ruff-format with settings that match HOOMD-blue.

glotzerlab · Nov 27, 2024 · df4bc80 · df4bc80
1 parent 43d8f7d
commit df4bc80
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Showing 49 changed files with 508 additions and 509 deletions.
diff --git a/.ruff.toml b/.ruff.toml
@@ -1,6 +1,6 @@
-target-version = "py38"
-
 extend-include = ["*.ipynb"]
+line-length = 88
+indent-width = 4
 
 [lint]
 
@@ -50,7 +50,8 @@ ignore = [
 convention = "google"
 
 [format]
-quote-style = "single"
+indent-style = "space"
+line-ending = "auto"
 
 [lint.flake8-import-conventions]
 # Prefer no import aliases

diff --git a/00-Introducing-HOOMD-blue/02-Performing-Hard-Particle-Monte-Carlo-Simulations.ipynb b/00-Introducing-HOOMD-blue/02-Performing-Hard-Particle-Monte-Carlo-Simulations.ipynb
@@ -76,7 +76,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mc.shape['octahedron'] = dict(\n",
+    "mc.shape[\"octahedron\"] = dict(\n",
     "    vertices=[\n",
     "        (-0.5, 0, 0),\n",
     "        (0.5, 0, 0),\n",
@@ -113,8 +113,8 @@
    "outputs": [],
    "source": [
     "mc.nselect = 2\n",
-    "mc.d['octahedron'] = 0.15\n",
-    "mc.a['octahedron'] = 0.2"
+    "mc.d[\"octahedron\"] = 0.15\n",
+    "mc.a[\"octahedron\"] = 0.2"
    ]
   },
   {

diff --git a/00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb b/00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb
@@ -50,7 +50,7 @@
    "source": [
     "import os\n",
     "\n",
-    "fn = os.path.join(os.getcwd(), 'lattice.gsd')\n",
+    "fn = os.path.join(os.getcwd(), \"lattice.gsd\")\n",
     "![ -e \"$fn\" ] && rm \"$fn\""
    ]
   },
@@ -85,18 +85,18 @@
     "device = fresnel.Device()\n",
     "tracer = fresnel.tracer.Path(device=device, w=300, h=300)\n",
     "\n",
-    "FRESNEL_MIN_VERSION = packaging.version.parse('0.13.0')\n",
-    "FRESNEL_MAX_VERSION = packaging.version.parse('0.14.0')\n",
+    "FRESNEL_MIN_VERSION = packaging.version.parse(\"0.13.0\")\n",
+    "FRESNEL_MAX_VERSION = packaging.version.parse(\"0.14.0\")\n",
     "\n",
     "\n",
     "def render(position, orientation, L):\n",
     "    if (\n",
-    "        'version' not in dir(fresnel)\n",
+    "        \"version\" not in dir(fresnel)\n",
     "        or packaging.version.parse(fresnel.version.version) < FRESNEL_MIN_VERSION\n",
     "        or packaging.version.parse(fresnel.version.version) >= FRESNEL_MAX_VERSION\n",
     "    ):\n",
     "        warnings.warn(\n",
-    "            f'Unsupported fresnel version {fresnel.version.version} - expect errors.'\n",
+    "            f\"Unsupported fresnel version {fresnel.version.version} - expect errors.\"\n",
     "        )\n",
     "    vertices = [\n",
     "        (-0.5, 0, 0),\n",
@@ -361,7 +361,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "frame.particles.types = ['octahedron']"
+    "frame.particles.types = [\"octahedron\"]"
    ]
   },
   {
@@ -393,7 +393,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with gsd.hoomd.open(name='lattice.gsd', mode='x') as f:\n",
+    "with gsd.hoomd.open(name=\"lattice.gsd\", mode=\"x\") as f:\n",
     "    f.append(frame)"
    ]
   },
@@ -430,7 +430,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.create_state_from_gsd(filename='lattice.gsd')"
+    "simulation.create_state_from_gsd(filename=\"lattice.gsd\")"
    ]
   },
   {

