Copier update: copier-base-template v0.2.0 (review-comment script, nested-folder Biome settings)

.claude/skills/address-pr-comments/post-reply.py

@@ -15,14 +15,12 @@
 """
 
 import argparse
-import json
-import subprocess
 import sys
 from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent))
 from utils import owner_repo_from_remote
-from utils import run_cmd
+from utils import post_via_gh_api
 
 
 def main() -> None:
@@ -38,11 +36,6 @@ def main() -> None:
     args = parser.parse_args()
 
     owner, repo = owner_repo_from_remote()
-    try:
-        body = args.body_file.read_text(encoding="utf-8")
-    except OSError as e:
-        _ = sys.stderr.write(f"Unable to read body file {args.body_file}: {e}\n")
-        sys.exit(1)
 
     if args.comment_type == "pulls/comments":
         # Reply directly into the inline review comment thread.
@@ -51,31 +44,7 @@ def main() -> None:
         # GitHub has no "reply" concept for issue comments — post a new top-level comment.
         endpoint = f"repos/{owner}/{repo}/issues/{args.pr}/comments"
 
-    try:
-        result = run_cmd(
-            [
-                "gh",
-                "api",
-                endpoint,
-                "--method",
-                "POST",
-                "--raw-field",
-                f"body={body}",
-            ],
-            timeout=30,
-            timeout_msg="gh api timed out while posting reply.",
-        )
-    except subprocess.CalledProcessError as e:
-        _ = sys.stderr.write(f"gh api error: {e.stderr}\n")
-        sys.exit(1)
-
-    response = json.loads(result.stdout)
-    _ = sys.stdout.write(f"Posted: {response.get('html_url', '(no URL in response)')}\n")
-
-    try:
-        args.body_file.unlink()
-    except OSError as e:
-        _ = sys.stderr.write(f"Warning: post succeeded but could not delete body file {args.body_file}: {e}\n")
+    post_via_gh_api(endpoint=endpoint, body_file=args.body_file, timeout_msg="gh api timed out while posting reply.")
 
 
 if __name__ == "__main__":

.claude/skills/address-pr-comments/post-review-comment.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python3
+"""Post a new inline review comment on a PR diff via the GitHub API.
+
+Usage:
+  # Comment on one line of the new file:
+  post-review-comment.py --pr <number> --path <repo-relative path> --line <n> --body-file <path>
+
+  # Comment spanning a range of lines (start and end must be in the same diff hunk):
+  post-review-comment.py --pr <number> --path <repo-relative path> --start-line <n> --line <m> --body-file <path>
+
+  # Comment on a removed line (the old file's numbering):
+  post-review-comment.py --pr <number> --path <repo-relative path> --line <n> --side LEFT --body-file <path>
+
+Line numbers are those of the file at --commit-id (default: the PR's current head) for --side RIGHT, or of the base
+file for --side LEFT. Owner and repo are derived from the git remote automatically.
+
+This script exists so that gh api calls are covered by the skills allow-list
+rather than requiring manual approval each time.
+"""
+
+import argparse
+import subprocess
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).parent))
+from utils import owner_repo_from_remote
+from utils import post_via_gh_api
+from utils import run_cmd
+
+
+def pr_head_sha(*, owner: str, repo: str, pr: int) -> str:
+    try:
+        result = run_cmd(
+            ["gh", "api", f"repos/{owner}/{repo}/pulls/{pr}", "--jq", ".head.sha"],
+            timeout=30,
+            timeout_msg="gh api timed out while reading the PR head commit.",
+        )
+    except subprocess.CalledProcessError as e:
+        _ = sys.stderr.write(f"gh api error reading PR #{pr}: {e.stderr}\n")
+        sys.exit(1)
+    return result.stdout.strip()
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    _ = parser.add_argument("--pr", type=int, required=True, help="PR number")
+    _ = parser.add_argument("--path", required=True, help="File path relative to the repo root")
+    _ = parser.add_argument("--line", type=int, required=True, help="Line the comment ends on")
+    _ = parser.add_argument("--start-line", type=int, help="First line of a multi-line comment")
+    _ = parser.add_argument("--side", choices=["RIGHT", "LEFT"], default="RIGHT", help="RIGHT = new file, LEFT = old")
+    _ = parser.add_argument("--start-side", choices=["RIGHT", "LEFT"], help="Defaults to --side")
+    _ = parser.add_argument("--commit-id", help="Commit the line numbers refer to (default: the PR's head)")
+    _ = parser.add_argument("--body-file", required=True, type=Path)
+    args = parser.parse_args()
+
+    if args.start_line is not None and args.start_line >= args.line:
+        _ = sys.stderr.write(f"--start-line ({args.start_line}) must be less than --line ({args.line})\n")
+        sys.exit(1)
+
+    owner, repo = owner_repo_from_remote()
+
+    commit_id = args.commit_id
+    if commit_id is None:
+        commit_id = pr_head_sha(owner=owner, repo=repo, pr=args.pr)
+
+    string_fields = {"commit_id": commit_id, "path": args.path, "side": args.side}
+    int_fields = {"line": args.line}
+    if args.start_line is not None:
+        string_fields["start_side"] = args.side if args.start_side is None else args.start_side
+        int_fields["start_line"] = args.start_line
+
+    post_via_gh_api(
+        endpoint=f"repos/{owner}/{repo}/pulls/{args.pr}/comments",
+        body_file=args.body_file,
+        string_fields=string_fields,
+        int_fields=int_fields,
+        timeout_msg="gh api timed out while posting the review comment.",
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+# ============== WARNING ==============================================================================
+# File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git
+# See .config/.copier-managed-files.json for details.
+#
+# You are welcome to make changes to this file in your repo if they are custom to your project,
+# but if the change should be shared with other projects, please backport it to the template repo.
+# =====================================================================================================

