Merge branch 'master' into rocm3

548cec82 · Jeff Daily · 2f7bd8ef · 5dbfcdc4 · 548cec82 · 548cec82
Commit 548cec82 authored Oct 21, 2025 by Jeff Daily
20 changed files
--- a/.ci/append-comment.sh
+++ b/.ci/append-comment.sh
 #!/bin/bash
 #
 # [description]
-#     Update comment appending a given body to the specified original comment.
+#     Post a comment to a pull request.
 #
 # [usage]
-#     append-comment.sh <COMMENT_ID> <BODY>
+#     append-comment.sh <PULL_REQUEST_ID> <BODY>
 #
-# COMMENT_ID: ID of comment that should be modified.
+# PULL_REQUEST_ID: ID of PR to post the comment on.
 #
-# BODY: Text that will be appended to the original comment body.
+# BODY: Text of the comment to be posted.

 set -e -E -u -o pipefail

@@ -18,20 +18,13 @@ if [ -z "$GITHUB_ACTIONS" ]; then
 fi

 if [ $# -ne 2 ]; then
-  echo "Usage: $0 <COMMENT_ID> <BODY>"
+  echo "Usage: $0 <PULL_REQUEST_ID> <BODY>"
  exit 1
 fi

-comment_id=$1
+pr_id=$1
 body=$2

-old_comment_body=$(
-  curl -sL \
-    -H "Accept: application/vnd.github.v3+json" \
-    -H "Authorization: token $SECRETS_WORKFLOW" \
-    "${GITHUB_API_URL}/repos/microsoft/LightGBM/issues/comments/$comment_id" | \
-  jq '.body'
-)
 body=${body/failure/failure ❌}
 body=${body/error/failure ❌}
 body=${body/cancelled/failure ❌}
@@ -39,12 +32,13 @@ body=${body/timed_out/failure ❌}
 body=${body/success/success ✔️}
 data=$(
  jq -n \
-    --argjson body "${old_comment_body%?}\r\n\r\n$body\"" \
-    '{"body":$body}'
+    --argjson body "\"$body\"" \
+    '{"body": $body}'
 )
 curl -sL \
-  -X PATCH \
+  --fail \
+  -X POST \
  -H "Accept: application/vnd.github.v3+json" \
-  -H "Authorization: token $SECRETS_WORKFLOW" \
+  -H "Authorization: token ${GITHUB_TOKEN}" \
  -d "$data" \
-  "${GITHUB_API_URL}/repos/microsoft/LightGBM/issues/comments/$comment_id"
+  "${GITHUB_API_URL}/repos/microsoft/LightGBM/issues/${pr_id}/comments"
--- a/.ci/test-docs.sh
+++ b/.ci/test-docs.sh
@@ -10,11 +10,4 @@ conda env create \
 # shellcheck disable=SC1091
 source activate test-env

