Add diagnostics for species tree rendering

[Ulthran]

Motivation

• The species page sometimes showed an empty box when a Newick tree was loaded without any visible error, so rendering failures needed to be explicit and debuggable.
• Improve robustness by normalizing Newick input and surfacing library/load/parse errors in the UI so users and developers can quickly identify the root cause.

Description

• Add a visible status element above the tree container (#tree-status) that reports loading, success, or error messages to the user.
• Add client-side validation and normalization of the Newick string (trim and ensure a trailing ;) and log basic diagnostics (console.debug of length and preview).
• Add checks for the presence of the phylotree library and wrap the render call in a try/catch to display parsing/render errors instead of leaving the container blank.
• Apply a small formatting change to app/nl_query.py via black (no behavior change) to keep the codebase formatted.

Testing

• Ran black . which reformatted files and completed successfully.
• Ran pytest tests/ and all tests passed (9 passed).

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Codex Task

[Copilot]

Pull request overview

This PR enhances the species tree visualization page by adding comprehensive error handling and diagnostics for phylotree rendering failures. Previously, rendering failures resulted in an empty container with no visible feedback to users.

Changes:

• Added a visible status element that reports loading, success, or error messages for tree rendering
• Implemented client-side validation and normalization of Newick strings with diagnostic logging
• Added error handling for library loading failures and parsing/rendering errors
• Applied Black formatting to app/nl_query.py (no functional change)

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
app/templates/show_species.html	Added status element, Newick validation/normalization, library checks, and try-catch error handling for phylotree rendering
app/nl_query.py	Applied Black formatting to lambda expression (multi-line wrapping with parentheses)

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[Copilot]

The Newick string is being trimmed twice in the ternary expression. Consider storing the trimmed value in a variable first to avoid redundant operations. For example:

const trimmedNewick = rawNewick.trim();
const newick = trimmedNewick.endsWith(";") ? trimmedNewick : `${trimmedNewick};`;