From 7bedf6a0573edb19af2c5aa07fb72fd1cbb7a806 Mon Sep 17 00:00:00 2001
From: Maxwell Murphy <murphy2122@berkeley.edu>
Date: Wed, 30 Oct 2024 16:01:48 -0700
Subject: [PATCH] Increment version number to 3.5.0

---
 DESCRIPTION |  2 +-
 NEWS.md     | 28 ++++++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 837be75..1a69378 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: moire
 Title: Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data
-Version: 3.4.0
+Version: 3.5.0
 Authors@R: c(
     person(given = "Maxwell",
            family = "Murphy",
diff --git a/NEWS.md b/NEWS.md
index 89ec3a0..38af0d0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,31 @@
+# moire 3.5.0
+
+## New Features
+
+* Implemented maximum runtime functionality (#34)
+  - The user can now specify a maximum runtime for the MCMC. After the maximum runtime is reached, the MCMC will stop and the current state of the MCMC will be returned.
+  - Enabled by setting `max_runtime = {time in minutes}` in `run_mcmc()`
+
+
+## Bug Fixes
+
+* Fixed handling of NA values in allele frequency vector
+  - NA values are now replaced with 0
+  - Warning message added to alert users of potential MCMC chain issues or loci lacking diversity (#20)
+
+* Fixed memory crash in `prob_any_missing()` function (#38)
+
+## Other Changes
+
+* Modified data loading to ungroup input data when loading long form (#37)
+
+* Updated citation and manuscript information
+
+* Added OpenMP detection utility
+
+* Implement logging of individual sample log likelihoods
+  - May be useful for diagnosing issues with particular samples, such as those that come from different populations
+
 # moire 3.4.0
 ## New features