Add namespace-scoped performance indexes on projects

docs/changelog.md

@@ -3,6 +3,9 @@
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
 
+## [Unreleased]
+- Added namespace-oriented performance indexes on `projects`: composite `(namespace, last_update_date)` for namespace project listings, a covering partial index `(namespace) INCLUDE (number_of_samples, name) WHERE private IS FALSE` for namespace aggregation, and a trigram GIN index on `namespace` for `ILIKE` search
+
 ## [0.13.0] -- 2026-07-01
 - Migrated from `peppy` to `peprs` across all modules (project, sample, view, models, utils)
 - Updated subsample key constant: `SUBSAMPLE_RAW_LIST_KEY` → `SUBSAMPLE_RAW_DICT_KEY`

pepdbagent/db_utils.py

@@ -166,6 +166,30 @@ class Projects(Base):
         Index("ix_projects_last_update_date", "last_update_date"),
         Index("ix_projects_submission_date", "submission_date"),
         Index("ix_projects_number_of_stars", "number_of_stars"),
+        # Composite for namespace project listings
+        # (WHERE namespace = ? ORDER BY last_update_date DESC LIMIT n): a bounded
+        # index range scan instead of walking the global last_update_date index
+        # and filtering by namespace (the plan flip that scans most of the table
+        # for a namespace whose rows are not near the date tip), and no full sort.
+        Index("ix_projects_namespace_update_date", "namespace", "last_update_date"),
+        # Covering partial index for namespace aggregation
+        # (SELECT namespace, count(name), sum(number_of_samples) GROUP BY namespace):
+        # an index-only scan (~25 MB) instead of a ~250 MB heap seq scan. Covers
+        # only the public rows aggregated and INCLUDEs the summed/counted columns.
+        # (Needs a fresh visibility map — run VACUUM ANALYZE projects afterward.)
+        Index(
+            "ix_projects_ns_agg",
+            "namespace",
+            postgresql_include=["number_of_samples", "name"],
+            postgresql_where=text("private IS FALSE"),
+        ),
+        # Trigram GIN on namespace for namespace ILIKE '%str%' search.
+        Index(
+            "trgm_index_namespace",
+            "namespace",
+            postgresql_using="gin",
+            postgresql_ops={"namespace": "gin_trgm_ops"},
+        ),
     )