From e6299a718c21b347ded7063721dc1380fcb65fcf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 12 Aug 2024 19:32:31 +0000
Subject: [PATCH 01/24] [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 → v0.5.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.6...v0.5.7)
---
 .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 3efbaccd..fdcf53c7 100644
--- 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: v0.5.6 # Ruff version
+    rev: v0.5.7 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 46323ea59e37daf24871cda4a7da1480c4e0c634 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 14:24:49 -0600
Subject: [PATCH 02/24] [pre-commit.ci] pre-commit autoupdate (#158)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](https://github.com/astral-sh/ruff-pre-commit/compare/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 <chrisjones4@u.boisestate.edu>
---
 .pre-commit-config.yaml                    |  2 +-
 tutorials/1-flowerMD-basics.ipynb          | 34 ++++++----
 tutorials/2-flowerMD-advanced.ipynb        | 42 ++++++++----
 tutorials/3-flowerMD-coarse-graining.ipynb | 13 +++-
 tutorials/4-flowerMD-welding.ipynb         | 75 ++++++++++++++--------
 tutorials/5-flowerMD-surface-wetting.ipynb | 64 +++++++++---------
 6 files changed, 146 insertions(+), 84 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fdcf53c7..44af9a1d 100644
--- 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
index d6ad4cd2..2d83458d 100644
--- 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
index de0fbd46..fc3d2135 100644
--- 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
index 476a31a6..7d1d70f0 100644
--- 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()"
    ]
   },
diff --git a/tutorials/4-flowerMD-welding.ipynb b/tutorials/4-flowerMD-welding.ipynb
index 7fb9d4d6..c4b71feb 100644
--- a/tutorials/4-flowerMD-welding.ipynb
+++ b/tutorials/4-flowerMD-welding.ipynb
@@ -33,8 +33,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    " import warnings\n",
-    "warnings.filterwarnings('ignore')"
+    "import warnings\n",
+    "\n",
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -97,9 +98,15 @@
     "\n",
     "system = Pack(\n",
     "    molecules=molecule,\n",
-    "    density=1.1 * u.g/u.cm**3,\n",
+    "    density=1.1 * u.g / u.cm**3,\n",
     ")\n",
-    "system.apply_forcefield(r_cut=2.5, force_field=OPLS_AA(), auto_scale=True,remove_charges=True, remove_hydrogens=True)"
+    "system.apply_forcefield(\n",
+    "    r_cut=2.5,\n",
+    "    force_field=OPLS_AA(),\n",
+    "    auto_scale=True,\n",
+    "    remove_charges=True,\n",
+    "    remove_hydrogens=True,\n",
+    ")"
    ]
   },
   {
@@ -134,7 +141,7 @@
    "source": [
     "sim = SlabSimulation.from_system(\n",
     "    system=system,\n",
-    "    interface_axis=(1,0,0),\n",
+    "    interface_axis=(1, 0, 0),\n",
     "    gsd_file_name=\"slab_x_interface.gsd\",\n",
     ")"
    ]
@@ -232,9 +239,13 @@
     }
    ],
    "source": [
-    "target_box = flowermd.utils.get_target_box_mass_density(density=1.2*u.g/u.cm**3, mass=sim.mass.to(\"g\"))\n",
+    "target_box = flowermd.utils.get_target_box_mass_density(\n",
+    "    density=1.2 * u.g / u.cm**3, mass=sim.mass.to(\"g\")\n",
+    ")\n",
     "\n",
-    "sim.run_update_volume(final_box_lengths=target_box, n_steps=5e4, kT=5.0, period=100, tau_kt=0.001)"
+    "sim.run_update_volume(\n",
+    "    final_box_lengths=target_box, n_steps=5e4, kT=5.0, period=100, tau_kt=0.001\n",
+    ")"
    ]
   },
   {
@@ -294,7 +305,7 @@
     }
    ],
    "source": [
-    "sim.remove_walls(wall_axis=(1,0,0))\n",
+    "sim.remove_walls(wall_axis=(1, 0, 0))\n",
     "sim.pickle_forcefield()\n",
     "sim.flush_writers()"
    ]
@@ -328,7 +339,9 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"slab_x_interface.gsd\", view_axis=(0, 1, 0), frame=-1)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"slab_x_interface.gsd\", view_axis=(0, 1, 0), frame=-1\n",
+    ")\n",
     "sim_viewer.view()"
    ]
   },
@@ -392,7 +405,7 @@
     }
    ],
    "source": [
-    "sim_viewer.view_axis = (1,0,0)\n",
+    "sim_viewer.view_axis = (1, 0, 0)\n",
     "sim_viewer.view()"
    ]
   },
@@ -428,7 +441,9 @@
     }
    ],
    "source": [
-    "interface = Interface(gsd_files=[\"slab_x_interface.gsd\"], interface_axis=(1, 0, 0), gap=0.05)\n",
+    "interface = Interface(\n",
+    "    gsd_files=[\"slab_x_interface.gsd\"], interface_axis=(1, 0, 0), gap=0.05\n",
+    ")\n",
     "\n",
     "print(type(interface.hoomd_snapshot))\n",
     "print(\"Slab number of particles:\", system.n_particles)\n",
@@ -512,7 +527,7 @@
     "    gsd_file_name=\"weld.gsd\",\n",
