From a70b20646282355e5e653b5830ab9f15d0c2737e Mon Sep 17 00:00:00 2001
From: Andrey Prjibelski <andrewprzh@gmail.com>
Date: Fri, 2 Aug 2024 16:58:02 +0300
Subject: [PATCH] 3.5.0

---
 README.md     |  2 +-
 VERSION       |  2 +-
 changelog.md  | 11 +++++++++++
 make-targz.sh |  3 ++-
 4 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 4e65d13a..d547fb18 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 
 
 
-# IsoQuant 3.4 manual
+# IsoQuant 3.5 manual
 
 [New IsoQuant documentation](https://ablab.github.io/IsoQuant/) is available. This README will be removed at some point.
 
diff --git a/VERSION b/VERSION
index 4d9d11cf..1545d966 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.4.2
+3.5.0
diff --git a/changelog.md b/changelog.md
index e176278c..458d6751 100644
--- a/changelog.md
+++ b/changelog.md
@@ -1,5 +1,16 @@
 # IsoQuant changelog
 
+## IsoQuant 3.5.0, 2 August 2024
+
+- New visualization software developed by @jackfreeman88. See more [here](https://ablab.github.io/IsoQuant/visualization.html).
+
+- Dramatically reduce RAM consumption for grouped counts, about 10-20x decrease on datasets with large number of groups.
+  Important fix for single-cell data processing. Should fix [#189](https://github.com/ablab/IsoQuant/issues/189).
+
+- Fix [#195](https://github.com/ablab/IsoQuant/issues/195): output GTF contained very similar isoforms and estimated their expression as 0.
+
+- New documentation is now available at [ablab.github.io/IsoQuant](https://ablab.github.io/IsoQuant/).
+
 ## IsoQuant 3.4.2, 13 July 2024
 
 - Dramatically reduce RAM consumption.
diff --git a/make-targz.sh b/make-targz.sh
index 26f7a8a0..b90f4a86 100755
--- a/make-targz.sh
+++ b/make-targz.sh
@@ -22,10 +22,11 @@ rm -rf ./tests/.config/
 
 cp -r ./src $TARGET_DIR/
 cp -r ./tests $TARGET_DIR/
-cp -r ./figs $TARGET_DIR/
+cp -r ./docs $TARGET_DIR/
 
 
 cp isoquant.py $TARGET_DIR/
+cp visualize.py $TARGET_DIR/
 cp README.md $TARGET_DIR/
 cp VERSION $TARGET_DIR/
 cp LICENSE $TARGET_DIR/