Enable Branch Indexing by MarcSkovMadsen · Pull Request #151 · MarcSkovMadsen/holoviz-mcp

MarcSkovMadsen · 2026-02-22T14:17:33Z

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Pull request overview

Updates the HoloViz MCP servers and documentation indexer to improve tool registration consistency and to better respect configured git refs (branch/tag) when cloning/updating documentation repositories.

Changes:

Add unit tests covering git clone/update behavior when branch/tag are configured.
Update MCP tool decorators across servers from @mcp.tool to @mcp.tool().
Adjust DocumentationIndexer._clone_or_update_repo_sync to detect stale checkouts and re-clone when the configured ref changes.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
`tests/docs_mcp/test_data.py`	Adds tests for branch/tag clone/update behavior.
`src/holoviz_mcp/holoviz_mcp/data.py`	Implements ref-aware clone/update logic and minor log formatting tweaks.
`src/holoviz_mcp/holoviz_mcp/server.py`	Switches to `@mcp.tool()` and comments out the `update_index` tool decorator.
`src/holoviz_mcp/panel_mcp/server.py`	Switches tools to `@mcp.tool()`.
`src/holoviz_mcp/hvplot_mcp/server.py`	Switches tools to `@mcp.tool()`.
`src/holoviz_mcp/holoviews_mcp/server.py`	Switches tools to `@mcp.tool()`.

Comments suppressed due to low confidence (1)

src/holoviz_mcp/holoviz_mcp/server.py:356

update_index’s docstring and examples describe it as an MCP tool, but the @mcp.tool(enabled=False) decorator has been commented out, so it’s no longer registered at all. Either restore the decorator (if you want it present-but-disabled) or adjust/remove the docstring/examples to avoid advertising a tool that can’t be called.

# @mcp.tool(enabled=False)
async def update_index(ctx: Context) -> str:
    """Update the documentation index by re-cloning repositories and re-indexing content.

    DO use this tool periodically (weekly) to ensure the documentation index is up-to-date

Copilot · 2026-02-22T14:21:02Z

+                expected_ref = repo_config.branch or repo_config.tag
+
+                if expected_ref:
+                    try:
+                        current_ref = repo.active_branch.name
+                    except TypeError:
+                        current_ref = None  # Detached HEAD (e.g. tag/commit checkout)
+
+                    if current_ref != expected_ref:
+                        logger.info(f"Stale checkout for {repo_name}: on '{current_ref}', expected '{expected_ref}'. " "Deleting and re-cloning...")
+                        shutil.rmtree(repo_path)
+                        # Fall through to clone below
+                    else:
+                        logger.info(f"Updating {repo_name} repository at {repo_path}...")
+                        repo.remotes.origin.pull()
+                        return repo_path
+                else:
+                    logger.info(f"Updating {repo_name} repository at {repo_path}...")
+                    repo.remotes.origin.pull()
                    return repo_path


Using repo.active_branch to determine the current ref breaks for tag-based clones: cloning a tag via --branch <tag> typically leaves the repo in a detached HEAD where active_branch raises and current_ref becomes None, causing unnecessary re-clones (or always re-cloning) even when the correct tag is already checked out. Consider handling repo_config.tag separately by comparing the checked-out commit to the tag’s commit (or using an exact-match tag check), and avoid relying on active_branch for tags.

Suggested change

expected_ref = repo_config.branch or repo_config.tag

if expected_ref:

try:

current_ref = repo.active_branch.name

except TypeError:

current_ref = None # Detached HEAD (e.g. tag/commit checkout)

if current_ref != expected_ref:

logger.info(f"Stale checkout for {repo_name}: on '{current_ref}', expected '{expected_ref}'. " "Deleting and re-cloning...")

shutil.rmtree(repo_path)

# Fall through to clone below

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

# If a tag is specified, avoid relying on active_branch (HEAD will be detached).

if repo_config.tag:

tag_name = repo_config.tag

tag_ref = next((t for t in repo.tags if t.name == tag_name), None)

if tag_ref is not None and repo.head.commit == tag_ref.commit:

# Already at the expected tag commit; nothing to update for immutable tags.

logger.info(

f"Repository {repo_name} at {repo_path} already checked out at tag '{tag_name}'."

)

return repo_path

logger.info(

f"Stale or mismatched tag checkout for {repo_name}: expected tag '{tag_name}'. "

"Deleting and re-cloning..."

)

shutil.rmtree(repo_path)

# Fall through to clone below

else:

# Branch-based (or default) checkout: use active_branch when available.

expected_ref = repo_config.branch

if expected_ref:

try:

current_ref = repo.active_branch.name

except Exception:

# Detached HEAD or other issue; treat as unknown branch.

current_ref = None

if current_ref != expected_ref:

logger.info(

f"Stale checkout for {repo_name}: on '{current_ref}', expected '{expected_ref}'. "

"Deleting and re-cloning..."