     "    log_file_name=\"weld_log.txt\",\n",
     "    log_write_freq=500,\n",
-    "    dt=0.0003\n",
+    "    dt=0.0003,\n",
     ")"
    ]
   },
@@ -616,7 +631,9 @@
    ],
    "source": [
     "weld_sim.run_NVT(kT=10.0, n_steps=7e4, tau_kt=0.001)\n",
-    "cooling_ramp = weld_sim.temperature_ramp(n_steps=2e4, kT_start=10.0, kT_final=2.0)\n",
+    "cooling_ramp = weld_sim.temperature_ramp(\n",
+    "    n_steps=2e4, kT_start=10.0, kT_final=2.0\n",
+    ")\n",
     "weld_sim.run_NVT(kT=cooling_ramp, n_steps=2e4, tau_kt=0.001)\n",
     "weld_sim.save_restart_gsd(\"weld_restart.gsd\")\n",
     "weld_sim.flush_writers()"
@@ -651,10 +668,12 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"weld.gsd\", view_axis=(0, 1, 0), frame=0, height=12)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"weld.gsd\", view_axis=(0, 1, 0), frame=0, height=12\n",
+    ")\n",
     "weld_colors = np.zeros_like(sim_viewer.positions)\n",
-    "weld_colors[:weld_colors.shape[0]//2 + 1] = np.array([0.5, 0.25, 0.5])\n",
-    "weld_colors[weld_colors.shape[0]//2 + 1:] = np.array([0.5, 0.1, 0.1])\n",
+    "weld_colors[: weld_colors.shape[0] // 2 + 1] = np.array([0.5, 0.25, 0.5])\n",
+    "weld_colors[weld_colors.shape[0] // 2 + 1 :] = np.array([0.5, 0.1, 0.1])\n",
     "sim_viewer.colors = weld_colors\n",
     "sim_viewer.view(width=500, height=500)"
    ]
@@ -737,7 +756,9 @@
     "sim_data = np.genfromtxt(\"weld_log.txt\", names=True)\n",
     "lj_energy = sim_data[\"mdpairLJenergy\"]\n",
     "time_step = sim_data[\"flowermdmodulesweldingWeldSimulationtimestep\"]\n",
-    "plt.plot(time_step, lj_energy/interface.hoomd_snapshot.particles.N, linewidth=3)\n",
+    "plt.plot(\n",
+    "    time_step, lj_energy / interface.hoomd_snapshot.particles.N, linewidth=3\n",
+    ")\n",
     "plt.ylabel(\"$\\dfrac{\\epsilon}{N}$\", fontsize=15)\n",
     "plt.xlabel(\"Time step\", fontsize=15)"
    ]
@@ -775,16 +796,16 @@
     "# Open and load the forcefield picke file\n",
     "with open(\"forcefield.pickle\", \"rb\") as f:\n",
     "    hoomd_forces = pickle.load(f)\n",
-    "    \n",
+    "\n",
     "tensile_sim = Tensile(\n",
     "    initial_state=\"weld_restart.gsd\",\n",
     "    forcefield=hoomd_forces,\n",
-    "    tensile_axis=(1,0,0),\n",
+    "    tensile_axis=(1, 0, 0),\n",
     "    gsd_file_name=\"tensile.gsd\",\n",
     "    gsd_write_freq=1000,\n",
     "    log_file_name=\"tensile_log.txt\",\n",
     "    log_write_freq=500,\n",
-    "    fix_ratio=0.30\n",
+    "    fix_ratio=0.30,\n",
     ")"
    ]
   },
@@ -945,7 +966,9 @@
     }
    ],
    "source": [
-    "tensile_sim.run_tensile(n_steps=1e5, strain=0.30, period=500, kT=2.0, tau_kt=0.001)\n",
+    "tensile_sim.run_tensile(\n",
+    "    n_steps=1e5, strain=0.30, period=500, kT=2.0, tau_kt=0.001\n",
+    ")\n",
     "tensile_sim.flush_writers()"
    ]
   },
@@ -975,10 +998,12 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"tensile.gsd\", view_axis=(0, 1, 0), frame=0, height=12)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"tensile.gsd\", view_axis=(0, 1, 0), frame=0, height=12\n",
+    ")\n",
     "weld_colors = np.zeros_like(sim_viewer.positions)\n",
-    "weld_colors[:weld_colors.shape[0]//2 + 1] = np.array([0.5, 0.25, 0.5])\n",
-    "weld_colors[weld_colors.shape[0]//2 + 1:] = np.array([0.5, 0.1, 0.1])\n",
+    "weld_colors[: weld_colors.shape[0] // 2 + 1] = np.array([0.5, 0.25, 0.5])\n",
+    "weld_colors[weld_colors.shape[0] // 2 + 1 :] = np.array([0.5, 0.1, 0.1])\n",
     "sim_viewer.colors = weld_colors\n",
     "sim_viewer.view(width=500, height=500)"
    ]
@@ -1059,7 +1084,7 @@
     "    new_x = snap.configuration.box[0]\n",
     "    strain = (new_x - initial_x_len) / initial_x_len\n",
     "    energy = snap.log[\"md/pair/LJ/energy\"]\n",
-    "    plt.plot(strain, energy/snap.particles.N, \"ro\")\n",
+    "    plt.plot(strain, energy / snap.particles.N, \"ro\")\n",
     "\n",
     "plt.show()"
    ]
diff --git a/tutorials/5-flowerMD-surface-wetting.ipynb b/tutorials/5-flowerMD-surface-wetting.ipynb
index 46254ec7..2817a1b2 100644
--- a/tutorials/5-flowerMD-surface-wetting.ipynb
+++ b/tutorials/5-flowerMD-surface-wetting.ipynb
@@ -65,9 +65,8 @@
     "from cmeutils.visualize import FresnelGSD\n",
     "import unyt\n",
     "import warnings\n",
-    "import os\n",
     "\n",
-    "warnings.filterwarnings('ignore')"
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -111,13 +110,13 @@
    ],
    "source": [
     "polyethylene = PolyEthylene(num_mols=70, lengths=25)\n",
-    "droplet_system = Pack(molecules=polyethylene, density=1.0 * unyt.g/unyt.cm**3)\n",
