From 83bcee517323687a86b888faea2f23463cf8649c Mon Sep 17 00:00:00 2001
From: AlgoFoe <varun.singh10011@gmail.com>
Date: Thu, 20 Aug 2026 18:25:40 +0530
Subject: [PATCH 1/2] add script and python helper for precommit settings

---
 bash/update_precommit_config.sh | 149 ++++++++++++++++++++++++++++++++
 python/precommit_updater.py     |  63 ++++++++++++++
 2 files changed, 212 insertions(+)
 create mode 100644 bash/update_precommit_config.sh
 create mode 100644 python/precommit_updater.py

diff --git a/bash/update_precommit_config.sh b/bash/update_precommit_config.sh
new file mode 100644
index 0000000..43fc053
--- /dev/null
+++ b/bash/update_precommit_config.sh
@@ -0,0 +1,149 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+ORG="brainglobe"
+BRANCH_NAME="update/standardize-precommit"
+PR_TITLE="ci: standardise pre-commit config"
+PR_BODY="Drops black in favor of ruff-format and bumps pre-commit-hooks/ruff/mypy/check-manifest/codespell revs to match the rest of BrainGlobe. Repo-specific hooks are left untouched."
+WORK_DIR="$(pwd)/.brainglobe_precommit_work"
+DRY_RUN=false
+ONLY_REPO=""
+
+REPOS=(
+    "brainglobe-atlasapi"
+    "brainglobe-ccf-translator"
+    "brainglobe-heatmap"
+    "brainrender-napari"
+    "brainrender"
+    "cellfinder"
+    "morphapi"
+    "brainglobe-registeration"
+)
+
+# parsing args
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --dry-run)  DRY_RUN=true ; shift ;;
+        --repo)     ONLY_REPO="$2" ; shift 2 ;;
+        *) echo "Unknown argument: $1" ; exit 1 ;;
+    esac
+done
+
+log()  { echo "[INFO]  $*" ; }
+warn() { echo "[WARN]  $*" >&2 ; }
+die()  { echo "[ERROR] $*" >&2 ; exit 1 ; }
+
+require_cmd() {
+    command -v "$1" &>/dev/null || die "'$1' is required but not found in PATH."
+}
+
+require_cmd git
+require_cmd gh
+require_cmd python3
+
+mkdir -p "$WORK_DIR"
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+PYTHON_HELPER="$SCRIPT_DIR/../python/precommit_updater.py"
+[[ -f "$PYTHON_HELPER" ]] || die "Cannot find Python helper: $PYTHON_HELPER"
+
+process_repo() {
+    local repo="$1"
+    local repo_dir="$WORK_DIR/$repo"
+
+    log "Processing: $ORG/$repo"
+
+    # 1. Clone/update
+    if [[ -d "$repo_dir/.git" ]]; then
+        log "Repo exists locally, resetting to origin/main…"
+        git -C "$repo_dir" fetch origin --prune
+        git -C "$repo_dir" checkout main 2>/dev/null \
+            || git -C "$repo_dir" checkout master 2>/dev/null \
+            || { warn "Cannot find main/master for $repo - skipping."; return 0; }
+        git -C "$repo_dir" reset --hard origin/HEAD
+    else
+        log "Cloning $ORG/$repo…"
+        if ! gh repo clone "$ORG/$repo" "$repo_dir" -- --depth=1 2>&1; then
+            warn "Could not clone $ORG/$repo - skipping."
+            return 0
+        fi
+    fi
+
+    # 2. Find pre-commit config
+    local config="$repo_dir/.pre-commit-config.yaml"
+    if [[ ! -f "$config" ]]; then
+        warn "No .pre-commit-config.yaml found in $repo - skipping."
+        return 0
+    fi
+
+    log "Config: $config"
+
+    # 3. Check if branch already exists remotely
+    if git -C "$repo_dir" ls-remote --exit-code --heads origin "$BRANCH_NAME" &>/dev/null; then
+        warn "Branch '$BRANCH_NAME' already exists on $repo - skipping."
+        return 0
+    fi
+
+    # 4. Create branch
+    git -C "$repo_dir" checkout -b "$BRANCH_NAME"
+
+    # 5. Run standardize.py
+    log "Running pre-commit standardizer…"
+    if ! python3 "$PYTHON_HELPER" "$config"; then
+        warn "Standardizer failed for $repo - skipping."
+        git -C "$repo_dir" checkout -f main 2>/dev/null || true
+        git -C "$repo_dir" branch -D "$BRANCH_NAME" 2>/dev/null || true
+        return 0
+    fi
+
+    # 6. Check for actual diff
+    if git -C "$repo_dir" diff --quiet; then
+        log "No changes needed for $repo - skipping PR."
+        git -C "$repo_dir" checkout -f main 2>/dev/null || true
+        git -C "$repo_dir" branch -D "$BRANCH_NAME" 2>/dev/null || true
+        return 0
+    fi
+
+    log "Diff preview:"
+    git -C "$repo_dir" diff -- "$(basename "$config")" || true
+
+    if [[ "$DRY_RUN" == true ]]; then
+        log "[DRY RUN] Would commit, push, and open PR for $repo."
+        return 0
+    fi
+
+    # 7. Commit
+    git -C "$repo_dir" add "$(basename "$config")"
+    git -C "$repo_dir" commit -m "$PR_TITLE"
+
+    # 8. Push
+    log "Pushing branch $BRANCH_NAME to origin…"
+    git -C "$repo_dir" push origin "$BRANCH_NAME"
+
+    # 9. Open PR
+    log "Opening PR…"
+    gh pr create \
+        --repo "$ORG/$repo" \
+        --head "$BRANCH_NAME" \
+        --base main \
+        --title "$PR_TITLE" \
+        --body "$PR_BODY" \
+        --label "maintenance" \
+    && log "PR opened for $repo." \
+    || warn "PR creation failed for $repo (maybe label doesn't exist - try without --label)."
+
+    log "Done: $repo"
+}
+
+# Main
+if [[ -n "$ONLY_REPO" ]]; then
+    process_repo "$ONLY_REPO"
+else
+    for repo in "${REPOS[@]}"; do
+        process_repo "$repo" || warn "Unhandled error for $repo - continuing."
+    done
+fi
+
+log "All repos processed."
+log "Work directory: $WORK_DIR"
\ No newline at end of file
diff --git a/python/precommit_updater.py b/python/precommit_updater.py
new file mode 100644
index 0000000..5857e38
--- /dev/null
+++ b/python/precommit_updater.py
@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+"""
+Standardize a single .pre-commit-config.yaml in place:
+  - bump pre-commit-hooks / ruff-pre-commit / mypy / check-manifest / codespell revs
+  - drop the black hook entirely
+  - make sure ruff-pre-commit has both `ruff` and `ruff-format`, each with
+    args: [--config=pyproject.toml]
+Everything else (napari-plugin-checks, exclude:, ci:, extra mypy deps, etc.)
+is left untouched.
+"""
+import sys
+from ruamel.yaml import YAML
+
+yaml = YAML()
+yaml.preserve_quotes = True
+yaml.width = 4096
+yaml.indent(mapping=4, sequence=4, offset=2)
+
+REVS = {
+    "https://github.com/pre-commit/pre-commit-hooks": "v6.0.0",
+    "https://github.com/astral-sh/ruff-pre-commit": "v0.16.1",
+    "https://github.com/pre-commit/mirrors-mypy": "v1.13.0",
+    "https://github.com/mgedmin/check-manifest": "0.50",
+    "https://github.com/codespell-project/codespell": "v2.4.3",
+}
+BLACK_REPO = "https://github.com/psf/black-pre-commit-mirror"
+RUFF_REPO = "https://github.com/astral-sh/ruff-pre-commit"
+RUFF_ARGS = ["--config=pyproject.toml"]
+
+
+def fix_ruff_hooks(entry):
+    ids = {h["id"] for h in entry["hooks"]}
+    for h in entry["hooks"]:
+        h["args"] = list(RUFF_ARGS)
+    if "ruff-format" not in ids:
+        fmt = type(entry["hooks"][0])()
+        fmt["id"] = "ruff-format"
+        fmt["args"] = list(RUFF_ARGS)
+        entry["hooks"].append(fmt)
+
+
+def standardize(path):
+    with open(path) as f:
+        data = yaml.load(f)
+
+    new_repos = []
+    for entry in data["repos"]:
+        url = entry["repo"]
+        if url == BLACK_REPO:
+            continue  # drop black entirely
+        if url in REVS:
+            entry["rev"] = REVS[url]
+        if url == RUFF_REPO:
+            fix_ruff_hooks(entry)
+        new_repos.append(entry)
+    data["repos"] = new_repos
+
+    with open(path, "w") as f:
+        yaml.dump(data, f)
+
+
+standardize(sys.argv[1] if len(sys.argv) > 1 else ".pre-commit-config.yaml")
+print(f"standardized {sys.argv[1] if len(sys.argv) > 1 else '.pre-commit-config.yaml'}")
\ No newline at end of file

