[pre-commit.ci] pre-commit autoupdate (#158)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.7...v0.6.1) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix indent --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: chrisjonesBSU <[email protected]>
cmelab · Aug 19, 2024 · 46323ea · 46323ea
1 parent c74aa85
commit 46323ea
Show file tree

Hide file tree

Showing 6 changed files with 146 additions and 84 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7 # Ruff version
+    rev: v0.6.1 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

diff --git a/tutorials/1-flowerMD-basics.ipynb b/tutorials/1-flowerMD-basics.ipynb
@@ -55,7 +55,8 @@
    "outputs": [],
    "source": [
     "import warnings\n",
-    "warnings.filterwarnings('ignore')"
+    "\n",
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -78,9 +79,7 @@
      ]
     }
    ],
-   "source": [
-    "import flowermd"
-   ]
+   "source": []
   },
   {
    "cell_type": "markdown",
@@ -149,6 +148,7 @@
    "outputs": [],
    "source": [
     "from flowermd.base import Pack\n",
+    "\n",
     "system = Pack(molecules=molecules, density=0.5, packing_expand_factor=5)"
    ]
   },
@@ -199,7 +199,9 @@
    "source": [
     "from flowermd.library import OPLS_AA_PPS\n",
     "\n",
-    "system.apply_forcefield(r_cut=2.5, force_field=OPLS_AA_PPS(), auto_scale=True, scale_charges=True)"
+    "system.apply_forcefield(\n",
+    "    r_cut=2.5, force_field=OPLS_AA_PPS(), auto_scale=True, scale_charges=True\n",
+    ")"
    ]
   },
   {
@@ -358,7 +360,9 @@
    "source": [
     "from flowermd.base import Simulation\n",
     "\n",
-    "sim = Simulation.from_system(system=system, gsd_write_freq=100, log_write_freq=100)"
+    "sim = Simulation.from_system(\n",
+    "    system=system, gsd_write_freq=100, log_write_freq=100\n",
+    ")"
    ]
   },
   {
@@ -390,7 +394,9 @@
    "source": [
     "from flowermd.utils import get_target_box_mass_density\n",
     "\n",
-    "target_box = get_target_box_mass_density(density=system.density, mass=system.mass.to(\"g\"))\n",
+    "target_box = get_target_box_mass_density(\n",
+    "    density=system.density, mass=system.mass.to(\"g\")\n",
+    ")\n",
     "print(target_box)"
    ]
   },
@@ -446,7 +452,9 @@
     }
    ],
    "source": [
-    "sim.run_update_volume(n_steps=1000, period=1, kT=1, tau_kt=1, final_box_lengths=target_box)"
+    "sim.run_update_volume(\n",
+    "    n_steps=1000, period=1, kT=1, tau_kt=1, final_box_lengths=target_box\n",
+    ")"
    ]
   },
   {
@@ -483,6 +491,7 @@
    "outputs": [],
    "source": [
     "import hoomd\n",
+    "\n",
     "for writer in sim.operations.writers:\n",
     "    if isinstance(writer, hoomd.write.GSD):\n",
     "        writer.flush()"
@@ -508,9 +517,10 @@
    "source": [
     "from cmeutils.visualize import FresnelGSD\n",
     "\n",
-    "sim_visualizer = FresnelGSD(gsd_file=\"trajectory.gsd\", frame=0, view_axis=(1, 1, 1))\n",
-    "sim_visualizer.view()\n",
-    "                            "
+    "sim_visualizer = FresnelGSD(\n",
+    "    gsd_file=\"trajectory.gsd\", frame=0, view_axis=(1, 1, 1)\n",
+    ")\n",
+    "sim_visualizer.view()"
    ]
   },
   {
@@ -614,7 +624,7 @@
     }
    ],
    "source": [
-    "sim_visualizer.frame=-1\n",
+    "sim_visualizer.frame = -1\n",
     "sim_visualizer.view()"
    ]
   },