+    "droplet_system = Pack(molecules=polyethylene, density=1.0 * unyt.g / unyt.cm**3)\n",
     "droplet_system.apply_forcefield(\n",
-    "    force_field=OPLS_AA(), \n",
-    "    remove_charges=True,         \n",
-    "    remove_hydrogens=True, \n",
+    "    force_field=OPLS_AA(),\n",
+    "    remove_charges=True,\n",
+    "    remove_hydrogens=True,\n",
     "    auto_scale=True,\n",
-    "    r_cut=2.5\n",
+    "    r_cut=2.5,\n",
     ")"
    ]
   },
@@ -141,7 +140,7 @@
     "droplet_sim = DropletSimulation.from_system(\n",
     "    droplet_system,\n",
     "    gsd_file_name=\"droplet_trajectory.gsd\",\n",
-    "    log_file_name=\"droplet_sim_data.txt\"\n",
+    "    log_file_name=\"droplet_sim_data.txt\",\n",
     ")"
    ]
   },
@@ -798,9 +797,8 @@
    "outputs": [],
    "source": [
     "import gsd.hoomd\n",
-    "import pickle\n",
     "\n",
-    "droplet_snapshot = gsd.hoomd.open('data/polyethylene_droplet.gsd')[0]"
+    "droplet_snapshot = gsd.hoomd.open(\"data/polyethylene_droplet.gsd\")[0]"
    ]
   },
   {
@@ -840,7 +838,9 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"data/polyethylene_droplet.gsd\", view_axis=(0, 1, 0), frame=-1)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"data/polyethylene_droplet.gsd\", view_axis=(0, 1, 0), frame=-1\n",
+    ")\n",
     "sim_viewer.view()"
    ]
   },
@@ -870,11 +870,11 @@
     "polyethylene_small = PolyEthylene(num_mols=10, lengths=5)\n",
     "droplet_system_small = Pack(molecules=polyethylene_small, density=1.0)\n",
     "droplet_system_small.apply_forcefield(\n",
-    "    force_field=OPLS_AA(), \n",
-    "    remove_charges=True,         \n",
-    "    remove_hydrogens=True, \n",
+    "    force_field=OPLS_AA(),\n",
+    "    remove_charges=True,\n",
+    "    remove_hydrogens=True,\n",
     "    auto_scale=True,\n",
-    "    r_cut=2.5\n",
+    "    r_cut=2.5,\n",
     ")"
    ]
   },
@@ -938,16 +938,10 @@
     "from flowermd.library.surfaces import Graphene\n",
     "\n",
     "graphene = Graphene(\n",
-    "    x_repeat=30,\n",
-    "    y_repeat=30,\n",
-    "    n_layers=2,\n",
-    "    base_units=droplet_ref_values\n",
+    "    x_repeat=30, y_repeat=30, n_layers=2, base_units=droplet_ref_values\n",
     ")\n",
     "graphene.apply_forcefield(\n",
-    "    force_field=OPLS_AA(),\n",
-    "    remove_charges=True,\n",
-    "    auto_scale=False,\n",
-    "    r_cut=2.5\n",
+    "    force_field=OPLS_AA(), remove_charges=True, auto_scale=False, r_cut=2.5\n",
     ")"
    ]
   },
@@ -985,7 +979,7 @@
     "    drop_ff=droplet_ff,\n",
     "    drop_ref_values=droplet_ref_values,\n",
     "    box_height=12 * u.nm,\n",
-    "    gap=0.4 * u.nm\n",
+    "    gap=0.4 * u.nm,\n",
     ")"
    ]
   },
@@ -1062,7 +1056,9 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"surface_wetting_init.gsd\", view_axis=(0, 1.5, 0), frame=-1)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"surface_wetting_init.gsd\", view_axis=(0, 1.5, 0), frame=-1\n",
+    ")\n",
     "sim_viewer.view()"
    ]
   },
@@ -1111,7 +1107,7 @@
     "    forcefield=wetting_forcefield,\n",
     "    fix_surface=True,\n",
     "    gsd_file_name=\"wetting_trajectory.gsd\",\n",
-    "    log_file_name=\"wetting_sim_data.txt\"\n",
+    "    log_file_name=\"wetting_sim_data.txt\",\n",
     ")"
    ]
   },
@@ -1211,8 +1207,8 @@
    "source": [
     "# Uncomment to run surface wetting simulation\n",
     "\n",
-    "#wetting_sim.run_NVT(kT=3.0, n_steps=3e5, tau_kt=wetting_sim.dt*100)\n",
-    "#wetting_sim.flush_writers()"
+    "# wetting_sim.run_NVT(kT=3.0, n_steps=3e5, tau_kt=wetting_sim.dt*100)\n",
+    "# wetting_sim.flush_writers()"
    ]
   },
   {
@@ -1239,7 +1235,9 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"wetting_trajectory.gsd\", view_axis=(0, 1.5, 0), frame=-1)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"wetting_trajectory.gsd\", view_axis=(0, 1.5, 0), frame=-1\n",
+    ")\n",
     "sim_viewer.view()"
    ]
   },
@@ -1295,8 +1293,8 @@
    "source": [
     "# Uncomment to run the surface wetting simulation longer:\n",
     "\n",
-    "#wetting_sim.run_NVT(kT=3.0, n_steps=2e5, tau_kt=wetting_sim.dt*100)\n",
-    "#wetting_sim.flush_writers()"
+    "# wetting_sim.run_NVT(kT=3.0, n_steps=2e5, tau_kt=wetting_sim.dt*100)\n",
+    "# wetting_sim.flush_writers()"
    ]
   },
   {
@@ -1318,7 +1316,9 @@
     }
    ],
    "source": [
-    "sim_viewer = FresnelGSD(gsd_file=\"wetting_trajectory.gsd\", view_axis=(0, 1.5, 0), frame=-1)\n",
+    "sim_viewer = FresnelGSD(\n",
+    "    gsd_file=\"wetting_trajectory.gsd\", view_axis=(0, 1.5, 0), frame=-1\n",
+    ")\n",
     "sim_viewer.view()"
    ]
   },

