From a7b37f5660f63f7784222bc61946dadcd41f08e7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 19 Aug 2024 22:23:24 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.6 → v0.6.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.6...v0.6.1) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 07ae08a0..bf6aba4d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.5.6 + rev: v0.6.1 hooks: # Run the linter. - id: ruff From 9c3ef9a1542da989f3bb4892f0677a6173ca0715 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 19 Aug 2024 22:23:29 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- examples/01_Model_Training.ipynb | 13 +++++++------ examples/02_Molecular_Dynamics.ipynb | 17 ++++++++++------- examples/03_Transfer_Learning.ipynb | 12 +++++++++--- examples/04_Batch_Data_Selection.ipynb | 13 ++++++------- 4 files changed, 32 insertions(+), 23 deletions(-) diff --git a/examples/01_Model_Training.ipynb b/examples/01_Model_Training.ipynb index a0fc88d0..6db1644b 100644 --- a/examples/01_Model_Training.ipynb +++ b/examples/01_Model_Training.ipynb @@ -7,6 +7,7 @@ "outputs": [], "source": [ "import warnings\n", + "\n", "warnings.simplefilter('ignore')" ] }, @@ -31,7 +32,8 @@ "outputs": [], "source": [ "from pathlib import Path\n", - "from apax.utils.datasets import mod_md_datasets, download_etoh_ccsdt\n", + "\n", + "from apax.utils.datasets import download_etoh_ccsdt, mod_md_datasets\n", "\n", "data_path = Path(\"project\")\n", "\n", @@ -187,9 +189,9 @@ "metadata": {}, "outputs": [], "source": [ - "from apax.utils.helpers import mod_config\n", "import yaml\n", "\n", + "from apax.utils.helpers import mod_config\n", "\n", "config_path = Path(\"config.yaml\")\n", "\n", @@ -311,7 +313,6 @@ "from apax.train.run import run\n", "from apax.utils.helpers import mod_config\n", "\n", - "\n", "config_path = Path(\"config.yaml\")\n", "\n", "config_updates = {\n", @@ -342,9 +343,9 @@ } ], "source": [ - "import csv\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", + "\n", "from apax.utils.helpers import load_csv_metrics\n", "\n", "metrics_path = \"project/models/ethanol_ccsd_t_script/log.csv\"\n", @@ -354,7 +355,7 @@ "\n", "fig, axes = plt.subplots(2, 2, constrained_layout=True)\n", "axes = axes.ravel()\n", - "fig.suptitle(f'Metrics', fontsize=16)\n", + "fig.suptitle('Metrics', fontsize=16)\n", "\n", "for id, key in enumerate(keys):\n", " val = np.array(data_dict[f\"val_{key}\"])\n", @@ -440,7 +441,7 @@ "\n", "fig, axes = plt.subplots(1, 4, constrained_layout=True)\n", "axes = axes.ravel()\n", - "fig.suptitle(f'Metrics', fontsize=16)\n", + "fig.suptitle('Metrics', fontsize=16)\n", "\n", "for id, key in enumerate(keys):\n", " test = np.array(data_dict[f\"test_{key}\"])\n", diff --git a/examples/02_Molecular_Dynamics.ipynb b/examples/02_Molecular_Dynamics.ipynb index 261479a7..da89282a 100644 --- a/examples/02_Molecular_Dynamics.ipynb +++ b/examples/02_Molecular_Dynamics.ipynb @@ -7,6 +7,7 @@ "outputs": [], "source": [ "import warnings\n", + "\n", "warnings.simplefilter('ignore')" ] }, @@ -55,11 +56,12 @@ ], "source": [ "from pathlib import Path\n", - "from apax.utils.datasets import download_etoh_ccsdt, mod_md_datasets\n", - "from apax.train.run import run\n", - "from apax.utils.helpers import mod_config\n", + "\n", "import yaml\n", "\n", + "from apax.train.run import run\n", + "from apax.utils.datasets import download_etoh_ccsdt, mod_md_datasets\n", + "from apax.utils.helpers import mod_config\n", "\n", "# Download and modify the dataset\n", "data_path = Path(\"project\")\n", @@ -118,12 +120,12 @@ "metadata": {}, "outputs": [], "source": [ - "from ase.io import read\n", - "from apax.md import ASECalculator\n", - "from ase.md.langevin import Langevin\n", "from ase import units\n", + "from ase.io import read\n", "from ase.io.trajectory import Trajectory\n", + "from ase.md.langevin import Langevin\n", "\n", + "from apax.md import ASECalculator\n", "\n", "# read starting structure and define modelpath\n", "atoms = read(train_file_path, index=0)\n", @@ -164,6 +166,7 @@ "import matplotlib.pyplot as plt\n", "import numpy as np\n", "\n", + "\n", "def plot_bondlength_distribution(traj, indices: list, bins: int=25):\n", " oh_dist = []\n", " for atoms in traj:\n", @@ -253,9 +256,9 @@ "metadata": {}, "outputs": [], "source": [ - "from apax.utils.helpers import mod_config\n", "import yaml\n", "\n", + "from apax.utils.helpers import mod_config\n", "\n", "md_config_path = Path(\"md_config.yaml\")\n", "\n", diff --git a/examples/03_Transfer_Learning.ipynb b/examples/03_Transfer_Learning.ipynb index 9ecdf64a..04fa3e24 100644 --- a/examples/03_Transfer_Learning.ipynb +++ b/examples/03_Transfer_Learning.ipynb @@ -53,9 +53,15 @@ "outputs": [], "source": [ "from pathlib import Path\n", - "from apax.utils.datasets import download_md22_benzene_CCSDT, mod_md_datasets, download_benzene_DFT\n", - "from apax.utils.helpers import mod_config\n", - "import yaml" + "\n", + "import yaml\n", + "\n", + "from apax.utils.datasets import (\n", + " download_benzene_DFT,\n", + " download_md22_benzene_CCSDT,\n", + " mod_md_datasets,\n", + ")\n", + "from apax.utils.helpers import mod_config" ] }, { diff --git a/examples/04_Batch_Data_Selection.ipynb b/examples/04_Batch_Data_Selection.ipynb index 1075a7c4..b13caac2 100644 --- a/examples/04_Batch_Data_Selection.ipynb +++ b/examples/04_Batch_Data_Selection.ipynb @@ -21,17 +21,16 @@ "outputs": [], "source": [ "from pathlib import Path\n", - "import yaml\n", "\n", - "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n", + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "import yaml\n", "from ase import units\n", + "from ase.io import read\n", + "from ase.io.trajectory import TrajectoryWriter\n", "from ase.md.langevin import Langevin\n", + "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n", "from ase.optimize.fire import FIRE\n", - "from ase.io.trajectory import TrajectoryWriter\n", - "from ase.io import read\n", - "import numpy as np\n", - "import matplotlib.pyplot as plt\n", - "\n", "\n", "from apax.bal import api\n", "from apax.md import ASECalculator\n",