Use Ruff formatting and linting. Install configuration moved to pyproject.toml

.github/workflows/check_tutorials.yml

@@ -37,10 +37,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         # Version range or exact version of a Python version to use, using SemVer's version range syntax.
         python-version: ${{ matrix.python-version}}
@@ -50,37 +50,31 @@ jobs:
     # Cache pip dependencies
     # Source: https://github.com/actions/cache/blob/main/examples.md#python---pip
     - name: Cache dependencies
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
-        # Cache the full python environment, this is more efficient than just caching pip
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
         path: ${{ env.pythonLocation }}
-        # Hash both ordinary requirements and those specific for developmnet.
-        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('**/requirements.txt', '**/requirements-dev.txt') }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install external libraries
       run: |
         # Various packages that must be installed 
         sudo apt-get install libglu1-mesa libgeos-dev libffi-dev
         export LD_LIBRARY_PATH=/usr/local/lib64/:$LD_LIBRARY_PATH
 
-    - name: Install requirements
+    # Install the requirements, including the extras needed for testing, and PorePy
+    # itself.
+    - name: Install requirements and PorePy
       run: |
         pip install -U pip
-        # Install requirements, using eager updates to avoid stalled dependencies due to caching
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
-        pip install --upgrade --upgrade-strategy eager -r requirements.txt
+        pip install .[testing]
+        pip freeze
 
+    # Install jupyter - needed to run the tutorial notebooks.
     - name: Install jupyter
       run: |
         pip install jupyter 
 
-    - name: Install PorePy
-      run: |
-        pip install .
-        pip freeze       
-
     - name: Check tutorials
       if: ${{always()}}
       run: pytest tests -m tutorials

.github/workflows/run-pytest-all.yml

@@ -28,10 +28,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         # Version range or exact version of a Python version to use, using SemVer's version range syntax.
         python-version: ${{ matrix.python-version}}
@@ -41,44 +41,30 @@ jobs:
     # Cache pip dependencies
     # Source: https://github.com/actions/cache/blob/main/examples.md#python---pip
     - name: Cache dependencies
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
-        # Cache the full python environment, this is more efficient than just caching pip
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
         path: ${{ env.pythonLocation }}
-        # Hash requirements.
-        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('**/requirements.txt') }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install external libraries
       run: |
         # Various packages that must be installed 
         sudo apt-get install libglu1-mesa libgeos-dev libffi-dev
         export LD_LIBRARY_PATH=/usr/local/lib64/:$LD_LIBRARY_PATH
 
-    - name: Install requirements
+    # Install the requirements, including the extras needed for testing, and PorePy
+    # itself.
+    - name: Install requirements and PorePy
       run: |
         pip install -U pip
-        # Install requirements, using eager updates to avoid stalled dependencies due to caching
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
-        pip install --upgrade --upgrade-strategy eager -r requirements.txt
+        pip install .[testing]
+        pip freeze
 
     - name: Install pypardiso
       run: |
         pip install pypardiso
 
-    - name: Install jupyter
-      run: |
-        pip install jupyter 
-
-    - name: Install PorePy
-      run: |
-        pip install .
-        pip freeze       
-
     - name: all tests
       if: ${{always()}}
-      run: pytest --run-skipped -m "not tutorials"
-
-
-
+      run: pytest --run-skipped -m "not tutorials"

.github/workflows/run-pytest.yml

@@ -36,10 +36,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         # Version range or exact version of a Python version to use, using SemVer's version range syntax.
         python-version: ${{ matrix.python-version}}
@@ -49,32 +49,25 @@ jobs:
     # Cache pip dependencies
     # Source: https://github.com/actions/cache/blob/main/examples.md#python---pip
     - name: Cache dependencies
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
-        # Cache the full python environment, this is more efficient than just caching pip
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
         path: ${{ env.pythonLocation }}
-        # Hash requirements.
-        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('**/requirements.txt') }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install external libraries
       run: |
         # Various packages that must be installed 
         sudo apt-get install libglu1-mesa libgeos-dev libffi-dev
         export LD_LIBRARY_PATH=/usr/local/lib64/:$LD_LIBRARY_PATH
 
-    - name: Install requirements
+    # Install the requirements, including the extras needed for testing, and PorePy
+    # itself.
+    - name: Install requirements and PorePy
       run: |
         pip install -U pip
-        # Install requirements, using eager updates to avoid stalled dependencies due to caching
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
-        pip install --upgrade --upgrade-strategy eager -r requirements.txt
-
-    - name: Install PorePy
-      run: |
-        pip install .
-        pip freeze       
+        pip install .[testing]
+        pip freeze
 
     - name: Run tests
       if: ${{always()}}

.github/workflows/run-static-checks.yml

@@ -1,4 +1,4 @@
-# Run static tests for code quality: Isort, black, flake8, mypy.
+# Run static tests for code quality: Isort, ruff (formatting and linting), mypy.
 
 name: Static tests
 
@@ -55,10 +55,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it.
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Setup Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         # Version range or exact version of a Python version to use, using SemVer's version range syntax.
         python-version: ${{ matrix.python-version}}
@@ -68,43 +68,51 @@ jobs:
     # Cache pip dependencies
     # Source: https://github.com/actions/cache/blob/main/examples.md#python---pip
     - name: Cache dependencies
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
-        # Cache the full python environment, this is more efficient than just caching pip
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
         path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('**/requirements.txt', '**/requirements-dev.txt') }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Cache mypy
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-mypy
       with:
         path: mypy-cache-${{ matrix.python-version}}
         key: ${{ runner.os }}-mypy
 