From dceb6313d5e6fadcce4b9196b529550590f6beca Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 26 Aug 2024 13:47:21 -0600
Subject: [PATCH 03/24] [pre-commit.ci] pre-commit autoupdate (#159)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.1 → v0.6.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.1...v0.6.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 44af9a1d..09884528 100644
--- 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: v0.6.1 # Ruff version
+    rev: v0.6.2 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 2cab21517ec240a6ef79dd77ab3851a302ee7c83 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 2 Sep 2024 15:53:43 -0600
Subject: [PATCH 04/24] [pre-commit.ci] pre-commit autoupdate (#162)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 09884528..be9feeeb 100644
--- 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: v0.6.2 # Ruff version
+    rev: v0.6.3 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 6e96d91d1747f0a2ed559985d516c9da118e454a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Sep 2024 13:52:17 -0600
Subject: [PATCH 05/24] [pre-commit.ci] pre-commit autoupdate (#163)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.3 → v0.6.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.3...v0.6.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 be9feeeb..e244b53c 100644
--- 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: v0.6.3 # Ruff version
+    rev: v0.6.4 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From e9205c3f411e90293288cc0abcf2f07a37663346 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Sep 2024 14:18:52 -0600
Subject: [PATCH 06/24] [pre-commit.ci] pre-commit autoupdate (#164)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.4 → v0.6.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.4...v0.6.5)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 e244b53c..dfdf0233 100644
--- 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: v0.6.4 # Ruff version
+    rev: v0.6.5 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From de5b32483aa968ec8b61dcece18de6f83582339b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 23 Sep 2024 13:58:44 -0600
Subject: [PATCH 07/24] [pre-commit.ci] pre-commit autoupdate (#165)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.5...v0.6.7)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 dfdf0233..c7b19fa0 100644
--- 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: v0.6.5 # Ruff version
+    rev: v0.6.7 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 74fc05f1b2591c4be4065b07e05cff4fbbbe39e9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 15:18:13 -0600
Subject: [PATCH 08/24] [pre-commit.ci] pre-commit autoupdate (#166)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.7 → v0.6.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.7...v0.6.8)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 c7b19fa0..db323289 100644
--- 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: v0.6.7 # Ruff version
+    rev: v0.6.8 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From c5255d770411ef975be3ef21adc21aafdcdfb236 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2024 20:35:09 +0000
Subject: [PATCH 09/24] [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: v0.6.8 → v0.6.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.8...v0.6.9)
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index db323289..0100a38c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,14 +9,14 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.8 # Ruff version
+    rev: v0.6.9 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]
       - id: ruff-format
         args: [ --line-length=80 ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer

