Test with python 3.13

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Expanded official Python compatibility to include Python 3.13 in project metadata and package requirements.
  • Updated CI workflows to use and test against Python 3.13; one workflow entry remains on Python 3.12 and should be aligned.
  • Refreshed package classifiers to list Python 3.13 support.

[coderabbitai]

Walkthrough

Updated CI workflow Python matrices and setup entries from 3.12 to 3.13 (one ubuntu matrix entry remains 3.12). Updated packaging metadata to allow Python <3.14 and added the Python 3.13 classifier. No other functional or control-flow changes.

Changes

Cohort / File(s)	Summary
CI workflow Python version updates .github/workflows/pipeline.yml	Replaced most python-version: '3.12' occurrences with 3.13 in setup and matrix entries; one ubuntu-latest matrix item still lists 3.12.
Packaging metadata pyproject.toml	Changed requires-python from ">=3.9, <3.13" to ">=3.9, <3.14" and added classifier Programming Language :: Python :: 3.13.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Poem

I hop from twelve up to thirteen's gate,
Nudge CI pins and update the crate.
One shy twelve peeks from under a leaf,
I twitch my nose and leave it a brief relief.
New classifier thumps — a joyous little trait.

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The title “Test with python 3.13” clearly conveys the primary change of updating testing to Python 3.13 in a concise, single-sentence format without extraneous details.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch py313

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[coderabbitai]

Actionable comments posted: 0

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

.github/workflows/pipeline.yml (1)

20-20: black_fix job never triggers as intended.

if: failure() at the job level doesn’t reference the result of the black job. Use the needs context.

Apply this diff:

   black_fix:  # in most cases pre-commit is faster
     needs: [black]
-    if: failure()
+    if: ${{ needs.black.result == 'failure' }}

🧹 Nitpick comments (2)

.github/workflows/pipeline.yml (2)

35-37: Guard commit when no changes after formatting.

Avoid failing the job if Black produces no diff (rare but safe). Replace the commit block with a no-op guard.

-        git config --local user.email "pyiron@mpie.de"
-        git config --local user.name "pyiron-runner"
-        git commit -m "Format black" -a
+        git config --local user.email "pyiron@mpie.de"
+        git config --local user.name "pyiron-runner"
+        if ! git diff --quiet; then
+          git commit -m "Format black" -a
+        else
+          echo "No changes to commit"
+        fi

---

56-63: Reduce duplication in setup-miniconda steps.

Consider YAML anchors or a small reusable workflow for the 3.13 conda setup to DRY repeated blocks.

Example with an anchor:

# Define once (e.g., near the top of the workflow file)
conda-313: &conda-313
  uses: conda-incubator/setup-miniconda@v3
  with:
    python-version: '3.13'
    miniforge-version: latest
    channels: conda-forge
    conda-remove-defaults: "true"
    environment-file: environment.yml

# Use in jobs:
- name: Setup Mambaforge
  <<: *conda-313

Also applies to: 86-94, 111-118, 137-144, 212-219, 240-247, 266-273, 290-297, 317-324, 366-373, 396-403

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 997a87a and 3958255.

📒 Files selected for processing (1)

• .github/workflows/pipeline.yml (12 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (13)

• GitHub Check: unittest_siesta
• GitHub Check: unittest_old
• GitHub Check: unittest_qe
• GitHub Check: unittest_matrix (ubuntu-latest, 3.13)
• GitHub Check: unittest_matrix (ubuntu-latest, 3.11)
• GitHub Check: coverage
• GitHub Check: unittest_sphinxdft
• GitHub Check: unittest_matrix (windows-latest, 3.13)
• GitHub Check: unittest_matrix (macos-latest, 3.13)
• GitHub Check: unittest_matrix (ubuntu-latest, 3.12)
• GitHub Check: unittest_mace
• GitHub Check: unittest_gpaw
• GitHub Check: notebooks

🔇 Additional comments (3)

.github/workflows/pipeline.yml (3)

58-63: 3.13 rollout looks consistent across jobs.

The version bumps to Python 3.13 in these jobs are coherent and align with the PR objective. LGTM.

Also applies to: 89-94, 113-118, 139-144, 160-161, 163-164, 166-167, 212-219, 240-247, 266-273, 290-297, 317-324, 366-373, 396-403

---

343-347: Intentional 3.12 for unittest_grace?

All other DFT/ASE jobs are on 3.13. If 3.12 is not required for the Grace toolchain, consider updating to 3.13 for parity; otherwise, a brief comment explaining the pin would prevent future “drift” changes.

---

39-41: Pin GitHub push-action to v1.0.0
In .github/workflows/pipeline.yml (lines 39–41), replace

uses: ad-m/github-push-action@master

with

uses: ad-m/github-push-action@v1.0.0

to lock to the latest stable release and reduce supply-chain risk.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.71%. Comparing base (847dc1b) to head (3958255).
⚠️ Report is 7 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #561   +/-   ##
=======================================
  Coverage   85.71%   85.71%           
=======================================
  Files          43       43           
  Lines        2591     2591           
=======================================
  Hits         2221     2221           
  Misses        370      370           

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