Update workflows (#6)

* Pre-commit and workflow updates * Fix typo * Add MacOS build tests * Fix style * Fix typo * Update mac tests * Update mac tests * Fix tests
pybamm-team · Oct 17, 2024 · 8a99bfc · 8a99bfc
1 parent 357ac25
commit 8a99bfc
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Showing 10 changed files with 185 additions and 65 deletions.
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -208,7 +208,7 @@ jobs:
             python install_KLU_Sundials.py
             python -m cibuildwheel --output-dir wheelhouse
         env:
-          # 10.13 for Intel (macos-12/macos-13), 11.0 for Apple Silicon (macos-14 and macos-latest)
+          # 10.13 for Intel (macos-13), 11.0 for Apple Silicon (macos-14 and macos-latest)
           MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-14' && '11.0' || '10.13' }}
           CIBW_ARCHS_MACOS: auto
           CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
@@ -253,7 +253,7 @@ jobs:
           if-no-files-found: error
 
   publish_pypi:
-    if: github.repository == 'pybamm-team/pybammsolvers'
+    if: ${{ github.event_name == 'release' && github.repository == 'pybamm-team/pybammsolvers' }}
     name: Upload package to PyPI
     needs: [
       build_manylinux_wheels,
@@ -279,7 +279,6 @@ jobs:
         run: ls -lA artifacts/
 
       - name: Publish to PyPI
-        if: github.event_name == 'release'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           packages-dir: artifacts/
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,19 @@
+name: Static analysis
+
+on:
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'true'
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -11,24 +11,42 @@ concurrency:
 
 jobs:
   pytest:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.11"]
+        os: [ ubuntu-latest, macos-13, macos-latest]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: 'true'
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+
+      - name: Install dependencies (Linux)
+        if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get install gfortran gcc libopenblas-dev
           pip install nox
 
+      - name: Install dependencies (MacOs)
+        if: matrix.os == 'macos-13' || matrix.os == 'macos-latest'
+        env:
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
+          NONINTERACTIVE: 1
+        run: |
+          brew analytics off
+          brew install libomp
+          brew reinstall gcc
+          pip install nox
+
       - name: Build and test
         run: |
           nox
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,13 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.3"
+    hooks:
+      - id: ruff
+        args: [--fix, --show-fixes]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
diff --git a/install_KLU_Sundials.py b/install_KLU_Sundials.py
@@ -21,7 +21,9 @@ def build_solvers():
     SUITESPARSE_CHECKSUM = (
         "7111b505c1207f6f4bd0be9740d0b2897e1146b845d73787df07901b4f5c1fb7"
     )
-    SUNDIALS_CHECKSUM = "4e0b998dff292a2617e179609b539b511eb80836f5faacf800e688a886288502"
+    SUNDIALS_CHECKSUM = (
+        "4e0b998dff292a2617e179609b539b511eb80836f5faacf800e688a886288502"
+    )
     DEFAULT_INSTALL_DIR = str(pathlib.Path(__file__).parent.resolve() / ".idaklu")
 
     def safe_remove_dir(path):
@@ -58,19 +60,19 @@ def install_suitesparse(download_dir):
                 # if in CI, set RPATH to the install directory for SuiteSparse_config
                 # dylibs to find libomp.dylib when repairing the wheel
                 if os.environ.get("CIBUILDWHEEL") == "1":
-                    env["CMAKE_OPTIONS"] = (
-                        f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib"
-                    )
+                    env[
+                        "CMAKE_OPTIONS"
+                    ] = f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib"
                 else:
                     env["CMAKE_OPTIONS"] = f"-DCMAKE_INSTALL_PREFIX={install_dir}"
             else:
                 # For AMD, COLAMD, BTF and KLU; do not set a BUILD RPATH but use an
                 # INSTALL RPATH in order to ensure that the dynamic libraries are found
                 # at runtime just once. Otherwise, delocate complains about multiple
                 # references to the SuiteSparse_config dynamic library (auditwheel does not).
-                env["CMAKE_OPTIONS"] = (
-                    f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE -DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"
-                )
+                env[
+                    "CMAKE_OPTIONS"
+                ] = f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE -DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"
             subprocess.run(make_cmd, cwd=build_dir, env=env, shell=True, check=True)
             subprocess.run(install_cmd, cwd=build_dir, check=True)
 