-# build docs
 make -C docs html || exit 1
-
-if [[ $TASK == "check-links" ]]; then
-    # check docs for broken links
-    pip install 'linkchecker>=10.5.0'
-    linkchecker --config=./docs/.linkcheckerrc ./docs/_build/html/*.html || exit 1
-fi
--- a/.ci/check-workflow-status.sh
+++ b/.ci/check-workflow-status.sh
+#!/bin/bash
+
+# [description]
+#
+#   Look for the last run of a given GitHub Actions workflow on a given branch.
+#   If there's never been one (as might be the case with optional workflows like valgrind),
+#   exit with 0.
+#
+#   Otherwise, check the status of that latest run.
+#   If it wasn't successful, exit with a non-0 exit code.
+#
+# [usage]
+#
+#     check-workflow-status.sh <BRANCH> <WORKFLOW_FILE>
+#
+# BRANCH: name of a branch involved in a pull request.
+#
+# WORKFLOW_FILE: filename (e.g. 'r_valgrind.yml') defining the GitHub Actions workflow.
+#
+
+set -e -u -o pipefail
+
+BRANCH="${1}"
+WORKFLOW_FILE="${2}"
+
+echo "Searching for latest run of '${WORKFLOW_FILE}' on branch '${BRANCH}'"
+
+LATEST_RUN_ID=$(
+    gh run list  \
+        --repo "microsoft/LightGBM" \
+        --branch "${BRANCH}" \
+        --workflow "${WORKFLOW_FILE}" \
+        --json 'createdAt,databaseId' \
+        --jq 'sort_by(.createdAt) | reverse | .[0] | .databaseId'
+)
+
+if [[ "${LATEST_RUN_ID}" == "" ]]; then
+    echo "No runs of '${WORKFLOW_FILE}' found on branch '${BRANCH}'"
+    exit 0
+fi
+
+echo "Checking status of workflow run '${LATEST_RUN_ID}'"
+gh run view \
+    --repo "microsoft/LightGBM" \
+    --exit-status \
+    "${LATEST_RUN_ID}"
--- a/.ci/get-workflow-status.py
+++ b/.ci/get-workflow-status.py
-# coding: utf-8
-"""Get the most recent status of workflow for the current PR.
-
-[usage]
-    python get-workflow-status.py TRIGGER_PHRASE
-
-TRIGGER_PHRASE: Code phrase that triggers workflow.
-"""
-
-import json
-from os import environ
-from sys import argv, exit
-from time import sleep
-from urllib import request
-
-
-def get_runs(trigger_phrase):
-    """Get all triggering workflow comments in the current PR.
-
-    Parameters
-    ----------
-    trigger_phrase : str
-        Code phrase that triggers workflow.
-
-    Returns
-    -------
-    pr_runs : list
-        List of comment objects sorted by the time of creation in decreasing order.
-    """
-    pr_runs = []
-    if environ.get("GITHUB_EVENT_NAME", "") == "pull_request":
-        pr_number = int(environ.get("GITHUB_REF").split("/")[-2])
-        page = 1
-        while True:
-            req = request.Request(
-                url="{}/repos/microsoft/LightGBM/issues/{}/comments?page={}&per_page=100".format(
-                    environ.get("GITHUB_API_URL"), pr_number, page
-                ),
-                headers={"Accept": "application/vnd.github.v3+json"},
-            )
-            url = request.urlopen(req)
-            data = json.loads(url.read().decode("utf-8"))
-            url.close()
-            if not data:
-                break
-            runs_on_page = [
-                i
-                for i in data
-                if i["author_association"].lower() in {"owner", "member", "collaborator"}
-                and i["body"].startswith("/gha run {}".format(trigger_phrase))
-            ]
-            pr_runs.extend(runs_on_page)
-            page += 1
-    return pr_runs[::-1]
-
-
-def get_status(runs):
-    """Get the most recent status of workflow for the current PR.
-
-    Parameters
-    ----------
-    runs : list
-        List of comment objects sorted by the time of creation in decreasing order.
-
-    Returns
-    -------
-    status : str
-        The most recent status of workflow.
-        Can be 'success', 'failure' or 'in-progress'.
-    """
-    status = "success"
-    for run in runs:
-        body = run["body"]
-        if "Status: " in body:
-            if "Status: skipped" in body:
-                continue
-            if "Status: failure" in body:
-                status = "failure"
-                break
-            if "Status: success" in body:
-                status = "success"
-                break
-        else:
-            status = "in-progress"
-            break
-    return status
-
-
-if __name__ == "__main__":
-    trigger_phrase = argv[1]
-    while True:
-        status = get_status(get_runs(trigger_phrase))
-        if status != "in-progress":
-            break
-        sleep(60)
-    if status == "failure":
-        exit(1)
--- a/.ci/lint-all.sh
+++ b/.ci/lint-all.sh
@@ -8,21 +8,14 @@ pwsh -file ./.ci/lint-powershell.ps1 || exit 1

 conda create -q -y -n test-env \
    "python=3.13[build=*_cp*]" \
-    'biome>=1.9.3' \
-    'matplotlib-base>=3.9.1' \
-    'mypy>=1.11.1' \
    'pre-commit>=3.8.0' \
-    'pyarrow-core>=17.0' \
-    'scikit-learn>=1.5.2' \
    'r-lintr>=3.1.2'

