From 1951ad68778d4197745e6e9b3c1e7c492297cf05 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Wed, 13 Nov 2024 13:37:30 -0500
Subject: [PATCH 1/3] update from python 3.9 to 3.10 for vcell-batch

---
 Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 243f19ea..41d6c950 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.9.7-slim AS build
+FROM python:3.10.15-slim AS build
 
 RUN apt-get -y update && apt-get install -y apt-utils && \
     apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
@@ -38,12 +38,12 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM python:3.9.7-slim
+FROM python:3.10.15-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH="${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
-# now we have Java 17 and Python 3.9
+# now we have Java 17 and Python 3.10.15 installed
 ENV DEBIAN_FRONTEND=noninteractive
 ENV LANG=en_US.UTF-8
 

From 9509da0867d3d5b3d591844b28f9b1d206245b8a Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Wed, 13 Nov 2024 14:33:54 -0500
Subject: [PATCH 2/3] force python 3.10 on all platforms for github runner

---
 .github/workflows/cd.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
index ec460a97..600879e9 100644
--- a/.github/workflows/cd.yml
+++ b/.github/workflows/cd.yml
@@ -53,6 +53,10 @@ jobs:
       - name: checkout vcell-solvers repo
         uses: actions/checkout@v4
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
       - name: Install Intel MacOS dependencies
         if: matrix.platform == 'macos-13'
         shell: bash
@@ -69,6 +73,7 @@ jobs:
           gcc --version
           gfortran --version
           cmake --version
+          python --version
           brew info boost
           brew info hdf5
 

From 23f4976feb598b4ea3b127209c6d22d9c627794b Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Wed, 13 Nov 2024 14:56:52 -0500
Subject: [PATCH 3/3] generalize HDF5 lib directory for macos amd64

---
 Stochastic/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Stochastic/CMakeLists.txt b/Stochastic/CMakeLists.txt
index a6c6faa2..c192480f 100644
--- a/Stochastic/CMakeLists.txt
+++ b/Stochastic/CMakeLists.txt
@@ -40,7 +40,7 @@ if (APPLE)
 	if (PROCESSOR_ARCHITECTURE STREQUAL "arm64")
 		link_directories("/opt/homebrew/lib")
 	else ()
-		link_directories("/usr/local/Cellar/hdf5/1.14.3_1/lib")
+		link_directories("/usr/local/lib")
 	endif()
 endif()