diff --git a/00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb b/00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb
@@ -47,7 +47,7 @@
    "source": [
     "import os\n",
     "\n",
-    "fn = os.path.join(os.getcwd(), 'random.gsd')\n",
+    "fn = os.path.join(os.getcwd(), \"random.gsd\")\n",
     "![ -e \"$fn\" ] && rm \"$fn\""
    ]
   },
@@ -82,18 +82,18 @@
     "device = fresnel.Device()\n",
     "tracer = fresnel.tracer.Path(device=device, w=300, h=300)\n",
     "\n",
-    "FRESNEL_MIN_VERSION = packaging.version.parse('0.13.0')\n",
-    "FRESNEL_MAX_VERSION = packaging.version.parse('0.14.0')\n",
+    "FRESNEL_MIN_VERSION = packaging.version.parse(\"0.13.0\")\n",
+    "FRESNEL_MAX_VERSION = packaging.version.parse(\"0.14.0\")\n",
     "\n",
     "\n",
     "def render(snapshot):\n",
     "    if (\n",
-    "        'version' not in dir(fresnel)\n",
+    "        \"version\" not in dir(fresnel)\n",
     "        or packaging.version.parse(fresnel.version.version) < FRESNEL_MIN_VERSION\n",
     "        or packaging.version.parse(fresnel.version.version) >= FRESNEL_MAX_VERSION\n",
     "    ):\n",
     "        warnings.warn(\n",
-    "            f'Unsupported fresnel version {fresnel.version.version} - expect errors.'\n",
+    "            f\"Unsupported fresnel version {fresnel.version.version} - expect errors.\"\n",
     "        )\n",
     "    L = snapshot.configuration.box[0]\n",
     "    vertices = [\n",
@@ -166,7 +166,7 @@
     "simulation = hoomd.Simulation(device=cpu, seed=12)\n",
     "\n",
     "mc = hoomd.hpmc.integrate.ConvexPolyhedron()\n",
-    "mc.shape['octahedron'] = dict(\n",
+    "mc.shape[\"octahedron\"] = dict(\n",
     "    vertices=[\n",
     "        (-0.5, 0, 0),\n",
     "        (0.5, 0, 0),\n",
@@ -178,7 +178,7 @@
     ")\n",
     "\n",
     "simulation.operations.integrator = mc\n",
-    "simulation.create_state_from_gsd(filename='lattice.gsd')"
+    "simulation.create_state_from_gsd(filename=\"lattice.gsd\")"
    ]
   },
   {
@@ -480,7 +480,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hoomd.write.GSD.write(state=simulation.state, mode='xb', filename='random.gsd')"
+    "hoomd.write.GSD.write(state=simulation.state, mode=\"xb\", filename=\"random.gsd\")"
    ]
   },
   {

diff --git a/00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb b/00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb
@@ -47,7 +47,7 @@
    "source": [
     "import os\n",
     "\n",
-    "fn = os.path.join(os.getcwd(), 'compressed.gsd')\n",
+    "fn = os.path.join(os.getcwd(), \"compressed.gsd\")\n",
     "![ -e \"$fn\" ] && rm \"$fn\""
    ]
   },
@@ -82,18 +82,18 @@
     "device = fresnel.Device()\n",
     "tracer = fresnel.tracer.Path(device=device, w=300, h=300)\n",
     "\n",
-    "FRESNEL_MIN_VERSION = packaging.version.parse('0.13.0')\n",
-    "FRESNEL_MAX_VERSION = packaging.version.parse('0.14.0')\n",
+    "FRESNEL_MIN_VERSION = packaging.version.parse(\"0.13.0\")\n",
+    "FRESNEL_MAX_VERSION = packaging.version.parse(\"0.14.0\")\n",
     "\n",
     "\n",
     "def render(snapshot):\n",
     "    if (\n",
-    "        'version' not in dir(fresnel)\n",
+    "        \"version\" not in dir(fresnel)\n",
     "        or packaging.version.parse(fresnel.version.version) < FRESNEL_MIN_VERSION\n",
     "        or packaging.version.parse(fresnel.version.version) >= FRESNEL_MAX_VERSION\n",
     "    ):\n",
     "        warnings.warn(\n",
-    "            f'Unsupported fresnel version {fresnel.version.version} - expect errors.'\n",
+    "            f\"Unsupported fresnel version {fresnel.version.version} - expect errors.\"\n",
     "        )\n",
     "    L = snapshot.configuration.box[0]\n",
     "    vertices = [\n",
@@ -153,7 +153,7 @@
    "source": [
     "cpu = hoomd.device.CPU()\n",
     "simulation = hoomd.Simulation(device=cpu, seed=12)\n",
-    "simulation.create_state_from_gsd(filename='random.gsd')"
+    "simulation.create_state_from_gsd(filename=\"random.gsd\")"
    ]
   },
   {
@@ -222,7 +222,7 @@
    "outputs": [],
    "source": [
     "mc = hoomd.hpmc.integrate.ConvexPolyhedron()\n",
-    "mc.shape['octahedron'] = dict(\n",
+    "mc.shape[\"octahedron\"] = dict(\n",
     "    vertices=[\n",
     "        (-0.5, 0, 0),\n",
     "        (0.5, 0, 0),\n",
@@ -311,7 +311,7 @@
    "source": [
     "periodic = hoomd.trigger.Periodic(10)\n",
     "tune = hoomd.hpmc.tune.MoveSize.scale_solver(\n",
-    "    moves=['a', 'd'],\n",
+    "    moves=[\"a\", \"d\"],\n",
     "    target=0.2,\n",
     "    trigger=periodic,\n",
     "    max_translation_move=0.2,\n",
@@ -383,7 +383,7 @@
    "outputs": [],
    "source": [
     "if not compress.complete:\n",
-    "    message = 'Compression failed to complete'\n",
+    "    message = \"Compression failed to complete\"\n",
     "    raise RuntimeError(message)"
    ]
   },
@@ -411,7 +411,7 @@
     }
    ],
    "source": [
-    "mc.a['octahedron']"
+    "mc.a[\"octahedron\"]"
    ]
   },
   {
@@ -431,7 +431,7 @@
     }
    ],
    "source": [
-    "mc.d['octahedron']"
+    "mc.d[\"octahedron\"]"
    ]
   },
   {
@@ -475,7 +475,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hoomd.write.GSD.write(state=simulation.state, mode='xb', filename='compressed.gsd')"
+    "hoomd.write.GSD.write(state=simulation.state, mode=\"xb\", filename=\"compressed.gsd\")"
    ]
   }
  ],

