Adds test suite and benchmarks (#69)

* Fix: CasADi linking to work with pip isolated build environments

This commit resolves a build failure that occurred when building the package
with pip/nox due to pip's use of isolated and changing build environments.

Problem:
- CMake was using find_library() to get the absolute path to libcasadi.dylib
  during configuration in one temporary pip build environment
- By the time the actual build ran, pip had switched to a different temporary
  build environment, making the hard-coded library path invalid
- This caused: "No rule to make target .../libcasadi.dylib" error

Solution:
- Link against CasADi by library name instead of absolute path, relying on
  target_link_directories() to provide the search path during build
- Use relative RPATH (@loader_path on macOS, $ORIGIN on Linux) so the built
  module can find CasADi in the same Python environment at runtime
- Set BUILD_RPATH for the build environment and INSTALL_RPATH for runtime
- Remove duplicate casadi link (already added in USE_PYTHON_CASADI section)

* tests: adds initial test suite w/ basic functionality

* infra: adds __version__ to package, adds nox to dev dependencies w/ uv backend preference

* tests: adds benchmark session, uv backend for nox, updates to unit suite, integration_tests.yml uses nox session, updates docs

* benchmarks: remove icons

* Fix: RPath installation bool, updates PYBAMM_ENV in noxfile, adds nox install to workflow

* test: try condition RPATH

* fix: precommit, integration workflow missing uv

* benchmarks: update regression threshold, increase repeats, try: fix windows build

* fix: integration workflow

* CI: unifi package management

* benchmarks: timeit implementation

* test: adds casadi-based integration tests, removes simplistic unit tests (#70)

* precommit additions

* Suggestions from review

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* precommit additions

* fix: avoid single-element vector operations for MacOS-intel

* another test: separate negate from casadi symbol

* infra: skip macosx_x86_x64 tests for build_wheels.yml

* infra: test level skip instead of workflow level

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

Author: BradyPlanden

.github/workflows/benchmarks.yml

@@ -0,0 +1,49 @@
+name: Benchmarks
+
+on:
+  pull_request:
+    branches:
+      - "main"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest]
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: 'recursive'
+
+      - name: Install dependencies (macOS)
+        if: matrix.os == 'macos-15-intel' || 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
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        run: |
+          pip install uv
+
+      - name: Run benchmarks
+        run: |
+          uvx nox -s benchmarks

.github/workflows/integration_tests.yml

@@ -39,28 +39,11 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Clone PyBaMM repository
-        uses: actions/checkout@v5
-        with:
-          repository: pybamm-team/PyBaMM
-          path: PyBaMM
-          fetch-depth: 0
-          fetch-tags: true
+      - name: Install uv
+        run: |
+          pip install uv
 
       - name: Build and test
         run: |
-          # Install PyBaMM with dependencies
-          cd ./PyBaMM
-          pip install -e ".[all,dev,jax]"
-          cd ..
-
-          # Replace PyBaMM solvers
-          pip uninstall pybammsolvers --yes
-          python install_KLU_Sundials.py
-          pip install "numpy>=2" --upgrade
-          pip install .
-
-          # Run pybamm tests
-          cd ./PyBaMM
-          pytest tests/unit
-          pytest tests/integration
+          # Use PyBaMM-tests nox session
+          uvx nox -s pybamm-tests

.github/workflows/unit_tests.yml

@@ -44,10 +44,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install nox
+      - name: Install uv
         run: |
-          pip install nox
+          pip install uv
 
       - name: Build and test
         run: |
-          nox
+          uvx nox

.gitignore

@@ -16,3 +16,7 @@ build
 # Extra directories for local work
 workspace
 deploy
+PyBaMM
+
+# benchmark results
+performance_results.json

CMakeLists.txt

@@ -137,25 +137,51 @@ if (${USE_PYTHON_CASADI})
         message("Found Python CasADi library directory: ${CASADI_LIB_DIR}")
         target_link_directories(idaklu PRIVATE ${CASADI_LIB_DIR})
 
