[codekongdev]

What does this pull request do, and why?

cmake and ninja are installed into the Python environment together with amici (as requirements of cmake-build-extension), but cmake_build_extension.BuildExtension.run looks them up only on PATH (shutil.which). If the interpreter of a virtual environment is run without activating the environment (IDE, scheduler job, /path/to/venv/bin/python script.py), every model build fails with Required command 'ninja' not found (or 'cmake'), or uses some other cmake from PATH.

Changes:

• build_model_extension now prepends the scripts directory of the running interpreter (sysconfig.get_path("scripts"), the directory _get_env_swig() already uses for SWIG) to PATH for the setup.py subprocess, if it is not on PATH already. This is what activating the environment would do.
• If the directory is already on PATH (activated environment, or a deliberately chosen order, e.g. a module-loaded cmake in front), PATH is left unchanged. I chose this over always prepending because for a system interpreter the scripts directory is e.g. /usr/local/bin, and always moving it to the front could change which tools are used for setups that work today.
• A test in python/tests/test_misc.py and a changelog fragment.

Testing (Ubuntu, Python 3.14.4, amici installed from this branch with pip install -e python/sdist --no-build-isolation; no system cmake/ninja/swig):

• Reproducer from Model build fails with "Required command 'ninja' not found" when the environment is not activated, although cmake and ninja are installed in it #3505, run as env -i HOME=$HOME PATH=/usr/bin:/bin /path/to/venv/bin/python repro.py: on main it fails with Required command 'cmake' not found; with this change the model builds. With another cmake but no ninja first on PATH: Required command 'ninja' not found on main; builds with this change. With the environment's bin on PATH: builds, as before.
• pytest python/tests/test_misc.py with the environment on PATH: 20 passed, 1 failed. test_cmake_compilation needs the C++ CMake build in build/, which I did not do; it fails the same way on main.
• The same without the environment on PATH (PATH=/usr/bin:/bin): on main the shared model fixture fails to build (2 errors). With this change, 19 passed. The two failures are test_cmake_compilation (as above) and test_model_rebuild_reruns_swig_on_swig_change, which looks up swig with shutil.which("swig") in the test itself.
• The new test fails on main ([False] case) and passes with this change.

Related issues

Closes #3505

Use of AI tools

Claude Code (Claude Opus 5.5) drafted the code change, the test, the changelog entry, and this description, and ran the tests listed above.

Checklist

• I have run the relevant tests locally
• I have added a changelog entry in changelog.d/ (or it is not needed)

🤖 Generated with Claude Code