Add support for pyproject.toml

.github/workflows/publish_pypi.yml

@@ -1,13 +1,16 @@
-name: Build and publish package to PyPI
-
+# name: Build and publish package to PyPI
+name: Test building wheels
+# Temporarily disable publishing to PyPI and enable
+# building wheels on pull requests
 on:
-  push:
-    branches: main
+  # push:
+  #   branches: main
+  pull_request:
   workflow_dispatch:
     inputs:
-      target:
-        description: 'Deployment target. Can be "pypi" or "testpypi"'
-        default: "pypi"
+      # target:
+      #   description: 'Deployment target. Can be "pypi" or "testpypi"'
+      #   default: "pypi"
       debug_enabled:
           type: boolean
           description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
@@ -153,34 +156,34 @@ jobs:
           path: ./dist/*.tar.gz
           if-no-files-found: error
 
-  publish_pypi:
-    name: Upload package to PyPI
-    needs: [build_wheels, build_windows_wheels, build_sdist]
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download all artifacts
-        uses: actions/download-artifact@v3
-
-      - name: Move all package files to files/
-        run: |
-          mkdir files
-          mv windows_wheels/* wheels/* sdist/* files/
-
-      - name: Publish on PyPI
-        if: |
-          github.event.inputs.target == 'pypi' ||
-          (github.event_name == 'push' && github.ref == 'refs/heads/main')
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
-          packages_dir: files/
-
-      - name: Publish on TestPyPI
-        if: github.event.inputs.target == 'testpypi'
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.TESTPYPI_TOKEN }}
-          packages_dir: files/
-          repository_url: https://test.pypi.org/legacy/
+  # publish_pypi:
+  #   name: Upload package to PyPI
+  #   needs: [build_wheels, build_windows_wheels, build_sdist]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Download all artifacts
+  #       uses: actions/download-artifact@v3
+
+  #     - name: Move all package files to files/
+  #       run: |
+  #         mkdir files
+  #         mv windows_wheels/* wheels/* sdist/* files/
+
+  #     - name: Publish on PyPI
+  #       if: |
+  #         github.event.inputs.target == 'pypi' ||
+  #         (github.event_name == 'push' && github.ref == 'refs/heads/main')
+  #       uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         user: __token__
+  #         password: ${{ secrets.PYPI_TOKEN }}
+  #         packages_dir: files/
+
+  #     - name: Publish on TestPyPI
+  #       if: github.event.inputs.target == 'testpypi'
+  #       uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         user: __token__
+  #         password: ${{ secrets.TESTPYPI_TOKEN }}
+  #         packages_dir: files/
+  #         repository_url: https://test.pypi.org/legacy/

.github/workflows/test_on_push.yml

@@ -4,6 +4,9 @@ on:
   workflow_dispatch:
   pull_request:
 
+env:
+  FORCE_COLOR: 3
+
 concurrency:
   # github.workflow: name of the workflow, so that we don't cancel other workflows
   # github.event.pull_request.number || github.ref: pull request number or branch name if not a pull request
@@ -87,10 +90,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -147,10 +149,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -230,10 +231,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -290,10 +290,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -351,10 +350,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3

CMakeLists.txt

@@ -63,8 +63,9 @@ execute_process(
 
 if (CASADI_DIR)
   file(TO_CMAKE_PATH ${CASADI_DIR} CASADI_DIR)
+  message("Found python casadi path: ${CASADI_DIR}")
 endif()
-message("Found python casadi path: ${CASADI_DIR}")
+message("Could not find python casadi path")
 
 if(${USE_PYTHON_CASADI})
   message("Trying to link against python casadi package")

docs/source/user_guide/installation/windows-wsl.rst

@@ -22,13 +22,13 @@ Get PyBaMM's Source Code
 
      sudo apt install git-core
 
-3. Clone the PyBaMM repository::
+3. Clone the PyBaMM repository:
 
 .. code:: bash
 
      git clone https://github.com/pybamm-team/PyBaMM.git
 
-4. Enter the PyBaMM Directory by running::
+4. Enter the PyBaMM Directory by running:
 
 .. code:: bash
 

noxfile.py

@@ -16,9 +16,7 @@
     "SUNDIALS_INST": f"{homedir}/.local",
     "LD_LIBRARY_PATH": f"{homedir}/.local/lib:",
 }
-# Do not stdout ANSI colours on GitHub Actions
 if os.getenv("CI") == "true":
-    os.environ["NO_COLOR"] = "1"
     # The setup-python action installs and caches dependencies by default, so we skip
     # installing them again in nox environments. The dev and docs sessions will still
     # require a virtual environment, but we don't run them in the CI

