Stabilize new build in separate repository, and get CI/CD working

.github/scripts/install_name_tool_macos.sh

@@ -8,11 +8,12 @@ shopt -s -o nounset
 for exe in `ls *_x64`
 do
     echo "fixing paths in ${exe}"
-    for libpath in `otool -L ${exe} | grep "/" | grep -v "System" | awk '{print $1}'`
+    for libpath in `otool -L ${exe} | grep "/" | grep -v "/usr/lib" | grep -v "System" | awk '{print $1}'`
     do
 		libfilename=${libpath##*/}
 		echo install_name_tool -change $libpath @executable_path/$libfilename  $exe
 		install_name_tool -change $libpath @executable_path/$libfilename  $exe
+		cp libpath "$(pwd)"
   	done
 done
 
@@ -29,7 +30,7 @@ do
 	echo install_name_tool -id "@loader_path/$libfilename"  $libfilename
     install_name_tool -id "@loader_path/$libfilename"  $libfilename
 
-	for dependentlibpath in `otool -L ${libfilename} | grep "/" | grep -v "System" | awk '{print $1}'`
+	for dependentlibpath in `otool -L ${libfilename} | grep "/" | grep -v "/usr/lib" | grep -v "System" | awk '{print $1}'`
 	do
 		dependentlibfilename=${dependentlibpath##*/}
 		#

.github/workflows/docker-deploy.yml

@@ -1,6 +1,14 @@
 name: docker-deploy
 
-on: [push, release]
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+  release:
+    types:
+      - published
 
 env:
   REGISTRY: ghcr.io
@@ -9,6 +17,12 @@ env:
 jobs:
   build-and-push-image:
     runs-on: ubuntu-latest
+    services:
+      activemq:
+        image: rmohr/activemq:latest # Or a specific version like rmohr/activemq:5.15.9
+        ports:
+          - 30163:30163 # JMS port
+          - 8161:8161   # Web console port
     permissions:
       contents: read
       packages: write

.gitignore

@@ -1,30 +1,40 @@
-/build-linux64-server/
-/build-dockcross-win64/
+
 /.project
 /.cproject
-/build-win64/
 /.DS_Store
-/build-linux64/
-/build-macos/
 /packages/
-/build_archive/
-/build-linux64-ubuntu/
+
+/dist
 /conan/
 /singularity/
-/cmake-build*
-/build*
-/debug-build*
 /.idea/
-/nfsim/
-/all_solvers/*
 
 .DS_Store
 
-NFsim_v1.11/tests/smoke/SimID_273069657_0_.gdat
-NFsim_v1.11/tests/smoke/SimID_273069657_0_.species
-
-IDAWin/tests/smoke/SimID_1489333437_0_.ida
+*.ida
 
 CMakeUserPresets.json
+
+/build-linux64-server/
+/build-dockcross-win64/
+/build-win64/
+/build-linux64/
+/build-macos/
+/build_archive/
+/build-linux64-ubuntu/
+/build*
+/cmake-build*
+/debug-build*
 conan-build
 conan-build/*
+conan_provider.cmake
+
+wheelhouse/
+
+# Covers every package dir, including pyvcell_odesolver/_internal/, which the
+# previous per-directory entries missed.
+__pycache__/
+
+pyvcell_odesolver/lib/*.dylib
+pyvcell_odesolver/lib/*.dll
+pyvcell_odesolver/lib/*.so

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "vcell-messaging"]
+	path = vcell-messaging
+	url = https://github.com/virtualcell/vcell-messaging.git
+[submodule "vcell-expressionparser"]
+	path = vcell-expressionparser
+	url = https://github.com/virtualcell/vcell-expressionparser.git