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

Author: david-zwicker

.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