pyproject.toml

@@ -0,0 +1,180 @@
+# From the pip documentation:
+
+# Fallback Behaviour
+# If a project does not have a pyproject.toml file containing a build-system section,
+# it will be assumed to have the following backend settings:
+
+# [build-system]
+# requires = ["setuptools>=40.8.0", "wheel"]
+# build-backend = "setuptools.build_meta:__legacy__"
+
+# TODO: add appropriate build-system section
+[build-system]
+# TODO: specify minimum version of setuptools otherwise scikits.odes, NumPy, and others
+# will fail to install
+requires = [
+    "setuptools",
+    "wheel",
+    "casadi>=3.6.0; platform_system!='Windows'",
+    "cmake; platform_system=='Linux'",
+    ]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pybamm"
+# TODO: try picking up version from the package itself
+# dynamic = ["version", "readme"]
+# [tool.setuptools.dynamic]
+# version = {attr = "my_package.VERSION"}
+version = "23.5"
+# Unsure: specify BSD-3-Clause?
+# license = {text = "BSD-3-Clause"}
+license = { file = "LICENSE.txt" }
+
+# TODO: add appropriate long description
+description = "Python Battery Mathematical Modelling"
+
+# TODO: correctly specify all authors and maintainers
+# Note: these are currently missing when running `pip show pybamm`, so we should add
+# them in some form
+authors = [{name = "The PyBaMM Team", email = "[email protected]"}]
+maintainers = [{name = "The PyBaMM Team", email = "[email protected]"}]
+requires-python = ">=3.8, <3.12"
+readme = "README.md"
+
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering",
+]
+
+dependencies = [
+    "numpy>=1.16",
+    "scipy>=1.3",
+    "casadi>=3.6.0",
+    "xarray",
+]
+
+[project.optional-dependencies]
+# For the generation of documentation
+docs = [
+    "sphinx>=6",
+    "sphinx_rtd_theme>=0.5",
+    "pydata-sphinx-theme",
+    "sphinx_design",
+    "sphinx-copybutton",
+    "myst-parser",
+    "sphinx-inline-tabs",
+    "sphinxcontrib-bibtex",
+    "sphinx-autobuild",
+    "sphinx-last-updated-by-git",
+    "nbsphinx",
+    "ipykernel",
+    "ipywidgets",
+    "sphinx-gallery",
+    "sphinx-hoverxref",
+    "sphinx-docsearch",
+]
+# For example notebooks
+examples = [
+    "jupyter",
+]
+# Plotting functionality
+plot = [
+    "imageio>=2.9.0",
+    # Note: Matplotlib is loaded for debug plots, but to ensure pybamm runs
+    # on systems without an attached display, it should never be imported
+    # outside of plot() methods.
+    "matplotlib>=2.0",
+]
+# For the Citations class
+cite = [
+    "pybtex>=0.24.0",
+]
+# To generate LaTeX strings
+latexify = [
+    "sympy>=1.8",
+]
+# Battery Parameter eXchange format
+bpx = [
+    "bpx",
+]
+# Low-overhead progress bars
+tqdm = [
+    "tqdm",
+]
+# Dependencies intended for use by developers
+dev = [
+    # For code style checking
+    "pre-commit",
+    # For code style auto-formatting
+    "ruff",
+    # For running testing sessions
+    "nox",
+]
+# Reading CSV files
+pandas =  [
+    "pandas>=0.24",
+]
+# For the Jax solver
+jax = [
+    "jax==0.4.8",
+    "jaxlib==0.4.7",
+]
+# For the scikits.odes solver
+odes = [
+    "scikits.odes"
+]
+# Contains all optional dependencies, except for odes, jax, and dev dependencies
+all = [
+    "anytree>=2.4.3",
+    "autograd>=1.2",
+    "pandas>=0.24",
+    "scikit-fem>=0.2.0",
+    "imageio>=2.9.0",
+    "matplotlib>=2.0",
+    "pybtex>=0.24.0",
+    "sympy>=1.8",
+    "bpx",
+    "tqdm",
+    "jupyter",
+]
+
+# Equivalent to the console scripts in the entry_points section of the setup()
+# function in setup.py
+[project.scripts]
+pybamm_edit_parameter = "pybamm.parameters_cli:edit_parameter"
+pybamm_add_parameter = "pybamm.parameters_cli:add_parameter"
+pybamm_rm_parameter = "pybamm.parameters_cli:remove_parameter"
+pybamm_install_odes = "pybamm.install_odes:main"
+pybamm_install_jax = "pybamm.util:install_jax"
+
+# Equivalent to the "pybamm_parameter_sets" entry_points section of the setup()
+# function in setup.py
+[project.entry-points."pybamm_parameter_sets"]
+Sulzer2019 = "pybamm.input.parameters.lead_acid.Sulzer2019:get_parameter_values"
+Ai2020 = "pybamm.input.parameters.lithium_ion.Ai2020:get_parameter_values"
+Chen2020 = "pybamm.input.parameters.lithium_ion.Chen2020:get_parameter_values"
+Chen2020_composite = "pybamm.input.parameters.lithium_ion.Chen2020_composite:get_parameter_values"
+Ecker2015 = "pybamm.input.parameters.lithium_ion.Ecker2015:get_parameter_values"
+Marquis2019 = "pybamm.input.parameters.lithium_ion.Marquis2019:get_parameter_values"
+Mohtat2020 = "pybamm.input.parameters.lithium_ion.Mohtat2020:get_parameter_values"
+NCA_Kim2011 = "pybamm.input.parameters.lithium_ion.NCA_Kim2011:get_parameter_values"
+OKane2022 = "pybamm.input.parameters.lithium_ion.OKane2022:get_parameter_values"
+ORegan2022 = "pybamm.input.parameters.lithium_ion.ORegan2022:get_parameter_values"
+Prada2013 = "pybamm.input.parameters.lithium_ion.Prada2013:get_parameter_values"
+Ramadass2004 = "pybamm.input.parameters.lithium_ion.Ramadass2004:get_parameter_values"
+Xu2019 = "pybamm.input.parameters.lithium_ion.Xu2019:get_parameter_values"
+ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
+
+# [tool.setuptools.packages.find]
+# include = ["pybamm", "pybamm.*"]