apply formatting

pdebench/__init__.py

@@ -19,6 +19,7 @@
 
 
 """
+
 from __future__ import annotations
 
 import logging

pdebench/data_gen/data_gen_NLE/AdvectionEq/advection_exact_Hydra.py

@@ -143,6 +143,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import logging

pdebench/data_gen/data_gen_NLE/AdvectionEq/advection_multi_solution_Hydra.py

@@ -143,6 +143,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import random
@@ -165,6 +166,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 def _pass(carry):
     return carry
 
@@ -233,7 +235,6 @@ def _show(_carry):
         t, tsave, steps, i_save, dt, u, uu = lax.while_loop(cond_fun, _body_fun, carry)
         return uu.at[-1].set(u)
 
-
     @jax.jit
     def simulation_fn(i, carry):
         u, t, dt, steps, tsave = carry

pdebench/data_gen/data_gen_NLE/BurgersEq/burgers_Hydra.py

@@ -143,6 +143,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import logging

pdebench/data_gen/data_gen_NLE/BurgersEq/burgers_multi_solution_Hydra.py

@@ -143,6 +143,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import logging
@@ -233,7 +234,6 @@ def _show(_carry):
         t, tsave, steps, i_save, dt, u, uu = lax.while_loop(cond_fun, _body_fun, carry)
         return uu.at[-1].set(u)
 
-
     @jax.jit
     def simulation_fn(i, carry):
         u, t, dt, steps, tsave = carry

pdebench/data_gen/gen_radial_dam_break.py

@@ -101,7 +101,6 @@ def main(config: DictConfig):
     # Change back to the hydra working directory
     os.chdir(temp_path)
 
-
     work_path = Path(config.work_dir)
     output_path = work_path / config.data_dir / config.output_path
     if not output_path.is_dir():

pdebench/data_gen/notebooks/Analysis.ipynb

@@ -76,8 +76,8 @@
     }
    ],
    "source": [
-    "data_path = resolve_path('${WORKING_DIR}/*/*/*/*/*/*.h5', idx=-1, unique=False)\n",
-    "print(data_path)  # noqa: T201\n"
+    "data_path = resolve_path(\"${WORKING_DIR}/*/*/*/*/*/*.h5\", idx=-1, unique=False)\n",
+    "print(data_path)  # noqa: T201"
    ]
   },
   {
@@ -97,7 +97,7 @@
     }
    ],
    "source": [
-    "data_f = h5py.File(data_path, 'r')\n",
+    "data_f = h5py.File(data_path, \"r\")\n",
     "data_f.keys()"
    ]
   },
@@ -118,7 +118,7 @@
     }
    ],
    "source": [
-    "data_f['particles'].shape"
+    "data_f[\"particles\"].shape"
    ]
   },
   {
@@ -140,16 +140,15 @@
     }
    ],
    "source": [
-    "\n",
     "columns = 5\n",
     "fsize = 12\n",
     "\n",
-    "arr = data_f['particles'][0, :columns, :, :, 0]\n",
+    "arr = data_f[\"particles\"][0, :columns, :, :, 0]\n",
     "\n",
-    "fig = plt.figure(figsize=(fsize, fsize/columns))\n",
-    "plt.imshow(rearrange(arr, 't x y -> x (t y)'))\n",
+    "fig = plt.figure(figsize=(fsize, fsize / columns))\n",
+    "plt.imshow(rearrange(arr, \"t x y -> x (t y)\"))\n",
     "plt.gca().set_axis_off()\n",
-    "plt.tight_layout(pad = 1)\n",
+    "plt.tight_layout(pad=1)\n",
     "plt.show()"
    ]
   },
@@ -172,16 +171,15 @@
     }
    ],
    "source": [
-    "\n",
     "columns = 5\n",
     "fsize = 12\n",
     "\n",
-    "arr = data_f['particles'][0, 1000:1000+columns, :, :, 0]\n",
+    "arr = data_f[\"particles\"][0, 1000 : 1000 + columns, :, :, 0]\n",
     "\n",
-    "fig = plt.figure(figsize=(fsize, fsize/columns))\n",
-    "plt.imshow(rearrange(arr, 't x y -> x (t y)'))\n",
+    "fig = plt.figure(figsize=(fsize, fsize / columns))\n",
+    "plt.imshow(rearrange(arr, \"t x y -> x (t y)\"))\n",
     "plt.gca().set_axis_off()\n",
-    "plt.tight_layout(pad = 1)\n",
+    "plt.tight_layout(pad=1)\n",
     "plt.show()"
    ]
   },
@@ -204,16 +202,15 @@
     }
    ],
    "source": [
-    "\n",
     "columns = 5\n",
     "fsize = 12\n",
     "\n",
-    "arr = data_f['force'][:columns, :, :, 0]\n",
+    "arr = data_f[\"force\"][:columns, :, :, 0]\n",
     "\n",
-    "fig = plt.figure(figsize=(fsize, fsize/columns))\n",
-    "plt.imshow(rearrange(arr, 'b x y -> x (b y)'))\n",
+    "fig = plt.figure(figsize=(fsize, fsize / columns))\n",
+    "plt.imshow(rearrange(arr, \"b x y -> x (b y)\"))\n",
     "plt.gca().set_axis_off()\n",
-    "plt.tight_layout(pad = 1)\n",
+    "plt.tight_layout(pad=1)\n",
     "plt.show()"
    ]
   },

