From 24c646706617aaf06b45c2ca5cb8e8edf79a63f4 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Mon, 25 Jul 2022 23:26:37 +0100
Subject: [PATCH 01/49] moved install scripts into Dockerfile

---
 CI/Dockerfile | 164 ++++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 131 insertions(+), 33 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 2f25be054b..80be45d3d3 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,4 +1,23 @@
 ARG UBUNTU_VERSION=18.04
+# or clang
+
+
+ARG ci_jobs=8
+ARG MOAB_BRANCH=5.4.0
+ARG build_dir=/root/build_dir
+ARG install_dir=/root/opt
+ARG geant4_version=10.5.1
+ARG EMBREE_BRANCH='v3.6.1'
+ARG HDF5_VERSION=1.10.4
+ARG HDF5_VERSION_major=1.10
+
+# if clang then change cc and cxx
+# ARG COMPILER=gcc
+# or clang
+ARG CC=gcc
+# or clang++
+ARG CXX=g++
+
 FROM ubuntu:${UBUNTU_VERSION} AS base
 
 # Use bash as the default shell
@@ -34,60 +53,139 @@ RUN apt-get -y update; \
     pip install cython;
 
 
-# Copy scripts to docker image
-RUN mkdir -p /root/etc/
-COPY CI/ /root/etc/CI
-#TODO move sh file contents into this Dockerfile
-ENV docker_env=/root/etc/CI/env.sh
-
-ENV build_dir=/root/build_dir
-ENV install_dir=/root/opt
 
 
 FROM base as external_deps
 
-#setting the COMPILER variable
-ARG COMPILER=gcc
-ENV COMPILER=${COMPILER}
-
-# Set Geant4 env variable
+ARG build_dir
+ARG install_dir
+ARG COMPILER
+ARG ci_jobs
+ARG geant4_version
+ARG CC
+ARG CXX
+ARG EMBREE_BRANCH
+
+ENV geant4_basename=geant4-v${geant4_version}
+ENV geant4_tarball=${geant4_basename}.tar.gz
+ENV geant4_shasum=2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e39
 ENV geant4_build_dir=${build_dir}/geant4
 ENV geant4_install_dir=${install_dir}/geant4
 
-# Build Geant4
-#TODO move sh file contents into this Dockerfile
-RUN /root/etc/CI/docker/build_geant4.sh
-
+RUN mkdir -p ${geant4_build_dir}/bld
+RUN cd ${geant4_build_dir} && \
+    wget https://gitlab.cern.ch/geant4/geant4/-/archive/v${geant4_version}/${geant4_tarball} --no-check-certificate && \
+    tar -xzf ${geant4_tarball} && \
+    cd bld && \
+    cmake ../${geant4_basename} -DBUILD_STATIC_LIBS=ON \
+                -DGEANT4_USE_SYSTEM_EXPAT=OFF \
+                -DCMAKE_BUILD_TYPE=Release \
+                -DCMAKE_C_COMPILER=${CC} \
+                -DCMAKE_CXX_COMPILER=${CXX} \
+                -DCMAKE_INSTALL_RPATH=${geant4_install_dir}/lib \
+                -DCMAKE_INSTALL_PREFIX=${geant4_install_dir} && \
+    make -j${ci_jobs} && \
+    make install && \
+    cd && \
+    rm -rf ${geant4_build_dir}
+
+# these don't appear to be used yet
 ENV double_down_build_dir=${build_dir}/double-down/
 ENV double_down_install_dir=${install_dir}/double-down/
 
-# Build Embree
-#TODO move sh file contents into this Dockerfile
-RUN /root/etc/CI/docker/build_embree.sh
+ENV embree_install_dir=${install_dir}/embree
+
+RUN mkdir EMBREE && \
+    cd EMBREE && \
+    git clone -b ${EMBREE_BRANCH} https://github.com/embree/embree && \
+    mkdir build && \
+    cd build && \
+    cmake ../embree -DCMAKE_INSTALL_PREFIX=${embree_install_dir} \
+        -DEMBREE_ISPC_SUPPORT=OFF \
+        -DEMBREE_TASKING_SYSTEM=INTERNAL \
+        -DEMBREE_TUTORIALS=OFF \
+        -DEMBREE_TBB_ROOT=/usr && \
+    make -j2 && make -j2 install && \
+    rm -rf $HOME/EMBREE/embree
+
 
 FROM external_deps AS hdf5
 
+ARG build_dir
+ARG install_dir
+ARG ci_jobs
+ARG HDF5_VERSION
+ARG HDF5_VERSION_major
+ARG CC
+ARG CXX
+
 # Set HDF5 env variable
 ENV hdf5_build_dir=${build_dir}/hdf5
 ENV hdf5_install_dir=${install_dir}/hdf5
 
-# Build HDF5
-# HDF5 argument possible value: 1.10.4 or system
-ARG HDF5=1.10.4
-ENV HDF5_VERSION=${HDF5}
-#TODO move sh file contents into this Dockerfile
-RUN /root/etc/CI/docker/build_hdf5.sh
+RUN mkdir -p ${hdf5_build_dir}/bld && \
+    cd ${hdf5_build_dir} && \
+    wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION_major}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz && \
+    tar -xzf hdf5-${HDF5_VERSION}.tar.gz && \
+    cd bld && \
+    ../hdf5-${HDF5_VERSION}/configure --enable-shared \
+        --prefix=${hdf5_install_dir} \
+        CC=${CC} \
+        CXX=${CXX} && \
+    make -j${ci_jobs} && \
+    make install && \
+    cd && \
+    rm -rf ${hdf5_build_dir}
+
 
 FROM hdf5 AS moab
 
+ARG ci_jobs
+ARG MOAB_BRANCH
+ARG CC
+ARG CXX
+ARG build_dir
+ARG install_dir
+
 # Set MOAB env variable
 ENV moab_build_dir=${build_dir}/moab
 ENV moab_install_dir=${install_dir}/moab
 
-ARG MOAB=5.3.0
-ENV MOAB_VERSION ${MOAB}
-#TODO move sh file contents into this Dockerfile
-RUN if [ "${MOAB_VERSION}" != "master" ] && [ "${MOAB_VERSION}" != "develop" ]; then \
-        /root/etc/CI/docker/build_moab.sh; \
-    fi;
-
+RUN mkdir -p ${moab_build_dir}/bld
+RUN cd ${moab_build_dir} && \
+    git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \
+    cd bld && \
+    cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
+                -DENABLE_BLASLAPACK=OFF \
+                -DENABLE_FORTRAN=OFF \
+                -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+                -DCMAKE_C_COMPILER=${CC} \
+                -DCMAKE_CXX_COMPILER=${CXX} \
+                -DBUILD_SHARED_LIBS=OFF && \
+    make -j${ci_jobs} && \
+    make install && \
+    rm -rf * && \
+    cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
+                -DENABLE_PYMOAB=ON \
+                -DENABLE_BLASLAPACK=OFF \
+                -DENABLE_FORTRAN=OFF \
+                -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+                -DCMAKE_C_COMPILER=${CC} \
+                -DCMAKE_CXX_COMPILER=${CXX} \
+                -DBUILD_SHARED_LIBS=ON \
+                -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib && \
+    # ensure that the installation directory for python packages exist
+    for d in $(echo $PYTHONPATH | tr : '\n'); do mkdir -p $d; done && \
+    make -j${ci_jobs} && \
+    make install && \
+    cd && \
+    rm -rf ${moab_build_dir}
+
+ENV dagmc_build_dir=${build_dir}/DAGMC
+ENV dagmc_install_dir=${install_dir}/DAGMC
+
+ENV dagmc_build_dir_shared=${dagmc_build_dir}-shared
+ENV dagmc_install_dir_shared=${dagmc_install_dir}-shared
+
+ENV dagmc_build_dir_static=${dagmc_build_dir}-static
+ENV dagmc_install_dir_static=${dagmc_install_dir}-static

From c2dba7a81edc7ce7e93d0676f00276007c012587 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Mon, 25 Jul 2022 23:52:36 +0100
Subject: [PATCH 02/49] improved docs/comments

---
 CI/Dockerfile | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 80be45d3d3..6cc619959f 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,21 +1,23 @@
-ARG UBUNTU_VERSION=18.04
-# or clang
+# Svalinn DAGMC Dockerfile
 
+ARG UBUNTU_VERSION=18.04
 
 ARG ci_jobs=8
 ARG MOAB_BRANCH=5.4.0
-ARG build_dir=/root/build_dir
-ARG install_dir=/root/opt
-ARG geant4_version=10.5.1
 ARG EMBREE_BRANCH='v3.6.1'
+ARG geant4_version=10.5.1
+
 ARG HDF5_VERSION=1.10.4
+# currently major version must be manually set to match HDF5 version
 ARG HDF5_VERSION_major=1.10
 
-# if clang then change cc and cxx
-# ARG COMPILER=gcc
-# or clang
+ARG build_dir=/root/build_dir
+ARG install_dir=/root/opt
+
+# clang and gcc are options for the compiler but to use them CC and CXX must be set
+# if clang then change cc to clang and cxx to clang++
+# if gcc then change cc to gcc and cxx to g++
 ARG CC=gcc
-# or clang++
 ARG CXX=g++
 
 FROM ubuntu:${UBUNTU_VERSION} AS base
@@ -53,8 +55,6 @@ RUN apt-get -y update; \
     pip install cython;
 
