Minor fixes (#614)

Author: david-zwicker

examples/trajectory_io.py

@@ -18,12 +18,11 @@
 eq = pde.PDE({"s": "-0.1 * s", "v": "-v"})
 
 # get a temporary file to write data to
-path = NamedTemporaryFile(suffix=".hdf5")
+with NamedTemporaryFile(suffix=".hdf5") as path:
+    # run a simulation and write the results
+    writer = pde.FileStorage(path.name, write_mode="truncate")
+    eq.solve(state, t_range=32, dt=0.01, tracker=writer.tracker(1))
 
-# run a simulation and write the results
-writer = pde.FileStorage(path.name, write_mode="truncate")
-eq.solve(state, t_range=32, dt=0.01, tracker=writer.tracker(1))
-
-# read the simulation back in again
-reader = pde.FileStorage(path.name, write_mode="read_only")
-pde.plot_kymographs(reader)
+    # read the simulation back in again
+    reader = pde.FileStorage(path.name, write_mode="read_only")
+    pde.plot_kymographs(reader)

pde/tools/docstrings.py

@@ -15,7 +15,7 @@
 import re
 import textwrap
 from functools import partial
-from typing import TypeVar
+from typing import Callable, TypeVar
 
 DOCSTRING_REPLACEMENTS = {
     # description of function arguments
@@ -121,7 +121,7 @@ def get_text_block(identifier: str) -> str:
     return "".join(textwrap.dedent(raw_text))
 
 
-TFunc = TypeVar("TFunc")
+TFunc = TypeVar("TFunc", bound=Callable)
 
 
 def replace_in_docstring(

tests/_notebooks/Test PlotTracker for different backend.ipynb

@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -78,18 +78,18 @@
    ],
    "source": [
     "eq = pde.DiffusionPDE()\n",
-    "movie_file = tempfile.NamedTemporaryFile(delete=False, suffix=\".mov\").name\n",
-    "plot_tracker = pde.PlotTracker(\n",
-    "    0.1, title=\"Visible – {time:.2g}\", show=True, movie=movie_file\n",
-    ")\n",
-    "_, info = eq.solve(\n",
-    "    field,\n",
-    "    t_range=2,\n",
-    "    dt=0.1,\n",
-    "    backend=\"numpy\",\n",
-    "    ret_info=True,\n",
-    "    tracker=[\"progress\", plot_tracker],\n",
-    ")"
+    "with tempfile.NamedTemporaryFile(delete=False, suffix=\".mov\") as movie_file:\n",
+    "    plot_tracker = pde.PlotTracker(\n",
+    "        0.1, title=\"Visible – {time:.2g}\", show=True, movie=movie_file.name\n",
+    "    )\n",
+    "    _, info = eq.solve(\n",
+    "        field,\n",
+    "        t_range=2,\n",
+    "        dt=0.1,\n",
+    "        backend=\"numpy\",\n",
+    "        ret_info=True,\n",
+    "        tracker=[\"progress\", plot_tracker],\n",
+    "    )"
    ]
   },
   {
@@ -144,7 +144,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -164,18 +164,18 @@
    ],
    "source": [
     "eq = pde.DiffusionPDE()\n",
-    "movie_file = tempfile.NamedTemporaryFile(delete=False, suffix=\".mov\").name\n",
-    "plot_tracker = pde.PlotTracker(\n",
-    "    0.1, title=\"Hidden – {time:.2g}\", show=False, movie=movie_file\n",
-    ")\n",
-    "_, info = eq.solve(\n",
-    "    field,\n",
-    "    t_range=2,\n",
-    "    dt=0.1,\n",
-    "    backend=\"numpy\",\n",
-    "    ret_info=True,\n",
-    "    tracker=[\"progress\", plot_tracker],\n",
-    ")"
+    "with tempfile.NamedTemporaryFile(delete=False, suffix=\".mov\") as movie_file:\n",
+    "    plot_tracker = pde.PlotTracker(\n",
+    "        0.1, title=\"Hidden – {time:.2g}\", show=False, movie=movie_file.name\n",
+    "    )\n",
+    "    _, info = eq.solve(\n",
+    "        field,\n",
+    "        t_range=2,\n",
+    "        dt=0.1,\n",
+    "        backend=\"numpy\",\n",
+    "        ret_info=True,\n",
+    "        tracker=[\"progress\", plot_tracker],\n",
+    "    )"
    ]
   },
   {
@@ -236,7 +236,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -263,22 +263,22 @@
    ],
    "source": [
     "eq = pde.PDE({\"a\": \"laplace(a)\", \"b\": \"laplace(b)\"})\n",
-    "movie_file = tempfile.NamedTemporaryFile(delete=False, suffix=\".mov\").name\n",
-    "plot_tracker = pde.PlotTracker(\n",
-    "    0.5,\n",
-    "    title=\"Visible Plot Collection – {time:.2g}\",\n",
-    "    show=True,\n",
-    "    movie=movie_file,\n",
-    "    plot_args={\"colorbar\": True},\n",
-    ")\n",
-    "_, info = eq.solve(\n",
-    "    fc,\n",
-    "    t_range=2,\n",
-    "    dt=0.1,\n",
-    "    backend=\"numpy\",\n",
-    "    ret_info=True,\n",
-    "    tracker=[\"progress\", plot_tracker],\n",
-    ")"
+    "with tempfile.NamedTemporaryFile(delete=False, suffix=\".mov\") as movie_file:\n",
+    "    plot_tracker = pde.PlotTracker(\n",
+    "        0.5,\n",
+    "        title=\"Visible Plot Collection – {time:.2g}\",\n",
+    "        show=True,\n",
+    "        movie=movie_file.name,\n",
+    "        plot_args={\"colorbar\": True},\n",
+    "    )\n",
+    "    _, info = eq.solve(\n",
+    "        fc,\n",
+    "        t_range=2,\n",
+    "        dt=0.1,\n",
+    "        backend=\"numpy\",\n",
+    "        ret_info=True,\n",
+    "        tracker=[\"progress\", plot_tracker],\n",
+    "    )"
    ]
   },
   {