-    # Install the requirements. Mypy needs this to access stubs for numpy etc.
+    # Install the dependencies, which is needed to make mypy happy. Unravelling of the
+    # second command: The expression in the angular brackets is a python command that
+    # fetches the dependencies section in pyproject.toml; this is then made available to
+    # pip via -r. Option --no-bulid-isolation makes pip not use an isolated environment
+    # for the install (hence the installed packages are sure to be available also after
+    # the build), while --no-deps will only install the specified packages (in this
+    # case, the dependencies of PorePy). The third line similarly installs the
+    # development dependencies.
+    #
+    # Thanks, copilot!
     - name: Install requirements
       run: |
         pip install -U pip
-        # Install requirements, using eager updates to avoid stalled dependencies due to caching
-        # https://blog.allenai.org/python-caching-in-github-actions-e9452698e98d
-        pip install --upgrade --upgrade-strategy eager -r requirements.txt
+        pip install toml
+        pip install --no-build-isolation --no-deps -r <(python -c "import toml; print('\n'.join(toml.load('pyproject.toml')['project']['dependencies']))")
+        pip install --no-build-isolation --no-deps -r <(python -c "import toml; print('\n'.join(toml.load('pyproject.toml')['project']['optional-dependencies']['development']))")
         pip freeze
 
-    # Run black, isort, flake8, and mypy.
-    # Note that since these are static checks, we have not installed PorePy.
-    - name: black
+    # Run the various checks
+    - name: Ruff linting
       if: ${{ always() }}
-      run: black --check src
+      run: ruff check src
 
-    - name: isort
+    - name: Ruff formatting
       if: ${{always()}}
-      run: isort --check src
+      run: ruff format --check src
 
-    - name: flake8
+      # EK note to self: Ruff may introduce sorting of imports in the future, if so, we
+      # should use that instead of isort.
+    - name: isort 
       if: ${{ always() }}
-      run: flake8 src 
+      run: isort src 
 
     - name: mypy
       if: ${{ always() }}

Readme.md

@@ -1,6 +1,7 @@
 ![Pytest](https://github.com/pmgbergen/porepy/actions/workflows/run-pytest.yml/badge.svg)
 ![Pytest including slow](https://github.com/pmgbergen/porepy/actions/workflows/run-pytest-all.yml/badge.svg)
-![Mypy, black, isort, flake8](https://github.com/pmgbergen/porepy/actions/workflows/run-static-checks.yml/badge.svg)
+![Mypy, ruff, isort](https://github.com/pmgbergen/porepy/actions/workflows/run-static-checks.yml/badge.svg)
+![Tutorials](https://github.com/pmgbergen/porepy/actions/workflows/check_tutorials.yml/badge.svg)
 [![DOI](https://zenodo.org/badge/89228838.svg)](https://zenodo.org/badge/latestdoi/89228838)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 

pyproject.toml

@@ -0,0 +1,81 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+# Project information.
+[project]
+name = "porepy"
+version = "1.10.0"
+description = "Simulation tool for fractured and deformable porous media"
+readme = "Readme.md"
+license = { text = "GPL" }
+keywords = ["porous media simulation fractures deformable"]
+maintainers = [
+    { name = "Eirik Keilegavlen", email = "Eirik.Keilegavlen@uib.no" },
+    { name = "Ivar Stefansson", email = "Ivar.Stefansson@uib.no" },
+    { name = "Jakub Both", email = "Jakub.Both@uib.no" }
+]
+urls = { "Homepage" = "https://github.com/pmgbergen/porepy" }
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License (GPL)",
+    "Operating System :: OS Independent"
+]
+dependencies = [
+    "deepdiff",
+    "future",
+    "gmsh",
+    "matplotlib < 3.11",
+    "meshio",
+    "networkx",
+    "numba",
+    "numpy < 2.2",
+    "scipy",
+    "seaborn",
+    "shapely",
+    "six",
+    "sympy",
+    "typing_extensions",
+]
+
+[project.optional-dependencies]
+development = [
+    "isort",
+    "ruff",
+    "mypy",
+    "mypy-extensions"
+]
+testing = [
+    "pytest >= 4.6",
+    "pytest-cov",
+    "pytest-runner"
+]
+
+# Information for the build system.
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"porepy" = [
+    "py.typed",
+    "applications/md_grids/gmsh_file_library/**/*.csv",
+    "applications/md_grids/gmsh_file_library/**/*.geo"
+]
+
+# Testing.
+[tool.pytest.ini_options]
+python_files = "tests/*.py"
+addopts = "--cov=src/porepy --cov-report term-missing -p no:warnings"
+
+# Static analysis.
+[tool.ruff.lint]
+ignore = [
+    "E731",  # do not assign a lambda expression, use a def
+    "E266",  # too many leading '#' for block comment
+]
+exclude = [
+    "src/porepy/__init__.py",
+    "src/porepy/numerics/ad/__init__.py",
+    "src/porepy/compositional/__init__.py"
+]