 
-
-
 FROM base as external_deps
 
 ARG build_dir
@@ -89,7 +89,9 @@ RUN cd ${geant4_build_dir} && \
     cd && \
     rm -rf ${geant4_build_dir}
 
-# these don't appear to be used yet
+# these two double down ENVs don't appear to be used yet
+# However they were in orginal dockerfile, so they have been kept
+# TODO add double down to the dockerfile
 ENV double_down_build_dir=${build_dir}/double-down/
 ENV double_down_install_dir=${install_dir}/double-down/
 
@@ -119,7 +121,6 @@ ARG HDF5_VERSION_major
 ARG CC
 ARG CXX
 
-# Set HDF5 env variable
 ENV hdf5_build_dir=${build_dir}/hdf5
 ENV hdf5_install_dir=${install_dir}/hdf5
 

From 5255950082fc2e668e0cf9171632606bea7e060f Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Mon, 25 Jul 2022 23:59:27 +0100
Subject: [PATCH 03/49] added PR 817

---
 doc/CHANGELOG.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/doc/CHANGELOG.rst b/doc/CHANGELOG.rst
index 0cbcc6a5e1..abbd7f9f0d 100644
--- a/doc/CHANGELOG.rst
+++ b/doc/CHANGELOG.rst
@@ -10,6 +10,7 @@ Next version
 **Changed:**
 
    * Using multi stage Dockerfile to reduce the number of Dockerfile (#813)
+   * Move install scripts into Dockerfile (#817)
 
 
 v3.2.2

From 14a929150920f2a7969edc8484053cbdb2889111 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Thu, 18 Aug 2022 16:07:36 +0100
Subject: [PATCH 04/49] [skip ci] compile cores review suggestion by @gonuke

Co-authored-by: Paul Wilson <paul.wilson@wisc.edu>
---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index f23b87e5c1..92e6d89724 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -107,7 +107,7 @@ RUN mkdir EMBREE && \
         -DEMBREE_TASKING_SYSTEM=INTERNAL \
         -DEMBREE_TUTORIALS=OFF \
         -DEMBREE_TBB_ROOT=/usr && \
-    make -j2 && make -j2 install && \
+    make -j${ci_jobs} && make -j${ci_jobs} install && \
     rm -rf $HOME/EMBREE/embree
 
 

From ad88096b9074cd6d08de1ebed525deebcfa16efd Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:13:04 +0100
Subject: [PATCH 05/49] [skip ci] removed compiler arg fully

---
 CI/Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 92e6d89724..8f87339c69 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -58,8 +58,7 @@ RUN apt-get -y update; \
 FROM base as external_deps
 
 ARG build_dir
-ARG install_dir
-ARG COMPILER
+ARG install_dir 
 ARG ci_jobs
 ARG geant4_version
 ARG CC

From 8c8d57936fc1e5c9c54045cd8acce7f7655cf7d7 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:26:39 +0100
Subject: [PATCH 06/49] more consistent dirs for build

---
 CI/Dockerfile | 78 +++++++++++++++++++++++++++------------------------
 1 file changed, 41 insertions(+), 37 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 8f87339c69..f3f057e421 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,5 +1,7 @@
 # Svalinn DAGMC Dockerfile
 
+# build this docker file
+
 ARG UBUNTU_VERSION=18.04
 
 ARG ci_jobs=8
@@ -71,18 +73,18 @@ ENV geant4_shasum=2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e
 ENV geant4_build_dir=${build_dir}/geant4
 ENV geant4_install_dir=${install_dir}/geant4
 
-RUN mkdir -p ${geant4_build_dir}/bld
+RUN mkdir -p ${geant4_build_dir}/build
 RUN cd ${geant4_build_dir} && \
     wget https://gitlab.cern.ch/geant4/geant4/-/archive/v${geant4_version}/${geant4_tarball} --no-check-certificate && \
     tar -xzf ${geant4_tarball} && \
-    cd bld && \
-    cmake ../${geant4_basename} -DBUILD_STATIC_LIBS=ON \
-                -DGEANT4_USE_SYSTEM_EXPAT=OFF \
-                -DCMAKE_BUILD_TYPE=Release \
-                -DCMAKE_C_COMPILER=${CC} \
-                -DCMAKE_CXX_COMPILER=${CXX} \
-                -DCMAKE_INSTALL_RPATH=${geant4_install_dir}/lib \
-                -DCMAKE_INSTALL_PREFIX=${geant4_install_dir} && \
+    cd build && \
+    cmake ../${geant4_basename} -DCMAKE_INSTALL_RPATH=${geant4_install_dir}/lib \
+                                -DCMAKE_INSTALL_PREFIX=${geant4_install_dir} \
+                                -DGEANT4_USE_SYSTEM_EXPAT=OFF \
+                                -DCMAKE_BUILD_TYPE=Release \
+                                -DCMAKE_CXX_COMPILER=${CXX} \
+                                -DCMAKE_C_COMPILER=${CC} \
+                                -DBUILD_STATIC_LIBS=ON && \
     make -j${ci_jobs} && \
     make install && \
     cd && \
@@ -95,18 +97,20 @@ ENV double_down_build_dir=${build_dir}/double-down/
 ENV double_down_install_dir=${install_dir}/double-down/
 
 ENV embree_install_dir=${install_dir}/embree
+ENV embree_build_dir=${build_dir}/embree
 
-RUN mkdir EMBREE && \
-    cd EMBREE && \
+RUN mkdir -p ${hdf5_build_dir}/build && \
+    cd ${hdf5_build_dir} && \
     git clone -b ${EMBREE_BRANCH} https://github.com/embree/embree && \
     mkdir build && \
     cd build && \
     cmake ../embree -DCMAKE_INSTALL_PREFIX=${embree_install_dir} \
-        -DEMBREE_ISPC_SUPPORT=OFF \
-        -DEMBREE_TASKING_SYSTEM=INTERNAL \
-        -DEMBREE_TUTORIALS=OFF \
-        -DEMBREE_TBB_ROOT=/usr && \
-    make -j${ci_jobs} && make -j${ci_jobs} install && \
+                    -DEMBREE_TASKING_SYSTEM=INTERNAL \
+                    -DEMBREE_ISPC_SUPPORT=OFF \
+                    -DEMBREE_TUTORIALS=OFF \
+                    -DEMBREE_TBB_ROOT=/usr && \
+    make -j${ci_jobs} && \
+    make -j${ci_jobs} install && \
     rm -rf $HOME/EMBREE/embree
 
 
@@ -123,15 +127,15 @@ ARG CXX
 ENV hdf5_build_dir=${build_dir}/hdf5
 ENV hdf5_install_dir=${install_dir}/hdf5
 
-RUN mkdir -p ${hdf5_build_dir}/bld && \
+RUN mkdir -p ${hdf5_build_dir}/build && \
     cd ${hdf5_build_dir} && \
     wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION_major}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz && \
     tar -xzf hdf5-${HDF5_VERSION}.tar.gz && \
-    cd bld && \
+    cd build && \
     ../hdf5-${HDF5_VERSION}/configure --enable-shared \
         --prefix=${hdf5_install_dir} \
-        CC=${CC} \
-        CXX=${CXX} && \
+        CXX=${CXX} \
+        CC=${CC} && \
     make -j${ci_jobs} && \
     make install && \
     cd && \
@@ -151,29 +155,29 @@ ARG install_dir
 ENV moab_build_dir=${build_dir}/moab
 ENV moab_install_dir=${install_dir}/moab
 
-RUN mkdir -p ${moab_build_dir}/bld
+RUN mkdir -p ${moab_build_dir}/build
 RUN cd ${moab_build_dir} && \
     git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \
-    cd bld && \
+    cd build && \
     cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
-                -DENABLE_BLASLAPACK=OFF \
-                -DENABLE_FORTRAN=OFF \
-                -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
-                -DCMAKE_C_COMPILER=${CC} \
-                -DCMAKE_CXX_COMPILER=${CXX} \
-                -DBUILD_SHARED_LIBS=OFF && \
+                  -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+                  -DCMAKE_CXX_COMPILER=${CXX} \
+                  -DCMAKE_C_COMPILER=${CC} \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DBUILD_SHARED_LIBS=OFF \
+                  -DENABLE_FORTRAN=OFF && \
     make -j${ci_jobs} && \
     make install && \
     rm -rf * && \
-    cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
-                -DENABLE_PYMOAB=ON \
-                -DENABLE_BLASLAPACK=OFF \
-                -DENABLE_FORTRAN=OFF \
-                -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
-                -DCMAKE_C_COMPILER=${CC} \
-                -DCMAKE_CXX_COMPILER=${CXX} \
-                -DBUILD_SHARED_LIBS=ON \
-                -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib && \
+    cmake ../moab -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib && \
+                  -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
+                  -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+                  -DCMAKE_CXX_COMPILER=${CXX} \
+                  -DCMAKE_C_COMPILER=${CC} \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DBUILD_SHARED_LIBS=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_PYMOAB=ON \
     # ensure that the installation directory for python packages exist
     for d in $(echo $PYTHONPATH | tr : '\n'); do mkdir -p $d; done && \
     make -j${ci_jobs} && \

From 21af7e74566da3d179ab9f47a7d976619efd136a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:33:55 +0100
Subject: [PATCH 07/49] ordering and intenting args