diff --git a/00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb b/00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb
@@ -47,7 +47,7 @@
    "source": [
     "import os\n",
     "\n",
-    "fn = os.path.join(os.getcwd(), 'trajectory.gsd')\n",
+    "fn = os.path.join(os.getcwd(), \"trajectory.gsd\")\n",
     "![ -e \"$fn\" ] && rm \"$fn\""
    ]
   },
@@ -84,18 +84,18 @@
     "device = fresnel.Device()\n",
     "tracer = fresnel.tracer.Path(device=device, w=300, h=300)\n",
     "\n",
-    "FRESNEL_MIN_VERSION = packaging.version.parse('0.13.0')\n",
-    "FRESNEL_MAX_VERSION = packaging.version.parse('0.14.0')\n",
+    "FRESNEL_MIN_VERSION = packaging.version.parse(\"0.13.0\")\n",
+    "FRESNEL_MAX_VERSION = packaging.version.parse(\"0.14.0\")\n",
     "\n",
     "\n",
     "def render(snapshot):\n",
     "    if (\n",
-    "        'version' not in dir(fresnel)\n",
+    "        \"version\" not in dir(fresnel)\n",
     "        or packaging.version.parse(fresnel.version.version) < FRESNEL_MIN_VERSION\n",
     "        or packaging.version.parse(fresnel.version.version) >= FRESNEL_MAX_VERSION\n",
     "    ):\n",
     "        warnings.warn(\n",
-    "            f'Unsupported fresnel version {fresnel.version.version} - expect errors.'\n",
+    "            f\"Unsupported fresnel version {fresnel.version.version} - expect errors.\"\n",
     "        )\n",
     "\n",
     "    L = snapshot.configuration.box[0]\n",
@@ -158,7 +158,7 @@
     "cpu = hoomd.device.CPU()\n",
     "simulation = hoomd.Simulation(device=cpu, seed=12)\n",
     "mc = hoomd.hpmc.integrate.ConvexPolyhedron()\n",
-    "mc.shape['octahedron'] = dict(\n",
+    "mc.shape[\"octahedron\"] = dict(\n",
     "    vertices=[\n",
     "        (-0.5, 0, 0),\n",
     "        (0.5, 0, 0),\n",
@@ -185,7 +185,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.create_state_from_gsd(filename='compressed.gsd')"
+    "simulation.create_state_from_gsd(filename=\"compressed.gsd\")"
    ]
   },
   {
@@ -209,7 +209,7 @@
    "outputs": [],
    "source": [
     "gsd_writer = hoomd.write.GSD(\n",
-    "    filename='trajectory.gsd', trigger=hoomd.trigger.Periodic(1000), mode='xb'\n",
+    "    filename=\"trajectory.gsd\", trigger=hoomd.trigger.Periodic(1000), mode=\"xb\"\n",
     ")\n",
     "simulation.operations.writers.append(gsd_writer)"
    ]
@@ -236,7 +236,7 @@
    "outputs": [],
    "source": [
     "tune = hoomd.hpmc.tune.MoveSize.scale_solver(\n",
-    "    moves=['a', 'd'],\n",
+    "    moves=[\"a\", \"d\"],\n",
     "    target=0.2,\n",
     "    trigger=hoomd.trigger.And(\n",
     "        [hoomd.trigger.Periodic(100), hoomd.trigger.Before(simulation.timestep + 5000)]\n",