 # shellcheck disable=SC1091
 source activate test-env

-bash ./.ci/run-pre-commit-mypy.sh || exit 1
+echo "Running pre-commit checks"
+pre-commit run --all-files || exit 1

 echo "Linting R code"
 Rscript ./.ci/lint-r-code.R "$(pwd)" || exit 1
-
-echo "Linting JavaScript code"
-bash ./.ci/lint-js.sh || exit 1
--- a/.ci/lint-js.sh
+++ b/.ci/lint-js.sh
-#!/bin/bash
-
-set -e -E -u -o pipefail
-
-biome ci --config-path=./biome.json --diagnostic-level=info --error-on-warnings ./
--- a/.ci/parameter-generator.py
+++ b/.ci/parameter-generator.py
@@ -289,7 +289,13 @@ def gen_parameter_code(
 * This file is auto generated by LightGBM\.ci\parameter-generator.py from LightGBM\include\LightGBM\config.h file.
 */
 """
-    str_to_write += "#include<LightGBM/config.h>\nnamespace LightGBM {\n"
+    str_to_write += "#include <LightGBM/config.h>\n\n"
+    str_to_write += "#include <string>\n"
+    str_to_write += "#include <unordered_map>\n"
+    str_to_write += "#include <unordered_set>\n"
+    str_to_write += "#include <vector>\n\n"
+    str_to_write += "namespace LightGBM {\n"
+
    # alias table
    str_to_write += "const std::unordered_map<std::string, std::string>& Config::alias_table() {\n"
    str_to_write += "  static std::unordered_map<std::string, std::string> aliases({\n"

--- a/.ci/rerun-workflow.sh
+++ b/.ci/rerun-workflow.sh
@@ -31,7 +31,7 @@ pr_branch=$3
 runs=$(
  curl -sL \
    -H "Accept: application/vnd.github.v3+json" \
-    -H "Authorization: token $SECRETS_WORKFLOW" \
+    -H "Authorization: token ${GITHUB_TOKEN}" \
    "${GITHUB_API_URL}/repos/microsoft/LightGBM/actions/workflows/${workflow_id}/runs?event=pull_request&branch=${pr_branch}" | \
  jq '.workflow_runs'
 )
@@ -42,6 +42,6 @@ if [[ $(echo "${runs}" | jq 'length') -gt 0 ]]; then
  curl -sL \
    -X POST \
    -H "Accept: application/vnd.github.v3+json" \
-    -H "Authorization: token $SECRETS_WORKFLOW" \
+    -H "Authorization: token ${GITHUB_TOKEN}" \
    "${GITHUB_API_URL}/repos/microsoft/LightGBM/actions/runs/$(echo "${runs}" | jq '.[0].id')/rerun"
 fi
--- a/.ci/run-pre-commit-mypy.sh
+++ b/.ci/run-pre-commit-mypy.sh
-#!/bin/bash
-
-set -e -E -u -o pipefail
-
-echo "running pre-commit checks"
-pre-commit run --all-files || exit 1
-echo "done running pre-commit checks"
-
-echo "running mypy"
-mypy \
-    --config-file=./python-package/pyproject.toml \
-    ./python-package \
-|| true
-echo "done running mypy"
--- a/.ci/set-commit-status.sh
+++ b/.ci/set-commit-status.sh
@@ -46,8 +46,9 @@ data=$(
 )