.claude/skills/address-pr-comments/utils.py

@@ -5,9 +5,12 @@
 # You are welcome to make changes to this file in your repo if they are custom to your project,
 # but if the change should be shared with other projects, please backport it to the template repo.
 # =====================================================================================================
+import json
 import re
 import subprocess
 import sys
+from collections.abc import Mapping
+from pathlib import Path
 
 
 def run_cmd(
@@ -48,3 +51,55 @@ def owner_repo_from_remote() -> tuple[str, str]:
         _ = sys.stderr.write(f"Cannot parse GitHub owner/repo from remote: {url}\n")
         sys.exit(1)
     return match.group(1), match.group(2)
+
+
+def _read_body_file(body_file: Path) -> str:
+    try:
+        return body_file.read_text(encoding="utf-8")
+    except OSError as e:
+        _ = sys.stderr.write(f"Unable to read body file {body_file}: {e}\n")
+        sys.exit(1)
+
+
+def post_via_gh_api(
+    *,
+    endpoint: str,
+    body_file: Path,
+    string_fields: Mapping[str, str] | None = None,
+    int_fields: Mapping[str, int] | None = None,
+    timeout_msg: str,
+) -> None:
+    """POST a comment to a GitHub API endpoint with gh api, print its URL, then delete the body file it came from.
+
+    The comment's `body` field is read from body_file. string_fields are sent as strings (--raw-field) and int_fields as
+    JSON numbers (--field), which is what GitHub expects for values like line numbers.
+
+    Exits with status 1 if gh api fails. Once gh api succeeds the comment exists, so an unparsable response still counts
+    as posted and the body file is still deleted (otherwise a retry would post a duplicate). A failure to delete the body
+    file only warns.
+    """
+    body = _read_body_file(body_file)
+    cmd = ["gh", "api", endpoint, "--method", "POST", "--raw-field", f"body={body}"]
+    if string_fields is not None:
+        for key, value in string_fields.items():
+            cmd += ["--raw-field", f"{key}={value}"]
+    if int_fields is not None:
+        for key, value in int_fields.items():
+            cmd += ["--field", f"{key}={value}"]
+
+    try:
+        result = run_cmd(cmd, timeout=30, timeout_msg=timeout_msg)
+    except subprocess.CalledProcessError as e:
+        _ = sys.stderr.write(f"gh api error: {e.stderr}\n")
+        sys.exit(1)
+
+    try:
+        url = json.loads(result.stdout).get("html_url", "(no URL in response)")
+    except json.JSONDecodeError:
+        url = "(unparsable response)"
+    _ = sys.stdout.write(f"Posted: {url}\n")
+
+    try:
+        body_file.unlink()
+    except OSError as e:
+        _ = sys.stderr.write(f"Warning: post succeeded but could not delete body file {body_file}: {e}\n")