From 362adbb4f6de9c03ba90a328bdac33c0b652c379 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Oct 2024 13:54:06 -0600
Subject: [PATCH 10/24] [pre-commit.ci] pre-commit autoupdate (#168)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.9...v0.7.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 0100a38c..e2eba3b2 100644
--- 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: v0.6.9 # Ruff version
+    rev: v0.7.0 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 2d89be9813f105e30f2442c3ffca175c7c294e27 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:05:26 -0600
Subject: [PATCH 11/24] [pre-commit.ci] pre-commit autoupdate (#169)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.7.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.0...v0.7.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 e2eba3b2..e7883227 100644
--- 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: v0.7.0 # Ruff version
+    rev: v0.7.1 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 87cb6c44a65862cf8f9d975474f15e079f1ce962 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 12:59:16 -0700
Subject: [PATCH 12/24] [pre-commit.ci] pre-commit autoupdate (#170)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.1 → v0.7.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.1...v0.7.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 e7883227..82f7fe42 100644
--- 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: v0.7.1 # Ruff version
+    rev: v0.7.2 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 99b4b2c9f6c6936d73d25bf5e6dd5c11cf5ce3cd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 11 Nov 2024 13:26:14 -0700
Subject: [PATCH 13/24] [pre-commit.ci] pre-commit autoupdate (#171)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.7.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.2...v0.7.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 82f7fe42..a07a279e 100644
--- 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: v0.7.2 # Ruff version
+    rev: v0.7.3 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 5ae979aad56a07dd015deffe1d649ebd8f31a836 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 12:50:09 -0700
Subject: [PATCH 14/24] [pre-commit.ci] pre-commit autoupdate (#172)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.3 → v0.7.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.3...v0.7.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 a07a279e..3fa374c6 100644
--- 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: v0.7.3 # Ruff version
+    rev: v0.7.4 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 579332a36d1afe27de20718fcf29f372a6801ead Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Nov 2024 19:44:56 +0000
Subject: [PATCH 15/24] [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: v0.7.4 → v0.8.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.4...v0.8.0)
---
 .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 3fa374c6..9126b87c 100644
--- 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: v0.7.4 # Ruff version
+    rev: v0.8.0 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 5a8406981833e6d51c26af47250cd04d3d53601b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 3 Dec 2024 09:29:56 -0700
Subject: [PATCH 16/24] [pre-commit.ci] pre-commit autoupdate (#174)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.0 → v0.8.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.0...v0.8.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 9126b87c..a5a1f4e4 100644
--- 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: v0.8.0 # Ruff version
+    rev: v0.8.1 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 867c085c7ba6d070c8eec3414da61c858da36cea Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 10 Dec 2024 06:20:46 -0700
Subject: [PATCH 17/24] [pre-commit.ci] pre-commit autoupdate (#175)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.1 → v0.8.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.1...v0.8.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 a5a1f4e4..cd638105 100644
--- 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: v0.8.1 # Ruff version
+    rev: v0.8.2 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From ce26407395f6e1cd42a76a01b64e5c88e25ad90d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 13:05:34 -0700
Subject: [PATCH 18/24] [pre-commit.ci] pre-commit autoupdate (#176)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.2 → v0.8.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.2...v0.8.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 cd638105..30b2f1f6 100644
--- 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: v0.8.2 # Ruff version
+    rev: v0.8.3 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 956eb148bf9cf283df7b479b91f97f112a186ecb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 23 Dec 2024 19:53:22 +0000
Subject: [PATCH 19/24] [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: v0.8.3 → v0.8.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.3...v0.8.4)
---
 .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 30b2f1f6..4c8fd163 100644
--- 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: v0.8.3 # Ruff version
+    rev: v0.8.4 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From f6da360bf8edd7bcc39d778664c5faa88a519302 Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Sat, 18 Jan 2025 14:27:39 -0700
Subject: [PATCH 20/24] Update CI file and environments (#180)