-        set_target_properties(
-                idaklu PROPERTIES
-                INSTALL_RPATH "${CASADI_LIB_DIR}"
-                INSTALL_RPATH_USE_LINK_PATH TRUE
-        )
-        # Attempt to link the casadi library directly if found
-        find_library(CASADI_LIBRARY NAMES casadi PATHS ${CASADI_LIB_DIR} NO_DEFAULT_PATH)
-        if (CASADI_LIBRARY)
-            message("Found CasADi library: ${CASADI_LIBRARY}")
-            target_link_libraries(idaklu PRIVATE ${CASADI_LIBRARY})
-        else ()
-            message(WARNING "CasADi library not found in ${CASADI_LIB_DIR}. The target will rely on transitive linkage via CMake config if available.")
-        endif ()
+        # Set RPATH to find libraries relative to the module location
+        # This allows finding casadi in the same Python environment at runtime
+        # Module is at: site-packages/pybammsolvers/idaklu.so
+        # CasADi is at: site-packages/casadi/libcasadi.dylib
+        # SuiteSparse/SUNDIALS are found via DYLD_LIBRARY_PATH/LD_LIBRARY_PATH
+        # (set by noxfile or user environment) pointing to .idaklu/lib
+        # Note: Windows uses vcpkg with static linking, no RPATH needed
+        
+        # For CI wheel builds, use BUILD_WITH_INSTALL_RPATH=FALSE so that
+        # wheel repair tools (delocate/auditwheel) can properly analyze dependencies.
+        # For local development, use BUILD_WITH_INSTALL_RPATH=TRUE so the module
+        # works immediately after pip install without wheel repair.
+        if(DEFINED ENV{CIBUILDWHEEL})
+            set(USE_INSTALL_RPATH_AT_BUILD FALSE)
+        else()
+            set(USE_INSTALL_RPATH_AT_BUILD TRUE)
+        endif()
+        
+        if (APPLE)
+            set_target_properties(
+                    idaklu PROPERTIES
+                    BUILD_RPATH "${CASADI_LIB_DIR}"
+                    BUILD_RPATH_USE_LINK_PATH FALSE
+                    INSTALL_RPATH "@loader_path/../casadi"
+                    BUILD_WITH_INSTALL_RPATH ${USE_INSTALL_RPATH_AT_BUILD}
+            )
+        else()
+            set_target_properties(
+                    idaklu PROPERTIES
+                    BUILD_RPATH "${CASADI_LIB_DIR}"
+                    BUILD_RPATH_USE_LINK_PATH FALSE
+                    INSTALL_RPATH "$ORIGIN/../casadi"
+                    BUILD_WITH_INSTALL_RPATH ${USE_INSTALL_RPATH_AT_BUILD}
+            )
+        endif()
+        # Link against casadi by name, not absolute path, to avoid issues with
+        # pip's isolated build environments changing paths between configure and build
+        target_link_libraries(idaklu PRIVATE casadi)
     else ()
         message(FATAL_ERROR "Could not find CasADi library directory")
     endif ()
 else ()
     message("Trying to link against any casadi package apart from the Python one")
     find_package(casadi CONFIG REQUIRED)
+    target_link_libraries(idaklu PRIVATE casadi)
 endif ()
 
 # openmp
@@ -180,7 +206,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
 find_package(SUNDIALS REQUIRED)
 message("SUNDIALS found in ${SUNDIALS_INCLUDE_DIR}: ${SUNDIALS_LIBRARIES}")
 target_include_directories(idaklu PRIVATE ${SUNDIALS_INCLUDE_DIR})
-target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES} casadi)
+target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES})
 
 # link suitesparse
 # if using vcpkg, use config mode to

README.md

@@ -13,11 +13,13 @@ pip install pybammsolvers
 The following solvers are available:
 - PyBaMM's IDAKLU solver
 
-## Local builds
+## Development
+
+### Local builds
 
 For testing new solvers and unsupported architectures, local builds are possible.
 
-### Nox
+#### Nox (Recommended)
 
 Nox can be used to do a quick build:
 ```bash
@@ -26,7 +28,7 @@ nox
 ```
 This will setup an environment and attempt to build the library.
 
-### MacOS
+#### MacOS
 
 Mac dependencies can be installed using brew
 ```bash
@@ -37,7 +39,7 @@ python install_KLU_Sundials.py
 pip install .
 ```
 
-### Linux
+#### Linux
 
 Linux installs may vary based on the distribution, however, the basic build can
 be performed with the following commands:
@@ -48,3 +50,33 @@ pip install cmake casadi setuptools wheel "pybind11[global]"
 python install_KLU_Sundials.py
 pip install .
 ```
+
+### Testing
+
+The project includes comprehensive test suites:
+
+#### Unit Tests
+Test pybammsolvers functionality in isolation:
+```bash
+nox -s unit            # Run all unit tests
+nox -s integration     # Run all integration tests
+```
+
+#### PyBaMM Integration Tests
+Verify compatibility with PyBaMM:
+```bash
+nox -s pybamm-tests                    # Clone/update PyBaMM and run all tests
+nox -s pybamm-tests -- --unit-only     # Run only unit tests
+nox -s pybamm-tests -- --integration-only  # Run only integration tests
+nox -s pybamm-tests -- --no-update     # Skip git pull (use current version)
+nox -s pybamm-tests -- --pybamm-dir ./custom/path  # Use existing PyBaMM clone
+nox -s pybamm-tests -- --branch develop  # Use specific branch/tag
+```
+
+The integration tests ensure that changes to pybammsolvers don't break PyBaMM functionality.
+
+### Benchmarks
+Test for performance regressions against released PyBaMM:
+```bash
+nox -s benchmarks
+```