Merge branch 'master' into modelrunner

.github/workflows/check_docs.yml

@@ -0,0 +1,14 @@
+name: "Check documentation"
+
+on: [push]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "docs/"

.github/workflows/coverage_report.yml

@@ -5,37 +5,57 @@ on: [push]
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
+
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install FFmpeg
       continue-on-error: true
       run: |
         sudo apt-get install ffmpeg
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
-    - uses: mpi4py/setup-mpi@v1
+        python-version: '3.11'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r tests/requirements_mpi.txt
+        pip install -r tests/requirements_full.txt
         pip install -r tests/requirements.txt
 
-    - name: Generate coverage report
+    - name: Generate serial coverage report
+      env:
+        NUMBA_DISABLE_JIT: 1
+        MPLBACKEND: agg
+        PYPDE_TESTRUN: 1
+      run: |
+        export PYTHONPATH="${PYTHONPATH}:`pwd`"
+        pytest --cov-config=pyproject.toml --cov=pde -n auto tests
+
+    - name: Setup MPI
+      uses: mpi4py/setup-mpi@v1
+
+    - name: Generate parallel coverage report
+      env:
+        NUMBA_DISABLE_JIT: 1
+        MPLBACKEND: agg
+        PYPDE_TESTRUN: 1
       run: |
-        export NUMBA_DISABLE_JIT=1
-        export MPLBACKEND="agg"
         export PYTHONPATH="${PYTHONPATH}:`pwd`"
-        pytest --cov-config=tests/.coveragerc --cov-report xml:report_coverage.xml --cov=pde --runslow pde
-        mpiexec -n 2 pytest --cov-config=tests/.coveragerc --cov-report xml:report_coverage.xml --cov-append --cov=pde --use_mpi pde 
+        pip install -r tests/requirements_mpi.txt
+        mpiexec -n 2 pytest --cov-config=pyproject.toml --cov-append --cov=pde --use_mpi tests
+
+    - name: Create coverage report
+      run: |
+        coverage xml -o coverage_report.xml 
 
-    - name: Upload coverage to Codecov  
+    - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./report_coverage.xml
+        file: ./coverage_report.xml
         flags: unittests
         name: codecov-pydev
         fail_ci_if_error: true

.github/workflows/release_pip.yml

@@ -7,24 +7,33 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.8'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
+
+    - name: Prepare build
+      run: |
+        python -m build 2>&1 | tee build.log
+        # exit `fgrep -i warning build.log | wc -l`
+
+    - name: Check the package
+      run: twine check --strict dist/*
 
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        python -m twine upload dist/*
+      run: python -m twine upload dist/*

.github/workflows/tests_all.yml

@@ -8,12 +8,14 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Install dependencies
       # install all requirements
@@ -27,5 +29,5 @@ jobs:
         NUMBA_WARNINGS: 1
         MPLBACKEND: agg
       run: |
-        cd tests
-        python run_tests.py --unit --num_cores auto --showconfig
+        cd scripts
+        python run_tests.py --unit --runslow --num_cores auto --showconfig

.github/workflows/tests_minversion.yml

@@ -8,10 +8,12 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest]  # windows-latest
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.8'
 
@@ -27,6 +29,5 @@ jobs:
         NUMBA_WARNINGS: 1
         MPLBACKEND: agg
       run: |
-        pip install pytest pytest-cov
-        cd tests
-        python run_tests.py --unit --num_cores auto --showconfig
+        cd scripts
+        python run_tests.py --unit --runslow --num_cores auto --showconfig

.github/workflows/tests_mpi.yml

@@ -6,14 +6,16 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest, windows-latest]
+        os: [macos-latest, ubuntu-latest] #, windows-latest]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - uses: mpi4py/setup-mpi@v1
 
     - name: Install dependencies
@@ -28,5 +30,5 @@ jobs:
         NUMBA_WARNINGS: 1
         MPLBACKEND: agg
       run: |
-        cd tests
+        cd scripts
         python run_tests.py --unit --use_mpi --showconfig

.github/workflows/tests_types.yml

@@ -5,15 +5,15 @@ on: [push]
 jobs:
   build:
     runs-on: ubuntu-latest
-
     strategy:
       matrix:
-        pyversion: ['3.8', '3.10']
+        pyversion: ['3.8', '3.11']
+    timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.pyversion }}
 
@@ -26,4 +26,4 @@ jobs:
     - name: Test types with mypy
       continue-on-error: true
       run: |
-        python -m mypy --config-file tests/mypy.ini --pretty --package pde
+        python -m mypy --config-file pyproject.toml --pretty --package pde

.gitignore

@@ -4,6 +4,7 @@ docs/source/examples_gallery/
 docs/paper/paper.pdf
 tests/coverage/
 tests/mypy-report/
+pde/_version.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -6,12 +6,9 @@
 [![PyPI version](https://badge.fury.io/py/py-pde.svg)](https://badge.fury.io/py/py-pde)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/py-pde.svg)](https://anaconda.org/conda-forge/py-pde)
 [![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
-
 [![Build Status](https://github.com/zwicker-group/py-pde/actions/workflows/tests_all.yml/badge.svg)](https://github.com/zwicker-group/py-pde/actions/workflows/tests_all.yml)
 [![codecov](https://codecov.io/gh/zwicker-group/py-pde/branch/master/graph/badge.svg)](https://codecov.io/gh/zwicker-group/py-pde)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/zwicker-group/py-pde.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/zwicker-group/py-pde/context:python)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/zwicker-group/py-pde/master?filepath=examples%2Fjupyter)
-
 [![Documentation Status](https://readthedocs.org/projects/py-pde/badge/?version=latest)](https://py-pde.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02158/status.svg)](https://doi.org/10.21105/joss.02158)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
@@ -25,36 +22,35 @@ dynamical systems in physics. The focus of the package lies on easy usage to
 explore the behavior of PDEs. However, core computations can be compiled
 transparently using numba for speed.
 
-[Try it out online!](https://mybinder.org/v2/gh/zwicker-group/py-pde/master?filepath=examples%2Fjupyter)
+[Try it online!](https://mybinder.org/v2/gh/zwicker-group/py-pde/master?filepath=examples%2Fjupyter)
 
 
 Installation
 ------------
 
-`py-pde` is available on `pypi`, so you should be able to install it through
-`pip`:
+`py-pde` is available on `pypi`, so you should be able to install it through `pip`:
 
 ```bash
 pip install py-pde
 ```
 
-In order to have all features of the package available, you might also want to 
+In order to have all features of the package available, you might want to 
 install the following optional packages:
 
 ```bash
-pip install h5py pandas tqdm
+pip install h5py pandas mpi4py numba-mpi
 ```
 
 Moreover, `ffmpeg` needs to be installed for creating movies.
 
 As an alternative, you can install `py-pde` through [conda](https://docs.conda.io/en/latest/)
-using [conda-forge](https://conda-forge.org/) channel:
+using the [conda-forge](https://conda-forge.org/) channel:
 
 ```bash
 conda install -c conda-forge py-pde
 ```
 
-Installation with `conda` includes all required dependencies to have all features of `py-pde`.
+Installation with `conda` includes all dependencies of `py-pde`.
 
 Usage
 -----