Add conda installation workflow (#2839)

Add GitHub Actions workflow to verify conda installations on Linux and macOS.

Fixes crashes on macos under conda related to linking libpython.

Adds some CMake debug output.

---------

Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>

Author: FFroehlich

.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)
 

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:
 

python/sdist/amici/exporters/sundials/templates/CMakeLists.template.cmake

@@ -4,6 +4,12 @@ cmake_policy(VERSION 3.22...3.31)
 
 project(TPL_MODELNAME)
 
+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)

swig/CMakeLists.txt

@@ -20,6 +20,10 @@ find_package(
   Python3
   COMPONENTS Interpreter Development NumPy
   REQUIRED)
+message(
+  STATUS
+    "Python3_INCLUDE_DIRS: ${Python3_INCLUDE_DIRS}; Python3_LIBRARIES: ${Python3_LIBRARIES}"
+)
 message(
   STATUS
     "Found numpy ${Python3_NumPy_VERSION} include dir ${Python3_NumPy_INCLUDE_DIRS}"
@@ -112,7 +116,7 @@ set_target_properties(
 # NOTE: No public definitions of any dependency are forwarded to swig, they are
 # only used for compiling the swig-generated source file. Any definition that
 # are relevant for swig-code generation, need to be forwarded manually.
-target_link_libraries(_amici amici Python3::Python)
+target_link_libraries(_amici amici Python3::Module)
 if(WIN32)
   add_custom_command(
     TARGET _amici