pdebench/data_gen/plot.py

@@ -3,6 +3,7 @@
 
 @author: timot
 """
+
 from __future__ import annotations
 
 import os
@@ -63,6 +64,5 @@ def main(config: DictConfig):
     )
 
 
-
 if __name__ == "__main__":
     main()

pdebench/data_gen/src/plots.py

@@ -2,6 +2,7 @@
 Author : John Kim, Simon Brown, Timothy Praditia
 PDE Simulation packages
 """
+
 from __future__ import annotations
 
 import h5py
@@ -18,7 +19,7 @@ def plot_data(data, t, dim, channel, t_fraction, config, filename):
     plt.figure()
     plt.title(f"$t={t[t_idx]}$")
     if dim == 1:
-        with h5py.File(config.data_path, 'r') as h5_file:
+        with h5py.File(config.data_path, "r") as h5_file:
             x = np.array(h5_file["grid"]["x"], dtype="f")
         plt.plot(x.squeeze(), data[t_idx, ..., channel])
         plt.xlabel("$x$")

pdebench/data_gen/src/sim_diff_react.py

@@ -157,5 +157,3 @@ def rc_ode(self, t, y):  # noqa: ARG002
 
         # Stack the time derivative into a single array y_t
         return np.concatenate((u_t, v_t))
-
-

pdebench/data_gen/src/sim_ns_incomp_2d.py

@@ -2,6 +2,7 @@
 Author : John Kim, Ran Zhang, Dan MacKinlay
 PDE Simulation packages
 """
+
 from __future__ import annotations
 
 import logging

pdebench/data_gen/src/sim_radial_dam_break.py

@@ -10,6 +10,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 class Basic2DScenario(ABC):
     name = ""
 

pdebench/data_gen/src/utils.py

@@ -19,7 +19,7 @@ def matching_paths(glob_exp):
     return a list of paths matching a glob expression
     """
     path = os.path.expandvars(Path(glob_exp).expanduser())
-    return list(Path(path).glob('*'))
+    return list(Path(path).glob("*"))
 
 
 def resolve_path(path, idx=None, unique=True):

pdebench/data_gen/src/vorticity.py

@@ -1,4 +1,4 @@
-r""" Generate vorticity field :math:`\boldsymbol{\omega} = \nabla \times \boldsymbol{v}` given
+r"""Generate vorticity field :math:`\boldsymbol{\omega} = \nabla \times \boldsymbol{v}` given
      velocity field :math:`\boldsymbol{v}` using numerical approximation.
 
 Assuming the velocitiy field of shape [n, sx, sy, sz, 3] (5D) consists of a trajectory of equidistant cells,
@@ -15,6 +15,7 @@
 
 for approximating the vorticity field.
 """
+
 from __future__ import annotations
 
 import jax

pdebench/data_gen/velocity2vorticity.py

@@ -1,6 +1,7 @@
-""" Convert velocity- to vorticity field assuming 3D CFD exampe was downloaded.
-    The resulting .hdf5 file does not store pressure and density.
+"""Convert velocity- to vorticity field assuming 3D CFD exampe was downloaded.
+The resulting .hdf5 file does not store pressure and density.
 """
+
 from __future__ import annotations
 
 import argparse

pdebench/models/analyse_result_forward.py

@@ -144,6 +144,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import _pickle as cPickle

pdebench/models/analyse_result_inverse.py

@@ -144,6 +144,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import matplotlib.pyplot as plt

pdebench/models/fno/fno.py

@@ -24,6 +24,7 @@
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
+
 from __future__ import annotations
 
 import torch

pdebench/models/fno/train.py

@@ -14,6 +14,7 @@
 # np.random.seed(0)
 device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
+
 def run_training(
     if_training,
     continue_training,

pdebench/models/fno/utils.py

@@ -146,6 +146,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import math as mt

pdebench/models/inverse/inverse.py

@@ -144,6 +144,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import pyro

pdebench/models/inverse/train.py

@@ -144,6 +144,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import logging

pdebench/models/inverse/utils.py

@@ -144,6 +144,7 @@
 
        THIS HEADER MAY NOT BE EXTRACTED OR MODIFIED IN ANY WAY.
 """
+
 from __future__ import annotations
 
 import logging
@@ -157,6 +158,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 def plot_ic_solution_mcmc(
     latent,
     x,