* update ci workflows and env file

* uncomment mambaforge version

* replace Mambaforge with Miniforge

* Fix Miniforge name

* fix version

* update unit tests

* fix variable name

* add python 3.12 to test matrix
---
 .github/workflows/pytest.yml         | 18 +++++++++---------
 environment-dev.yml                  |  4 ++--
 environment.yml                      |  4 ++--
 flowermd/tests/base/test_molecule.py | 10 +++++-----
 4 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 9e46e8b0..93275870 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -29,8 +29,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-latest, macOS-13, ubuntu-latest]
-        python-version: ['3.10', '3.11']
+        os: [macos-14, ubuntu-24.04]
+        python-version: ['3.10', '3.11', '3.12']
 
     runs-on: ${{ matrix.os }}
 
@@ -43,8 +43,8 @@ jobs:
       with:
         environment-file: environment-dev.yml
         python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
+        miniforge-variant: Miniforge3
+        miniforge-version: 24.11.0-0
         use-mamba: true
 
     - name: Install package
@@ -63,7 +63,7 @@ jobs:
 
   test-tutorials:
     if: ${{ github.event.issue.pull_request && github.event.comment.body== '/testtutorials'}}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
     - name: Put a reaction to the comment
       run: gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
@@ -96,14 +96,14 @@ jobs:
         PR_NUMBER: ${{ github.event.issue.number }}
 
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         environment-file: environment-dev.yml
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
+        miniforge-variant: Miniforge3
+        miniforge-version: 24.11.0-0
         use-mamba: true
 
     - name: Install package
diff --git a/environment-dev.yml b/environment-dev.yml
index 3285b1f1..0f881fa2 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -8,7 +8,7 @@ dependencies:
   - gmso >=0.12.0
   - gsd >=3.0
   - grits >=0.5.0
-  - hoomd >=4.5
+  - hoomd >=4.5, <5.0
   - mbuild >=0.17.0
   - numpy <2.0
   - openbabel >=3
@@ -18,6 +18,6 @@ dependencies:
   - pytest
   - pytest-cov
   - nbmake
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3
diff --git a/environment.yml b/environment.yml
index 4caf1ddc..3305ba5d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,12 +8,12 @@ dependencies:
   - gmso >=0.12.0
   - gsd >=3.0
   - grits >=0.5.0
-  - hoomd >=4.5
+  - hoomd >=4.5, <5.0
   - mbuild >=0.17.0
   - numpy <2.0
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3
diff --git a/flowermd/tests/base/test_molecule.py b/flowermd/tests/base/test_molecule.py
index b6ad615c..351f722e 100644
--- a/flowermd/tests/base/test_molecule.py
+++ b/flowermd/tests/base/test_molecule.py
@@ -207,8 +207,8 @@ def test_polymer_different_chain_lengths(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 53
-        assert len(polymer.molecules[0].labels["Compound"]) == 3
-        assert len(polymer.molecules[1].labels["Compound"]) == 4
+        assert len(polymer.molecules[0].children) == 3
+        assert len(polymer.molecules[1].children) == 4
 
     def test_polymer_different_num_mol(self, dimethylether_smiles):
         polymer = Polymer(
@@ -220,9 +220,9 @@ def test_polymer_different_num_mol(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 55
-        assert len(polymer.molecules[0].labels["Compound"]) == 3
-        assert len(polymer.molecules[1].labels["Compound"]) == 2
-        assert len(polymer.molecules[2].labels["Compound"]) == 2
+        assert len(polymer.molecules[0].children) == 3
+        assert len(polymer.molecules[1].children) == 2
+        assert len(polymer.molecules[2].children) == 2
 
     def test_polymer_unequal_num_mol_length(self, dimethylether_smiles):
         with pytest.raises(ValueError):

From 7d8d8c15ac23b2f4b92e504078f39b44340f9be9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 19 Jan 2025 10:53:43 -0700
Subject: [PATCH 21/24] [pre-commit.ci] pre-commit autoupdate (#179)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](https://github.com/astral-sh/ruff-pre-commit/compare/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

