more efficient types

pyproject.toml

@@ -51,9 +51,6 @@ exclude = '''
 files = ["src", "scripts"]
 
 ignore_missing_imports = true
-allow_redefinition = true
-show_error_context = false
-show_column_numbers = true
 
 [tool.pytest.ini_options]
 log_cli = true

src/gemini3d/grid/uniform.py

@@ -58,14 +58,14 @@ def non_uniform1d(xmax: float, parms: list[float]):
     ell = parms[3]  # transition length of degradation
     x2 = xmax - degdist
 
-    x = [dx0 / 2.0]
+    x = np.array([dx0 / 2.0])
     # start offset from zero so we can have an even number (better for mpi)
 
     while x[-1] < xmax:
         dx = dx0 + dxincr * (1 / 2 + 1 / 2 * math.tanh((x[-1] - x2) / ell))
-        x.append(x[-1] + dx)
+        x = np.append(x, x[-1] + dx)
 
-    x = np.append(-np.array(x[::-1]), x)
+    x = np.append(-x[::-1], x)
 
     return x
 
@@ -78,14 +78,13 @@ def altitude_grid(
     if alt_max <= alt_min:
         raise ValueError("grid_max must be greater than grid_min")
 
-    alt = [alt_min]
+    alt = np.array([alt_min])
 
     while alt[-1] < alt_max:
         # dalt=10+9.5*tanh((alt(i-1)-500)/150)
         dalt = d[0] + d[1] * math.tanh((alt[-1] - d[2]) / d[3])
-        alt.append(alt[-1] + dalt)
+        alt = np.append(alt, alt[-1] + dalt)
 
-    alt = np.asarray(alt)
     if alt.size < 10:
         raise ValueError("grid too small")
 

src/gemini3d/job.py

@@ -169,22 +169,22 @@ def check_compiler():
         raise EnvironmentError("Cannot find Fortran compiler e.g. Gfortran")
 
 
-def check_mpiexec(mpiexec: str, gemexe: Path) -> str:
+def check_mpiexec(mpiexec_name: str, gemexe: Path) -> str:
     """
     check if specified mpiexec exists on this system.
     If not, error as most runs are exceedingly slow with one CPU core.
     """
 
-    if not mpiexec:
-        mpiexec = "mpiexec"
+    if not mpiexec_name:
+        mpiexec_name = "mpiexec"
 
     mpi_root = os.environ.get("MPI_ROOT", None)
     if mpi_root:
         mpi_root += "/bin"
 
-    mpiexec = shutil.which(mpiexec, path=mpi_root)
+    mpiexec = shutil.which(mpiexec_name, path=mpi_root)
     if not mpiexec:
-        raise FileNotFoundError(f"Cannot find mpiexec {mpiexec}")
+        raise FileNotFoundError(f"Cannot find mpiexec {mpiexec_name}")
 
     ret = subprocess.run([mpiexec, "-help"], capture_output=True, text=True, timeout=5)
     if ret.returncode != 0:

src/gemini3d/magcalc.py

@@ -93,6 +93,6 @@ def magcalc(
         nargs="?",
         default=1.5,
     )
-    P = P.parse_args()
+    args = P.parse_args()
 
-    magcalc(P.direc, P.dang)
+    magcalc(args.direc, args.dang)

src/gemini3d/magtools.py

@@ -12,7 +12,7 @@
 
 
 def makegrid(
-    direc: str,
+    direc: Path,
     dang: float = 1.5,
     ltheta: int = 16,
     lphi: int = 16,
@@ -89,7 +89,7 @@ def makegrid(
 
 
 def makegrid_full(
-    direc: str,
+    direc: Path,
     ltheta: int = 16,
     lphi: int = 16,
     write_grid: bool = False,

src/gemini3d/read.py

@@ -9,7 +9,6 @@
 import typing as T
 
 import numpy as np
-import xarray
 
 from .config import read_nml
 from . import find
@@ -76,7 +75,7 @@ def frame(
     *,
     cfg: dict[str, T.Any] | None = None,
     xg: dict[str, T.Any] | None = None,
-) -> xarray.Dataset:
+):
     """
     load a frame of simulation data, automatically selecting the correct
     functions based on simulation parameters
@@ -93,6 +92,12 @@ def frame(
         to avoid reading config.nml
     xg: dict
         to avoid reading simgrid.*, useful to save time when reading data files in a loop
+
+    Returns
+    -------
+
+    dat: xarray.Dataset
+        simulation data from this time
     """
 
     # %% default variables