@@ -106,7 +108,9 @@ def install_sundials(download_dir, install_dir):
                 OpenMP_C_LIB_NAMES = "omp"
                 OpenMP_omp_LIBRARY = "/opt/homebrew/opt/libomp/lib/libomp.dylib"
             elif platform.processor() == "i386":
-                OpenMP_C_FLAGS = "-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include"
+                OpenMP_C_FLAGS = (
+                    "-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include"
+                )
                 OpenMP_C_LIB_NAMES = "omp"
                 OpenMP_omp_LIBRARY = "/usr/local/opt/libomp/lib/libomp.dylib"
             else:
@@ -305,7 +309,9 @@ def parallel_download(urls, download_dir):
             "The '--force' option is activated: installation will be forced, ignoring any existing libraries."
         )
         safe_remove_dir(os.path.join(download_dir, "build_sundials"))
-        safe_remove_dir(os.path.join(download_dir, f"SuiteSparse-{SUITESPARSE_VERSION}"))
+        safe_remove_dir(
+            os.path.join(download_dir, f"SuiteSparse-{SUITESPARSE_VERSION}")
+        )
         safe_remove_dir(os.path.join(download_dir, f"sundials-{SUNDIALS_VERSION}"))
         sundials_found, suitesparse_found = False, False
     else:
@@ -334,5 +340,6 @@ def parallel_download(urls, download_dir):
             parallel_download([(SUITESPARSE_URL, SUITESPARSE_CHECKSUM)], download_dir)
             install_suitesparse(download_dir)
 
+
 if __name__ == "__main__":
     build_solvers()
diff --git a/noxfile.py b/noxfile.py
@@ -114,6 +114,7 @@ def run_pybamm_requires(session):
     else:
         session.error("nox -s idaklu-requires is only available on Linux & macOS.")
 
+
 @nox.session(name="unit")
 def run_unit(session):
     """Run the unit tests."""
@@ -131,4 +132,3 @@ def run_unit(session):
             silent=False,
         )
     session.run("pytest", "tests")
-
diff --git a/pyproject.toml b/pyproject.toml
@@ -19,11 +19,14 @@ license = {file = "LICENSE"}
 dynamic = ["version", "readme"]
 dependencies = [
     "casadi",
+    "numpy<2.0"
 ]
 
 [project.optional-dependencies]
 dev = [
     "pytest",
+    "setuptools",
+    "wheel",
 ]
 
 [tool.setuptools.packages.find]

diff --git a/ruff.toml b/ruff.toml
@@ -0,0 +1,59 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    "__init__.py",
+    "docs",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+
+line-length = 88
+indent-width = 4
+
+target-version = "py310"
+
+[lint]
+select = [
+    "W",
+    "E",
+    "F",
+    "B",
+    "A",
+    "U",
+    "SLF",
+]
+ignore = [
+    "E501", # Line length check conflicted with the formatter
+    "B018", # Useless expression checks were a problem for notebooks
+    "B905", # Requires zip to have explict strict flag. Enable in the future
+]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
diff --git a/setup.py b/setup.py
@@ -178,8 +178,9 @@ def move_output(self, ext):
 
 # ---------- end of CMake steps --------------------------------------------------------
 
+
 class CustomInstall(install):
-    """A custom install command to add 2 build options"""
+    """A custom installation command to add 2 build options"""
 
     user_options = [
         *install.user_options,
@@ -207,7 +208,7 @@ def run(self):
 
 
 class bdist_wheel(orig.bdist_wheel):
-    """A custom install command to add 2 build options"""
+    """A custom installation command to add 2 build options"""
 
     user_options = [
         *orig.bdist_wheel.user_options,
@@ -231,52 +232,53 @@ def run(self):
         orig.bdist_wheel.run(self)
 