 curl -sL \
+  --fail \
  -X POST \
  -H "Accept: application/vnd.github.v3+json" \
-  -H "Authorization: token $SECRETS_WORKFLOW" \
+  -H "Authorization: token ${GITHUB_TOKEN}" \
  -d "$data" \
  "${GITHUB_API_URL}/repos/microsoft/LightGBM/statuses/$sha"
--- a/.ci/trigger-dispatch-run.sh
+++ b/.ci/trigger-dispatch-run.sh
-#!/bin/bash
-#
-# [description]
-#     Trigger manual workflow run by a dispatch event.
-#
-# [usage]
-#     trigger-dispatch-run.sh <PR_URL> <COMMENT_ID> <DISPATCH_NAME>
-#
-# PR_URL: URL of pull request from which dispatch is triggering.
-#
-# COMMENT_ID: ID of comment that is triggering a dispatch.
-#
-# DISPATCH_NAME: Name of a dispatch to be triggered.
-
-set -e -E -u -o pipefail
-
-if [ -z "$GITHUB_ACTIONS" ]; then
-  echo "Must be run inside GitHub Actions CI"
-  exit 1
-fi
-
-if [ $# -ne 3 ]; then
-  echo "Usage: $0 <PR_URL> <COMMENT_ID> <DISPATCH_NAME>"
-  exit 1
-fi
-
-pr_url=$1
-comment_id=$2
-dispatch_name=$3
-
-pr=$(
-  curl -sL \
-    -H "Accept: application/vnd.github.v3+json" \
-    -H "Authorization: token $SECRETS_WORKFLOW" \
-    "$pr_url"
-)
-data=$(
-  jq -n \
-    --arg event_type "$dispatch_name" \
-    --arg pr_number "$(echo "$pr" | jq '.number')" \
-    --arg pr_sha "$(echo "$pr" | jq '.head.sha')" \
-    --arg pr_branch "$(echo "$pr" | jq '.head.ref')" \
-    --arg comment_number "$comment_id" \
-    '{"event_type":$event_type,"client_payload":{"pr_number":$pr_number,"pr_sha":$pr_sha,"pr_branch":$pr_branch,"comment_number":$comment_number}}'
-)
-curl -sL \
-  -X POST \
-  -H "Accept: application/vnd.github.v3+json" \
-  -H "Authorization: token $SECRETS_WORKFLOW" \
-  -d "$data" \
-  "${GITHUB_API_URL}/repos/microsoft/LightGBM/dispatches"
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -4,3 +4,5 @@
 1b792e716682254c33ddb5eb845357e84018636d
 # enable ruff-format on main library Python code (#6336)
 dd31208ab7a7aea86762830697b00666f843ded9
+# enable whitespace/indent_namespace rule from cpplint (#7056)
+50f11a9f3c066eadee475ea567f9e9d49e6bb827
--- a/.github/workflows/linkchecker.yml
+++ b/.github/workflows/linkchecker.yml
@@ -23,9 +23,21 @@ jobs:
          fetch-depth: 5
          persist-credentials: false
          submodules: false
-      - name: Setup and run tests
+      - name: Build docs
        run: |
          export CONDA=${HOME}/miniforge
          export PATH=${CONDA}/bin:${HOME}/.local/bin:${PATH}
          $GITHUB_WORKSPACE/.ci/setup.sh || exit 1
-          $GITHUB_WORKSPACE/.ci/test-docs.sh || exit 1
+          $GITHUB_WORKSPACE/.ci/build-docs.sh || exit 1
+      - name: Check links
+        uses: lycheeverse/lychee-action@v2.6.1
+        with:
+          args: >-
+            --config=./docs/.lychee.toml
+            --
+            "**/*.rst"
+            "**/*.md"
+            "./R-package/**/*.Rd"
+            "./docs/_build/html/*.html"
+          fail: true
+          failIfEmpty: true
--- a/.github/workflows/optional_checks.yml
+++ b/.github/workflows/optional_checks.yml
@@ -7,8 +7,10 @@ on:

 jobs:
  all-optional-checks-successful:
-    timeout-minutes: 120
+    timeout-minutes: 30
    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ github.token }}
    steps:
      - name: Checkout repository
        uses: actions/checkout@v5
@@ -16,19 +18,12 @@ jobs:
          fetch-depth: 5
          persist-credentials: false
          submodules: false
-      - name: Check that all tests succeeded
+      - name: Check valgrind workflow
        shell: bash
        run: |
-            workflows=(
-                "R valgrind tests;r-valgrind"
-            )
-            for i in "${workflows[@]}"; do
-                workflow_name=${i%;*}
-                comment="The last reported status from workflow \"$workflow_name\" is failure."
-                comment="${comment} Commit fixes and rerun the workflow."
-                trigger_phrase=${i#*;}
-                python \
-                    "$GITHUB_WORKSPACE/.ci/get-workflow-status.py" \
-                    "$trigger_phrase" \
-                || { echo "${comment}"; exit 1; }
-            done
+            # ref: https://docs.github.com/en/actions/reference/workflows-and-actions/contexts#github-context
+            PR_BRANCH="${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}"
+            echo "checking status for branch '${PR_BRANCH}'"
+            ./.ci/check-workflow-status.sh \
+                "${PR_BRANCH}" \
+                'r_valgrind.yml'
--- a/.github/workflows/r_configure.yml
+++ b/.github/workflows/r_configure.yml
 name: R generate configure

 on:
-  repository_dispatch:
-    types: [gha_run_r_configure]
+  workflow_dispatch:
+    inputs:
+      pr-branch:
+        type: string
+        description: |
+          Branch in microsoft/LightGBM to update.
+
+permissions:
+  actions: none
+  checks: none
+  contents: write
+  deployments: none
+  discussions: none
+  id-token: write
+  issues: none
+  packages: none
+  pages: none
+  pull-requests: read
+  repository-projects: none
+  security-events: none
+  statuses: none