From 52525cee9eb2a5e872e90689f08192c731ee9d92 Mon Sep 17 00:00:00 2001
From: AlgoFoe <varun.singh10011@gmail.com>
Date: Thu, 20 Aug 2026 18:33:51 +0530
Subject: [PATCH 2/2] update pr body

---
 bash/update_precommit_config.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bash/update_precommit_config.sh b/bash/update_precommit_config.sh
index 43fc053..35b2047 100644
--- a/bash/update_precommit_config.sh
+++ b/bash/update_precommit_config.sh
@@ -4,8 +4,8 @@ set -euo pipefail
 
 ORG="brainglobe"
 BRANCH_NAME="update/standardize-precommit"
-PR_TITLE="ci: standardise pre-commit config"
-PR_BODY="Drops black in favor of ruff-format and bumps pre-commit-hooks/ruff/mypy/check-manifest/codespell revs to match the rest of BrainGlobe. Repo-specific hooks are left untouched."
+PR_TITLE="ci: standardize pre-commit config"
+PR_BODY="Standardizes the pre-commit configuration across BrainGlobe repositories while preserving repo-specific hooks and settings."
 WORK_DIR="$(pwd)/.brainglobe_precommit_work"
 DRY_RUN=false
 ONLY_REPO=""
@@ -88,7 +88,7 @@ process_repo() {
     # 4. Create branch
     git -C "$repo_dir" checkout -b "$BRANCH_NAME"
 
-    # 5. Run standardize.py
+    # 5. Run python helper
     log "Running pre-commit standardizer…"
     if ! python3 "$PYTHON_HELPER" "$config"; then
         warn "Standardizer failed for $repo - skipping."