---
 CI/Dockerfile | 37 ++++++++++++++++++++-----------------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index f3f057e421..ec2cb50df5 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,7 +1,5 @@
 # Svalinn DAGMC Dockerfile
 
-# build this docker file
-
 ARG UBUNTU_VERSION=18.04
 
 ARG ci_jobs=8
@@ -22,11 +20,13 @@ ARG install_dir=/root/opt
 ARG CC=gcc
 ARG CXX=g++
 
+
 FROM ubuntu:${UBUNTU_VERSION} AS base
 
 # Use bash as the default shell
 SHELL ["/bin/bash", "-c"]
-# Ubuntu Setup
+
+# timezone setup
 ENV TZ=America/Chicago
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
@@ -59,13 +59,14 @@ RUN apt-get -y update; \
 
 FROM base as external_deps
 
-ARG build_dir
+# accessing gloabl ARGs in build stage
+ARG geant4_version
+ARG EMBREE_BRANCH
 ARG install_dir 
+ARG build_dir
 ARG ci_jobs
-ARG geant4_version
-ARG CC
 ARG CXX
-ARG EMBREE_BRANCH
+ARG CC
 
 ENV geant4_basename=geant4-v${geant4_version}
 ENV geant4_tarball=${geant4_basename}.tar.gz
@@ -116,13 +117,14 @@ RUN mkdir -p ${hdf5_build_dir}/build && \
 
 FROM external_deps AS hdf5
 
-ARG build_dir
+# accessing gloabl ARGs in build stage
+ARG HDF5_VERSION_major
+ARG HDF5_VERSION
 ARG install_dir
+ARG build_dir
 ARG ci_jobs
-ARG HDF5_VERSION
-ARG HDF5_VERSION_major
-ARG CC
 ARG CXX
+ARG CC
 
 ENV hdf5_build_dir=${build_dir}/hdf5
 ENV hdf5_install_dir=${install_dir}/hdf5
@@ -144,12 +146,13 @@ RUN mkdir -p ${hdf5_build_dir}/build && \
 
 FROM hdf5 AS moab
 
-ARG ci_jobs
+# accessing gloabl ARGs in build stage
+ARG install_dir
 ARG MOAB_BRANCH
-ARG CC
-ARG CXX
 ARG build_dir
-ARG install_dir
+ARG ci_jobs
+ARG CXX
+ARG CC
 
 # Set MOAB env variable
 ENV moab_build_dir=${build_dir}/moab
@@ -169,7 +172,7 @@ RUN cd ${moab_build_dir} && \
     make -j${ci_jobs} && \
     make install && \
     rm -rf * && \
-    cmake ../moab -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib && \
+    cmake ../moab -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib \
                   -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
                   -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
                   -DCMAKE_CXX_COMPILER=${CXX} \
@@ -177,7 +180,7 @@ RUN cd ${moab_build_dir} && \
                   -DENABLE_BLASLAPACK=OFF \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_FORTRAN=OFF \
-                  -DENABLE_PYMOAB=ON \
+                  -DENABLE_PYMOAB=ON && \
     # ensure that the installation directory for python packages exist
     for d in $(echo $PYTHONPATH | tr : '\n'); do mkdir -p $d; done && \
     make -j${ci_jobs} && \

From 5571c7a0bdc8a11bfe87e19da93c1800e8691232 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:34:13 +0100
Subject: [PATCH 08/49] reduced layers

---
 CI/Dockerfile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index ec2cb50df5..0bbc2a4c2b 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -74,8 +74,8 @@ ENV geant4_shasum=2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e
 ENV geant4_build_dir=${build_dir}/geant4
 ENV geant4_install_dir=${install_dir}/geant4
 
-RUN mkdir -p ${geant4_build_dir}/build
-RUN cd ${geant4_build_dir} && \
+RUN mkdir -p ${geant4_build_dir}/build && \
+    cd ${geant4_build_dir} && \
     wget https://gitlab.cern.ch/geant4/geant4/-/archive/v${geant4_version}/${geant4_tarball} --no-check-certificate && \
     tar -xzf ${geant4_tarball} && \
     cd build && \
@@ -158,8 +158,8 @@ ARG CC
 ENV moab_build_dir=${build_dir}/moab
 ENV moab_install_dir=${install_dir}/moab
 
-RUN mkdir -p ${moab_build_dir}/build
-RUN cd ${moab_build_dir} && \
+RUN mkdir -p ${moab_build_dir}/build && \
+    cd ${moab_build_dir} && \
     git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \
     cd build && \
     cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \

From 5cdad9aafe3caa8174aeb500fb675c94c0ac1a2d Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:37:08 +0100
Subject: [PATCH 09/49] added missing hdf5 install dir env

---
 CI/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 0bbc2a4c2b..6cb92bfc75 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -158,6 +158,9 @@ ARG CC
 ENV moab_build_dir=${build_dir}/moab
 ENV moab_install_dir=${install_dir}/moab
 
+# Set the hdf5 install dir as this is also needed by moab compile
+ENV hdf5_install_dir=${install_dir}/hdf5
+
 RUN mkdir -p ${moab_build_dir}/build && \
     cd ${moab_build_dir} && \
     git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \

From e331db4a780a49578ee969efcdff368f06b8c043 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:41:14 +0100
Subject: [PATCH 10/49] commented out moab static build

---
 CI/Dockerfile | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 6cb92bfc75..63b779be7e 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -165,16 +165,17 @@ RUN mkdir -p ${moab_build_dir}/build && \
     cd ${moab_build_dir} && \
     git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \
     cd build && \
-    cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
-                  -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
-                  -DCMAKE_CXX_COMPILER=${CXX} \
-                  -DCMAKE_C_COMPILER=${CC} \
-                  -DENABLE_BLASLAPACK=OFF \
-                  -DBUILD_SHARED_LIBS=OFF \
-                  -DENABLE_FORTRAN=OFF && \
-    make -j${ci_jobs} && \
-    make install && \
-    rm -rf * && \
+    # static building of moab is also an option and was required for older versions
+    # cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
+    #               -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+    #               -DCMAKE_CXX_COMPILER=${CXX} \
+    #               -DCMAKE_C_COMPILER=${CC} \
+    #               -DENABLE_BLASLAPACK=OFF \
+    #               -DBUILD_SHARED_LIBS=OFF \
+    #               -DENABLE_FORTRAN=OFF && \
+    # make -j${ci_jobs} && \
+    # make install && \
+    # rm -rf * && \
     cmake ../moab -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib \
                   -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
                   -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \

From 8507e48f4a00d67e432f4d0d2c4c12111caa8fe2 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:42:59 +0100
Subject: [PATCH 11/49] corrected embree dirs

---
 CI/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 63b779be7e..e9399ec527 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -100,8 +100,8 @@ ENV double_down_install_dir=${install_dir}/double-down/
 ENV embree_install_dir=${install_dir}/embree
 ENV embree_build_dir=${build_dir}/embree
 
-RUN mkdir -p ${hdf5_build_dir}/build && \
-    cd ${hdf5_build_dir} && \
+RUN mkdir -p ${embree_build_dir}/build && \
+    cd ${embree_build_dir} && \
     git clone -b ${EMBREE_BRANCH} https://github.com/embree/embree && \
     mkdir build && \
     cd build && \

From 75d2419e50fd5205794681d8ef84f9121fe1d093 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:44:37 +0100
Subject: [PATCH 12/49] using embree dir in rm -rf cmd

---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index e9399ec527..44a85d9c52 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -112,7 +112,7 @@ RUN mkdir -p ${embree_build_dir}/build && \
                     -DEMBREE_TBB_ROOT=/usr && \
     make -j${ci_jobs} && \
     make -j${ci_jobs} install && \
-    rm -rf $HOME/EMBREE/embree
+    rm -rf ${embree_build_dir}
 
 
 FROM external_deps AS hdf5

From 3881de6197f24b9cacc225ae1d7d50f949426297 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 18 Aug 2022 16:45:25 +0100
Subject: [PATCH 13/49] cd to safe place

---
 CI/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 44a85d9c52..c8af1b5989 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -112,6 +112,7 @@ RUN mkdir -p ${embree_build_dir}/build && \
                     -DEMBREE_TBB_ROOT=/usr && \
     make -j${ci_jobs} && \
     make -j${ci_jobs} install && \
+    cd && \
     rm -rf ${embree_build_dir}
 
 

From 85884d6a87ba6978fb852b69b0a364e9210b1ed9 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 19 Aug 2022 17:44:28 +0100
Subject: [PATCH 14/49] removed 2nd mkdir build in embree compile

---
 CI/Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index c8af1b5989..7884bf0222 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -103,7 +103,6 @@ ENV embree_build_dir=${build_dir}/embree
 RUN mkdir -p ${embree_build_dir}/build && \
     cd ${embree_build_dir} && \
     git clone -b ${EMBREE_BRANCH} https://github.com/embree/embree && \
-    mkdir build && \
     cd build && \
     cmake ../embree -DCMAKE_INSTALL_PREFIX=${embree_install_dir} \
                     -DEMBREE_TASKING_SYSTEM=INTERNAL \

From d4723f89ce221e4725691612016708f498c3a34b Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Tue, 23 Aug 2022 20:43:28 +0100
Subject: [PATCH 15/49] remove env for dag

