[minor] drop 3.9 in favour of 3.13 #36

liamhuber · 2025-03-17T17:45:44Z

In lieu of 3.9

If the tests pass (I don't anticipate a reason they wouldn't), the support bounds can be changed accordingly

In lieu of 3.9

github-actions · 2025-03-17T17:45:55Z

👈 Launch a binder notebook on branch pyiron/pyiron_snippets/liamhuber-patch-1

codacy-production · 2025-03-17T17:47:08Z

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
✅ +0.00% (target: -1.00%)	✅ ∅

Coverage variation details

	Coverable lines	Covered lines	Coverage
Common ancestor commit (`c2205d5`)	560	532	95.00%
Head commit (`941a08d`)	560 (+0)	532 (+0)	95.00% (+0.00%)

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details

	Coverable lines	Covered lines	Diff coverage
Pull request (#36)	0	0	∅ (not applicable)

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

See your quality gate settings Change summary preferences

coveralls · 2025-03-17T17:49:37Z

Pull Request Test Coverage Report for Build 13907416732

Details

0 of 0 changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 95.0%

Totals
Change from base Build 13888350067:	0.0%
Covered Lines:	532
Relevant Lines:	560

💛 - Coveralls

jan-janssen · 2025-03-17T21:26:43Z

The coveralls python package does not support Python 3.13 yet. TheKevJames/coveralls-python#549 Is it required? Or is it possible to replace it with the coveralls GitHub action https://github.com/coverallsapp/github-action

# Conflicts: # .github/workflows/push-pull.yml

Signed-off-by: liamhuber <[email protected]>

codecov · 2025-05-08T00:57:13Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.00%. Comparing base (288377c) to head (2d6c7ac).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #36   +/-   ##
=======================================
  Coverage   95.00%   95.00%           
=======================================
  Files          13       13           
  Lines         560      560           
=======================================
  Hits          532      532           
  Misses         28       28

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liamhuber · 2025-05-08T01:01:48Z

Ah darnit, the codacy and coveralls env files are still getting included. I was just too sloppy verifying pyiron/actions#146 and there must still be a little bug. I'll fix it tomorrow.

Signed-off-by: liamhuber <[email protected]>

liamhuber · 2025-05-08T13:12:21Z

The action itself was (correctly) still maintaining the old env files by default, so in pyiron/actions#147 I just manually turned it off in the reusable workflows whenever we're not actually trying to calculate coverage.

liamhuber · 2025-05-08T13:17:26Z

The coverage env issues are resolved; 3.13 alone is failing with an exception that is new to me:

Run pip install --no-deps . --no-build-isolation
  pip install --no-deps . --no-build-isolation
  shell: /usr/bin/bash -l {0}
  env:
    WRITE_ENVIRONMENT_OUTPUT_ENV_FILE: ./environment.yml
    INPUT_RUN_POST: true
    CONDA: /home/runner/miniconda3
Processing /home/runner/work/pyiron_snippets/pyiron_snippets
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
ERROR: Exception:
Traceback (most recent call last):
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
    status = _inner_run()
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
    return self.run(options, args)
           ~~~~~~~~^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/cli/req_command.py", line 68, in wrapper
    return func(self, options, args)
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/commands/install.py", line 387, in run
    requirement_set = resolver.resolve(
        reqs, check_supported_wheels=not options.target_dir
    )
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 77, in resolve
    collected = self.factory.collect_root_requirements(root_reqs)
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements
    reqs = list(
        self._make_requirements_from_install_req(
    ...<2 lines>...
        )
    )
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req
    cand = self._make_base_candidate_from_link(
        ireq.link,
    ...<2 lines>...
        version=None,
    )
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link
    self._link_candidate_cache[link] = LinkCandidate(
                                       ~~~~~~~~~~~~~^
        link,
        ^^^^^
    ...<3 lines>...
        version=version,
        ^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__
    super().__init__(
    ~~~~~~~~~~~~~~~~^
        link=link,
        ^^^^^^^^^^
    ...<4 lines>...
        version=version,
        ^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__
    self.dist = self._prepare()
                ~~~~~~~~~~~~~^^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare
    dist = self._prepare_distribution()
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution
    return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement
    return self._prepare_linked_requirement(req, parallel_builds)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement
    dist = _get_prepared_distribution(
        req,
    ...<3 lines>...
        self.check_build_deps,
    )
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution
    abstract_dist.prepare_distribution_metadata(
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        finder, build_isolation, check_build_deps
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata
    self.req.prepare_metadata()
    ~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/req/req_install.py", line 575, in prepare_metadata
    self.metadata_directory = generate_metadata(
                              ~~~~~~~~~~~~~~~~~^
        build_env=self.build_env,
        ^^^^^^^^^^^^^^^^^^^^^^^^^
        backend=self.pep517_backend,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        details=details,
        ^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/operations/build/metadata.py", line 34, in generate_metadata
    distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir)
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_internal/utils/misc.py", line 723, in prepare_metadata_for_build_wheel
    return super().prepare_metadata_for_build_wheel(
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        metadata_directory=metadata_directory,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        config_settings=cs,
        ^^^^^^^^^^^^^^^^^^^
        _allow_fallback=_allow_fallback,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 224, in prepare_metadata_for_build_wheel
    return self._call_hook(
           ~~~~~~~~~~~~~~~^
        "prepare_metadata_for_build_wheel",
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<4 lines>...
        },
        ^^
    )
    ^
  File "/home/runner/work/pyiron_snippets/pyiron_snippets/cached-miniforge/my-env/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 402, in _call_hook
    raise BackendUnavailable(
    ...<4 lines>...
    )
pip._vendor.pyproject_hooks._impl.BackendUnavailable: Cannot import 'setuptools.build_meta'

liamhuber · 2025-05-08T13:26:40Z

I find this rather confusing, as it complains about the availability of setuptools.build_meta, but the head of my pyproject.toml suggests this should be available:

