docker: Add Python 3.13 free-threaded Docker images

[enwask]

Adds an additional base layer for building Python 3.13 from source with disable-gil, and makes the necessary changes to the rest of the build process as well as Docker build workflows.

[mloubout]

Some minor comments but it looks good

[Copilot]

Pull Request Overview

This PR adds support for Python 3.13 free-threaded (GIL-disabled) Docker images to the Devito project. The changes enable building Docker containers with a custom Python 3.13 build that has the Global Interpreter Lock (GIL) disabled, allowing for true parallelism in Python code.

Key changes include:

• Creation of a new Dockerfile for building Python 3.13 from source with GIL disabled
• Modification of existing Dockerfiles to conditionally use either system Python or the custom free-threaded build
• Updates to GitHub Actions workflows to build both standard and nogil variants of all Docker images

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
docker/Dockerfile.nogil	New Dockerfile that builds Python 3.13 from source with --disable-gil flag
docker/Dockerfile.nvidia	Modified to accept parameterized base image and conditionally install Python
docker/Dockerfile.intel	Updated to use configurable base image and conditional Python installation
docker/Dockerfile.devito	Added logic to handle free-threaded builds and skip incompatible packages like Jupyter
docker/Dockerfile.cpu	Modified to support parameterized base image and conditional Python setup
docker/Dockerfile.amd	Updated to copy Python build from base image and handle conditional installation
.github/workflows/docker-devito.yml	Added nogil variants for all existing Docker image configurations
.github/workflows/docker-bases.yml	Extended workflow matrix to build both standard and nogil versions of all base images

Comments suppressed due to low confidence (1)

[Copilot]

Using a specific branch '3.13' may cause issues if the branch is updated or removed. Consider pinning to a specific commit hash or tag for reproducible builds.

Suggested change

	RUN git clone --depth 1 --branch 3.13 https://github.com/python/cpython.git /usr/src/cpython
	RUN git clone --depth 1 https://github.com/python/cpython.git /usr/src/cpython && \
	cd /usr/src/cpython && \
	git checkout <COMMIT_HASH>

[EdCaunt]

It would probably be worth adding a run to CI-core which runs the tests with free-threaded Python

[enwask]

It would probably be worth adding a run to CI-core which runs the tests with free-threaded Python

Thought about this but I think lots of things will fail off the bat so not sure it should be in CI yet

[EdCaunt]

Thought about this but I think lots of things will fail off the bat so not sure it should be in CI yet

That's a reasonable contention, but they will all need fixing eventually. We've been tripped up like this before (CXX anyone?)

[enwask]

That's a reasonable contention, but they will all need fixing eventually. We've been tripped up like this before (CXX anyone?)

Yeah, just wasn't sure that we want CI to always be red from now on—I think this is above my paygrade though so I'll defer to consensus

[mloubout]

I agree with @EdCaunt that at least one basic test needs to be added to the base no-mpi (i.e., pytest-core-nompi.py, possibly with just test_operator.py). This test file contains very little runtime and mostly just operator build, which should ensure that the base of Devito works with it.

[mloubout]

Looks like it fails to build

https://github.com/devitocodes/devito/actions/runs/16507922396/job/46683232942

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.73%. Comparing base (69ffd48) to head (3054e73).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2681      +/-   ##
==========================================
- Coverage   92.10%   87.73%   -4.37%     
==========================================
  Files         248      248              
  Lines       49654    49654              
  Branches     4368     4368              
==========================================
- Hits        45734    43566    -2168     
- Misses       3213     5326    +2113     
- Partials      707      762      +55     

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pytest-gpu-nvc-nvidiaX	?

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[mloubout]

Just need the CI fixed but GTG. Need some rebase/cleanup of commits.

[FabioLuporini]

why this switch?

[enwask]

The default is used for automated runs, so with a default of false none of the automated runs actually built any images

[EdCaunt]

Commit history will want a cleanup before merge