Changelog¶

All notable changes to this project are documented here.

[Unreleased]¶

BLAST capacity: the pipeline now builds five BLAST databases (phages, proteins, hosts, private, combined) via workflow/rules/blast.smk, with private-vs-public duplicate detection.
BlastSearcher class in the pbi package, pbi blast-search / pbi blast-diagnose CLI commands, and REST API endpoints (POST /blast/search, GET /blast/databases, GET /blast/status).
09_blast_search.ipynb notebook demonstrating sequence similarity search.
Restored private_data/test_private/ synthetic example dataset so notebooks can demonstrate private-data ingestion end to end.

Documentation refreshed for v0.6.0: BLAST pipeline stage and outputs, first-run timing warnings (downloading, host resolution, file merging, BLAST database building), PBI-Scope naming consistency, and reference-page index.

GFF3 gene annotation retrieval: GFF3Retriever class, API endpoints, and 07_gff3_annotations.ipynb notebook.
Continuous integration pipeline with automated pipeline and pbi package tests (see CI Tests).

Phage-only private data ingestion: the hosts/ directory is now optional for private sources. When all Host_ID and Host_name values are unknown, the source is valid without host FASTA files.
Detailed VS Code remote connection guide (SSH + Dev Containers) in Analysis Container Guide.
Security warning section in analysis-guide.md, installation.md, and docker-guide.md explaining the implications of --ServerApp.disable_check_xsrf=True and the broader lack of authentication.

Expanded Dockerfile.analysis CMD comment to explicitly document the security risks of disabling token auth, password auth, and XSRF protection, with guidance on hardening steps.
Updated private data ingestion documentation with phage-only mode examples and updated directory structure requirements.

Updated project naming consistency to Phage Bacteria Interactions across code/docs.
Refreshed documentation structure and core pages for current infrastructure.
Added one-read storytelling page describing end-to-end flow.
Clarified private data ingestion behavior and mandatory host sequence requirements.
Updated home/current-status sections with dedicated private-data status.
Documented current API limitation (not supported for sequence-heavy retrieval).
Added VS Code Dev Containers recommendation in analysis workflow docs.