Create Optional Dependencies

.github/workflows/run_periodic_tests.yml

@@ -86,46 +86,35 @@ jobs:
 
       - name: Install standard python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools
-          python -m pip install "tox<4"
-
+          python -m pip install --upgrade pip wheel setuptools nox
+
       - name: Install SuiteSparse and Sundials
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e pybamm-requires
+        run: nox -s pybamm-requires
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10
         if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11
-        run: python -m tox -e unit
+        run: nox -s unit
 
       - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: python -m tox -e coverage
+        run: nox -s coverage
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/codecov-action@v2.1.0
 
-      - name: Run integration tests for GNU/Linux
-        if: matrix.os == 'ubuntu-latest'
-        run: python -m tox -e integration
+      - name: Run integration tests
+        run: nox -s integration
 
       - name: Run unit tests for Windows and MacOS
         if: matrix.os != 'ubuntu-latest'
-        run: python -m tox -e mac-windows-unit
-
-      - name: Run integration tests for Windows and MacOS
-        if: matrix.os != 'ubuntu-latest'
-        run: python -m tox -e mac-windows-integration
+        run: nox -s unit
 
       - name: Install docs dependencies and run doctests
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e doctests
+        run: nox -s doctests
 
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e examples
-
-      - name: Install scikits.odes and test pybamm_install_odes
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          tox -e odes
+        run: nox -s examples

.github/workflows/test_on_push.yml

@@ -96,36 +96,36 @@ jobs:
       - name: Install standard Python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools
-          python -m pip install "tox<4"
+          python -m pip install "nox"
 
       - name: Install SuiteSparse and Sundials
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e pybamm-requires
+        run: nox -s pybamm-requires
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10
         if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11
-        run: python -m tox -e unit
+        run: nox -s unit
 
       - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: python -m tox -e coverage
+        run: nox -s coverage
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/codecov-action@v2.1.0
 
       - name: Run integration tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: python -m tox -e integration
+        run: nox -s integration
 
       - name: Run unit tests for Windows and MacOS with all Python versions
         if: matrix.os != 'ubuntu-latest'
-        run: python -m tox -e mac-windows-unit
+        run: nox -s unit
 
       - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: tox -e doctests
+        run: nox -s doctests
 
       - name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: tox -e examples
+        run: nox -s examples

docs/requirements.txt

@@ -11,6 +11,7 @@ jupyter  # For example notebooks
 pybtex
 sympy >= 1.8
 xarray
+tqdm
 # 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.

noxfile.py

@@ -0,0 +1,123 @@
+import nox
+import os
+import sys
+
+
+@nox.session(name="pybamm-requires")
+def run_pybamm_requires(session):
+    homedir = os.getenv("HOME")
+    session.env["SUNDIALS_INST"] = session.env.get("SUNDIALS_INST", f"{homedir}/.local")
+    session.env[
+        "LD_LIBRARY_PATH"
+    ] = f"{homedir}/.local/lib:{session.env.get('LD_LIBRARY_PATH')}"
+    if sys.platform != "win32" or sys.platform != "darwin":
+        session.install("wget", "cmake")
+        session.run("python", "scripts/install_KLU_Sundials.py")
+        session.run(
+            "git",
+            "clone",
+            "https://github.com/pybind/pybind11.git",
+            "pybind11/",
+            external=True,
+        )
+
+
+@nox.session(name="coverage")
+def run_coverage(session):
+    homedir = os.getenv("HOME")
+    session.env["SUNDIALS_INST"] = session.env.get("SUNDIALS_INST", f"{homedir}/.local")
+    session.env[
+        "LD_LIBRARY_PATH"
+    ] = f"{homedir}/.local/lib:{session.env.get('LD_LIBRARY_PATH')}"
+    session.install("coverage")
+    session.install("-e", ".[dev]")
+    if sys.platform != "win32" or sys.platform != "darwin":
+        session.install("scikits.odes")
+        session.run("pybamm_install_jax")
+    session.run("coverage", "run", "--rcfile=.coveragerc", "run-tests.py", "--nosub")
+    session.run("coverage", "combine")
+    session.run("coverage", "xml")
+
+
+@nox.session(name="integration", reuse_venv=True)
+def run_integration(session):
+    homedir = os.getenv("HOME")
+    session.env["SUNDIALS_INST"] = session.env.get("SUNDIALS_INST", f"{homedir}/.local")
+    session.env[
+        "LD_LIBRARY_PATH"
+    ] = f"{homedir}/.local/lib:{session.env.get('LD_LIBRARY_PATH')}"
+    session.install("-e", ".[dev]")
+    if sys.platform == "linux":
+        session.install("scikits.odes")
+    session.run("python", "run-tests.py", "--integration")
+
+
+@nox.session(name="doctests", reuse_venv=True)
+def run_doctests(session):
+    session.install("-e", ".[dev]")
+    session.install("-e", ".[docs]")
+    session.run("python", "run-tests.py", "--doctest")
+
+
+@nox.session(name="unit", reuse_venv=True)
+def run_unit(session):
+    homedir = os.getenv("HOME")
+    session.env["SUNDIALS_INST"] = session.env.get("SUNDIALS_INST", f"{homedir}/.local")
+    session.env[
+        "LD_LIBRARY_PATH"
+    ] = f"{homedir}/.local/lib:{session.env.get('LD_LIBRARY_PATH')}"
+    session.install("-e", ".[dev]")
+    if sys.platform == "linux":
+        session.run("pybamm_install_jax")
+        session.install("scikits.odes")
+    session.run("python", "run-tests.py", "--unit")
+
+
+@nox.session(name="examples", reuse_venv=True)
+def run_examples(session):
+    session.install("-e", ".[dev]")
+    session.install("-e", ".[examples]")
+    session.run("python", "run-tests.py", "--examples")
+
+
+@nox.session(name="dev", reuse_venv=True)
+def set_dev(session):
+    homedir = os.getenv("HOME")
+    LD_LIBRARY_PATH = f"{homedir}/.local/lib:{session.env.get('LD_LIBRARY_PATH')}"
+    envbindir = session.bin
+    session.install("-e", ".[dev]")
+    session.install("cmake")
+    session.run(
+        "echo",
+        "export",
+        f"LD_LIBRARY_PATH={LD_LIBRARY_PATH}",
+        ">>",
+        f"{envbindir}/activate",
+    )
+
+
+@nox.session(name="tests", reuse_venv=True)
+def run_tests(session):
+    session.install("-e", ".[dev]")
+    if sys.platform == "linux":
+        session.run("pybamm_install_jax")
+    session.run("python", "run-tests.py", "--all")
+
+
+@nox.session(name="docs", reuse_venv=True)
+def build_docs(session):
+    envbindir = session.bin
+    session.install("-e", ".[dev]")
+    session.install(
+        "sphinx>=1.5",
+        "pydata-sphinx-theme",
+        "sphinx-autobuild",
+        "sphinx_design",
+        "sphinx-copybutton",
+        "myst-parser",
+        "sphinx-inline-tabs",
+    )
+    session.chdir("docs/")
+    session.run(
+        "sphinx-autobuild", "--open-browser", "-qT", ".", f"{envbindir}/../tmp/html"
+    )