[build-system]
requires = [
    "setuptools",
    "versioneer[toml]==0.29",
]
build-backend = "setuptools.build_meta"

@jan-janssen, I peeked at executorlib for a reference, but your pyproject file looks quite similar (and identical in terms of setuptools and the build-backend), yet works fine on 3.13. Have you seen this error before?

liamhuber · 2025-05-08T19:34:23Z

I didn't find anything similar on a web search; I tried re-running; I tried deleting the p3.13 cache and re-running. Unfortunately, no progress.

.binder/environment.yml

jan-janssen · 2025-05-08T19:35:16Z

.ci_support/environment.yml

@@ -1,4 +1,4 @@
 channels:
 - conda-forge
 dependencies:
- python >=3.9,<3.13
+- python >=3.10,<3.14


Suggested change

- python >=3.10,<3.14

- python >=3.10,<3.14

- setuptools

jan-janssen · 2025-05-08T19:36:08Z

docs/environment.yml

@@ -7,4 +7,4 @@ dependencies:
 - sphinx-gallery
 - sphinx-rtd-theme
 - versioneer
- python >=3.9,<3.13
+- python >=3.10,<3.14


Suggested change

- python >=3.10,<3.14

- setuptools

- python >=3.10,<3.14

jan-janssen · 2025-05-08T19:37:05Z

I didn't find anything similar on a web search; I tried re-running; I tried deleting the p3.13 cache and re-running. Unfortunately, no progress.

It might be just missing setuptools in the environment.yml.

liamhuber · 2025-05-08T19:44:28Z

Yeah, I was just poking deeper and see setuptools is pinned in your env file

They [were removed](https://conda-forge.org/news/2024/08/21/sunsetting-pip-deps/?utm_source=chatgpt.com) Signed-off-by: liamhuber <[email protected]>

liamhuber · 2025-05-08T19:59:21Z

I didn't find anything similar on a web search; I tried re-running; I tried deleting the p3.13 cache and re-running. Unfortunately, no progress.

It might be just missing setuptools in the environment.yml.

Thank you for the pointer. I let the bot handle the changes rather than the suggestions, but this was indeed the issue.

It turns out that since there are so many build tools available now conda-forge is no longer packaging setuptools and wheel by default. I'll go through the rest of the release process for snippets and then give a little report on Monday.

Signed-off-by: liamhuber <[email protected]>

…r-patch-1

Test 3.13

30b7ba2

In lieu of 3.9

liamhuber added 3 commits March 17, 2025 10:52

Update pyproject.toml (#37)

6f49e9f

Update environment.yml (#38)

494dab9

Update environment.yml (#39)

941a08d

liamhuber mentioned this pull request Mar 17, 2025

Python 3.13 Support #35

Closed

liamhuber mentioned this pull request Mar 24, 2025

Switch from coveralls to codecov pyiron/actions#143

Open

liamhuber added 2 commits May 7, 2025 17:53

Merge branch 'main' into liamhuber-patch-1

5e395ff

# Conflicts: # .github/workflows/push-pull.yml

Update push-pull target

e496bf1

Signed-off-by: liamhuber <[email protected]>

liamhuber changed the title ~~Test 3.13~~ [minor] drop 3.9 in favour of 3.13 May 8, 2025

Target action patch

0d982af

Signed-off-by: liamhuber <[email protected]>

liamhuber mentioned this pull request May 8, 2025

[patch] Limit coverage env pyiron/actions#147

Merged

jan-janssen reviewed May 8, 2025

View reviewed changes

.binder/environment.yml Show resolved Hide resolved

jan-janssen reviewed May 8, 2025

View reviewed changes

liamhuber and others added 2 commits May 8, 2025 12:55

Explicitly add setuptools and wheel

1775aa4

They [were removed](https://conda-forge.org/news/2024/08/21/sunsetting-pip-deps/?utm_source=chatgpt.com) Signed-off-by: liamhuber <[email protected]>

[dependabot skip] Update env file

d160cc7

Target the latest pyiron/actions

19583bd

Signed-off-by: liamhuber <[email protected]>

Merge remote-tracking branch 'origin/liamhuber-patch-1' into liamhube…

2d6c7ac

…r-patch-1

liamhuber merged commit a2694e0 into main May 8, 2025
21 checks passed

liamhuber deleted the liamhuber-patch-1 branch May 8, 2025 20:07

[minor] drop 3.9 in favour of 3.13 #36

[minor] drop 3.9 in favour of 3.13 #36

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