Merge pull request #2525 from dweindl/release_0.26.3

Release 0.26.3

.github/workflows/deploy_release.yml

@@ -36,11 +36,6 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    - name: Remove direct dependencies from setup.cfg
-      # Remove any "git+https"-based dependencies that are not supported
-      #  by PyPI and are only required for testing.
-      run: sed -i '/git+https/d' python/sdist/pyproject.toml
-
     - name: sdist
       run: scripts/buildSdist.sh
 

.github/workflows/test_benchmark_collection_models.yml

@@ -68,7 +68,7 @@ jobs:
     - name: Run Gradient Checks
       run: |
         pip install git+https://github.com/ICB-DCM/fiddy.git \
-          && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
+          && cd tests/benchmark-models && pytest --durations=10 ./test_petab_benchmark.py
 
     # upload results
     - uses: actions/upload-artifact@v4

.github/workflows/test_petab_test_suite.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     name: PEtab Testsuite
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     env:
       ENABLE_GCOV_COVERAGE: TRUE
@@ -68,6 +68,12 @@ jobs:
             && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
+      - name: Install PEtab benchmark collection
+        run: |
+          git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+            && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+            && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
       - name: Install petab
         run: |
           source ./venv/bin/activate \

.github/workflows/test_python_cplusplus.yml

@@ -338,6 +338,12 @@ jobs:
         path: ${{ env.pooch-cache }}
         key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
 
+    - name: Install PEtab benchmark collection
+      run: |
+        git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \

.gitignore

@@ -204,3 +204,4 @@ cache_fiddy/*
 debug/*
 tests/benchmark-models/cache_fiddy/*
 venv/*
+.coverage

CHANGELOG.md

@@ -4,6 +4,29 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+
+### v0.26.3 (2024-10-03)
+
+**Fixes**
+
+* Skip building SuiteSparse shared libraries and build all subprojects together
+  for slightly faster package installation
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2514
+  and https://github.com/AMICI-dev/AMICI/pull/2519
+
+* Got rid of petab `DeprecationWarnings` when using the `amici_import_petab`
+  CLI
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2517
+
+* Now also sundials and suitesparse are built in debug mode when installing
+  with `ENABLE_AMICI_DEBUGGING=TRUE`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2515
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.2...v0.26.3
+
 ### v0.26.2 (2024-09-25)
 
 **Fixes**

CMakeLists.txt

@@ -1,10 +1,10 @@
 #
 # Build AMICI library
 #
-cmake_minimum_required(VERSION 3.15)
+cmake_minimum_required(VERSION 3.22)
 # When updating the policy version, please also update it in
 # src/CMakeLists.template.cmake
-cmake_policy(VERSION 3.15...3.30)
+cmake_policy(VERSION 3.22...3.30)
 
 project(amici)
 
@@ -130,7 +130,8 @@ elseif(AMICI_TRY_ENABLE_HDF5)
 endif()
 
 set(VENDORED_SUNDIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/sundials)
-set(SUNDIALS_PRIVATE_INCLUDE_DIRS "${VENDORED_SUNDIALS_DIR}/src")
+set(SUNDIALS_PRIVATE_INCLUDE_DIRS
+    "${VENDORED_SUNDIALS_DIR}/src;${VENDORED_SUNDIALS_DIR}/src/sundials")
 # Handle different sundials build/install dirs, depending on whether we are
 # building the Python extension only or the full C++ interface
 if(AMICI_PYTHON_BUILD_EXT_ONLY)
@@ -224,7 +225,14 @@ set(AMICI_CXX_OPTIONS
     ""
     CACHE STRING "C++ options for libamici (semicolon-separated)")
 target_compile_options(${PROJECT_NAME} PRIVATE "${AMICI_CXX_OPTIONS}")
-
+set_property(
+  SOURCE src/solver_cvodes.cpp
+  APPEND
+  PROPERTY INCLUDE_DIRECTORIES "${SUNDIALS_PRIVATE_INCLUDE_DIRS}")
+set_property(
+  SOURCE src/solver_idas.cpp
+  APPEND
+  PROPERTY INCLUDE_DIRECTORIES "${SUNDIALS_PRIVATE_INCLUDE_DIRS}")
 add_dependencies(${PROJECT_NAME} version)
 
 file(GLOB PUBLIC_HEADERS include/amici/*.h)
@@ -237,8 +245,7 @@ target_include_directories(
          $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
          $<BUILD_INTERFACE:${GSL_LITE_INCLUDE_DIR}>
          $<INSTALL_INTERFACE:${CMAKE_INSTALL_DATADIR}/amici/swig>
-         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>
-  PRIVATE ${SUNDIALS_PRIVATE_INCLUDE_DIRS})
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>)
 
 if("$ENV{ENABLE_AMICI_DEBUGGING}"
    OR "$ENV{ENABLE_GCOV_COVERAGE}"