How can I configure Windows to use Python 3.13 for pip installations instead of MSYS2's Python?

The error indicates that your build is using the MSYS2-installed Python 3.11 rather than your newly installed Python 3.13. The missing header (Python.h) is usually provided with the development files for a given Python installation. In your case, because the MSYS2 Python is being detected first, its include files (or lack thereof) are used instead of what you expect from Python 3.13.

Here are a few steps to resolve the issue:

1. Check Which Python Is Being Used

   Run the following command in your shell to see the full path of the python executable:

   BASHCopied
   where python

   (or in MSYS2 bash shell use which python). You’ll likely see that the MSYS2 path (something like C:\msys64\ucrt64\bin\python.exe) comes before the official installation.

2. Adjust Your PATH Order

   You need to place the directory for Python 3.13 (for example, C:\Users\<User>\AppData\Local\Programs\Python\Python313\) at the top of your PATH environment variable. This tells Windows to use Python 3.13 rather than the MSYS2 version. After updating the PATH, restart your shell/command prompt and verify:

   BASHCopied
   python --version

   It should now report version 3.13.x.

3. Invoke Python Explicitly

   If adjusting the PATH is inconvenient, you can directly call Python 3.13 via its full path:

   BASHCopied
   "C:\Path\To\Python313\python.exe" -m pip install numpy

   This bypasses the issue of multiple installations in PATH.

4. Using Windows vs. MSYS2 Environment

   If you’re working in an MSYS2 environment, many tools there are tuned to its own ecosystem. You have two choices:

   • Option A: Use the official Windows command prompt (or PowerShell) with the Python 3.13 installation.
   • Option B: If you want to use MSYS2’s shell, consider uninstalling or temporarily renaming the MSYS2 Python executables, so that the Windows Python takes precedence in the MSYS2 PATH.

5. Ensure Developer Headers Are Installed

   Official Python installations (from python.org) generally come with the include directory (and Python.h). Make sure during installation you selected options such as “Install for all users” or “Add Python to PATH” and that the installation wasn’t missing the development headers.

By ensuring that your environment is using the correct Python 3.13 interpreter (with its associated headers), the build process for numpy should then be able to locate Python.h and proceed without that error.