From 0183ddea67c209da71cc13876240e5f601047f4c Mon Sep 17 00:00:00 2001
From: "41898282+github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 17 Sep 2026 17:34:24 +0000
Subject: [PATCH 1/2] =?UTF-8?q?chore:=20=F0=9F=A4=96=20prepare=20release?=
 =?UTF-8?q?=20v1.3.0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 CHANGELOG.md | 2 +-
 CITATION.cff | 4 ++--
 VERSION      | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1961861..9a3bd7a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-## ASPEN development version
+## ASPEN 1.3.0
 
 - Generate Tn5 nicking-site and read counts matrices, and the corresponding DiffATAC/DESeq2 results, from both `dedup.bam` (PCR/optical duplicates removed) and `filtered.bam` (duplicates retained, labeled `nondedup`), written to separate `dedup`/`nondedup` output subfolders under `visualization/` and `peaks/{peakcaller}/{fixed_width/counts,DiffATAC}/`; previously only the duplicate-retaining `filtered.bam` was used. `dedup` is recommended for standard differential accessibility testing. (#138, @kopardev)
 - Fail fast with a clear, actionable error message when a replicate has 0 reads aligned to the spike-in genome, instead of crashing with an opaque `ZeroDivisionError` in `_compute_downsampling_scaling_factors.py`; the error is now also captured in a dedicated `results/spikein/compute_scaling_factors.log`. (#139, @kopardev)
diff --git a/CITATION.cff b/CITATION.cff
index f8b6a85..263338a 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -29,5 +29,5 @@ identifiers:
     type: doi
     value: 10.5281/zenodo.13755867
 doi: 10.5281/zenodo.13755867
-version: v1.1.2
-date-released: "2025-07-17"
+version: v1.3.0
+date-released: "2026-09-17"
diff --git a/VERSION b/VERSION
index 0c64b5c..f0bb29e 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.2.0-dev
+1.3.0

From eb527bfd03531d72805ba5cb7181581452e107c0 Mon Sep 17 00:00:00 2001
From: "41898282+github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 17 Sep 2026 17:41:46 +0000
Subject: [PATCH 2/2] chore: bump changelog & version after release of v1.3.0

---
 CHANGELOG.md | 2 ++
 VERSION      | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a3bd7a..47f3622 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,5 @@
+## ASPEN development version
+
 ## ASPEN 1.3.0
 
 - Generate Tn5 nicking-site and read counts matrices, and the corresponding DiffATAC/DESeq2 results, from both `dedup.bam` (PCR/optical duplicates removed) and `filtered.bam` (duplicates retained, labeled `nondedup`), written to separate `dedup`/`nondedup` output subfolders under `visualization/` and `peaks/{peakcaller}/{fixed_width/counts,DiffATAC}/`; previously only the duplicate-retaining `filtered.bam` was used. `dedup` is recommended for standard differential accessibility testing. (#138, @kopardev)
diff --git a/VERSION b/VERSION
index f0bb29e..b6bb93f 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.3.0
+1.3.0-dev