Tl;Dr: System Python installed by actions/setup-python is working but not the Python installed by uv.

I made up a simple project to demonstrate this issue: https://github.com/kdeldycke/nuitka-issue-3325

Works with actions/setup-python

This project is a simple CLI compiled to a standalone binary on all major platforms (Ubuntu, macOS and Windows) and 2 different architectures (x86_64 and arm64).

This is performed by a GitHub workflow available at: https://github.com/kdeldycke/nuitka-issue-3325/blob/main/.github/workflows/system-python.yaml

The process works perfectly on all platforms.

Note that in the logs, Nuitka is picking the right Python version from the system:

Nuitka: Starting Python compilation with Nuitka '2.6.4' on Python (flavor GitHub Actions Python), '3.13' commercial grade 'not installed'.

Issue with uv

Now let's modify the working workflow used above, and completely remove the use of actions/setup-python. Instead, we will rely on uv alone to install our target Python version, by invoking:

$ uv venv --python 3.13

That new workflow is available at: https://github.com/kdeldycke/nuitka-issue-3325/blob/main/.github/workflows/uv-python.yaml

Here is an explicit highlight of the differences between the two workflows:

$ diff -ru ./.github/workflows/system-python.yaml ./.github/workflows/uv-python.yaml        
--- ./.github/workflows/system-python.yaml	2025-02-03 10:49:36
+++ ./.github/workflows/uv-python.yaml	2025-02-03 10:49:36
@@ -6,7 +6,7 @@
 
 jobs:
 
-  system-python:
+  uv-python:
     strategy:
       matrix:
         os:
@@ -19,15 +19,12 @@
     continue-on-error: true
     steps:
       - uses: actions/checkout@v4.2.2
-      - uses: actions/setup-python@v5.4.0
-        with:
-          python-version: "3.13"
       - name: Install uv
         run: |
           python -m pip install "uv == 0.5.28"
       - name: Install Nuitka
         run: |
-          uv --no-progress venv
+          uv --no-progress venv --python 3.13
           uv --no-progress pip install "nuitka == 2.6.4"
 
       - name: uv run -m nuitka --version

Despite these differences, I expect no change in the results. But this is not the case as you can see in this run: https://github.com/kdeldycke/nuitka-issue-3325/actions/runs/13151107465

All the Ubuntu builds fail. The binary is still produced on these platforms, but running them ends up with this error message:

my-cli-ubuntu-24.04.bin: error while loading shared libraries: libpython3.13.so.1.0: cannot open shared object file: No such file or directory

Note that in this case, Nuitka properly reports the Python 3.13 flavor as sourced from uv:

Nuitka: Starting Python compilation with Nuitka '2.6.4' on Python (flavor UV-Python), '3.13' commercial grade 'not installed'.

Context

This has been tested with:

• Latest nuitka: 2.6.4
• Latest uv: 0.5.28
• Latest Python: 3.13
• Latest actions/setup-python: 5.4.0

This issue has also been reported at: Nuitka/Nuitka#3325