---
 CI/Dockerfile | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 7884bf0222..0c3a36f111 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -192,12 +192,4 @@ RUN mkdir -p ${moab_build_dir}/build && \
     cd && \
     rm -rf ${moab_build_dir}
 
-ENV dagmc_build_dir=${build_dir}/DAGMC
-ENV dagmc_install_dir=${install_dir}/DAGMC
-
-ENV dagmc_build_dir_shared=${dagmc_build_dir}-shared
-ENV dagmc_install_dir_shared=${dagmc_install_dir}-shared
-
-ENV dagmc_build_dir_static=${dagmc_build_dir}-static
-ENV dagmc_install_dir_static=${dagmc_install_dir}-static
 

From 7c93d5dab4e016f63da4138cb5ca6697dc6c4316 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Wed, 24 Aug 2022 19:58:46 +0100
Subject: [PATCH 16/49] Remove making python path folders

---
 CI/Dockerfile | 2 --
 1 file changed, 2 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 0c3a36f111..b91e310aaf 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -185,8 +185,6 @@ RUN mkdir -p ${moab_build_dir}/build && \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_FORTRAN=OFF \
                   -DENABLE_PYMOAB=ON && \
-    # ensure that the installation directory for python packages exist
-    for d in $(echo $PYTHONPATH | tr : '\n'); do mkdir -p $d; done && \
     make -j${ci_jobs} && \
     make install && \
     cd && \

From 421e7ad2daeaabd5f31b29fb8e115ed613b2f0c2 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Sat, 27 Aug 2022 15:15:38 -0500
Subject: [PATCH 17/49] prepend pythonpath as fix for MOAB build

---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index b91e310aaf..411b1f28a2 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -185,7 +185,7 @@ RUN mkdir -p ${moab_build_dir}/build && \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_FORTRAN=OFF \
                   -DENABLE_PYMOAB=ON && \
-    make -j${ci_jobs} && \
+    PYTHONPATH=${moab_build_dir}/pymoab/lib/python3.6/site-packages make -j${ci_jobs} && \
     make install && \
     cd && \
     rm -rf ${moab_build_dir}

From 48a97a06fbfe2d816ed7e5c7e5dad6dd8cf37d00 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Sat, 27 Aug 2022 15:16:58 -0500
Subject: [PATCH 18/49] keep previous pythonpath as well

---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 411b1f28a2..676296ae0a 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -185,7 +185,7 @@ RUN mkdir -p ${moab_build_dir}/build && \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_FORTRAN=OFF \
                   -DENABLE_PYMOAB=ON && \
-    PYTHONPATH=${moab_build_dir}/pymoab/lib/python3.6/site-packages make -j${ci_jobs} && \
+    PYTHONPATH=${moab_build_dir}/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make -j${ci_jobs} && \
     make install && \
     cd && \
     rm -rf ${moab_build_dir}

From f77d7215f3cb6dd9444b31523a3305e46133d5db Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Sat, 27 Aug 2022 15:18:51 -0500
Subject: [PATCH 19/49] whitespace change to changelog

---
 doc/CHANGELOG.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/CHANGELOG.rst b/doc/CHANGELOG.rst
index 6f545e7a93..f4c5625271 100644
--- a/doc/CHANGELOG.rst
+++ b/doc/CHANGELOG.rst
@@ -12,7 +12,7 @@ Next version
    * Using multi stage Dockerfile to reduce the number of Dockerfile (#813)
    * Adding safe folder to allow CI to compile DAGMC (#814)
    * Correction to CMake variable name in OpenMC install instructions (#817)
-   * Move install scripts into Dockerfile (#822)
+   * Move install scripts into Dockerfile  (#822)
    * Updating documentation publishing URL (#823)
 
 

From dc2945cc852cd3ef35c471f1fcf72a76aecd1578 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Sun, 28 Aug 2022 14:04:12 -0500
Subject: [PATCH 20/49] correct pythonpath

---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 676296ae0a..bbfa1bab6a 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -185,7 +185,7 @@ RUN mkdir -p ${moab_build_dir}/build && \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_FORTRAN=OFF \
                   -DENABLE_PYMOAB=ON && \
-    PYTHONPATH=${moab_build_dir}/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make -j${ci_jobs} && \
+    PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make -j${ci_jobs} && \
     make install && \
     cd && \
     rm -rf ${moab_build_dir}

From de0f876ce01eaa353b76cbf529c3d308186a2067 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Mon, 29 Aug 2022 05:52:54 -0500
Subject: [PATCH 21/49] need to mkdir for temp install

---
 CI/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index bbfa1bab6a..3af3cdf1f0 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -185,6 +185,7 @@ RUN mkdir -p ${moab_build_dir}/build && \
                   -DBUILD_SHARED_LIBS=ON \
                   -DENABLE_FORTRAN=OFF \
                   -DENABLE_PYMOAB=ON && \
+    mkdir -p ${moab_build_dir}/build/pymoab/lib/python3.6/site-packages && \
     PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make -j${ci_jobs} && \
     make install && \
     cd && \

From 0b20fb3ebe9099627ef7b250648c9cb6a63b75d2 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Mon, 29 Aug 2022 12:56:43 -0500
Subject: [PATCH 22/49] add pythonpath for install as well

---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 3af3cdf1f0..f1c471e400 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -187,7 +187,7 @@ RUN mkdir -p ${moab_build_dir}/build && \
                   -DENABLE_PYMOAB=ON && \
     mkdir -p ${moab_build_dir}/build/pymoab/lib/python3.6/site-packages && \
     PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make -j${ci_jobs} && \
-    make install && \
+    PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make install && \
     cd && \
     rm -rf ${moab_build_dir}
 

From 10162c56bb8c67e80f5973d9bf33bf9301a2e88f Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Mon, 29 Aug 2022 20:41:05 -0500
Subject: [PATCH 23/49] comment out env source b/c it should all be in docker
 image

---
 CI/scripts/housekeeping.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/scripts/housekeeping.sh b/CI/scripts/housekeeping.sh
index d4ac1d9a9c..0e44feb414 100755
--- a/CI/scripts/housekeeping.sh
+++ b/CI/scripts/housekeeping.sh
@@ -2,7 +2,7 @@
 
 set -ex
 
-source ${docker_env}
+#source ${docker_env}
 
 cd ${dagmc_build_dir}
 

From da899cc71cc5cb9e89b5d3b1a6cf1e5fcafdd18a Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Mon, 29 Aug 2022 20:52:38 -0500
Subject: [PATCH 24/49] Add build and install dir to the environment

---
 CI/Dockerfile | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index f1c471e400..ae05906d0e 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -56,6 +56,11 @@ RUN apt-get -y update; \
     update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10; \
     pip install cython;
 
+ARG build_dir
+ARG install_dir
+
+ENV build_dir=${build_dir}
+ENV install_dir=${install_dir}
 
 FROM base as external_deps
 

From 5a84ef1fb5cc56dc80c7f77f9ea4211650aa15e6 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Mon, 29 Aug 2022 20:53:44 -0500
Subject: [PATCH 25/49] define build_dir from env

---
 CI/scripts/housekeeping.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CI/scripts/housekeeping.sh b/CI/scripts/housekeeping.sh
index 0e44feb414..4032cc9971 100755
--- a/CI/scripts/housekeeping.sh
+++ b/CI/scripts/housekeeping.sh
@@ -4,6 +4,7 @@ set -ex
 
 #source ${docker_env}
 
+export dagmc_build_dir=${build_dir}/dagmc
 cd ${dagmc_build_dir}
 
 # Ensure clang-format is there

From f5c70dd09cdb016e10241a40ad576e03d3301d01 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Mon, 29 Aug 2022 21:06:10 -0500
Subject: [PATCH 26/49] read build dir from the env

---
 CI/scripts/housekeeping.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/CI/scripts/housekeeping.sh b/CI/scripts/housekeeping.sh
index 4032cc9971..ea19bd40da 100755
--- a/CI/scripts/housekeeping.sh
+++ b/CI/scripts/housekeeping.sh
@@ -2,8 +2,6 @@
 
 set -ex
 
-#source ${docker_env}
-
 export dagmc_build_dir=${build_dir}/dagmc
 cd ${dagmc_build_dir}
 

From 488bf87613b120fa8316186493a674e4a6586ee8 Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Tue, 30 Aug 2022 05:40:29 -0500
Subject: [PATCH 27/49] workflow changes to correct directory

---
 CI/scripts/housekeeping.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/CI/scripts/housekeeping.sh b/CI/scripts/housekeeping.sh
index ea19bd40da..552c39f1ae 100755
--- a/CI/scripts/housekeeping.sh
+++ b/CI/scripts/housekeeping.sh
@@ -2,9 +2,6 @@
 
 set -ex
 
-export dagmc_build_dir=${build_dir}/dagmc
-cd ${dagmc_build_dir}
-
 # Ensure clang-format is there
 if ! command -v clang-format &> /dev/null
 then

From 5340950645833bddd87d20d4ea7e663af9d58ded Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Sun, 1 Jan 2023 20:33:16 +0000
Subject: [PATCH 28/49] moved hdf5_install_dir to global ARGs

---
 CI/Dockerfile | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index ae05906d0e..bf358a4688 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,5 +1,6 @@
 # Svalinn DAGMC Dockerfile
 
+# Global ARGS set before the first build stage are accessable by all build stages
 ARG UBUNTU_VERSION=18.04
 
