Add species pages with treefile lookup

[Ulthran]

Motivation

• Provide per-species pages so users can click species names and view related data and trees.
• Allow the app to load iqtree/newick treefiles from a configurable filesystem root via an env var.
• Surface counts of TaxonomicAssignment records matching a species to help navigation and filtering.

Description

• Add MARC_TREE_FP environment variable and helper treefile_for_species() to map a species name to a {lower_with_underscores}.treefile filename.
• Add route @app.route('/species/<path:species_name>') that counts matching TaxonomicAssignment rows and reads the treefile from MARC_TREE_FP if present, exposing tree_content, tree_path, and tree_error to templates.
• Link suspected organism and taxonomic classification values to the new species page by updating app/templates/show_isolate.html, app/templates/show_taxonomic_assignment.html, and app/templates/show_assembly.html.
• Add new template app/templates/show_species.html to display the assignment count and either the treefile contents, an error message, or guidance to set MARC_TREE_FP.
• Small prompt-formatting tweak in app/nl_query.py (reworked GENERATE_QUERY_PROMPT lambda formatting).

Testing

• Ran black . which reformatted one file and completed successfully.
• Ran pytest tests/ and all automated tests passed (9 passed reported).

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Codex Task

[Copilot]

Pull request overview

This pull request adds per-species pages to the web interface, enabling users to view taxonomic assignment counts and associated phylogenetic tree files for each species. The implementation reads tree files from a configurable directory via the MARC_TREE_FP environment variable.

Changes:

• Added /species/<path:species_name> route that queries taxonomic assignment counts and reads corresponding tree files
• Converted species/organism names in templates to clickable links that navigate to the new species pages
• Added treefile_for_species() helper function that maps species names to treefile filenames using a lowercase-with-underscores convention

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
app/app.py	Added MARC_TREE_FP environment variable, treefile_for_species() helper, and show_species() route with database query and file reading logic
app/templates/show_species.html	New template displaying species name, taxonomic assignment count, and tree file content with error handling
app/templates/show_taxonomic_assignment.html	Made classification field a clickable link to species page
app/templates/show_isolate.html	Made suspected organism field a clickable link to species page
app/templates/show_assembly.html	Made classification values in taxonomic assignments table clickable links to species pages
app/nl_query.py	Minor formatting change wrapping lambda assignment in parentheses (no functional change)

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