From 151a494822637d51d12d08d07ad5717d2fb06bf1 Mon Sep 17 00:00:00 2001
From: Maxwell Murphy <mm@maxmurphy.dev>
Date: Wed, 4 Nov 2026 10:20:40 -0800
Subject: [PATCH 1/2] Move pre-commit from runtime dependencies to the dev
 group.

pre-commit is only used for local hooks and CI, but listing it as a runtime
dependency pulls pre-commit -> virtualenv -> packaging into every install.
In Pyodide/stlite, latest virtualenv requires packaging>=26.3, which conflicts
with Streamlit's packaging<26 and intermittently breaks PMO Builder startup.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 pyproject.toml | 2 +-
 uv.lock        | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 660f4f9..8890c2c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,6 @@ dependencies = [
     "pandas>=2.2.2",
     "biopython>=1.83",
     "jsonschema>=4.23.0",
-    "pre-commit",
     "openpyxl>=3.1.5",
 ]
 
@@ -26,6 +25,7 @@ build-backend = "uv_build"
 
 [dependency-groups]
 dev = [
+    "pre-commit",
     "pytest>=8.4.1",
 ]
 
diff --git a/uv.lock b/uv.lock
index 96b1ced..6e280a3 100644
--- a/uv.lock
+++ b/uv.lock
@@ -292,11 +292,11 @@ dependencies = [
     { name = "jsonschema" },
     { name = "openpyxl" },
     { name = "pandas" },
-    { name = "pre-commit" },
 ]
 
 [package.dev-dependencies]
 dev = [
+    { name = "pre-commit" },
     { name = "pytest" },
 ]
 
@@ -306,11 +306,13 @@ requires-dist = [
     { name = "jsonschema", specifier = ">=4.23.0" },
     { name = "openpyxl", specifier = ">=3.1.5" },
     { name = "pandas", specifier = ">=2.2.2" },
-    { name = "pre-commit" },
 ]
 
 [package.metadata.requires-dev]
-dev = [{ name = "pytest", specifier = ">=8.4.1" }]
+dev = [
+    { name = "pre-commit" },
+    { name = "pytest", specifier = ">=8.4.1" },
+]
 
 [[package]]
 name = "pre-commit"

From ef034ecd925d4bc665c73efbc249f69a30bb1f47 Mon Sep 17 00:00:00 2001
From: kathryn1995 <kathryn.murie@ucsf.edu>
Date: Wed, 4 Nov 2026 10:34:52 -0800
Subject: [PATCH 2/2] Bump version to v1.2.2

Co-authored-by: Cursor <cursoragent@cursor.com>
---
 pyproject.toml | 2 +-
 uv.lock        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8890c2c..b6b695f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "pmotools"
-version = "v1.2.1"
+version = "v1.2.2"
 description = "Tools for building and analyzing PMO files"
 readme = "README.md"
 authors = [
diff --git a/uv.lock b/uv.lock
index 6e280a3..6d7e835 100644
--- a/uv.lock
+++ b/uv.lock
@@ -285,7 +285,7 @@ wheels = [
 
 [[package]]
 name = "pmotools"
-version = "1.2.1"
+version = "1.2.2"
 source = { editable = "." }
 dependencies = [
     { name = "biopython" },