 
-idaklu_ext = Extension(
-    name="pybammsolvers.idaklu",
-    # The sources list should mirror the list in CMakeLists.txt
-    sources=[
-        "src/pybammsolvers/idaklu_source/Expressions/Expressions.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/Base/Expression.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/Base/ExpressionSet.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/Base/ExpressionTypes.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/Base/ExpressionSparsity.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/Casadi/CasadiFunctions.cpp",
-        "src/pybammsolvers/idaklu_source/Expressions/Casadi/CasadiFunctions.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEBaseFunction.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEFunction.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEFunctions.cpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEFunctions.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/iree_jit.cpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/iree_jit.hpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/ModuleParser.cpp",
-        "src/pybammsolvers/idaklu_source/Expressions/IREE/ModuleParser.hpp",
-        "src/pybammsolvers/idaklu_source/idaklu_solver.hpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolver.cpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolver.hpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolverGroup.cpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolverGroup.hpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP.inl",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP.hpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP_solvers.cpp",
-        "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP_solvers.hpp",
-        "src/pybammsolvers/idaklu_source/sundials_functions.inl",
-        "src/pybammsolvers/idaklu_source/sundials_functions.hpp",
-        "src/pybammsolvers/idaklu_source/IdakluJax.cpp",
-        "src/pybammsolvers/idaklu_source/IdakluJax.hpp",
-        "src/pybammsolvers/idaklu_source/common.hpp",
-        "src/pybammsolvers/idaklu_source/common.cpp",
-        "src/pybammsolvers/idaklu_source/Solution.cpp",
-        "src/pybammsolvers/idaklu_source/Solution.hpp",
-        "src/pybammsolvers/idaklu_source/SolutionData.cpp",
-        "src/pybammsolvers/idaklu_source/SolutionData.hpp",
-        "src/pybammsolvers/idaklu_source/observe.cpp",
-        "src/pybammsolvers/idaklu_source/observe.hpp",
-        "src/pybammsolvers/idaklu_source/Options.hpp",
-        "src/pybammsolvers/idaklu_source/Options.cpp",
-        "src/pybammsolvers/idaklu.cpp",
-    ],
-)
-ext_modules = [idaklu_ext]
+ext_modules = [
+    Extension(
+        name="pybammsolvers.idaklu",
+        # The sources list should mirror the list in CMakeLists.txt
+        sources=[
+            "src/pybammsolvers/idaklu_source/Expressions/Expressions.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/Base/Expression.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/Base/ExpressionSet.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/Base/ExpressionTypes.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/Base/ExpressionSparsity.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/Casadi/CasadiFunctions.cpp",
+            "src/pybammsolvers/idaklu_source/Expressions/Casadi/CasadiFunctions.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEBaseFunction.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEFunction.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEFunctions.cpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/IREEFunctions.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/iree_jit.cpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/iree_jit.hpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/ModuleParser.cpp",
+            "src/pybammsolvers/idaklu_source/Expressions/IREE/ModuleParser.hpp",
+            "src/pybammsolvers/idaklu_source/idaklu_solver.hpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolver.cpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolver.hpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolverGroup.cpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolverGroup.hpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP.inl",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP.hpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP_solvers.cpp",
+            "src/pybammsolvers/idaklu_source/IDAKLUSolverOpenMP_solvers.hpp",
+            "src/pybammsolvers/idaklu_source/sundials_functions.inl",
+            "src/pybammsolvers/idaklu_source/sundials_functions.hpp",
+            "src/pybammsolvers/idaklu_source/IdakluJax.cpp",
+            "src/pybammsolvers/idaklu_source/IdakluJax.hpp",
+            "src/pybammsolvers/idaklu_source/common.hpp",
+            "src/pybammsolvers/idaklu_source/common.cpp",
+            "src/pybammsolvers/idaklu_source/Solution.cpp",
+            "src/pybammsolvers/idaklu_source/Solution.hpp",
+            "src/pybammsolvers/idaklu_source/SolutionData.cpp",
+            "src/pybammsolvers/idaklu_source/SolutionData.hpp",
+            "src/pybammsolvers/idaklu_source/observe.cpp",
+            "src/pybammsolvers/idaklu_source/observe.hpp",
+            "src/pybammsolvers/idaklu_source/Options.hpp",
+            "src/pybammsolvers/idaklu_source/Options.cpp",
+            "src/pybammsolvers/idaklu.cpp",
+        ],
+    )
+]
 
 # Project metadata was moved to pyproject.toml (which is read by pip). However, custom
 # build commands and setuptools extension modules are still defined here.

diff --git a/src/pybammsolvers/version.py b/src/pybammsolvers/version.py
@@ -1 +1 @@
-__version__="0.0.1"
+__version__ = "0.0.1"