tutorials/test_notebooks.py index 803f0aab7..91b8e0d87 100644 --- a/tutorials/test_notebooks.py +++ b/tutorials/test_notebooks.py @@ -10,8 +10,9 @@ def test_notebooks(): """ Test all notebooks in the examples directory. """ - - notebooks = glob.glob(os.path.join("examples", "**", "*.ipynb"), recursive=True) + + script_dir = os.path.dirname(os.path.abspath(__file__)) + notebooks = glob.glob(os.path.join(script_dir, "2-examples", "**", "*.ipynb"), recursive=True) failed_runs = [] for notebook in notebooks: print(f"Testing notebook: {notebook}...")