Repair pre-commit, drop pixi.lock, point .gitattributes at uv.lock (#67)

.pre-commit-config.yaml had rotted into a trap. It ran ruff-format while
CI enforces black, and the two disagree: black reports the tree clean,
ruff format rewrites five files, and black then rejects one of them. Any
contributor who ran `pre-commit install` would have had their commits
reformatted into a state that fails the lint job. It went unnoticed only
because nothing runs it -- no git hook is installed and no workflow
invokes it -- despite pre-commit sitting in the lint dependency group.

Formatting is now black's alone, running after ruff-check so the
formatter has the last word. Hook revs are current: ruff was pinned at
0.12.1 against a project on 0.16.3, and prettier pointed at
pre-commit/mirrors-prettier, which upstream archived; that moves to the
maintained rbubley fork. A pre-commit ecosystem is added to dependabot so
these stop drifting silently.

Deleting the config instead would have been simpler but would have
dropped codespell, validate-pyproject, and prettier, none of which CI
runs.

With the hooks working, codespell found eleven hits. Five were false
positives -- `lamda` is the LAMDA lab's domain in author emails, `anc` a
local for "ancestors" -- and are now in ignore-words-list with a note.
The other six are corrected, including "Subsequnce" in IKTOD's class
docstring and a misspelled variable in a doctest example, both
user-facing.

prettier also normalized indentation in three workflow files and removed
a blank line from mkdocs.yml, the first time it has run over them.
Verified the parsed YAML is identical before and after, and that the docs
still build under --strict.

pixi.lock is removed: 438K of lockfile with no pixi.toml and no
[tool.pixi] section, orphaned since the move to uv. .gitattributes
existed only to mark it generated, so it now does the same for uv.lock,
which collapses that file in diffs and keeps it out of language stats.

Author: xhan97

.gitattributes

@@ -1,4 +1,2 @@
-# GitHub syntax highlighting
-pixi.lock linguist-language=YAML linguist-generated=true
-# SCM syntax highlighting
-pixi.lock linguist-language=YAML linguist-generated=true
+# Collapse the lockfile in diffs and keep it out of language statistics.
+uv.lock linguist-language=TOML linguist-generated=true

.github/dependabot.yml

@@ -22,3 +22,16 @@ updates:
       github-actions:
         patterns:
           - "*"
+
+  # Without this the hook revs in .pre-commit-config.yaml drift silently, which
+  # is how they ended up pinned to ruff 0.12.1 and an archived prettier mirror.
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"
+    groups:
+      pre-commit:
+        patterns:
+          - "*"

.github/workflows/deploy-gh-pages.yml

@@ -3,7 +3,7 @@ name: Documentation
 on:
   push:
     branches:
-    - main
+      - main
     tags:
       - "v*"
   pull_request:
@@ -31,35 +31,35 @@ jobs:
       contents: write
 
     steps:
-    - uses: actions/checkout@v7
-      with:
-        fetch-depth: 0
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
 
-    - name: Set up Python
-      uses: actions/setup-python@v7
-      with:
-        python-version: "3.13"
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
 
-    - name: Set up uv
-      uses: astral-sh/setup-uv@v7
-      with:
-        enable-cache: true
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
 
-    - name: Install docs dependencies
-      run: uv sync --locked --no-default-groups --group docs
+      - name: Install docs dependencies
+        run: uv sync --locked --no-default-groups --group docs
 
-    - name: Deploy docs as dev
-      if: ${{ github.ref == 'refs/heads/main' }}
-      run: |
-        git config user.name "github-actions[bot]"
-        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-        uv run mike deploy --push --update-aliases dev
+      - name: Deploy docs as dev
+        if: ${{ github.ref == 'refs/heads/main' }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          uv run mike deploy --push --update-aliases dev
 
-    - name: Deploy versioned docs and update latest
-      if: ${{ startsWith(github.ref, 'refs/tags/v') }}
-      run: |
-        VERSION="${GITHUB_REF_NAME#v}"
-        git config user.name "github-actions[bot]"
-        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-        uv run mike deploy --push --update-aliases "$VERSION" latest
-        uv run mike set-default --push latest
+      - name: Deploy versioned docs and update latest
+        if: ${{ startsWith(github.ref, 'refs/tags/v') }}
+        run: |
+          VERSION="${GITHUB_REF_NAME#v}"
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          uv run mike deploy --push --update-aliases "$VERSION" latest
+          uv run mike set-default --push latest