 jobs:
  r-configure:
@@ -24,18 +43,19 @@ jobs:
        uses: actions/checkout@v5
        with:
          fetch-depth: 5
-          submodules: true
+          submodules: false
          repository: microsoft/LightGBM
-          ref: "refs/heads/${{ fromJSON(github.event.client_payload.pr_branch) }}"
-          token: ${{ secrets.WORKFLOW }}
+          ref: "refs/heads/${{ inputs.pr-branch }}"
+          token: ${{ github.token }}
          persist-credentials: true
      - name: Update configure
        shell: bash
        run: ./R-package/recreate-configure.sh || exit 1
      - name: Push changes
        run: |
-          git config --global user.name "GitHub Actions Bot"
-          git config --global user.email "githubactionsbot@users.noreply.github.com"
+          # source for this user and email: https://github.com/orgs/community/discussions/160496
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
          git add "./R-package/configure"
          git commit --allow-empty -m "Auto-update configure"
          git push
--- a/.github/workflows/r_valgrind.yml
+++ b/.github/workflows/r_valgrind.yml
 name: R valgrind tests

 on:
-  repository_dispatch:
-    types: [gha_run_r_valgrind]
+  workflow_dispatch:
+    inputs:
+      pr-branch:
+        type: string
+        description: |
+          Branch the PR was submitted from.
+          Branches from forks should be prefixed with the user/org they originate from,
+          like '{user}:{branch}'.
+      pr-number:
+        type: string
+        description: Pull request ID, found in the PR URL.
+
+permissions:
+  actions: none
+  checks: write
+  contents: read
+  deployments: none
+  discussions: none
+  id-token: write
+  issues: none
+  packages: none
+  pages: none
+  pull-requests: write
+  repository-projects: none
+  security-events: none
+  statuses: write

 jobs:
  test-r-valgrind:
@@ -11,7 +35,7 @@ jobs:
    runs-on: ubuntu-latest
    container: wch1/r-debug
    env:
-      SECRETS_WORKFLOW: ${{ secrets.WORKFLOW }}
+      GITHUB_TOKEN: ${{ github.token }}
    steps:
      - name: Install essential software before checkout
        shell: bash
@@ -30,20 +54,7 @@ jobs:
          submodules: true
          persist-credentials: false
          repository: microsoft/LightGBM
-          ref: "refs/pull/${{ github.event.client_payload.pr_number }}/merge"
-      - name: Send init status
-        if: ${{ always() }}
-        shell: bash
-        run: |
-          $GITHUB_WORKSPACE/.ci/set-commit-status.sh \
-            "${{ github.workflow }}" \
-            "pending" \
-            "${{ github.event.client_payload.pr_sha }}"
-          comment="Workflow **${{ github.workflow }}** has been triggered! 🚀\r\n"
-          comment="${comment}${GITHUB_SERVER_URL}/microsoft/LightGBM/actions/runs/${GITHUB_RUN_ID}"
-          $GITHUB_WORKSPACE/.ci/append-comment.sh \
-            "${{ github.event.client_payload.comment_number }}" \
-            "${comment}"
+          ref: "refs/pull/${{ inputs.pr-number }}/merge"
      - name: Run tests with valgrind
        shell: bash
        run: ./.ci/test-r-package-valgrind.sh
@@ -53,15 +64,18 @@ jobs:
          $GITHUB_WORKSPACE/.ci/set-commit-status.sh \
            "${{ github.workflow }}" \
            "${{ job.status }}" \
-            "${{ github.event.client_payload.pr_sha }}"
+            "${{ github.sha }}"
+          comment="Workflow **${{ github.workflow }}** has been triggered! 🚀\r\n"
+          comment="${comment}\r\n${GITHUB_SERVER_URL}/microsoft/LightGBM/actions/runs/${GITHUB_RUN_ID} \r\n"
+          comment="${comment}\r\nStatus: ${{ job.status }}"
          $GITHUB_WORKSPACE/.ci/append-comment.sh \
-            "${{ github.event.client_payload.comment_number }}" \
-            "Status: ${{ job.status }}."
+            "${{ inputs.pr-number }}" \
+            "${comment}"
      - name: Rerun workflow-indicator
        if: ${{ always() }}
        run: |
          bash $GITHUB_WORKSPACE/.ci/rerun-workflow.sh \
            "optional_checks.yml" \
-            "${{ github.event.client_payload.pr_number }}" \
-            "${{ github.event.client_payload.pr_branch }}" \
+            "${{ inputs.pr-number }}" \
+            "${{ inputs.pr-branch }}" \
            || true
--- a/.github/workflows/static_analysis.yml
+++ b/.github/workflows/static_analysis.yml
@@ -58,7 +58,7 @@ jobs:
          export CONDA=${HOME}/miniforge
          export PATH=${CONDA}/bin:$HOME/.local/bin:${PATH}
          $GITHUB_WORKSPACE/.ci/setup.sh || exit 1
-          $GITHUB_WORKSPACE/.ci/test-docs.sh || exit 1
+          $GITHUB_WORKSPACE/.ci/build-docs.sh || exit 1
  r-check-docs:
    name: r-package-check-docs
    timeout-minutes: 60