 ARG ci_jobs=8
@@ -13,6 +14,8 @@ ARG HDF5_VERSION_major=1.10
 
 ARG build_dir=/root/build_dir
 ARG install_dir=/root/opt
+# hdf5_install_dir is needed by moab and hdf5 build stages
+ARG hdf5_install_dir=${install_dir}/hdf5
 
 # clang and gcc are options for the compiler but to use them CC and CXX must be set
 # if clang then change cc to clang and cxx to clang++
@@ -124,6 +127,7 @@ FROM external_deps AS hdf5
 
 # accessing gloabl ARGs in build stage
 ARG HDF5_VERSION_major
+ARG hdf5_install_dir
 ARG HDF5_VERSION
 ARG install_dir
 ARG build_dir
@@ -132,7 +136,6 @@ ARG CXX
 ARG CC
 
 ENV hdf5_build_dir=${build_dir}/hdf5
-ENV hdf5_install_dir=${install_dir}/hdf5
 
 RUN mkdir -p ${hdf5_build_dir}/build && \
     cd ${hdf5_build_dir} && \
@@ -152,6 +155,7 @@ RUN mkdir -p ${hdf5_build_dir}/build && \
 FROM hdf5 AS moab
 
 # accessing gloabl ARGs in build stage
+ARG hdf5_install_dir
 ARG install_dir
 ARG MOAB_BRANCH
 ARG build_dir
@@ -163,9 +167,6 @@ ARG CC
 ENV moab_build_dir=${build_dir}/moab
 ENV moab_install_dir=${install_dir}/moab
 
-# Set the hdf5 install dir as this is also needed by moab compile
-ENV hdf5_install_dir=${install_dir}/hdf5
-
 RUN mkdir -p ${moab_build_dir}/build && \
     cd ${moab_build_dir} && \
     git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \
@@ -195,5 +196,3 @@ RUN mkdir -p ${moab_build_dir}/build && \
     PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make install && \
     cd && \
     rm -rf ${moab_build_dir}
-
-

From 1b438e8bff2fa53923a8ade99185e6a99db057be Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Sun, 1 Jan 2023 22:28:29 +0000
Subject: [PATCH 29/49] single ENV entry used in multiple stages

---
 CI/Dockerfile | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index bf358a4688..fb848d9c11 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -4,7 +4,7 @@
 ARG UBUNTU_VERSION=18.04
 
 ARG ci_jobs=8
-ARG MOAB_BRANCH=5.4.0
+ARG MOAB_BRANCH=5.4.1
 ARG EMBREE_BRANCH='v3.6.1'
 ARG geant4_version=10.5.1
 
@@ -14,8 +14,6 @@ ARG HDF5_VERSION_major=1.10
 
 ARG build_dir=/root/build_dir
 ARG install_dir=/root/opt
-# hdf5_install_dir is needed by moab and hdf5 build stages
-ARG hdf5_install_dir=${install_dir}/hdf5
 
 # clang and gcc are options for the compiler but to use them CC and CXX must be set
 # if clang then change cc to clang and cxx to clang++
@@ -127,7 +125,6 @@ FROM external_deps AS hdf5
 
 # accessing gloabl ARGs in build stage
 ARG HDF5_VERSION_major
-ARG hdf5_install_dir
 ARG HDF5_VERSION
 ARG install_dir
 ARG build_dir
@@ -136,6 +133,7 @@ ARG CXX
 ARG CC
 
 ENV hdf5_build_dir=${build_dir}/hdf5
+ENV hdf5_install_dir=${install_dir}/hdf5
 
 RUN mkdir -p ${hdf5_build_dir}/build && \
     cd ${hdf5_build_dir} && \
@@ -155,7 +153,6 @@ RUN mkdir -p ${hdf5_build_dir}/build && \
 FROM hdf5 AS moab
 
 # accessing gloabl ARGs in build stage
-ARG hdf5_install_dir
 ARG install_dir
 ARG MOAB_BRANCH
 ARG build_dir

From 28a5cbfc50db8c4f0887f23c86559014e47e452a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 5 Jan 2023 14:31:00 +0000
Subject: [PATCH 30/49] moab to 5.3.0

---
 .github/workflows/docker_publish.yml | 2 +-
 CI/Dockerfile                        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 18c03c4576..7dc819e506 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -163,7 +163,7 @@ jobs:
           1.10.4,
         ]
         moab_versions : [
-          5.4.0,
+          5.3.0,
           develop,
           master,
         ]
diff --git a/CI/Dockerfile b/CI/Dockerfile
index fb848d9c11..f70adddb4c 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -4,7 +4,7 @@
 ARG UBUNTU_VERSION=18.04
 
 ARG ci_jobs=8
-ARG MOAB_BRANCH=5.4.1
+ARG MOAB_BRANCH=5.3.0
 ARG EMBREE_BRANCH='v3.6.1'
 ARG geant4_version=10.5.1
 

From ebeaf5957f550a84cb1e287c7df5b1d379b873fb Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Thu, 5 Jan 2023 23:09:27 +0000
Subject: [PATCH 31/49] [skip ci] added double-down install, started adding
 dagmc stage

---
 CI/Dockerfile | 51 +++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 45 insertions(+), 6 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index f70adddb4c..af0ed52a70 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -2,7 +2,9 @@
 
 # Global ARGS set before the first build stage are accessable by all build stages
 ARG UBUNTU_VERSION=18.04
-
+ARG build_mw_reg_tests=OFF
+ARG double_down=ON
+ARG static_exe=OFF
 ARG ci_jobs=8
 ARG MOAB_BRANCH=5.3.0
 ARG EMBREE_BRANCH='v3.6.1'
@@ -97,15 +99,11 @@ RUN mkdir -p ${geant4_build_dir}/build && \
     cd && \
     rm -rf ${geant4_build_dir}
 
-# these two double down ENVs don't appear to be used yet
-# However they were in orginal dockerfile, so they have been kept
-# TODO add double down to the dockerfile
-ENV double_down_build_dir=${build_dir}/double-down/
-ENV double_down_install_dir=${install_dir}/double-down/
 
 ENV embree_install_dir=${install_dir}/embree
 ENV embree_build_dir=${build_dir}/embree
 
+# Clone and install Embree
 RUN mkdir -p ${embree_build_dir}/build && \
     cd ${embree_build_dir} && \
     git clone -b ${EMBREE_BRANCH} https://github.com/embree/embree && \
@@ -120,6 +118,19 @@ RUN mkdir -p ${embree_build_dir}/build && \
     cd && \
     rm -rf ${embree_build_dir}
 
+ENV double_down_build_dir=${build_dir}/double-down/
+ENV double_down_install_dir=${install_dir}/double-down/
+
+# Clone and install Double-Down
+RUN git clone --shallow-submodules --single-branch --branch v1.0.0 --depth 1 https://github.com/pshriwise/double-down.git && \
+    cd {double_down_build_dir} && \
+    mkdir build && \
+    cd build && \
+    cmake .. -DMOAB_DIR=/MOAB \
+             -DCMAKE_INSTALL_PREFIX=${double_down_install_dir} \
+             -DEMBREE_DIR=${embree_install_dir} \
+    make -j"$compile_cores" && \
+    make -j"$compile_cores" install
 
 FROM external_deps AS hdf5
 
@@ -193,3 +204,31 @@ RUN mkdir -p ${moab_build_dir}/build && \
     PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make install && \
     cd && \
     rm -rf ${moab_build_dir}
+
+FROM moab as dagmc
+
+ARG build_mw_reg_tests
+ARG install_dir
+ARG static_exe
+
+COPY src/ ${build_dir}
+
+RUN mkdir ${dagmc_build_dir} && \
+    cd dagmc_build_dir && \
+    mkdir build && \
+    cd build && \
+    cmake ${dagmc_build_dir} -DMOAB_DIR=${moab_install_dir} \
+                             -DBUILD_GEANT4=ON \
+                             -DGEANT4_DIR=${geant4_install_dir} \
+                             -DBUILD_CI_TESTS=ON \
+                             -DBUILD_MW_REG_TESTS=${build_mw_reg_tests} \
+                             -DBUILD_STATIC_EXE=${static_exe} \
+                             -DBUILD_STATIC_LIBS=${static_exe} \
+                             -DCMAKE_C_COMPILER=${CC} \
+                             -DCMAKE_CXX_COMPILER=${CXX} \
+                             -DCMAKE_Fortran_COMPILER=gfortran \
+                             -DCMAKE_INSTALL_PREFIX=${install_dir} \
+                             -DDOUBLE_DOWN=${double_down} \
+                             -Ddd_ROOT=${double_down_install_dir} && \
+    make -j${ci_jobs} && \
+    make install
\ No newline at end of file

From 6b89dd2d645d02e695e57d0b25f6e2ea2bd130dd Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 6 Jan 2023 12:52:07 +0000
Subject: [PATCH 32/49] building and testing dagmc in docker

---
 .github/workflows/docker_publish.yml | 45 ++++++++--------
 CI/Dockerfile                        | 78 +++++++++++++++++++---------
 2 files changed, 74 insertions(+), 49 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 7dc819e506..433b286e40 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -257,6 +257,10 @@ jobs:
          develop,
          master,
         ]
+        static_exe : [
+         OFF,
+         ON,
+        ]
     container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
 
     name: Installing and Testing DAGMC
@@ -266,30 +270,23 @@ jobs:
         with:
           submodules: recursive
 