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.4 → v0.9.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.4...v0.9.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: chrisjonesBSU <chrisjones4@u.boisestate.edu>
---
 .pre-commit-config.yaml                             | 2 +-
 flowermd/base/molecule.py                           | 3 +--
 flowermd/base/simulation.py                         | 3 +--
 flowermd/base/system.py                             | 3 +--
 flowermd/modules/surface_wetting/surface_wetting.py | 3 +--
 5 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4c8fd163..915bf97f 100644
--- 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: v0.8.4 # Ruff version
+    rev: v0.9.1 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]
diff --git a/flowermd/base/molecule.py b/flowermd/base/molecule.py
index c517f57b..aa33e603 100644
--- a/flowermd/base/molecule.py
+++ b/flowermd/base/molecule.py
@@ -525,8 +525,7 @@ def _build(self, length):
                 self.periodic_bond_axis, str
             ) or self.periodic_bond_axis.lower() not in ["x", "y", "z"]:
                 raise ValueError(
-                    "Valid choices for a `periodic_bond_axis` are "
-                    "'x', 'y', 'z'"
+                    "Valid choices for a `periodic_bond_axis` are 'x', 'y', 'z'"
                 )
             add_hydrogens = False
         else:
diff --git a/flowermd/base/simulation.py b/flowermd/base/simulation.py
index 4e62b832..db6fe52b 100644
--- a/flowermd/base/simulation.py
+++ b/flowermd/base/simulation.py
@@ -73,8 +73,7 @@ def __init__(
     ):
         if not isinstance(forcefield, Iterable) or isinstance(forcefield, str):
             raise ValueError(
-                "forcefield must be a sequence of "
-                "hoomd.md.force.Force objects."
+                "forcefield must be a sequence of hoomd.md.force.Force objects."
             )
         else:
             for obj in forcefield:
diff --git a/flowermd/base/system.py b/flowermd/base/system.py
index dc2b0107..820f0bd6 100644
--- a/flowermd/base/system.py
+++ b/flowermd/base/system.py
@@ -660,8 +660,7 @@ def __init__(
         if not isinstance(density, u.array.unyt_quantity):
             self.density = density * u.Unit("g") / u.Unit("cm**3")
             warnings.warn(
-                "Units for density were not given, assuming "
-                "units of g/cm**3."
+                "Units for density were not given, assuming units of g/cm**3."
             )
         else:
             self.density = density
diff --git a/flowermd/modules/surface_wetting/surface_wetting.py b/flowermd/modules/surface_wetting/surface_wetting.py
index 3f35383e..ea2e86aa 100644
--- a/flowermd/modules/surface_wetting/surface_wetting.py
+++ b/flowermd/modules/surface_wetting/surface_wetting.py
@@ -102,8 +102,7 @@ def run_droplet(
             shrink_density, u.array.unyt_quantity
         ) and not isinstance(final_density, u.array.unyt_quantity):
             warnings.warn(
-                "Units for density were not given, assuming "
-                "units of g/cm**3."
+                "Units for density were not given, assuming units of g/cm**3."
             )
             target_box_shrink = get_target_box_mass_density(
                 density=shrink_density * (u.g / (u.cm**3)),

From c2ad06897a9b951627278cdb6659a52559568f64 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 20 Jan 2025 13:34:17 -0700
Subject: [PATCH 22/24] [pre-commit.ci] pre-commit autoupdate (#181)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.1 → v0.9.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.1...v0.9.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 915bf97f..8b3006cc 100644
--- 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: v0.9.1 # Ruff version
+    rev: v0.9.2 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

From 0376b0535834f07fe14b29451b6623bd1d81b11a Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Fri, 24 Jan 2025 11:54:35 -0700
Subject: [PATCH 23/24] Replace `setup.py` with `pyproject.toml`, update CI
 (#182)

* update ci workflows and env file

* uncomment mambaforge version

* replace Mambaforge with Miniforge

* Fix Miniforge name

* fix version

* update unit tests

* fix variable name

* add python 3.12 to test matrix

* Replace setup.py with pyproject.toml file

* update version in pyproject.toml, use mamba runner instead of miniconda

* add comma

* put version in __init__.py
---
 .github/workflows/pytest.yml |  17 +++---
 flowermd/__init__.py         |   2 +
 flowermd/__version__.py      |   3 -
 pyproject.toml               |  43 +++++++++++++
 setup.py                     | 114 -----------------------------------
 5 files changed, 52 insertions(+), 127 deletions(-)
 delete mode 100644 flowermd/__version__.py
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 93275870..f9e5c973 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -39,13 +39,11 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        python-version: ${{ matrix.python-version }}
-        miniforge-variant: Miniforge3
-        miniforge-version: 24.11.0-0
-        use-mamba: true
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Install package
       shell: bash -l {0}
@@ -56,7 +54,7 @@ jobs:
       run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -99,12 +97,11 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        miniforge-variant: Miniforge3
-        miniforge-version: 24.11.0-0
-        use-mamba: true
+        create-args: >-
+          python=3.12
 