setup.py

@@ -206,21 +206,8 @@ def compile_KLU():
         "numpy>=1.16",
         "scipy>=1.3",
         "pandas>=0.24",
-        "anytree>=2.4.3",
-        "autograd>=1.2",
-        "scikit-fem>=0.2.0",
         "casadi>=3.6.0",
-        "imageio>=2.9.0",
-        "pybtex>=0.24.0",
-        "sympy>=1.8",
         "xarray",
-        "bpx",
-        "tqdm",
-        # 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.
-        # Should not be imported
-        "matplotlib>=2.0",
     ],
     extras_require={
         "docs": [
@@ -231,11 +218,72 @@ def compile_KLU():
             "myst-parser",
             "sphinx-inline-tabs",
         ],  # For doc generation
-        "dev": [
+        "examples": [
             "pre-commit",  # For code style checking
             "black",  # For code style auto-formatting
             "jupyter",  # For example notebooks
         ],
+        "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.
+            # Should not be imported
+            "matplotlib>=2.0",
+        ],
+        "cite": [
+            "pybtex>=0.24.0",
+        ],
+        "latexify": [
+            "sympy>=1.8",
+        ],
+        "bpx": [
+            "bpx",
+        ],
+        "tqdm": [
+            "tqdm",
+        ],
+        "dev": [
+            "numpy>=1.16",
+            "scipy>=1.3",
+            "pandas>=0.24",
+            "anytree>=2.4.3",
+            "autograd>=1.2",
+            "scikit-fem>=0.2.0",
+            "casadi>=3.6.0",
+            "imageio>=2.9.0",
+            "pybtex>=0.24.0",
+            "sympy>=1.8",
+            "xarray",
+            "bpx",
+            "tqdm",
+            "matplotlib>=2.0",
+        ],
+        "all": [
+            "numpy>=1.16",
+            "scipy>=1.3",
+            "pandas>=0.24",
+            "anytree>=2.4.3",
+            "autograd>=1.2",
+            "scikit-fem>=0.2.0",
+            "casadi>=3.6.0",
+            "imageio>=2.9.0",
+            "pybtex>=0.24.0",
+            "sympy>=1.8",
+            "xarray",
+            "bpx",
+            "tqdm",
+            "matplotlib>=2.0",
+            "sphinx>=1.5",
+            "pydata-sphinx-theme",
+            "sphinx_design",
+            "sphinx-copybutton",
+            "myst-parser",
+            "sphinx-inline-tabs",
+            "pre-commit",
+            "black",
+            "jupyter",
+        ],
     },
     entry_points={
         "console_scripts": [