diff --git a/pyproject.toml b/pyproject.toml
index 494ed38..7dd8410 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "pisa-analysis"
-version = "3.3.0"
+version = "3.3.1"
 description = "This python package works with PISA to analyse data for macromolecular interfaces and interactions in assemblies."
 authors = [
     { name = "Grisell Diaz Leines", email = "gdiazleines@ebi.ac.uk" },
diff --git a/requirements-dev.txt b/requirements-dev.txt
index d33bf1f..9b05aa9 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -11,7 +11,7 @@ packaging==26.0
 platformdirs==4.5.1
 pluggy==1.6.0
 pre-commit==4.5.1
-pygments==2.19.2
+pygments==2.20.0
 pytest==9.0.3
 pytest-cov==7.0.0
 pytest-mock==3.15.1
diff --git a/uv.lock b/uv.lock
index a4d3c6b..9f18f85 100644
--- a/uv.lock
+++ b/uv.lock
@@ -719,7 +719,7 @@ wheels = [
 
 [[package]]
 name = "pisa-analysis"
-version = "3.3.0"
+version = "3.3.1"
 source = { editable = "." }
 dependencies = [
     { name = "gemmi" },
@@ -932,11 +932,11 @@ wheels = [
 
 [[package]]
 name = "pygments"
-version = "2.19.2"
+version = "2.20.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/b0/77/a5b8c569bf593b0140bde72ea885a803b82086995367bf2037de0159d924/pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887", size = 4968631, upload-time = "2025-06-21T13:39:12.283Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c3/b2/bc9c9196916376152d655522fdcebac55e66de6603a76a02bca1b6414f6c/pygments-2.20.0.tar.gz", hash = "sha256:6757cd03768053ff99f3039c1a36d6c0aa0b263438fcab17520b30a303a82b5f", size = 4955991, upload-time = "2026-03-29T13:29:33.898Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/c7/21/705964c7812476f378728bdf590ca4b771ec72385c533964653c68e86bdc/pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b", size = 1225217, upload-time = "2025-06-21T13:39:07.939Z" },
+    { url = "https://files.pythonhosted.org/packages/f4/7e/a72dd26f3b0f4f2bf1dd8923c85f7ceb43172af56d63c7383eb62b332364/pygments-2.20.0-py3-none-any.whl", hash = "sha256:81a9e26dd42fd28a23a2d169d86d7ac03b46e2f8b59ed4698fb4785f946d0176", size = 1231151, upload-time = "2026-03-29T13:29:30.038Z" },
 ]
 
 [[package]]