-      - name: Setup
-        run: |
-          git config --global --add safe.directory ${GITHUB_WORKSPACE}
-          git config --global --add safe.directory /github/home/
-          git config --global --add safe.directory /github/home/.cache
-          git config --global --add safe.directory /github/home/.cache/pip
-          git config --global --add safe.directory /github/home/.cache/pip/http
-          echo "MOAB_VERSION=${{ matrix.moab_versions }}" >> $GITHUB_ENV
-          echo "COMPILER=${{ matrix.compiler }}" >> $GITHUB_ENV
-          echo "HDF5_VERSION=${{ matrix.hdf5_versions }}" >> $GITHUB_ENV
-          echo "REPO_SLUG=${GITHUB_REPOSITORY}" >> $GITHUB_ENV
-          echo "PULL_REQUEST=$(echo  $GITHUB_REF | cut -d"/" -f3)" >> $GITHUB_ENV
-          echo "DOUBLE_DOWN="OFF"" >> $GITHUB_ENV
-          ln -s $GITHUB_WORKSPACE /root/build_dir/DAGMC
-
-      - name: Install DAGMC
-        run: |
-          cd $GITHUB_WORKSPACE
-          /bin/bash "CI/scripts/install.sh"
-
-      - name: Run DAGMC Test
-        run: |
-          cd $GITHUB_WORKSPACE
-          /bin/bash "CI/scripts/tests.sh"
+      - name: Install DAGMC in Docker image and test
+        uses: docker/build-push-action@v2
+        with:
+          file: CI/Dockerfile
+          target: dagmc_test
+          context: .
+          push: false
+          build-args: |
+            OWNER=${{ github.repository_owner }}
+            TAG=ci_testing
+            UBUNTU_VERSION=${{ matrix.ubuntu_versions }}
+            COMPILER=${{ matrix.compiler }}
+            HDF5=${{ matrix.hdf5_versions }}
+            MOAB=${{ matrix.moab_versions }}
+            static_exe=OFF
+            build_mw_reg_tests=ON
+          tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-static_exe_dagmc_${{ matrix.static_exe }}:ci_testing
 
   pushing_housekeeping_stable_img:
     if: ${{ github.repository_owner == 'svalinn' }}
diff --git a/CI/Dockerfile b/CI/Dockerfile
index af0ed52a70..73f10bf311 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,17 +1,17 @@
 # Svalinn DAGMC Dockerfile
 
 # Global ARGS set before the first build stage are accessable by all build stages
-ARG UBUNTU_VERSION=18.04
 ARG build_mw_reg_tests=OFF
-ARG double_down=ON
-ARG static_exe=OFF
-ARG ci_jobs=8
-ARG MOAB_BRANCH=5.3.0
 ARG EMBREE_BRANCH='v3.6.1'
 ARG geant4_version=10.5.1
+ARG UBUNTU_VERSION=18.04
+ARG MOAB_BRANCH=5.3.0
+ARG double_down=OFF
+ARG static_exe=OFF
+ARG ci_jobs=20
 
 ARG HDF5_VERSION=1.10.4
-# currently major version must be manually set to match HDF5 version
+# currently HDF5 major version must be manually set to match HDF5 version
 ARG HDF5_VERSION_major=1.10
 
 ARG build_dir=/root/build_dir
@@ -65,6 +65,7 @@ ARG install_dir
 ENV build_dir=${build_dir}
 ENV install_dir=${install_dir}
 
+
 FROM base as external_deps
 
 # accessing gloabl ARGs in build stage
@@ -118,19 +119,6 @@ RUN mkdir -p ${embree_build_dir}/build && \
     cd && \
     rm -rf ${embree_build_dir}
 
-ENV double_down_build_dir=${build_dir}/double-down/
-ENV double_down_install_dir=${install_dir}/double-down/
-
-# Clone and install Double-Down
-RUN git clone --shallow-submodules --single-branch --branch v1.0.0 --depth 1 https://github.com/pshriwise/double-down.git && \
-    cd {double_down_build_dir} && \
-    mkdir build && \
-    cd build && \
-    cmake .. -DMOAB_DIR=/MOAB \
-             -DCMAKE_INSTALL_PREFIX=${double_down_install_dir} \
-             -DEMBREE_DIR=${embree_install_dir} \
-    make -j"$compile_cores" && \
-    make -j"$compile_cores" install
 
 FROM external_deps AS hdf5
 
@@ -205,19 +193,43 @@ RUN mkdir -p ${moab_build_dir}/build && \
     cd && \
     rm -rf ${moab_build_dir}
 
+ENV double_down_build_dir=${build_dir}/double-down
+ENV double_down_install_dir=${install_dir}/double-down
+
+# Clone and install Double-Down
+# performed after moab install as double-down requires moab
+RUN mkdir -p ${double_down_build_dir}/build && \
+    cd ${double_down_build_dir} && \
+    git clone --shallow-submodules --single-branch --branch v1.0.0 --depth 1 https://github.com/pshriwise/double-down.git && \
+    cd build && \
+    cmake ../double-down -DMOAB_DIR=${moab_install_dir} \
+                         -DCMAKE_INSTALL_PREFIX=${double_down_install_dir} \
+                         -DEMBREE_DIR=${embree_install_dir} && \
+    make -j${ci_jobs} && \
+    make -j${ci_jobs} install
+
+
 FROM moab as dagmc
 
+# accessing gloabl ARGs in build stage
 ARG build_mw_reg_tests
 ARG install_dir
 ARG static_exe
+ARG CXX
+ARG CC
 
-COPY src/ ${build_dir}
+ENV dagmc_build_dir=${build_dir}/dagmc
+ENV dagmc_install_dir=${install_dir}/dagmc
 
-RUN mkdir ${dagmc_build_dir} && \
-    cd dagmc_build_dir && \
-    mkdir build && \
+# copies the enitre git repo into the dockerfile to ensure the submodules can also be found
+RUN mkdir -p ${dagmc_build_dir}/build
+COPY . ${dagmc_build_dir}
+RUN cd  ${dagmc_build_dir} && git submodule update --init
+
+RUN mkdir -p ${dagmc_build_dir}/build && \
+    cd ${dagmc_build_dir} && \
     cd build && \
-    cmake ${dagmc_build_dir} -DMOAB_DIR=${moab_install_dir} \
+    cmake ../${dagmc} -DMOAB_DIR=${moab_install_dir} \
                              -DBUILD_GEANT4=ON \
                              -DGEANT4_DIR=${geant4_install_dir} \
                              -DBUILD_CI_TESTS=ON \
@@ -231,4 +243,20 @@ RUN mkdir ${dagmc_build_dir} && \
                              -DDOUBLE_DOWN=${double_down} \
                              -Ddd_ROOT=${double_down_install_dir} && \
     make -j${ci_jobs} && \
-    make install
\ No newline at end of file
+    make install
+
+
+FROM dagmc as dagmc_test
+
+# Test DAGMC executables
+RUN cd ${dagmc_build_dir}/build && \
+    make test
+
+# clean out config test directory for next build
+RUN cd ${dagmc_build_dir} && \
+    git clean -dxf .
+
+# Test DAGMC CMake configuration file
+RUN cd ${dagmc_build_dir}/cmake/test_config && \
+    cmake . -DDAGMC_ROOT=${dagmc_install_dir} && \
+    make all test

From 48ae87a58d9a4d68215fbe3b48254ee0e8ac295c Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Fri, 6 Jan 2023 23:13:18 +0000
Subject: [PATCH 33/49] removed static from tag

---
 .github/workflows/docker_publish.yml |  3 +--
 CI/Dockerfile                        | 24 ++++++++++++------------
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 433b286e40..06cf0c2569 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -284,9 +284,8 @@ jobs:
             COMPILER=${{ matrix.compiler }}
             HDF5=${{ matrix.hdf5_versions }}
             MOAB=${{ matrix.moab_versions }}
-            static_exe=OFF
             build_mw_reg_tests=ON
-          tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-static_exe_dagmc_${{ matrix.static_exe }}:ci_testing
+          tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
 
   pushing_housekeeping_stable_img:
     if: ${{ github.repository_owner == 'svalinn' }}
diff --git a/CI/Dockerfile b/CI/Dockerfile
index 73f10bf311..a37f9a573c 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -230,18 +230,18 @@ RUN mkdir -p ${dagmc_build_dir}/build && \
     cd ${dagmc_build_dir} && \
     cd build && \
     cmake ../${dagmc} -DMOAB_DIR=${moab_install_dir} \
-                             -DBUILD_GEANT4=ON \
-                             -DGEANT4_DIR=${geant4_install_dir} \
-                             -DBUILD_CI_TESTS=ON \
-                             -DBUILD_MW_REG_TESTS=${build_mw_reg_tests} \
-                             -DBUILD_STATIC_EXE=${static_exe} \
-                             -DBUILD_STATIC_LIBS=${static_exe} \
-                             -DCMAKE_C_COMPILER=${CC} \
-                             -DCMAKE_CXX_COMPILER=${CXX} \
-                             -DCMAKE_Fortran_COMPILER=gfortran \
-                             -DCMAKE_INSTALL_PREFIX=${install_dir} \
-                             -DDOUBLE_DOWN=${double_down} \
-                             -Ddd_ROOT=${double_down_install_dir} && \
+                      -DBUILD_GEANT4=ON \
+                      -DGEANT4_DIR=${geant4_install_dir} \
+                      -DBUILD_CI_TESTS=ON \
+                      -DBUILD_MW_REG_TESTS=${build_mw_reg_tests} \
+                      -DBUILD_STATIC_EXE=${static_exe} \
+                      -DBUILD_STATIC_LIBS=${static_exe} \
+                      -DCMAKE_C_COMPILER=${CC} \
+                      -DCMAKE_CXX_COMPILER=${CXX} \
+                      -DCMAKE_Fortran_COMPILER=gfortran \
+                      -DCMAKE_INSTALL_PREFIX=${install_dir} \
+                      -DDOUBLE_DOWN=${double_down} \
+                      -Ddd_ROOT=${double_down_install_dir} && \
     make -j${ci_jobs} && \
     make install
 

