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[xhan97]

update to uv manage and fix some bugs

[Copilot]

Pull request overview

This PR migrates the project tooling from pixi/setuptools to an uv + hatch-based workflow, refreshes dependency/tooling configuration, and includes a set of refactors and bug fixes across clustering/graph/stream utilities plus documentation updates.

Changes:

• Move packaging/versioning and CI workflows to uv (dependency groups, uv sync, uv build) and add docs checks with strict mkdocs builds.
• Refactor cluster internals (IDKC/PSKC/KCluster) and add an optional force_assign_unassigned behavior with corresponding tests.
• Update docs site navigation/content and enable notebook execution during docs builds.

Reviewed changes

Copilot reviewed 56 out of 57 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
pyproject_old.toml	Adds a snapshot of prior setuptools/pixi config.
pyproject.toml	Switches to hatch/uv-dynamic-versioning + uv dependency groups; updates deps and tooling config.
mkdocs.yml	Adds FAQ to nav; enables mkdocs-jupyter execution.
ikpykit/trajectory/utils.py	Modernizes typing imports/annotations.
ikpykit/trajectory/tests/test_ikat.py	Tightens expected exception type for not-fitted behavior.
ikpykit/trajectory/dataloader/base.py	Removes ABC base from Dataset.
ikpykit/timeseries/tests/test_iktod.py	Makes exception-message matching deterministic via escaped regex.
ikpykit/timeseries/anomaly/_iktod.py	Adds stacklevel to warnings.
ikpykit/stream/tests/test_icid.py	Adds per-module pytest timeout.
ikpykit/stream/cluster/utils/serialize_trees.py	Cleans imports and uses str.format for output writing.
ikpykit/stream/cluster/utils/logger.py	Adds typing for class var; simplifies class declaration.
ikpykit/stream/cluster/utils/file_utils.py	Improves readability of parsing + avoids redundant open args.
ikpykit/stream/cluster/utils/dendrogram_purity_pool.py	Small modernization (super call, prints, variable naming).
ikpykit/stream/cluster/utils/dendrogram_purity.py	Uses public tqdm import and cleans variable naming.
ikpykit/stream/cluster/utils/deltasep_utils.py	Cleans module header/docs and minor style tweaks.
ikpykit/stream/cluster/utils/Graphviz.py	Refactors string formatting + suppresses exceptions more cleanly.
ikpykit/stream/cluster/_streakhc.py	Modernizes typing (PEP 604 unions) and removes unused imports.
ikpykit/stream/cluster/_inode.py	Modernizes typing and minor comprehension cleanups.
ikpykit/stream/changedetect/_icid.py	Fixes mutable default arg + doc/formatting tweaks.
ikpykit/kernel/_isokernel.py	Improves error/warn messages and adds stacklevel.
ikpykit/kernel/_ik_inne.py	Removes unused variable binding.
ikpykit/group/utils.py	Modernizes typing imports/annotations.
ikpykit/graph/utils.py	Simplifies transpose handling.
ikpykit/graph/tests/test_isographkernel.py	Uses LIL then CSR to avoid sparse efficiency warnings.
ikpykit/graph/tests/test_ikgod.py	Uses LIL then CSR in synthetic adjacency construction; minor test edits.
ikpykit/graph/_isographkernel.py	Docstring dash normalization; adds stacklevel; minor loop var cleanup.
ikpykit/graph/_ikgod.py	Adds stacklevel to warnings.
ikpykit/graph/init.py	Reorders __all__.
ikpykit/cluster/tests/test_pskc.py	Removes unused test variable.
ikpykit/cluster/tests/test_idkc.py	Removes unused test vars; adds tests for force_assign_unassigned.
ikpykit/cluster/_pskc.py	Refactors clustering steps into helper methods; reuses KCluster helpers.
ikpykit/cluster/_kcluster.py	Refactors delete logic and adds shared helper methods.
ikpykit/cluster/_idkc.py	Adds force_assign_unassigned option + refactors post-process logic.
ikpykit/cluster/init.py	Reorders __all__.
ikpykit/anomaly/tests/test_inne.py	Removes unused variables in timing test.
ikpykit/anomaly/_inne.py	Improves messages/warnings formatting and adds stacklevel.
ikpykit/anomaly/_idkd.py	Improves messages/warnings formatting and adds stacklevel.
ikpykit/init.py	Reorders __all__.
examples/plot_inne.py	Import ordering/style cleanup.
docs/user_guides/table-of-contents.md	Updates INNE link to notebook.
docs/user_guides/inne.ipynb	Updates example to import/use INNE and refreshes notebook content.
docs/releases/releases.md	Adds a new changelog section for this release.
docs/quick-start/how-to-install.md	Recommends uv pip install; updates unstable install command.
docs/faq/table-of-contents.md	Replaces unrelated FAQ content with IKPyKit-specific FAQ.
docs/examples/examples_english.md	Updates INNE link to notebook.
docs/README.md	Updates badges and docs links; recommends uv.
README.md	Updates badges; recommends uv installation.
.python-version	Sets local dev Python to 3.13.
.pre-commit-config.yaml	Replaces hooks set; adds ruff format, validate-pyproject, codespell, etc.
.github/workflows/pytest.yml	Switches unit tests to uv sync + pytest matrix including 3.13.
.github/workflows/pypi.yml	Modernizes build/publish using uv build and OIDC publish; adds GitHub release step.
.github/workflows/lint.yml	Switches lint to uv sync + black/ruff.
.github/workflows/docs.yml	Adds strict docs build job with notebook execution.
.github/workflows/deploy-gh-pages.yml	Adds docs pre-check and versioned deployment via mike.
.github/workflows/ci.yml	Adds top-level CI workflow calling lint/tests/docs.
.github/dependabot.yml	Updates dependabot configuration and labels for dependency updates.

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[Copilot]

raise warn(...) is not valid exception handling: warn() returns None, so this will raise a TypeError at runtime. If the intent is to emit a warning and continue, call warn(...) without raise. If the intent is to stop execution, raise an actual exception type (e.g., ValueError) and do not call warn here.

Suggested change

	raise warn(
	warn(

[Copilot]

This is a no-op expression (np.random.rand(5, 2)) whose result is unused. With ruff’s bugbear rules enabled, this can be flagged as a “useless expression” and fail linting; remove it or assign it to a variable that’s used in the test.

[Copilot]

delete_points updates points_ before calling reduce_kernel_mean_, but reduce_kernel_mean_ uses self.n_points to scale the existing mean. After removal, self.n_points no longer matches the mean’s previous sample count, so the updated kernel_mean_ will be incorrect. Call reduce_kernel_mean_ before mutating points_, or pass the previous point count into the mean update logic.

Suggested change

	self.points_.remove(points)
	self.reduce_kernel_mean_(X)
	elif isinstance(points, Iterable):
	missing_points = [p for p in points if p not in self.points_]
	if missing_points:
	raise ValueError(f"Points {missing_points} not in cluster {self.id}")
	for p in points:
	self.points_.remove(p)
	self.reduce_kernel_mean_(X)
	# Update kernel mean before mutating points_ so that self.n_points
	# still reflects the original sample count used in kernel_mean_.
	self.reduce_kernel_mean_(X)
	self.points_.remove(points)
	elif isinstance(points, Iterable):
	missing_points = [p for p in points if p not in self.points_]
	if missing_points:
	raise ValueError(f"Points {missing_points} not in cluster {self.id}")
	# As above, update kernel mean before removing any points so that
	# self.n_points matches the count used for the current kernel_mean_.
	self.reduce_kernel_mean_(X)
	for p in points:
	self.points_.remove(p)