.config/.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.1.21
+_commit: v0.2.0
 _src_path: gh:LabAutomationAndScreening/copier-base-template.git
 copier_answers_directory: .config
 description: A web app that is hosted within a local intranet. Nuxt frontend, python

.config/.copier-managed-files.json

@@ -41,6 +41,7 @@
         ".claude/skills/address-pr-comments/commit-link.py",
         ".claude/skills/address-pr-comments/fetch-pr-comments.py",
         ".claude/skills/address-pr-comments/post-reply.py",
+        ".claude/skills/address-pr-comments/post-review-comment.py",
         ".claude/skills/address-pr-comments/utils.py",
         ".claude/skills/address-pr-comments/verify-env.py",
         ".claude/skills/caveman/SKILL.md",
@@ -152,6 +153,7 @@
         "template/.claude/skills/address-pr-comments/commit-link.py",
         "template/.claude/skills/address-pr-comments/fetch-pr-comments.py",
         "template/.claude/skills/address-pr-comments/post-reply.py",
+        "template/.claude/skills/address-pr-comments/post-review-comment.py",
         "template/.claude/skills/address-pr-comments/utils.py",
         "template/.claude/skills/address-pr-comments/verify-env.py",
         "template/.claude/skills/caveman/SKILL.md",

.devcontainer/devcontainer.json

@@ -22,7 +22,7 @@
       "extensions": [
         // basic tooling
         // "eamodio.gitlens@15.5.1",
-        "coderabbit.coderabbit-vscode@0.21.9",
+        "coderabbit.coderabbit-vscode@0.23.0",
         "ms-vscode.live-server@0.5.2025051301",
         "MS-vsliveshare.vsliveshare@1.0.5905",
         "anthropic.claude-code@2.1.283",
@@ -67,5 +67,5 @@
   "initializeCommand": "sh .devcontainer/initialize-command.sh",
   "onCreateCommand": "sh .devcontainer/on-create-command.sh",
   "postStartCommand": "sh .devcontainer/post-start-command.sh"
-  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): a45d1e87 # spellchecker:disable-line
+  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): 55943b35 # spellchecker:disable-line
 }

.devcontainer/on-create-command-boilerplate.sh

@@ -8,6 +8,28 @@ git config --local core.symlinks true
 
 sh .devcontainer/create-aws-profile.sh
 
+# The Biome VS Code extension starts a session per workspace folder and warns when folders nest. The root folder's
+# session already covers the nested ones, so Biome is switched off in their (gitignored) folder settings.
+root_folder_path="."
+for workspace_file in *.code-workspace; do
+    if [ ! -f "$workspace_file" ]; then
+        continue
+    fi
+    folders=$(sed -n 's/^[[:space:]]*"path":[[:space:]]*"\([^"]*\)".*/\1/p' "$workspace_file")
+    if ! echo "$folders" | grep -qxF "$root_folder_path"; then
+        continue
+    fi
+    printf '%s\n' "$folders" | while IFS= read -r folder; do
+        case "$folder" in
+        .. | ../* | /*) continue ;;
+        esac
+        if [ "$folder" != "$root_folder_path" ] && [ -d "$folder" ] && [ ! -e "$folder/.vscode/settings.json" ]; then
+            mkdir -p "$folder/.vscode"
+            echo '{ "biome.enabled": false }' >"$folder/.vscode/settings.json"
+        fi
+    done
+done
+
 # ============== WARNING ==============================================================================
 # File is managed by copier template: gh:LabAutomationAndScreening/copier-base-template.git
 # See .config/.copier-managed-files.json for details.

