Bump allowed python version to 3.12 (#473)

* Bumped allowed python version to 3.12
* Raised minimal python version to 3.9
* Bumped some more requirements
* Removed pyFFTW requirement until it supports python 3.12
* Updated jupyter notebooks

.github/workflows/check_docs.yml

@@ -8,7 +8,9 @@ jobs:
     timeout-minutes: 15
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - uses: ammaraskar/sphinx-action@master
       with:
         docs-folder: "docs/"
+        pre-build-command: "pip install --upgrade pip"

.github/workflows/release_pip.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: '3.9'
 
     - name: Install dependencies
       run: |

.github/workflows/tests_all.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install dependencies
       # install all requirements

.github/workflows/tests_minversion.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: '3.9'
 
     - name: Install dependencies
       # install packages in the exact version given in requirements.txt

.github/workflows/tests_mpi.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - uses: mpi4py/setup-mpi@v1
 
     - name: Install dependencies

.github/workflows/tests_types.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        pyversion: ['3.8', '3.11']
+        pyversion: ['3.9', '3.12']
     timeout-minutes: 30
 
     steps:

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.11"
   apt_packages:
     - graphviz
 

docs/requirements.txt

@@ -1,6 +1,6 @@
 -r ../requirements.txt
 h5py>=2.10
-pandas>=1.2
+pandas>=2
 Pillow>=7.0
 Sphinx>=4
 sphinx-autodoc-annotation>=1.0

docs/source/_static/requirements_main.csv

@@ -1,7 +1,7 @@
 Package,Minimal version,Usage
 matplotlib,3.1,Visualizing results
-numba,0.56,Just-in-time compilation to accelerate numerics
+numba,0.59,Just-in-time compilation to accelerate numerics
 numpy,1.22,Handling numerical data
 scipy,1.10,Miscellaneous scientific functions
 sympy,1.9,Dealing with user-defined mathematical expressions
-tqdm,4.60,Display progress bars during calculations
+tqdm,4.66,Display progress bars during calculations

docs/source/_static/requirements_optional.csv

@@ -1,9 +1,9 @@
 Package,Minimal version,Usage
 h5py,2.10,Storing data in the hierarchical file format
-ipywidgets,7,Jupyter notebook support
+ipywidgets,8,Jupyter notebook support
 mpi4py,3,Parallel processing using MPI
 napari,0.4.8,Displaying images interactively
 numba-mpi,0.22,Parallel processing using MPI+numba
-pandas,1.2,Handling tabular data
+pandas,2,Handling tabular data
 pyfftw,0.12,Faster Fourier transforms
-rocket-fft,0.2,Numba-compiled fast Fourier transforms
+rocket-fft,0.2.4,Numba-compiled fast Fourier transforms

examples/jupyter/Different solvers.ipynb

@@ -69,7 +69,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -83,7 +83,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.12.0"
   },
   "toc": {
    "base_numbering": 1,

examples/jupyter/Discretized Fields.ipynb

@@ -113,7 +113,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.12.0"
   },
   "toc": {
    "base_numbering": 1,

examples/jupyter/Solve PDEs.ipynb

@@ -83,16 +83,16 @@
     "class ChafeeInfantePDE(pde.PDEBase):\n",
     "    \"\"\"minimal model of a custom pde\n",
     "\n",
-    "    Taken from https://en.wikipedia.org/wiki/Chafee–Infante_equation\n",
+    "    Taken from https://en.wikipedia.org/wiki/Chafee-Infante_equation\n",
     "    \"\"\"\n",
     "\n",
-    "    def __init__(self, λ=1, bc=\"natural\"):\n",
+    "    def __init__(self, lmbd=1, bc=\"natural\"):\n",
     "        super().__init__()\n",
     "        self.bc = bc\n",
-    "        self.λ = λ\n",
+    "        self.lmbd = lmbd\n",
     "\n",
     "    def evolution_rate(self, state, t=0):\n",
-    "        return state.laplace(bc=self.bc) - self.λ * (state**3 - state)"
+    "        return state.laplace(bc=self.bc) - self.lmbd * (state**3 - state)"
    ]
   },
   {
@@ -123,7 +123,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.12.0"
   },
   "toc": {
    "base_numbering": 1,

examples/tutorial/Tutorial 1 - Grids and fields.ipynb

@@ -543,9 +543,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "(collection[0] + collection[1]).plot(\"image\");"
@@ -596,7 +594,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.12.0"
   },
   "toc": {
    "base_numbering": 1,

examples/tutorial/Tutorial 2 - Solving pre-defined partial differential equations.ipynb

@@ -366,9 +366,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "class KuramotoSivashinskyPDE(pde.PDEBase):\n",
@@ -449,9 +447,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# plot both fields and give the deviation as the title\n",
@@ -483,7 +479,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.12.0"
   },
   "toc": {
    "base_numbering": 1,

pde/fields/base.py

@@ -155,7 +155,7 @@ def _data_flat(self) -> np.ndarray:
         # flatten the first dimension of the internal data by creating a view and then
         # setting the new shape. This disallows accidental copying of the data
         data_flat = self._data_full.view()
-        data_flat.shape = (-1, *self.grid._shape_full)  # type: ignore
+        data_flat.shape = (-1, *self.grid._shape_full)
         return data_flat
 