--- a/.github/workflows/triggering_comments.yml
+++ b/.github/workflows/triggering_comments.yml
-name: Triggering comments
-
-on:
-  issue_comment:
-    types: [created]
-
-jobs:
-  triggering-tests:
-    if: |
-      github.event.issue.pull_request &&
-      contains('OWNER,MEMBER,COLLABORATOR', github.event.comment.author_association) &&
-      startsWith(github.event.comment.body, '/gha run')
-    runs-on: ubuntu-latest
-    env:
-      SECRETS_WORKFLOW: ${{ secrets.WORKFLOW }}
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v5
-        with:
-          fetch-depth: 5
-          persist-credentials: false
-          submodules: false
-
-      - name: Trigger R valgrind tests
-        if: github.event.comment.body == '/gha run r-valgrind'
-        run: |
-          $GITHUB_WORKSPACE/.ci/trigger-dispatch-run.sh \
-            "${{ github.event.issue.pull_request.url }}" \
-            "${{ github.event.comment.id }}" \
-            "gha_run_r_valgrind"
-
-      - name: Trigger update R configure
-        if: github.event.comment.body == '/gha run r-configure'
-        run: |
-          $GITHUB_WORKSPACE/.ci/trigger-dispatch-run.sh \
-            "${{ github.event.issue.pull_request.url }}" \
-            "${{ github.event.comment.id }}" \
-            "gha_run_r_configure"
--- a/.gitignore
+++ b/.gitignore
@@ -313,6 +313,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
@@ -320,8 +321,11 @@ nosetests.xml
 prof/
 *.prof
 coverage.xml
-*,cover
+*.cover
+*.py.cover
 .hypothesis/
+.pytest_cache/
+cover/
 **/coverage.html
 **/coverage.html.zip
 **/Rplots.pdf
@@ -469,3 +473,8 @@ dask-worker-space/

 # pixi environments
 .pixi
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,14 +21,15 @@ repos:
    rev: '1.4.3'
    hooks:
      - id: cmakelint
-        args: ["--linelength=120", "--filter=-convention/filename,-package/stdargs,-readability/wonkycase"]
+        args: ["--linelength=120"]
  - repo: https://github.com/cpplint/cpplint
    rev: '2.0.2'
    hooks:
      - id: cpplint
        args:
+          - --root=..  # workaround to get correct header guard pattern
          - --recursive
-          - --filter=-build/c++11,-build/include_subdir,-build/include_what_you_use,-build/header_guard,-whitespace/indent_namespace,-whitespace/line_length
+          - --filter=-build/include_subdir,-whitespace/line_length
  - repo: local
    hooks:
      - id: check-omp-pragmas
@@ -62,17 +63,22 @@ repos:
          - sphinx>=8.1.3
          - sphinx_rtd_theme>=3.0.1
  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
    rev: v0.14.0
    hooks:
-      # Run the linter.
      - id: ruff-check
        args: ["--config", "python-package/pyproject.toml"]
        types_or: [python, jupyter]
-      # Run the formatter.
      - id: ruff-format
        args: ["--config", "python-package/pyproject.toml"]
        types_or: [python, jupyter]
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.2.5
+    hooks:
+      - id: biome-ci
+        args:
+          - --config-path=./biome.json
+          - --diagnostic-level=info
+          - --error-on-warnings
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.10.0.1
    hooks:
@@ -88,3 +94,13 @@ repos:
    hooks:
      - id: validate-pyproject
        files: python-package/pyproject.toml$
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.18.2
+    hooks:
+      - id: mypy
+        verbose: true
+        entry: bash -c 'mypy --config-file=./python-package/pyproject.toml ./python-package || true'
+        additional_dependencies:
+          - matplotlib>=3.9.1
+          - pyarrow>=17.0
+          - scikit-learn>=1.5.2