diff --git a/tutorials/2-flowerMD-advanced.ipynb b/tutorials/2-flowerMD-advanced.ipynb
@@ -89,7 +89,8 @@
    "outputs": [],
    "source": [
     "import warnings\n",
-    "warnings.filterwarnings('ignore')"
+    "\n",
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -247,7 +248,9 @@
    },
    "outputs": [],
    "source": [
-    "phenol_mol = Molecule(num_mols=20, file=\"../flowermd/assets/molecule_files/IPH.mol2\")"
+    "phenol_mol = Molecule(\n",
+    "    num_mols=20, file=\"../flowermd/assets/molecule_files/IPH.mol2\"\n",
+    ")"
    ]
   },
   {
@@ -361,7 +364,7 @@
     "gmso_top = mb_compound.to_gmso()\n",
     "\n",
     "benzene_mol = Molecule(num_mols=20, compound=mb_compound)\n",
-    "benzene_mol = Molecule(num_mols=20, compound=gmso_top)\n"
+    "benzene_mol = Molecule(num_mols=20, compound=gmso_top)"
    ]
   },
   {
@@ -445,7 +448,9 @@
    "source": [
     "from flowermd.library import FF_from_file\n",
     "\n",
-    "benzene_ff = FF_from_file(forcefield_files=\"../flowermd/assets/forcefields/benzene_opls.xml\")"
+    "benzene_ff = FF_from_file(\n",
+    "    forcefield_files=\"../flowermd/assets/forcefields/benzene_opls.xml\"\n",
+    ")"
    ]
   },
   {
@@ -484,8 +489,18 @@
    "outputs": [],
    "source": [
     "from flowermd.base import BaseHOOMDForcefield\n",
+    "\n",
+    "\n",
     "class BeadSpring(BaseHOOMDForcefield):\n",
-    "    def __init__(self, r_cut, beads, bonds=None, angles=None, dihedrals=None,exclusions=[\"bond\", \"1-3\"]):\n",
+    "    def __init__(\n",
+    "        self,\n",
+    "        r_cut,\n",
+    "        beads,\n",
+    "        bonds=None,\n",
+    "        angles=None,\n",
+    "        dihedrals=None,\n",
+    "        exclusions=[\"bond\", \"1-3\"],\n",
+    "    ):\n",
     "        # ...\n",
     "        hoomd_forces = self._create_forcefield()\n",
     "        super(BeadSpring, self).__init__(hoomd_forces)\n",
@@ -494,8 +509,7 @@
     "        hoomd_forces = []\n",
     "        # generate hoomd forces for pair interactions, bonds, angles, dihedrals, etc.\n",
     "        # ...\n",
-    "        return hoomd_forces\n",
-    "\n"
+    "        return hoomd_forces"
    ]
   },
   {
@@ -716,8 +730,12 @@
     "\n",
     "dimethylether_mol = Molecule(num_mols=20, smiles=\"COC\")\n",
     "pps_mol = PPS(num_mols=10, lengths=4)\n",
-    "multi_type_system = Pack( molecules=[dimethylether_mol, pps_mol], density=0.8)\n",
-    "multi_type_system.apply_forcefield(r_cut=2.5, force_field=[OPLS_AA_DIMETHYLETHER(), OPLS_AA_PPS()], auto_scale=True)"
+    "multi_type_system = Pack(molecules=[dimethylether_mol, pps_mol], density=0.8)\n",
+    "multi_type_system.apply_forcefield(\n",
+    "    r_cut=2.5,\n",
+    "    force_field=[OPLS_AA_DIMETHYLETHER(), OPLS_AA_PPS()],\n",
+    "    auto_scale=True,\n",
+    ")"
    ]
   },
   {
@@ -899,10 +917,12 @@
     "\n",
     "molecule = Molecule(num_mols=30, smiles=\"c1ccccc1\")\n",
     "\n",
-    "system = Pack(molecules=molecule, density=0.5 * unyt.g/unyt.cm**3)\n",
+    "system = Pack(molecules=molecule, density=0.5 * unyt.g / unyt.cm**3)\n",
     "system.apply_forcefield(r_cut=2.5, force_field=OPLS_AA(), auto_scale=True)\n",
     "\n",
-    "sim = Simulation(initial_state=system.hoomd_snapshot, forcefield=system.hoomd_forcefield)\n",
+    "sim = Simulation(\n",
+    "    initial_state=system.hoomd_snapshot, forcefield=system.hoomd_forcefield\n",
+    ")\n",
     "\n",
     "sim.run_NVE(n_steps=1e3)"
    ]

diff --git a/tutorials/3-flowerMD-coarse-graining.ipynb b/tutorials/3-flowerMD-coarse-graining.ipynb
@@ -36,7 +36,8 @@
    "outputs": [],
    "source": [
     "import warnings\n",
-    "warnings.filterwarnings('ignore')"
+    "\n",
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -571,7 +572,11 @@
     }
    ],
    "source": [
-    "cg_sim = Simulation(initial_state=cg_system.hoomd_snapshot, forcefield=ff.hoomd_forces, gsd_write_freq=int(2e5/10))"
+    "cg_sim = Simulation(\n",
+    "    initial_state=cg_system.hoomd_snapshot,\n",
+    "    forcefield=ff.hoomd_forces,\n",
+    "    gsd_write_freq=int(2e5 / 10),\n",
+    ")"
    ]
   },
   {
@@ -650,7 +655,9 @@
    "source": [
     "from cmeutils.visualize import FresnelGSD\n",
     "\n",
-    "sim_visualizer = FresnelGSD(gsd_file=\"trajectory.gsd\", frame=-1, view_axis=(1, 1, 1))\n",
+    "sim_visualizer = FresnelGSD(\n",
+    "    gsd_file=\"trajectory.gsd\", frame=-1, view_axis=(1, 1, 1)\n",
+    ")\n",
     "sim_visualizer.view()"
    ]
   },