     - name: Install package
       shell: bash -l {0}
diff --git a/flowermd/__init__.py b/flowermd/__init__.py
index f8c66533..f88ad9cf 100644
--- a/flowermd/__init__.py
+++ b/flowermd/__init__.py
@@ -10,3 +10,5 @@
     Simulation,
     System,
 )
+
+__version__ = "1.3.1"
diff --git a/flowermd/__version__.py b/flowermd/__version__.py
deleted file mode 100644
index d00a693c..00000000
--- a/flowermd/__version__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-VERSION = (1, 3, 1)
-
-__version__ = ".".join(map(str, VERSION))
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..e8437a17
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.2", "versioningit"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "flowermd"
+description = "Framework for building and running coplex simulaiton workflows with MosDeF and HOOMD-Blue."
+readme = "README.md"
+authors = [
+  {name = "Chris Jones", email = "chrisjones4@u.boisestate.edu"},
+  {name = "Marjan Albooyeh", email = "marjanalbooyeh@u.boisestate.edu"},
+  {name = "Eric Jankowski", email = "ericjankowski@boisestate.edu"}
+]
+license= {text = "GPLv3"}
+classifiers=[
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+urls = {Homepage = "https://github.com/cmelab/flowermd"}
+requires-python = ">=3.10"
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages]
+find = {namespaces = false}
+
+[tool.setuptools.package-data]
+flowermd = [
+  '"modules/**"',
+  '"library/**"',
+  '"assets/forcefields/**"',
+  '"assets/molecule_files/**"',
+  '"utils/**"',
+  '"internal/**"',
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "flowermd.__version__"}
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 7369f8ab..00000000
--- a/setup.py
+++ /dev/null
@@ -1,114 +0,0 @@
-import os
-import sys
-from shutil import rmtree
-
-from setuptools import Command, find_packages, setup
-
-# Package meta-data.
-NAME = "flowermd"
-DESCRIPTION = (
-    "Package making it easier to build and simulate polymers in Hoomd-Blue."
-)
-URL = "https://github.com/cmelab/flowerMD"
-EMAIL = "chrisjones4@u.boisestate.edu"
-AUTHOR = "CME Lab"
-REQUIRES_PYTHON = ">=3.10.0"
-VERSION = None
-
-# What packages are required for this module to be executed?
-REQUIRED = []
-
-# Follow the README and use the environment.yml file to install
-# the needed packages.
-# ------------------------------------------------
-
-here = os.path.abspath(os.path.dirname(__file__))
-
-# Load the package's __version__.py module as a dictionary.
-about = {}
-if not VERSION:
-    with open(os.path.join(here, NAME, "__version__.py")) as f:
-        exec(f.read(), about)
-else:
-    about["__version__"] = VERSION
-
-
-class UploadCommand(Command):
-    """Support setup.py upload."""
-
-    description = "Build and publish the package."
-    user_options = []
-
-    @staticmethod
-    def status(s):
-        """Prints things in bold."""
-        print("\033[1m{0}\033[0m".format(s))
-
-    def initialize_options(self):
-        pass
-
-    def finalize_options(self):
-        pass
-
-    def run(self):
-        try:
-            self.status("Removing previous builds…")
-            rmtree(os.path.join(here, "dist"))
-        except OSError:
-            pass
-
-        self.status("Building Source and Wheel (universal) distribution…")
-        os.system(
-            "{0} setup.py sdist bdist_wheel --universal".format(sys.executable)
-        )
-
-        self.status("Uploading the package to PyPi via Twine…")
-        os.system("twine upload dist/*")
-
-        self.status("Pushing git tags…")
-        os.system("git tag v{0}".format(about["__version__"]))
-        os.system("git push --tags")
-
-        sys.exit()
-
-
-setup(
-    name=NAME,
-    version=about["__version__"],
-    description=DESCRIPTION,
-    author=AUTHOR,
-    author_email=EMAIL,
-    python_requires=REQUIRES_PYTHON,
-    url=URL,
-    packages=find_packages(
-        exclude=(
-            "tests",
-            "docs",
-        )
-    ),
-    package_data={
-        "flowermd": [
-            "modules/**",
-            "library/**",
-            "assets/forcefields/**",
-            "assets/molecule_files/**",
-            "utils/**",
-            "internal/**",
-        ],
-    },
-    install_requires=REQUIRED,
-    include_package_data=True,
-    license="GPLv3",
-    classifiers=[
-        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: Implementation :: CPython",
-        "Programming Language :: Python :: Implementation :: PyPy",
-    ],
-    # $ setup.py publish support.
-    cmdclass={
-        "upload": UploadCommand,
-    },
-)

From 95198060bd07b19270e40d0ce7eb59ea32a5183b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jan 2025 13:51:44 -0700
Subject: [PATCH 24/24] [pre-commit.ci] pre-commit autoupdate (#185)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.2 → v0.9.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.2...v0.9.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 8b3006cc..6cd72352 100644
--- 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: v0.9.2 # Ruff version
+    rev: v0.9.3 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]