Support umap-learn 0.5.12

[csadorf]

umap-learn 0.5.12 is the latest release but cuML currently caps support at <0.5.12.

Update dependency bounds and support-version docs to include 0.5.12. The upstream regression with numba >= 0.62.0 that caused test failures in older versions has been resolved, so remove the xfail markers that were guarding against it.

• dependencies.yaml, pyproject.toml, both conda env files, docs: relax upper bound from <0.5.12 to <0.5.13
• test_simpl_set.py, test_umap.py: remove numba ≥ 0.62.0 xfail strict markers (regression fixed, all 233 tests pass)
• xfail-list.yaml: remove three flaky tests verified passing 20/20 times under cuml.accel with this version

Closes #8070

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📝 Walkthrough

Walkthrough

This PR raises the umap-learn upper bound to <0.5.13 across envs/configs, removes three iris xfails from the upstream xfail list, and adds runtime umap-learn version gating and a shared UMAP_NUMBA_REGRESSION condition to several tests.

Changes

umap-learn 0.5.13 support

Layer / File(s)	Summary
Dependency version constraints conda/environments/all_cuda-129_arch-aarch64.yaml, conda/environments/all_cuda-129_arch-x86_64.yaml, conda/environments/all_cuda-131_arch-aarch64.yaml, conda/environments/all_cuda-131_arch-x86_64.yaml, dependencies.yaml, docs/source/supported_versions.rst, python/cuml/pyproject.toml	Update umap-learn upper bound from <0.5.12 to <0.5.13 in all environment and dependency declarations.
Upstream xfail list python/cuml/cuml_accel_tests/upstream/umap/xfail-list.yaml	Remove three iris-related test entries from the cuml_accel_flaky marker tests list.
Test version gating python/cuml/tests/test_umap_hypothesis.py, python/cuml/tests/test_umap.py	Import package-version helpers and add UMAP_VERSION constants; gate xfail decorators on UMAP_VERSION < 0.5.12 in addition to numba checks.
Test marker refactor and parametrization python/cuml/tests/test_simpl_set.py, python/cuml/tests/test_umap.py, python/cuml/tests/test_umap_hypothesis.py	Introduce UMAP_NUMBA_REGRESSION combining numba and UMAP-version checks; replace inline xfail conditions with the shared constant; update parametrization and an in-test TODO wording.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• rapidsai/cuml#7938: Modifies python/cuml/tests/test_umap.py to adjust pytest xfail expectations for UMAP-related tests.
• rapidsai/cuml#7850: Coordinated changes to umap-learn version constraints and related test gating/config.
• rapidsai/cuml#7879: Updates dependency specifications for umap-learn (env/pyproject changes).

Suggested reviewers

• betatim
• bdice

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 40.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Support umap-learn 0.5.12' directly and clearly describes the main change: relaxing dependency bounds to support a new version of the umap-learn library.
Description check	✅ Passed	The description is directly related to the changeset, explaining the rationale (umap-learn 0.5.12 is the latest release), listing specific file changes (dependencies.yaml, pyproject.toml, conda env files, docs), and documenting test improvements (removal of xfail markers and flaky tests).
Linked Issues check	✅ Passed	The PR fully addresses all objectives from issue #8070: dependency bounds updated from <0.5.12 to <0.5.13 across all configuration files, xfail markers for numba regression removed, flaky tests removed from xfail list, and upstream test compatibility validated.
Out of Scope Changes check	✅ Passed	All changes are directly scoped to supporting umap-learn 0.5.12: dependency version updates, removal of obsolete xfail markers, and removal of confirmed-passing flaky tests. No unrelated modifications detected.

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@python/cuml/tests/test_umap_hypothesis.py`:
- Around line 979-983: The test is being broadly marked with pytest.mark.xfail
based on Version(numba.__version__) >= Version("0.62.0"); remove this broad
xfail so the test will run normally (or replace it with a narrowly-scoped
condition that only xfails reproducible failure permutations), i.e., delete or
tighten the pytest.mark.xfail decorator that references Version and
numba.__version__ (do not just set strict=False); ensure the test function using
this decorator is no longer silently suppressed so real regressions become
visible.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

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Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

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Run ID: 86a30d49-490c-4530-af2f-9c7db3309b45

📥 Commits

Reviewing files that changed from the base of the PR and between 3fdc35c and d56fe39.

📒 Files selected for processing (10)

• conda/environments/all_cuda-129_arch-aarch64.yaml
• conda/environments/all_cuda-129_arch-x86_64.yaml
• conda/environments/all_cuda-131_arch-aarch64.yaml
• conda/environments/all_cuda-131_arch-x86_64.yaml
• dependencies.yaml
• docs/source/supported_versions.rst
• python/cuml/cuml_accel_tests/upstream/umap/xfail-list.yaml
• python/cuml/pyproject.toml
• python/cuml/tests/test_simpl_set.py
• python/cuml/tests/test_umap_hypothesis.py

💤 Files with no reviewable changes (1)

• python/cuml/cuml_accel_tests/upstream/umap/xfail-list.yaml

✅ Files skipped from review due to trivial changes (6)

• docs/source/supported_versions.rst
• conda/environments/all_cuda-129_arch-aarch64.yaml
• conda/environments/all_cuda-131_arch-aarch64.yaml
• python/cuml/pyproject.toml
• conda/environments/all_cuda-129_arch-x86_64.yaml
• python/cuml/tests/test_simpl_set.py

🚧 Files skipped from review as they are similar to previous changes (2)

• conda/environments/all_cuda-131_arch-x86_64.yaml
• dependencies.yaml

[jcrist]

(assuming tests pass)

[jcrist]

/merge