From 0ff7d8546fff36c6c05d397e47129c6e7dc34af4 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 13 Jan 2023 16:14:08 +0000
Subject: [PATCH 34/49] corrected install dir typo

---
 CI/Dockerfile | 28 ++++++++++++++++------------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 73f10bf311..529df6332d 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -214,6 +214,7 @@ FROM moab as dagmc
 # accessing gloabl ARGs in build stage
 ARG build_mw_reg_tests
 ARG install_dir
+ARG build_dir
 ARG static_exe
 ARG CXX
 ARG CC
@@ -230,24 +231,27 @@ RUN mkdir -p ${dagmc_build_dir}/build && \
     cd ${dagmc_build_dir} && \
     cd build && \
     cmake ../${dagmc} -DMOAB_DIR=${moab_install_dir} \
-                             -DBUILD_GEANT4=ON \
-                             -DGEANT4_DIR=${geant4_install_dir} \
-                             -DBUILD_CI_TESTS=ON \
-                             -DBUILD_MW_REG_TESTS=${build_mw_reg_tests} \
-                             -DBUILD_STATIC_EXE=${static_exe} \
-                             -DBUILD_STATIC_LIBS=${static_exe} \
-                             -DCMAKE_C_COMPILER=${CC} \
-                             -DCMAKE_CXX_COMPILER=${CXX} \
-                             -DCMAKE_Fortran_COMPILER=gfortran \
-                             -DCMAKE_INSTALL_PREFIX=${install_dir} \
-                             -DDOUBLE_DOWN=${double_down} \
-                             -Ddd_ROOT=${double_down_install_dir} && \
+                      -DBUILD_GEANT4=ON \
+                      -DGEANT4_DIR=${geant4_install_dir} \
+                      -DBUILD_CI_TESTS=ON \
+                      -DBUILD_MW_REG_TESTS=${build_mw_reg_tests} \
+                      -DBUILD_STATIC_EXE=${static_exe} \
+                      -DBUILD_STATIC_LIBS=${static_exe} \
+                      -DCMAKE_C_COMPILER=${CC} \
+                      -DCMAKE_CXX_COMPILER=${CXX} \
+                      -DCMAKE_Fortran_COMPILER=gfortran \
+                      -DCMAKE_INSTALL_PREFIX=${dagmc_install_dir} \
+                      -DDOUBLE_DOWN=${double_down} \
+                      -Ddd_ROOT=${double_down_install_dir} && \
     make -j${ci_jobs} && \
     make install
 
 
 FROM dagmc as dagmc_test
 
+ARG dagmc_build_dir
+ARG dagmc_install_dir
+
 # Test DAGMC executables
 RUN cd ${dagmc_build_dir}/build && \
     make test

From a30b95dc12cb160a5a366a839624df284dbd28e0 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Fri, 13 Jan 2023 23:46:26 +0000
Subject: [PATCH 35/49] updated actions

---
 .github/workflows/docker_publish.yml | 44 ++++++++++++++--------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 06cf0c2569..d5ad1fccc1 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -25,17 +25,17 @@ jobs:
         uses: actions/checkout@v3
       
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and Export Dockerfile_0_base
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile
           target: base
@@ -57,10 +57,10 @@ jobs:
 
     steps:
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -70,7 +70,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Build and push Dockerfile_1_housekeeping
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile_1_housekeeping
           context: .
@@ -102,10 +102,10 @@ jobs:
     name: Ubuntu ${{ matrix.ubuntu_versions }} + ${{ matrix.compiler }} hdf5 ${{ matrix.hdf5_versions }}
     steps:
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
@@ -115,7 +115,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Build and push Dockerfile_1_external_deps
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile
           target: external_deps
@@ -129,7 +129,7 @@ jobs:
           tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext:ci_testing
 
       - name: Build and export Dockerfile_2_hdf5
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile
           target: hdf5
@@ -172,10 +172,10 @@ jobs:
 
     steps:
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
@@ -185,7 +185,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Build and push Dockerfile_3_moab
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile
           target: moab
@@ -271,7 +271,7 @@ jobs:
           submodules: recursive
 
       - name: Install DAGMC in Docker image and test
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile
           target: dagmc_test
@@ -301,23 +301,23 @@ jobs:
     name: Housekeeping':' latest -> stable
     steps:
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Push Image as stable img
-        uses: akhilerm/tag-push-action@v1.0.0
+        uses: akhilerm/tag-push-action@v2.1.0
         with:
           src: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-housekeeping:ci_testing
           dst: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-housekeeping:stable
 
       - name: Push Image as latest img
-        uses: akhilerm/tag-push-action@v1.0.0
+        uses: akhilerm/tag-push-action@v2.1.0
         with:
           src: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-housekeeping:ci_testing
           dst: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-housekeeping:latest
@@ -353,23 +353,23 @@ jobs:
 
     steps:
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Push Image as stable img
-        uses: akhilerm/tag-push-action@v1.0.0
+        uses: akhilerm/tag-push-action@v2.1.0
         with:
           src: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
           dst: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:stable
 
       - name: Push Image as latest img
-        uses: akhilerm/tag-push-action@v1.0.0
+        uses: akhilerm/tag-push-action@v2.1.0
         with:
           src: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
           dst: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:latest
\ No newline at end of file

From a872a23f2cc0b88c0c22482684687e1ccbdf1e3d Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Sat, 14 Jan 2023 09:09:39 +0000
Subject: [PATCH 36/49] added docker buildx to step

---
 .github/workflows/docker_publish.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index d5ad1fccc1..e5eaedf80b 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -269,6 +269,9 @@ jobs:
         uses: actions/checkout@v3
         with:
           submodules: recursive
+        
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
 
       - name: Install DAGMC in Docker image and test
         uses: docker/build-push-action@v3

From 92db99cade7f273f4c784c5319f8fe20915d20ff Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 19 Jan 2023 14:40:00 +0000
Subject: [PATCH 37/49] added path before make test cmd

---
 CI/Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 529df6332d..fa27fbd8f4 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -1,5 +1,7 @@
 # Svalinn DAGMC Dockerfile
 
+
+
 # Global ARGS set before the first build stage are accessable by all build stages
 ARG build_mw_reg_tests=OFF
 ARG EMBREE_BRANCH='v3.6.1'
@@ -254,7 +256,7 @@ ARG dagmc_install_dir
 
 # Test DAGMC executables
 RUN cd ${dagmc_build_dir}/build && \
-    make test
+    PATH=${dagmc_install_dir}/bin:$PATH make test
 
 # clean out config test directory for next build
 RUN cd ${dagmc_build_dir} && \

From 97e1438fc42c63c4bd09492239ce66686203e905 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 2 Feb 2023 16:16:09 +0000
Subject: [PATCH 38/49] added inline CTEST_OUTPUT_ON_FAILURE=1

---
 CI/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index fa27fbd8f4..f634fcd859 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -256,7 +256,7 @@ ARG dagmc_install_dir
 
 # Test DAGMC executables
 RUN cd ${dagmc_build_dir}/build && \
-    PATH=${dagmc_install_dir}/bin:$PATH make test
+    PATH=${dagmc_install_dir}/bin:$PATH CTEST_OUTPUT_ON_FAILURE=1 make test
 
 # clean out config test directory for next build
 RUN cd ${dagmc_build_dir} && \
@@ -265,4 +265,4 @@ RUN cd ${dagmc_build_dir} && \
 # Test DAGMC CMake configuration file
 RUN cd ${dagmc_build_dir}/cmake/test_config && \
     cmake . -DDAGMC_ROOT=${dagmc_install_dir} && \
-    make all test
+    CTEST_OUTPUT_ON_FAILURE=1 make all test

From 26690987f3521ab412b4bed28aeffa1ef9fc87f5 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Mon, 6 Feb 2023 13:23:48 +0000
Subject: [PATCH 39/49] added ci stage for dagmc

---
 .github/workflows/docker_publish.yml | 64 ++++++++++++++++++++++++++--
 1 file changed, 61 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index e5eaedf80b..364b56f3ed 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -231,8 +231,8 @@ jobs:
         run: |
           cd $GITHUB_WORKSPACE
           /bin/bash "CI/scripts/housekeeping.sh"
-      
-  test_img:
+
+  build-dagmc-img:
     needs: [build-moab-img]
     runs-on: ubuntu-latest
     env:
@@ -263,6 +263,64 @@ jobs:
         ]
     container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
 
