Use swig from PyPI (#2774)

Use swig from PyPI (https://github.com/nightlark/swig-pypi / https://pypi.org/project/swig/) instead of requiring a system installation.

Closes #2737.

Author: dweindl

.github/actions/install-apt-dependencies/action.yml

@@ -11,6 +11,5 @@ runs:
               libboost-chrono-dev \
               libboost-math-dev \
               libboost-serialization-dev \
-              libhdf5-serial-dev \
-              swig
+              libhdf5-serial-dev
       shell: bash

.github/actions/install-macos-dependencies/action.yml

@@ -30,5 +30,5 @@ runs:
       # install hdf5 without dependencies, because pkgconf installation fails,
       # because it's already installed on the runners. install the other
       # hdf5 dependencies (libaec) manually
-      run: brew install libaec && brew install --ignore-dependencies hdf5 && brew install swig libomp boost
+      run: brew install libaec && brew install --ignore-dependencies hdf5 && brew install libomp boost
       shell: bash

.github/workflows/test_windows.yml

@@ -52,9 +52,7 @@ jobs:
     - name: Install deps
       shell: bash
       run: |
-        python -m pip install --upgrade pip \
-          && choco install -y ninja \
-          && choco install -y swig
+        python -m pip install --upgrade pip
 
     - name: Install OpenBLAS
       shell: powershell

binder/Dockerfile

@@ -14,7 +14,6 @@ RUN apt-get update && apt-get install -y \
     python3-dev \
     python3-pip \
     python3-venv \
-    swig \
     wget
 
 # BEGIN BINDER

container/Dockerfile

@@ -12,8 +12,7 @@ RUN apt-get update && apt-get install -y \
     python3 \
     python3-dev \
     python3-pip \
-    python3-venv \
-    swig
+    python3-venv
 
 # prepare python install
 

doc/python_installation.rst

@@ -9,7 +9,6 @@ Short guide
 Installation of the AMICI Python package has the following prerequisites:
 
 * Python>=3.11
-* :term:`SWIG`>=4.1
 * CBLAS compatible BLAS library
   (e.g., OpenBLAS, CBLAS, Atlas, Accelerate, Intel MKL)
 * a C++20 compatible C++ compiler and a C compiler
@@ -50,7 +49,7 @@ Install the AMICI dependencies via ``apt``
 
 .. code-block:: bash
 
-   sudo apt install libatlas-base-dev swig python3-dev
+   sudo apt install libatlas-base-dev python3-dev
 
    # optionally for HDF5 support:
    sudo apt install libhdf5-serial-dev
@@ -72,7 +71,7 @@ Install the AMICI dependencies via ``apt``
 
 .. code-block:: bash
 
-   sudo dnf install openblas-devel swig
+   sudo dnf install openblas-devel
 
 Install AMICI:
 
@@ -88,7 +87,7 @@ Install the AMICI dependencies via ``pacman``
 
 .. code-block:: bash
 
-   sudo pacman -S python swig openblas gcc hdf5 boost-libs
+   sudo pacman -S python openblas gcc hdf5 boost-libs
 
 Export the bash variables ``BLAS_CFLAGS`` and ``BLAS_LIBS`` to point to where BLAS was installed, e.g.:
 
@@ -109,13 +108,13 @@ Alternatively:
 
 .. code-block:: bash
 
-   sudo pacman -Si python swig openblas gcc hdf5 boost-libs
+   sudo pacman -Si python openblas gcc hdf5 boost-libs
 
 2. Upgrade installed packages if required mininum versions are not satisfied for AMICI installation.
 
 .. code-block:: bash
 
-   sudo pacman -Su python swig openblas gcc hdf5 boost-libs
+   sudo pacman -Su python openblas gcc hdf5 boost-libs
 
 3. Export the bash variables ``BLAS_CFLAGS`` and ``BLAS_LIBS`` to point to where BLAS was installed, e.g.:
 
@@ -138,8 +137,6 @@ Install the AMICI dependencies using homebrew:
 
 .. code-block:: bash
 
-    brew install swig
-
     # optionally for HDF5 support:
     brew install hdf5
 
@@ -399,8 +396,7 @@ To activate the environment, run:
 
 (and ``conda deactivate`` later to deactivate it again).
 
-:term:`SWIG` must be installed and available in your ``PATH``, and a
-CBLAS-compatible BLAS must be available. You can also use conda to
+A CBLAS-compatible BLAS must be available. You can also use conda to
 install the latter locally, using:
 
 .. code-block:: bash

python/sdist/pyproject.toml

@@ -6,6 +6,7 @@ requires = [
     "wheel",
     "numpy>=2.0",
     "cmake-build-extension==0.6.0",
+    "swig",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -27,6 +28,7 @@ dependencies = [
     "toposort",
     "setuptools>=48",
     "mpmath",
+    "swig"
 ]
 license = "BSD-3-Clause"
 authors = [

scripts/buildAmici.sh

@@ -48,7 +48,8 @@ fi
 
 # set python executable for cmake
 export PYTHON_EXECUTABLE="${amici_path}/venv/bin/python"
-python3 -m pip install numpy
+python3 -m pip install numpy swig
+export SWIG=$(which swig)
 
 suitesparse_root="${amici_path}/ThirdParty/SuiteSparse"
 

scripts/installAmiciSource.sh

@@ -33,7 +33,10 @@ fi
 export PYTHON_EXECUTABLE="${AMICI_PATH}/venv/bin/python"
 
 python -m pip install --upgrade pip wheel
-python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy petab
+# we need to install all build-system.requires manually, because of
+#  --no-build-isolation below.
+#  The latter is necessary for code coverage to work.
+python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy petab swig
 python -m pip install git+https://github.com/pysb/pysb@master # for SPM with compartments
 AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
   python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis,jax]" --no-build-isolation