From 5d7f9e49dced49d3220310fc90779e12186a0e53 Mon Sep 17 00:00:00 2001
From: Kevin Sitek <sitek.kevin@gmail.com>
Date: Fri, 11 Sep 2026 16:37:38 -0500
Subject: [PATCH] Addressed build failures by limiting actions to pushes and
 updating docker OS and python versions

---
 .github/workflows/docs.yml |  1 +
 Dockerfile                 | 11 +++++++++--
 Singularity.def            | 11 +++++++++--
 generate_images.sh         |  6 ++++--
 4 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 65ce573..8086ad8 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -34,6 +34,7 @@ jobs:
         run: uv run make -C docs clean html
 
       - name: GitHub Pages action
+        if: github.event_name == 'push'
         uses: peaceiris/actions-gh-pages@v3.6.1
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/Dockerfile b/Dockerfile
index 4437740..bddc98a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 # Generated by Neurodocker and Reproenv.
 
-FROM debian:bullseye-slim
+FROM debian:bookworm-slim
 ENV LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8" \
     ND_ENTRYPOINT="/neurodocker/startup.sh"
@@ -38,6 +38,7 @@ RUN curl -fsSL https://deno.land/install.sh | env DENO_INSTALL=/usr/local sh -s
 RUN curl -LsSf https://astral.sh/uv/install.sh | env UV_INSTALL_DIR=/usr/local/bin INSTALLER_NO_MODIFY_PATH=1 sh
 ENV UV_LINK_MODE="copy"
 ENV UV_PYTHON_INSTALL_DIR="/opt/uv-python"
+ENV UV_PYTHON="3.11"
 ENV UV_PROJECT_ENVIRONMENT="/home/ffrprep/.venv"
 ENV PYTHONDONTWRITEBYTECODE="1"
 COPY [".", \
@@ -61,7 +62,7 @@ RUN printf '{ \
     { \
       "name": "from_", \
       "kwds": { \
-        "base_image": "debian:bullseye-slim" \
+        "base_image": "debian:bookworm-slim" \
       } \
     }, \
     { \
@@ -127,6 +128,12 @@ RUN printf '{ \
         "UV_PYTHON_INSTALL_DIR": "/opt/uv-python" \
       } \
     }, \
+    { \
+      "name": "env", \
+      "kwds": { \
+        "UV_PYTHON": "3.11" \
+      } \
+    }, \
     { \
       "name": "env", \
       "kwds": { \
diff --git a/Singularity.def b/Singularity.def
index 45be799..9bf8f7d 100644
--- a/Singularity.def
+++ b/Singularity.def
@@ -1,7 +1,7 @@
 # Generated by Neurodocker and Reproenv.
 
 Bootstrap: docker
-From: debian:bullseye-slim
+From: debian:bookworm-slim
 
 %files
 . /home/ffrprep
@@ -12,6 +12,7 @@ export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
 export UV_LINK_MODE="copy"
 export UV_PYTHON_INSTALL_DIR="/opt/uv-python"
+export UV_PYTHON="3.11"
 export UV_PROJECT_ENVIRONMENT="/home/ffrprep/.venv"
 export PYTHONDONTWRITEBYTECODE="1"
 export IS_DOCKER="1"
@@ -78,7 +79,7 @@ printf '{ \
     { \
       "name": "from_", \
       "kwds": { \
-        "base_image": "debian:bullseye-slim" \
+        "base_image": "debian:bookworm-slim" \
       } \
     }, \
     { \
@@ -144,6 +145,12 @@ printf '{ \
         "UV_PYTHON_INSTALL_DIR": "/opt/uv-python" \
       } \
     }, \
+    { \
+      "name": "env", \
+      "kwds": { \
+        "UV_PYTHON": "3.11" \
+      } \
+    }, \
     { \
       "name": "env", \
       "kwds": { \
diff --git a/generate_images.sh b/generate_images.sh
index 35f9b04..fc94f91 100644
--- a/generate_images.sh
+++ b/generate_images.sh
@@ -25,7 +25,7 @@ INSTALL_GROUP_FLAG="--no-dev"
 
 generate_docker() {
   docker run --rm repronim/neurodocker:2.1.1 generate docker \
-    --base-image debian:bullseye-slim \
+    --base-image debian:bookworm-slim \
     --pkg-manager apt \
     --arg DEBIAN_FRONTEND=noninteractive \
     --install $OS_PACKAGES \
@@ -33,6 +33,7 @@ generate_docker() {
     --run "$UV_INSTALL" \
     --env UV_LINK_MODE=copy \
     --env UV_PYTHON_INSTALL_DIR=/opt/uv-python \
+    --env UV_PYTHON=3.11 \
     --env UV_PROJECT_ENVIRONMENT=/home/ffrprep/.venv \
     --env PYTHONDONTWRITEBYTECODE=1 \
     --copy . /home/ffrprep \
@@ -48,7 +49,7 @@ generate_docker() {
 
 generate_singularity() {
   docker run --rm repronim/neurodocker:2.1.1 generate singularity \
-    --base-image debian:bullseye-slim \
+    --base-image debian:bookworm-slim \
     --pkg-manager apt \
     --arg DEBIAN_FRONTEND=noninteractive \
     --install $OS_PACKAGES \
@@ -56,6 +57,7 @@ generate_singularity() {
     --run "$UV_INSTALL" \
     --env UV_LINK_MODE=copy \
     --env UV_PYTHON_INSTALL_DIR=/opt/uv-python \
+    --env UV_PYTHON=3.11 \
     --env UV_PROJECT_ENVIRONMENT=/home/ffrprep/.venv \
     --env PYTHONDONTWRITEBYTECODE=1 \
     --copy . /home/ffrprep \