Merge branch 'main' into fixed_parameters

Author: dweindl

.github/workflows/test_conda_install.yml

@@ -0,0 +1,58 @@
+name: Conda installation
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '48 4 * * *'
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  conda:
+    name: Conda installation
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-latest]
+        python-version: ['3.11', '3.12', '3.13']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+          activate-environment: amici
+      - name: Install requirements
+        shell: bash -l {0}
+        run: |
+          conda install -c conda-forge compilers cmake
+      - name: Install AMICI
+        shell: bash -l {0}
+        run: |
+          pip3 install -v ./python/sdist
+      - name: Show environment
+        shell: bash -l {0}
+        run: |
+          python -c "import os; import pprint; pprint.pprint(dict(os.environ))"
+          which cmake
+          which ninja
+          ls -l /Users/runner/miniconda3/envs/amici/bin || true
+      - name: Install test dependencies
+        shell: bash -l {0}
+        run: |
+          # Install test extras (pytest, scipy, etc.)
+          pip3 install pytest pytest-cov scipy h5py antimony
+      - name: Test import
+        shell: bash -l {0}
+        run: |
+          python -c "from amici import _amici; print(_amici)"
+          python -m amici
+      - name: Run SBML import test
+        shell: bash -l {0}
+        # FIXME
+        continue-on-error: true
+        run: |
+          cd python/tests
+          pytest test_sbml_import.py::test_steadystate_simulation -sv

CMakeLists.txt

@@ -6,6 +6,11 @@ cmake_minimum_required(VERSION 3.22)
 # src/CMakeLists.template.cmake
 cmake_policy(VERSION 3.22...3.31)
 
+# We aren't using C++20 modules, so disable scanning for them to avoid
+# clang-scan-deps-notfound errors.
+# See also https://discourse.cmake.org/t/cmake-3-28-cmake-cxx-compiler-clang-scan-deps-notfound-not-found/9244/3
+set(CMAKE_CXX_SCAN_FOR_MODULES OFF)
+
 project(amici)
 
 # misc options
@@ -27,6 +32,7 @@ message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
 message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
 message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
 message(STATUS "CMAKE_VERSION: ${CMAKE_VERSION}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
 
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 

cmake/AmiciFindBLAS.cmake

@@ -15,6 +15,11 @@ if(DEFINED ENV{AMICI_BLAS_USE_SCIPY_OPENBLAS})
       "Using AMICI_BLAS_USE_SCIPY_OPENBLAS=${AMICI_BLAS_USE_SCIPY_OPENBLAS} from environment variable."
   )
   set(AMICI_BLAS_USE_SCIPY_OPENBLAS $ENV{AMICI_BLAS_USE_SCIPY_OPENBLAS})
+elseif(NOT DEFINED AMICI_BLAS_USE_SCIPY_OPENBLAS
+       AND NOT AMICI_PYTHON_BUILD_EXT_ONLY)
+  # If were are not building the Python extension, it's unlikely that we want to
+  # use scipy-openblas
+  set(AMICI_BLAS_USE_SCIPY_OPENBLAS FALSE)
 endif()
 
 if((${BLAS} STREQUAL "MKL" OR DEFINED ENV{MKLROOT})

doc/conf.py

@@ -441,59 +441,6 @@ def process_docstring(app, what, name, obj, options, lines):
         )
 
