From 3f19fa8eb445719524002829ec0d881ea842d934 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Wed, 27 Nov 2024 12:25:13 -0500 Subject: [PATCH] pre-commit. --- .../03-Initializing-the-System-State.ipynb | 5 ----- .../04-Randomizing-the-System.ipynb | 5 ----- .../05-Compressing-the-System.ipynb | 5 ----- .../06-Equilibrating-the-System.ipynb | 5 ----- .../07-Analyzing-Trajectories.ipynb | 11 +++++------ 01-Introducing-Molecular-Dynamics/00-index.ipynb | 5 ----- .../01-Molecular-Dynamics-Simulations.ipynb | 5 ----- .../02-Initializing-a-Random-System.ipynb | 5 ----- .../03-Compressing-the-System.ipynb | 7 +------ 02-Logging/00-index.ipynb | 5 ----- 02-Logging/01-Logging-to-a-file.ipynb | 5 ----- 02-Logging/02-Saving-Array-Quantities.ipynb | 5 ----- 02-Logging/03-Storing-Particle-Shape.ipynb | 5 ----- 02-Logging/04-Writing-Formatted-Output.ipynb | 5 ----- .../01-Introduction-to-Rigid-Bodies.ipynb | 5 ----- .../02-Running-Rigid-Body-Simulations.ipynb | 7 +------ .../03-Preparing-a-General-Body.ipynb | 8 +------- .../02-Fixed-particles.ipynb | 5 ----- .../04-Wall-potential-MD.ipynb | 7 +------ .../05-Wall-potential-HPMC.ipynb | 5 ----- 20 files changed, 9 insertions(+), 106 deletions(-) diff --git a/00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb b/00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb index 08e2664..44c0139 100644 --- a/00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb +++ b/00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb @@ -448,11 +448,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb b/00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb index 558c56b..442bdda 100644 --- a/00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb +++ b/00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb @@ -498,11 +498,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb b/00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb index 9817661..d78f278 100644 --- a/00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb +++ b/00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb @@ -486,11 +486,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb b/00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb index 3173842..589e1f2 100644 --- a/00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb +++ b/00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb @@ -399,11 +399,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.ipynb b/00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.ipynb index 33542e2..ddcd218 100644 --- a/00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.ipynb +++ b/00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.ipynb @@ -53,6 +53,9 @@ "cell_type": "code", "execution_count": 2, "metadata": { + "jupyter": { + "source_hidden": true + }, "nbsphinx": "hidden", "tags": [] }, @@ -62,6 +65,7 @@ "# documentation (https://fresnel.readthedocs.io/) if you would like to learn more.\n", "\n", "import io\n", + "import os\n", "import warnings\n", "\n", "import fresnel\n", @@ -136,7 +140,7 @@ " scene.background_color = (1, 1, 1)\n", " samples = 2000\n", " if \"CI\" in os.environ:\n", - " samples = 100 \n", + " samples = 100\n", " return tracer.sample(scene, samples=samples)\n", "\n", "\n", @@ -1558,11 +1562,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/01-Introducing-Molecular-Dynamics/00-index.ipynb b/01-Introducing-Molecular-Dynamics/00-index.ipynb index b4b5332..3685e2f 100644 --- a/01-Introducing-Molecular-Dynamics/00-index.ipynb +++ b/01-Introducing-Molecular-Dynamics/00-index.ipynb @@ -40,11 +40,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/01-Introducing-Molecular-Dynamics/01-Molecular-Dynamics-Simulations.ipynb b/01-Introducing-Molecular-Dynamics/01-Molecular-Dynamics-Simulations.ipynb index 93b95c4..c88a802 100644 --- a/01-Introducing-Molecular-Dynamics/01-Molecular-Dynamics-Simulations.ipynb +++ b/01-Introducing-Molecular-Dynamics/01-Molecular-Dynamics-Simulations.ipynb @@ -871,11 +871,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb b/01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb index e2b9ccb..0983301 100644 --- a/01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb +++ b/01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb @@ -661,11 +661,6 @@ } ], "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb b/01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb index 61febf9..720d1b9 100644 --- a/01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb +++ b/01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb @@ -61,8 +61,8 @@ "# This is not intended as a full tutorial on fresnel - see the fresnel user\n", "# documentation (https://fresnel.readthedocs.io/) if you would like to learn more.