Merge pull request #323 from apax-hub/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate
apax-hub · Aug 20, 2024 · e66bfde · e66bfde
2 parents e3b1c66 + 9c3ef9a
commit e66bfde
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Showing 5 changed files with 33 additions and 24 deletions.
diff --git 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

diff --git 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
@@ -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
@@ -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
@@ -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",