     @_data_flat.setter

pde/fields/collection.py

@@ -9,7 +9,8 @@
 import json
 import logging
 import warnings
-from typing import Any, Callable, Iterator, Literal, Mapping, Sequence, overload
+from collections.abc import Iterator, Mapping, Sequence
+from typing import Any, Callable, Literal, overload
 
 import numpy as np
 from matplotlib import cm
@@ -21,7 +22,6 @@
 except ImportError:
     from matplotlib.cm import get_cmap
 
-
 from ..grids.base import GridBase
 from ..tools.docstrings import fill_in_docstring
 from ..tools.misc import Number, number_array

pde/fields/scalar.py

@@ -7,8 +7,9 @@
 from __future__ import annotations
 
 import numbers
+from collections.abc import Sequence
 from pathlib import Path
-from typing import TYPE_CHECKING, Callable, Literal, Sequence
+from typing import TYPE_CHECKING, Callable, Literal
 
 import numpy as np
 from numpy.typing import DTypeLike

pde/fields/tensorial.py

@@ -6,7 +6,8 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Callable, Sequence
+from collections.abc import Sequence
+from typing import TYPE_CHECKING, Callable
 
 import numpy as np
 from numpy.typing import DTypeLike

pde/fields/vectorial.py

@@ -6,7 +6,8 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Callable, Literal, Sequence
+from collections.abc import Sequence
+from typing import TYPE_CHECKING, Any, Callable, Literal
 
 import numba as nb
 import numpy as np

pde/grids/_mesh.py

@@ -7,8 +7,9 @@
 from __future__ import annotations
 
 import math
+from collections.abc import Sequence
 from enum import IntEnum
-from typing import Any, Sequence, TypeVar
+from typing import Any, TypeVar
 
 import numpy as np
 

pde/grids/base.py

@@ -14,17 +14,8 @@
 import math
 import warnings
 from abc import ABCMeta, abstractmethod
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Callable,
-    Generator,
-    Iterator,
-    Literal,
-    NamedTuple,
-    Sequence,
-    overload,
-)
+from collections.abc import Generator, Iterator, Sequence
+from typing import TYPE_CHECKING, Any, Callable, Literal, NamedTuple, overload
 
 import numba as nb
 import numpy as np

pde/grids/boundaries/axes.py

@@ -8,7 +8,8 @@
 
 from __future__ import annotations
 
-from typing import Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import numpy as np
 from numba.extending import register_jitable

pde/grids/boundaries/axis.py

@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Dict, Tuple, Union
+from typing import TYPE_CHECKING, Union
 
 import numpy as np
 from numba.extending import register_jitable
@@ -24,9 +24,9 @@
     from .._mesh import GridMesh
 
 BoundaryPairData = Union[
-    Dict[str, BoundaryData],
+    dict[str, BoundaryData],
     BoundaryData,
-    Tuple[BoundaryData, BoundaryData],
+    tuple[BoundaryData, BoundaryData],
     "BoundaryAxisBase",
 ]
 

pde/grids/boundaries/local.py

@@ -65,7 +65,7 @@
 import warnings
 from abc import ABCMeta, abstractmethod
 from numbers import Number
-from typing import TYPE_CHECKING, Any, Callable, Dict, Literal, Tuple, TypeVar, Union
+from typing import TYPE_CHECKING, Any, Callable, Literal, TypeVar, Union
 
 import numba as nb
 import numpy as np
@@ -86,7 +86,7 @@
     from .._mesh import GridMesh
 
 
-BoundaryData = Union[Dict, str, "BCBase"]
+BoundaryData = Union[dict, str, "BCBase"]
 
 
 class BCDataError(ValueError):
@@ -166,7 +166,7 @@ def _make_get_arr_1d(
         Consequently, `i = idx[axis]` and `arr[..., idx] == arr_1d[..., i]`.
     """
     assert 0 <= axis < dim
-    ResultType = Tuple[np.ndarray, int, Tuple]
+    ResultType = tuple[np.ndarray, int, tuple]
 
     # extract the correct indices
     if dim == 1:

pde/grids/cartesian.py

@@ -7,7 +7,8 @@
 from __future__ import annotations
 
 import itertools
-from typing import TYPE_CHECKING, Any, Generator, Sequence
+from collections.abc import Generator, Sequence
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 

pde/grids/cylindrical.py

@@ -6,7 +6,8 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Generator, Literal, Sequence
+from collections.abc import Generator, Sequence
+from typing import TYPE_CHECKING, Any, Literal
 
 import numpy as np
 

pde/solvers/__init__.py

@@ -30,7 +30,7 @@
     ExplicitMPISolver = None  # type: ignore
 
 
-def registered_solvers() -> List[str]:
+def registered_solvers() -> list[str]:
     """returns all solvers that are currently registered
 
     Returns:

pde/solvers/controller.py

@@ -9,7 +9,7 @@
 import datetime
 import logging
 import time
-from typing import TYPE_CHECKING, Any, Callable, Tuple, TypeVar, Union
+from typing import TYPE_CHECKING, Any, Callable, TypeVar, Union
 
 from .. import __version__
 from ..tools import mpi
@@ -25,7 +25,7 @@
     from ..fields.base import FieldBase
 
 
-TRangeType = Union[float, Tuple[float, float]]
+TRangeType = Union[float, tuple[float, float]]
 TState = TypeVar("TState", bound="FieldBase")