.github/workflows/docs.yml

@@ -29,4 +29,4 @@ jobs:
         run: uv sync --locked --no-default-groups --group docs
 
       - name: Build documentation (strict, execute notebooks)
-        run: uv run mkdocs build --strict
+        run: uv run mkdocs build --strict

.github/workflows/fresh-resolution.yml

@@ -11,7 +11,7 @@ name: Fresh Resolution
 
 on:
   schedule:
-    - cron: '0 3 * * 1' # Monday at 03:00
+    - cron: "0 3 * * 1" # Monday at 03:00
   workflow_dispatch:
 
 permissions:

.pre-commit-config.yaml

@@ -2,35 +2,44 @@ fail_fast: false
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.24.1
+    rev: v0.25
     hooks:
       - id: validate-pyproject
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.1.0
+  # pre-commit/mirrors-prettier was archived upstream; this is the maintained fork.
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.9.6
     hooks:
       - id: prettier
         types_or: [yaml, json5]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.12.1
+    rev: v0.16.3
     hooks:
-      # Run the linter.
+      # Linting only. Formatting is black's job below -- running ruff-format
+      # here as well rewrote files in ways black then rejected, so a commit made
+      # with these hooks installed would fail the lint job in CI.
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
-      # Run the formatter.
-      - id: ruff-format
+
+  # Runs after ruff so the formatter has the last word. Keep this rev in sync
+  # with the black pin in pyproject.toml; CI enforces that version.
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.5.1
+    hooks:
+      - id: black
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
+      # Redundant with branch protection on main, but fails locally and
+      # immediately rather than at push time.
       - id: no-commit-to-branch
         name: prevent commits to main
         args: [--branch, main]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.3
     hooks:
       - id: codespell # See pyproject.toml for args
         additional_dependencies:

docs/contributing/contribution.md

@@ -47,7 +47,7 @@ Tips
 - Anything in the `dev` branch should be deployable (no failing tests).
 - Never use `git add .`: it can add unwanted files;
 - Avoid using `git commit -a` unless you know what you're doing;
-- Check every change with `git diff` before adding then to the index (stage area) and with `git diff --cached` before commiting;
+- Check every change with `git diff` before adding then to the index (stage area) and with `git diff --cached` before committing;
 - If you have push access to the main repository, please do not commit directly to `dev`: your access should be used only to accept pull requests; if you want to make a new feature, you should use the same process as other developers so that your code can be reviewed.
 
 Documentation Guidelines
@@ -68,7 +68,7 @@ Code Guidelines
 Tests
 -----
 
-We use [Github Actions](https://github.com/features/actions)for continous integration
+We use [Github Actions](https://github.com/features/actions)for continuous integration
 and python [pytest](https://docs.pytest.org/en/stable/index.html) for writing tests.
 You should write tests for every feature you add or bug you solve in the code.
 Having automated tests for every line of our code let us make big changes

ikpykit/graph/_ikgod.py

@@ -85,7 +85,7 @@ class IKGOD(BaseEstimator):
     >>> # Fit model
     >>> model = IKGOD(n_estimators=100, h=2).fit(adj, features)
     >>> # Predict outliers
-    >>> lables = model.predict(features)
+    >>> labels = model.predict(features)
     """
 
     def __init__(

ikpykit/stream/cluster/_inode.py

@@ -140,7 +140,7 @@ def _delete_ancestors_ikv(self):
     def _find_and_delete_point(self, current_node, pt_id):
         while current_node.is_internal():
             current_node.pts.remove(pt_id)
-            # assert (p_id in curr_node.children[0].pts[0]) != (p_id in curr_node.children[1].pts[0]), "Except: Exsiting only in  one subtree, \
+            # assert (p_id in curr_node.children[0].pts[0]) != (p_id in curr_node.children[1].pts[0]), "Except: Existing only in  one subtree, \
             #                                                      Get: %s %s" % (p_id in curr_node.children[0].pts[0],
             #                                                                     p_id in curr_node.children[1].pts[0])
             if pt_id in current_node.children[0].pts:

ikpykit/stream/cluster/utils/deltasep_utils.py

@@ -55,7 +55,7 @@ def create_dataset(dims, size, num_clusters=20):
     a dataset of all points.
 
     Args:
-        dims - (int) the dimention of all data points.
+        dims - (int) the dimension of all data points.
         size - (int) the number of points to generate for each cluster.
         num_clusters - (int) the number of clusters.
     """