+    name: Installing and Testing DAGMC
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+        
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Install DAGMC in Docker image and test
+        uses: docker/build-push-action@v3
+        with:
+          file: CI/Dockerfile
+          target: dagmc
+          context: .
+          push: false
+          build-args: |
+            OWNER=${{ github.repository_owner }}
+            TAG=ci_testing
+            UBUNTU_VERSION=${{ matrix.ubuntu_versions }}
+            COMPILER=${{ matrix.compiler }}
+            HDF5=${{ matrix.hdf5_versions }}
+            MOAB=${{ matrix.moab_versions }}
+            build_mw_reg_tests=ON
+          tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc:ci_testing
+
+  test_img:
+    needs: [build-dagmc-img]
+    runs-on: ubuntu-latest
+    env:
+      hdf5_versions: 1.10.4
+      hdf5_build_dir: hdf5_build_dir
+
+    strategy:
+      matrix:
+        ubuntu_versions : [
+          18.04,
+          20.04,
+          ]
+        compiler : [
+          gcc,
+          clang,
+          ]
+        hdf5_versions : [
+         1.10.4,
+        ]
+        moab_versions : [
+         5.3.0,
+         develop,
+         master,
+        ]
+        static_exe : [
+         OFF,
+         ON,
+        ]
+    container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc-test:ci_testing
+
     name: Installing and Testing DAGMC
     steps:
       - name: Checkout repository
@@ -375,4 +433,4 @@ jobs:
         uses: akhilerm/tag-push-action@v2.1.0
         with:
           src: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
-          dst: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:latest
\ No newline at end of file
+          dst: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:latest

From b25e3c8a373987979db5551e3e73933af81b2f82 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Mon, 6 Feb 2023 13:25:39 +0000
Subject: [PATCH 40/49] dagmc_dirs as ENV not ARGS

---
 CI/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index f634fcd859..40ac16190a 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -251,8 +251,8 @@ RUN mkdir -p ${dagmc_build_dir}/build && \
 
 FROM dagmc as dagmc_test
 
-ARG dagmc_build_dir
-ARG dagmc_install_dir
+ENV dagmc_build_dir=${build_dir}/dagmc
+ENV dagmc_install_dir=${install_dir}/dagmc
 
 # Test DAGMC executables
 RUN cd ${dagmc_build_dir}/build && \

From ad9c95c1a4e663c0bd8c48e81b1fedb4b81d8709 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 7 Feb 2023 09:44:17 +0000
Subject: [PATCH 41/49] corrected tag and container names

---
 .github/workflows/docker_publish.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 364b56f3ed..76a054d976 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -263,7 +263,7 @@ jobs:
         ]
     container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
 
-    name: Installing and Testing DAGMC
+    name: Installing DAGMC
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
@@ -319,15 +319,15 @@ jobs:
          OFF,
          ON,
         ]
-    container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc-test:ci_testing
+    container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc:ci_testing
 
-    name: Installing and Testing DAGMC
+    name: Testing DAGMC
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
           submodules: recursive
-        
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 
@@ -346,7 +346,7 @@ jobs:
             HDF5=${{ matrix.hdf5_versions }}
             MOAB=${{ matrix.moab_versions }}
             build_mw_reg_tests=ON
-          tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
+          tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc-test:ci_testing
 
   pushing_housekeeping_stable_img:
     if: ${{ github.repository_owner == 'svalinn' }}

From 59e843ae5751c2a8e716ed1ab48f036412f15ea4 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 7 Feb 2023 17:08:38 +0000
Subject: [PATCH 42/49] pusing dagmc image so it can be found by testing image

---
 .github/workflows/docker_publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 76a054d976..eba019be3e 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -279,7 +279,7 @@ jobs:
           file: CI/Dockerfile
           target: dagmc
           context: .
-          push: false
+          push: true
           build-args: |
             OWNER=${{ github.repository_owner }}
             TAG=ci_testing

From 33f0e0754317e02a70d5ef37c9273e2c438df23a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Feb 2023 18:05:26 +0000
Subject: [PATCH 43/49] combining two steps

---
 .github/workflows/docker_publish.yml | 49 +++-------------------------
 1 file changed, 4 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index eba019be3e..94a0779bff 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -232,7 +232,7 @@ jobs:
           cd $GITHUB_WORKSPACE
           /bin/bash "CI/scripts/housekeeping.sh"
 
-  build-dagmc-img:
+  build-test-dagmc-img:
     needs: [build-moab-img]
     runs-on: ubuntu-latest
     env:
@@ -273,13 +273,13 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 
-      - name: Install DAGMC in Docker image and test
+      - name: Install DAGMC in Docker image
         uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile
           target: dagmc
           context: .
-          push: true
+          push: false
           build-args: |
             OWNER=${{ github.repository_owner }}
             TAG=ci_testing
@@ -290,48 +290,7 @@ jobs:
             build_mw_reg_tests=ON
           tags: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc:ci_testing
 
-  test_img:
-    needs: [build-dagmc-img]
-    runs-on: ubuntu-latest
-    env:
-      hdf5_versions: 1.10.4
-      hdf5_build_dir: hdf5_build_dir
-
-    strategy:
-      matrix:
-        ubuntu_versions : [
-          18.04,
-          20.04,
-          ]
-        compiler : [
-          gcc,
-          clang,
-          ]
-        hdf5_versions : [
-         1.10.4,
-        ]
-        moab_versions : [
-         5.3.0,
-         develop,
-         master,
-        ]
-        static_exe : [
-         OFF,
-         ON,
-        ]
-    container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}-dagmc:ci_testing
-
-    name: Testing DAGMC
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: Install DAGMC in Docker image and test
+      - name: Test DAGMC in Docker image
         uses: docker/build-push-action@v3
         with:
           file: CI/Dockerfile

From 051ec10981a2732faf95cb7aac5d7624e0d943be Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Feb 2023 18:08:25 +0000
Subject: [PATCH 44/49] making use of qemu, removed buildx

---
 .github/workflows/docker_publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 94a0779bff..17e0d58b76 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -270,8 +270,8 @@ jobs:
         with:
           submodules: recursive
         
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
 
       - name: Install DAGMC in Docker image
         uses: docker/build-push-action@v3

From 8e4da44ffadcbae4d32081d4d688dfae842da7db Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Feb 2023 18:10:19 +0000
Subject: [PATCH 45/49] housebuilding only if build-test works

---
 .github/workflows/docker_publish.yml | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 17e0d58b76..854222792f 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -264,15 +264,13 @@ jobs:
     container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
 
     name: Installing DAGMC
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-        
+    steps:        
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v2
 
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
       - name: Install DAGMC in Docker image
         uses: docker/build-push-action@v3
         with:
@@ -309,7 +307,7 @@ jobs:
 
   pushing_housekeeping_stable_img:
     if: ${{ github.repository_owner == 'svalinn' }}
-    needs: [test_img]
+    needs: [build-test-dagmc-img]
     runs-on: ubuntu-latest
     env:
       hdf5_versions: 1.10.4

From 5ddc8f8e2144a3d211d877f9e387b51e760420c3 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Feb 2023 18:11:06 +0000
Subject: [PATCH 46/49] housebuilding only if build-test works

---
 .github/workflows/docker_publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 854222792f..5d21c563b7 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -342,7 +342,7 @@ jobs:
 
   pushing_test_stable_img:
     if: ${{ github.repository_owner == 'svalinn' }}
-    needs: [test_img]
+    needs: [build-test-dagmc-img]
     runs-on: ubuntu-latest
     env:
       hdf5_versions: 1.10.4

From 4a123b5ea653833255d424bf11fbee62df5432d0 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 9 Feb 2023 09:40:31 +0000
Subject: [PATCH 47/49] docker qemu usage in dag step same as other stages

---
 .github/workflows/docker_publish.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 5d21c563b7..d732035aa5 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -169,7 +169,6 @@ jobs:
         ]
 
     name: Ubuntu ${{ matrix.ubuntu_versions }} + ${{ matrix.compiler }} hdf5 ${{ matrix.hdf5_versions }} + Moab ${{ matrix.moab_versions }}
-
     steps:
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v2
@@ -268,6 +267,13 @@ jobs:
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v2
 
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Checkout repository
         uses: actions/checkout@v3
 

From eb91b609621826568c3d57ca3599a1da12eda190 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 9 Feb 2023 14:57:43 +0000
Subject: [PATCH 48/49] not running dag intsall step in container

---
 .github/workflows/docker_publish.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index d732035aa5..1203060fea 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -260,7 +260,6 @@ jobs:
          OFF,
          ON,
         ]
-    container: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-ext-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}:ci_testing
 
     name: Installing DAGMC
     steps:        

From d3edab8c6d5eccf185adf113125ae88d7143379e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 17 Feb 2023 12:34:09 +0000
Subject: [PATCH 49/49] disable reg tests as models missing

---
 CI/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 40ac16190a..6e67c12d95 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -236,7 +236,8 @@ RUN mkdir -p ${dagmc_build_dir}/build && \
                       -DBUILD_GEANT4=ON \
                       -DGEANT4_DIR=${geant4_install_dir} \
                       -DBUILD_CI_TESTS=ON \
-                      -DBUILD_MW_REG_TESTS=${build_mw_reg_tests} \
+                      # reg tests disabled see issue https://github.com/svalinn/DAGMC/issues/858
+                      -DBUILD_MW_REG_TESTS=OFF \
                       -DBUILD_STATIC_EXE=${static_exe} \
                       -DBUILD_STATIC_LIBS=${static_exe} \
                       -DCMAKE_C_COMPILER=${CC} \