\n", "\n", - "import warnings\n", "import os\n", + "import warnings\n", "\n", "import fresnel\n", "import IPython\n", @@ -2274,11 +2274,6 @@ } ], "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/02-Logging/00-index.ipynb b/02-Logging/00-index.ipynb index cf6a55a..2779547 100644 --- a/02-Logging/00-index.ipynb +++ b/02-Logging/00-index.ipynb @@ -43,11 +43,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/02-Logging/01-Logging-to-a-file.ipynb b/02-Logging/01-Logging-to-a-file.ipynb index 55c31e9..dc54752 100644 --- a/02-Logging/01-Logging-to-a-file.ipynb +++ b/02-Logging/01-Logging-to-a-file.ipynb @@ -1580,11 +1580,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/02-Logging/02-Saving-Array-Quantities.ipynb b/02-Logging/02-Saving-Array-Quantities.ipynb index 8178d90..12bcef3 100644 --- a/02-Logging/02-Saving-Array-Quantities.ipynb +++ b/02-Logging/02-Saving-Array-Quantities.ipynb @@ -2207,11 +2207,6 @@ } ], "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/02-Logging/03-Storing-Particle-Shape.ipynb b/02-Logging/03-Storing-Particle-Shape.ipynb index 2553782..c40d2f1 100644 --- a/02-Logging/03-Storing-Particle-Shape.ipynb +++ b/02-Logging/03-Storing-Particle-Shape.ipynb @@ -301,11 +301,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/02-Logging/04-Writing-Formatted-Output.ipynb b/02-Logging/04-Writing-Formatted-Output.ipynb index 09a1494..8d27cd4 100644 --- a/02-Logging/04-Writing-Formatted-Output.ipynb +++ b/02-Logging/04-Writing-Formatted-Output.ipynb @@ -402,11 +402,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb b/06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb index f47471f..305aafe 100644 --- a/06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb +++ b/06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb @@ -1796,11 +1796,6 @@ } ], "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb b/06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb index 00ff71e..6df25c3 100644 --- a/06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb +++ b/06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb @@ -64,8 +64,8 @@ "# This is not intended as a full tutorial on fresnel - see the fresnel user\n", "# documentation (https://fresnel.readthedocs.io/) if you would like to learn more.\n", "\n", - "import warnings\n", "import os\n", + "import warnings\n", "\n", "import fresnel\n", "import IPython\n", @@ -659,11 +659,6 @@ } ], "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/06-Modelling-Rigid-Bodies/03-Preparing-a-General-Body.ipynb b/06-Modelling-Rigid-Bodies/03-Preparing-a-General-Body.ipynb index c94b676..16c52ff 100644 --- a/06-Modelling-Rigid-Bodies/03-Preparing-a-General-Body.ipynb +++ b/06-Modelling-Rigid-Bodies/03-Preparing-a-General-Body.ipynb @@ -4,7 +4,6 @@ "cell_type": "markdown", "id": "0", "metadata": { - "collapsed": true, "jupyter": { "outputs_hidden": true }, @@ -62,8 +61,8 @@ }, "outputs": [], "source": [ - "import warnings\n", "import os\n", + "import warnings\n", "\n", "import fresnel\n", "import IPython\n", @@ -465,11 +464,6 @@ } ], "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/08-Placing-Barriers-in-the-Simulation-Box/02-Fixed-particles.ipynb b/08-Placing-Barriers-in-the-Simulation-Box/02-Fixed-particles.ipynb index c31c6d3..82fc29d 100644 --- a/08-Placing-Barriers-in-the-Simulation-Box/02-Fixed-particles.ipynb +++ b/08-Placing-Barriers-in-the-Simulation-Box/02-Fixed-particles.ipynb @@ -679,11 +679,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/08-Placing-Barriers-in-the-Simulation-Box/04-Wall-potential-MD.ipynb b/08-Placing-Barriers-in-the-Simulation-Box/04-Wall-potential-MD.ipynb index f94669d..8b2e79e 100644 --- a/08-Placing-Barriers-in-the-Simulation-Box/04-Wall-potential-MD.ipynb +++ b/08-Placing-Barriers-in-the-Simulation-Box/04-Wall-potential-MD.ipynb @@ -143,7 +143,7 @@ " samples = 2000\n", " if \"CI\" in os.environ:\n", " samples = 100\n", - " return IPython.display.Image(tracer.sample(scene, samples=samples)._repr_png_()) " + " return IPython.display.Image(tracer.sample(scene, samples=samples)._repr_png_())" ] }, { @@ -395,11 +395,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython", diff --git a/08-Placing-Barriers-in-the-Simulation-Box/05-Wall-potential-HPMC.ipynb b/08-Placing-Barriers-in-the-Simulation-Box/05-Wall-potential-HPMC.ipynb index e0e54b1..a326816 100644 --- a/08-Placing-Barriers-in-the-Simulation-Box/05-Wall-potential-HPMC.ipynb +++ b/08-Placing-Barriers-in-the-Simulation-Box/05-Wall-potential-HPMC.ipynb @@ -339,11 +339,6 @@ "jupytext": { "notebook_metadata_filter": "-all" }, - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, "language_info": { "codemirror_mode": { "name": "ipython",