.github/pull_request_template.md

@@ -14,13 +14,13 @@
 
 
 
-## Test plan
+## How do we know this works?
 
-<!-- How do we know this works? Say which kinds of verification cover the change (unit, E2E, snapshot, manual in the
-app, physical device, deployed and checked live) and which part each one covers, any part none of them reaches, and
-whether a test was seen to fail with the code broken or the fix reverted. CI must pass on every PR, so leave out
-anything it covers: re-running its suites only counts somewhere CI can't (a Raspberry Pi, a lab PC). Don't list test
-names from the diff. -->
+<!-- For each part of the change, say which kind of verification pins it (unit, E2E, snapshot, manual in the app,
+physical device, deployed and checked live) and what it establishes, whether a test was seen to fail with the code
+broken or the fix reverted (and how it was broken), and any part nothing covers. Describe what the tests prove, never
+that they ran: CI reruns every suite on every push. Re-running a suite only
+counts somewhere CI can't (a Raspberry Pi, a lab PC). Don't list test names from the diff. -->
 
 
 ## Other

copier.yml

@@ -441,7 +441,7 @@ _tasks:
             fi
         fi
   - command: |
-        for script in .claude/skills/address-pr-comments/check-footer.py .claude/skills/address-pr-comments/commit-link.py .claude/skills/address-pr-comments/fetch-pr-comments.py .claude/skills/address-pr-comments/post-reply.py .claude/skills/address-pr-comments/verify-env.py; do
+        for script in .claude/skills/address-pr-comments/check-footer.py .claude/skills/address-pr-comments/commit-link.py .claude/skills/address-pr-comments/fetch-pr-comments.py .claude/skills/address-pr-comments/post-reply.py .claude/skills/address-pr-comments/post-review-comment.py .claude/skills/address-pr-comments/verify-env.py; do
             if [ -f "$script" ]; then
                 chmod +x "$script"
                 if git ls-files --error-unmatch "$script" > /dev/null 2>&1; then

template/.claude/skills/address-pr-comments/post-reply.py

@@ -15,14 +15,12 @@
 """
 
 import argparse
-import json
-import subprocess
 import sys
 from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent))
 from utils import owner_repo_from_remote
-from utils import run_cmd
+from utils import post_via_gh_api
 
 
 def main() -> None:
@@ -38,11 +36,6 @@ def main() -> None:
     args = parser.parse_args()
 
     owner, repo = owner_repo_from_remote()
-    try:
-        body = args.body_file.read_text(encoding="utf-8")
-    except OSError as e:
-        _ = sys.stderr.write(f"Unable to read body file {args.body_file}: {e}\n")
-        sys.exit(1)
 
     if args.comment_type == "pulls/comments":
         # Reply directly into the inline review comment thread.
@@ -51,31 +44,7 @@ def main() -> None:
         # GitHub has no "reply" concept for issue comments — post a new top-level comment.
         endpoint = f"repos/{owner}/{repo}/issues/{args.pr}/comments"
 
-    try:
-        result = run_cmd(
-            [
-                "gh",
-                "api",
-                endpoint,
-                "--method",
-                "POST",
-                "--raw-field",
-                f"body={body}",
-            ],
-            timeout=30,
-            timeout_msg="gh api timed out while posting reply.",
-        )
-    except subprocess.CalledProcessError as e:
-        _ = sys.stderr.write(f"gh api error: {e.stderr}\n")
-        sys.exit(1)
-
-    response = json.loads(result.stdout)
-    _ = sys.stdout.write(f"Posted: {response.get('html_url', '(no URL in response)')}\n")
-
-    try:
-        args.body_file.unlink()
-    except OSError as e:
-        _ = sys.stderr.write(f"Warning: post succeeded but could not delete body file {args.body_file}: {e}\n")
+    post_via_gh_api(endpoint=endpoint, body_file=args.body_file, timeout_msg="gh api timed out while posting reply.")
 
 
 if __name__ == "__main__":