 
-def fix_typehints(sig: str) -> str:
-    # cleanup types
-    if not isinstance(sig, str):
-        return sig
-
-    for old, new in typemaps.items():
-        sig = sig.replace(old, new)
-    sig = sig.replace("void", "None")
-    sig = sig.replace("amici::realtype", "float")
-    sig = sig.replace("std::string", "str")
-    sig = sig.replace("double", "float")
-    sig = sig.replace("long", "int")
-    sig = sig.replace("char const *", "str")
-    sig = sig.replace("amici::", "")
-    sig = sig.replace("sunindextype", "int")
-    sig = sig.replace("H5::H5File", "object")
-
-    # remove const / const&
-    sig = sig.replace(" const&? ", r" ")
-    sig = re.sub(r" const&?$", r"", sig)
-
-    # remove pass by reference
-    sig = re.sub(r" &(,|\))", r"\1", sig)
-    sig = re.sub(r" &$", r"", sig)
-
-    # turn gsl_spans and pointers into Iterables
-    sig = re.sub(r"([\w.]+) \*", r"Iterable[\1]", sig)
-    sig = re.sub(r"gsl::span< ([\w.]+) >", r"Iterable[\1]", sig)
-
-    # fix garbled output
-    sig = sig.replace(" >", "")
-    return sig
-
-
-def process_signature(
-    app, what: str, name: str, obj, options, signature, return_annotation
-):
-    if signature is None:
-        return
-
-    # only apply in the amici.amici module
-    split_name = name.split(".")
-    if len(split_name) < 2 or split_name[1] != "amici":
-        return
-
-    signature = fix_typehints(signature)
-    if hasattr(obj, "__annotations__"):
-        for ann in obj.__annotations__:
-            obj.__annotations__[ann] = fix_typehints(obj.__annotations__[ann])
-
-    return signature, return_annotation
-
-
 # this code fixes references in symlinked md files in documentation folder
 # link replacements must be in env.domains['std'].labels
 doclinks = {
@@ -600,7 +547,6 @@ def skip_member(app, what, name, obj, skip, options):
 
 def setup(app: "sphinx.application.Sphinx"):
     app.connect("autodoc-process-docstring", process_docstring, priority=0)
-    app.connect("autodoc-process-signature", process_signature, priority=0)
     app.connect("missing-reference", process_missing_ref, priority=0)
     app.connect("autodoc-skip-member", skip_member, priority=0)
     app.config.intersphinx_mapping = intersphinx_mapping

doc/python_installation.rst

@@ -249,12 +249,6 @@ Installation under conda
 There is no amici conda recipe available yet. However, you can install AMICI
 using pip in a conda environment.
 
-.. note::
-
-   It is possible, but we currently don't recommend using conda for installing
-   AMICI, as it commonly leads to conflicts with system installations of
-   libraries and compilers.
-
 Create a minimal conda environment via:
 
 .. code-block:: bash
@@ -286,25 +280,13 @@ Now, you are ready to use AMICI in the virtual environment.
 
    **conda on Mac**
 
-   If the above installation does not work for you, try installing AMICI via:
+   If the above installation does not work for you, try installing AMICI
+   using clang compilers provided by conda:
 
    .. code-block:: bash
 
-      CFLAGS="-stdlib=libc++" CC=clang CXX=clang pip3 install --verbose amici
-
-   This will use the ``clang`` compiler.
-
-   You will have to pass the same options when compiling any model later
-   on. This can be done by inserting the following code before model import:
-
-   .. code-block:: python
-
-      import os
-      os.environ['CC'] = 'clang'
-      os.environ['CXX'] = 'clang'
-      os.environ['CFLAGS'] = '-stdlib=libc++'
-
-   (For further discussion see https://github.com/AMICI-dev/AMICI/issues/357)
+      conda install -c conda-forge compilers
+      pip install amici --no-cache
 
 Known issues:
 

models/model_calvetti_py/CMakeLists.txt

@@ -4,6 +4,12 @@ cmake_policy(VERSION 3.22...3.31)
 
 project(model_calvetti_py)
 
+message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
+message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "CMAKE_VERSION: ${CMAKE_VERSION}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -30,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.1 REQUIRED HINTS
+find_package(Amici 0.34.2 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_calvetti_py/model_calvetti_py.h

@@ -549,7 +549,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.1";
+        return "0.34.2";
     }
 
     /**

models/model_calvetti_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.1"],
+    install_requires=["amici==0.34.2"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_dirac_py/CMakeLists.txt

@@ -4,6 +4,12 @@ cmake_policy(VERSION 3.22...3.31)
 
 project(model_dirac_py)
 
+message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
+message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "CMAKE_VERSION: ${CMAKE_VERSION}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -30,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.1 REQUIRED HINTS
+find_package(Amici 0.34.2 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_dirac_py/model_dirac_py.h

@@ -536,7 +536,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.1";
+        return "0.34.2";
     }
 
     /**