Update news.

Author: javh

NEWS.rst

@@ -4,28 +4,35 @@ Release Notes
 Version 0.3.0 pre-release notes:  September 11, 2024
 -------------------------------------------------------------------------------
 
-Exhaustive queries: 
+General:
+  + Various changes to utility functions to improve efficiency.
+  + Tutorials have been updated with new download links and analyses.
+
+Exhaustive queries:
   + Functionality to perform exhaustive queries has been added as the new
-    method `cell_query.search_exhaustive`.
-  + The kNN query method `cell_query.search` has been renamed to
-    `cell_query.search_nearest`.
+    method ``cell_query.search_exhaustive``.
+  + The kNN query method ``cell_query.search`` has been renamed to
+    ``cell_query.search_nearest``.
 
 Query result filtering and interpretation:
+  + The ``cell_query.compile_sample_metadata`` method has been expanded to
+    allow grouping by tissue and disease (in addition to study and sample).
+  + The methods ``utils.subset_by_unique_values``,
+    ``utils.subset_by_frequency``, and ``utils.categorize_and_sort_by_score``
+    have been added to provide tools for filtering, sorting and summarizing
+    query results.
+  + The "query_stability" quality control metric has been renamed to
+    "query_coherence" and is now deterministic (by setting a random seed).
   + Results from exhaustive queries can be constrained to specific
-    metadata criteria (e.g.  tissue, disease, in vitro vs in vivo, etc.)
-    using the `metadata_filter` argument to `cell_query.search_exhaustive`.
+    metadata criteria (e.g., tissue, disease, in vitro vs in vivo, etc).
+    using the ``metadata_filter`` argument to ``cell_query.search_exhaustive``.
   + Results from exhaustive queries can be constrained by distance-to-query
-    using the `max_dist` argument to `cell_query.search_exhaustive`.
-  + The `cell_query.compile_sample_metadata` method has been expanded to
-    allow grouping by tissue and disease (in addition to study and sample).
-  + The methods `utils.subset_by_unique_values`, `utils.subset_by_frequency`,
-    and `utils.categorize_and_sort_by_score` have been added to provide
-    tools for filtering, sorting and summarizing query results.
+    using the ``max_dist`` argument to ``cell_query.search_exhaustive``.
 
 Optimizations to training:
   + The ASW and NMSE training evaluation metrics were added to multiple
     methods.
-  + The `triplet_selector.get_asw` method was added to calculate ASW.
+  + The ``triplet_selector.get_asw`` method was added to calculate ASW.
   + Optimized sampling weights of study and cell type.