)

shutil.rmtree(repo_path)

# Fall through to clone below

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

Copilot · 2026-02-22T14:21:02Z

+                expected_ref = repo_config.branch or repo_config.tag
+
+                if expected_ref:
+                    try:
+                        current_ref = repo.active_branch.name
+                    except TypeError:
+                        current_ref = None  # Detached HEAD (e.g. tag/commit checkout)
+
+                    if current_ref != expected_ref:
+                        logger.info(f"Stale checkout for {repo_name}: on '{current_ref}', expected '{expected_ref}'. " "Deleting and re-cloning...")
+                        shutil.rmtree(repo_path)
+                        # Fall through to clone below
+                    else:
+                        logger.info(f"Updating {repo_name} repository at {repo_path}...")
+                        repo.remotes.origin.pull()
+                        return repo_path
+                else:
+                    logger.info(f"Updating {repo_name} repository at {repo_path}...")
+                    repo.remotes.origin.pull()
                    return repo_path


expected_ref only considers branch/tag, so a repo configured with a specific commit will be treated as having no expected ref when it already exists and will just pull(), potentially moving HEAD away from the configured commit. If repo_config.commit is meant to pin the checkout, add a commit check for existing repos (e.g., compare repo.head.commit.hexsha and reset/re-clone when it differs).

Suggested change

expected_ref = repo_config.branch or repo_config.tag

if expected_ref:

try:

current_ref = repo.active_branch.name

except TypeError:

current_ref = None # Detached HEAD (e.g. tag/commit checkout)

if current_ref != expected_ref:

logger.info(f"Stale checkout for {repo_name}: on '{current_ref}', expected '{expected_ref}'. " "Deleting and re-cloning...")

shutil.rmtree(repo_path)

# Fall through to clone below

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

# If a specific commit is configured, treat it as a pinned checkout.

if repo_config.commit:

current_commit = repo.head.commit.hexsha

expected_commit = repo_config.commit

# Allow expected_commit to be a short SHA prefix.

if not current_commit.startswith(expected_commit):

logger.info(

f"Stale checkout for {repo_name}: on commit '{current_commit}', "

f"expected '{expected_commit}'. Deleting and re-cloning..."

)

shutil.rmtree(repo_path)

# Fall through to clone below

else:

logger.info(

f"Repository {repo_name} already at desired commit '{expected_commit}'."

)

return repo_path

else:

expected_ref = repo_config.branch or repo_config.tag

if expected_ref:

try:

current_ref = repo.active_branch.name

except TypeError:

current_ref = None # Detached HEAD (e.g. tag/commit checkout)

if current_ref != expected_ref:

logger.info(

f"Stale checkout for {repo_name}: on '{current_ref}', expected '{expected_ref}'. "

"Deleting and re-cloning..."

)

shutil.rmtree(repo_path)

# Fall through to clone below

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

else:

logger.info(f"Updating {repo_name} repository at {repo_path}...")

repo.remotes.origin.pull()

return repo_path

Copilot · 2026-02-22T14:21:02Z

+
+        mock_repo = MagicMock()
+        mock_repo.active_branch.name = "v0.9.0"
+


These tag tests don’t reflect GitPython behavior for tag checkouts: in a tag-based clone the repo is usually in detached HEAD and accessing active_branch raises TypeError. As written (mock_repo.active_branch.name = ...), the test can’t catch the detached-HEAD path and will miss the real bug. Update the mock to raise on active_branch and assert the intended tag detection behavior (including a case where the correct tag is already checked out and does not trigger an rmtree/re-clone).

fix

a2a9614

Copilot AI review requested due to automatic review settings February 22, 2026 14:17

Copilot started reviewing on behalf of MarcSkovMadsen February 22, 2026 14:18 View session

MarcSkovMadsen changed the title ~~Fix~~ Enable Branch Indexing Feb 22, 2026

Copilot AI reviewed Feb 22, 2026

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copilot feedback

1b44672

MarcSkovMadsen merged commit 50dec2f into main Feb 22, 2026
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Enable Branch Indexing#151

Enable Branch Indexing#151
MarcSkovMadsen merged 2 commits into
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enhancment/fix-branch

MarcSkovMadsen commented Feb 22, 2026 •

edited

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		mock_repo = MagicMock()
		mock_repo.active_branch.name = "v0.9.0"

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Pull request overview

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MarcSkovMadsen commented Feb 22, 2026 •

edited

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