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build: add Python 3.13 to CI matrix across all repos #89
Description
Overview
Add Python 3.13 support to the CI test matrix for all five PyAuto library repos. Currently all CI runs only on Python 3.12. Since requires-python >= 3.12 already allows 3.13 installs, we need CI coverage to catch any 3.13-specific issues. The dependency sweep (#87) already raised version caps — JAX, numba, and all other deps support 3.13. AutoBuild will remain on 3.12 only per user request.
Plan
- Add
'3.13'to the Python version matrix in.github/workflows/main.ymlfor all five repos - Add
"Programming Language :: Python :: 3.13"classifier to eachpyproject.toml - Handle optional deps that lack 3.13 wheels: skip
tensorflow-probabilityinstall on 3.13 (it's optional and not needed for core tests) - Push branches, let CI run on both 3.12 and 3.13, then iterate on any failures
- Note: a previous
feature/python-3.12-3.13branch exists on 4 repos — we'll start fresh
Detailed implementation plan
Affected Repositories
- PyAutoConf (primary)
- PyAutoFit
- PyAutoArray
- PyAutoGalaxy
- PyAutoLens
Work Classification
Library
Branch Survey
| Repository | Current Branch | Dirty? | Prior branch? |
|---|---|---|---|
| PyAutoConf | main | clean | feature/python-3.12-3.13 exists |
| PyAutoFit | main | clean | feature/python-3.12-3.13 exists |
| PyAutoArray | main | clean | feature/python-3.12-3.13 exists |
| PyAutoGalaxy | main | clean | feature/python-3.12-3.13 exists |
| PyAutoLens | main | clean | none |
Suggested branch: feature/python-313
Worktree root: ~/Code/PyAutoLabs-wt/python-313/
Implementation Steps
-
For each repo, edit
.github/workflows/main.yml:- Change
python-version: ['3.12']topython-version: ['3.12', '3.13']
- Change
-
For each repo, edit
pyproject.toml:- Add
"Programming Language :: Python :: 3.13"to classifiers
- Add
-
For PyAutoArray only: conditionally skip
tensorflow-probabilityon 3.13 (no wheels). Either:- Use a matrix exclude, or
- Install
[optional]only on 3.12 and base deps on 3.13
-
Push all branches and monitor CI results on both Python versions
-
Fix any 3.13-specific failures that emerge
Key Files
PyAutoConf/.github/workflows/main.ymlPyAutoFit/.github/workflows/main.ymlPyAutoArray/.github/workflows/main.ymlPyAutoGalaxy/.github/workflows/main.ymlPyAutoLens/.github/workflows/main.yml- All five
pyproject.tomlfiles (classifiers only)
Known Compatibility
- jaxnnls==1.0.1: pure Python, works on 3.13 (no compiled extensions)
- JAX >=0.4.33: has 3.13 support
- numba >=0.60: has 3.13 support (optional dep)
- tensorflow-probability==0.25.0: NO 3.13 wheels (optional, skip on 3.13)
Original Prompt
Click to expand starting prompt
Can you add Python 3.13 to the Github actions of every PyAuto library repository, assess what errors or
bugs come up when they try to use 3.13, and then we will iterate on working out what to do
so that the package as a whole supports both 3.12 and 3.13.
When libraries are done, we'll then do an autobuild run, but at the end autobuild will still only run on
3.12 by default to avoid too many different actions and instances of things running.
Activity
build: add Python 3.13 to CI matrix and classifiers
build: add Python 3.13 to CI matrix and classifiers
build: add Python 3.13 to CI matrix and classifiers
build: add Python 3.13 to CI matrix and classifiers
build: add Python 3.13 to CI matrix and classifiers
Jammy2211 commentedon Apr 12, 2026
Smoke Test Results — 2026-04-12
All failures are pre-existing and unrelated to the Python 3.13 CI changes:
cookbooks/samples.py— test mode returns fewer samples than script expectsinterferometer/*— simulator subprocess fails (missing interferometer data/deps)aggregator/*— numerical precision ("probabilities do not sum to 1")jax_likelihood_functions/*— JAX vmap tolerance mismatch + interferometer simulatordatabase/scrape/general.py— missing dataset file in SMALL_DATASETS modeCore functionality (autofit searches, galaxy imaging, lens modeling, multi-wavelength) all passes.
PRs
Jammy2211 commentedon Apr 12, 2026
Shipped — 2026-04-12
PRs
Summary
Added Python 3.13 to the CI matrix across all 5 PyAuto library repos. All repos now test on both 3.12 and 3.13 with
fail-fast: false.Key fixes:
==2.8.14on 3.12,>=2.9.0on 3.13) to handle numpy 2.x requirement on 3.13. Fixed dict mutation during iteration inreplace_promise(). Added test exclusions for astropy/anesthetic/numpy-type incompatibilities on 3.13.Session Notes
anesthetic==2.8.14requiringnumpy<2.0.0, which has no Python 3.13 wheels. PEP 508 environment markers solved this cleanly.recursion.py.SettingWithCopyWarning, numpy 2.x float type changes). These could be addressed in future PRs.