From 8889e7972266140a72e06c6f4ea9b504bb87a27c Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Tue, 16 Apr 2024 19:42:31 -0500
Subject: [PATCH 1/9] modify pyinstall process

---
 CMakeLists.txt        | 23 ++++++++++++++++-------
 cyclus/CMakeLists.txt |  3 ---
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d974fde905..e8203738ae 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -307,10 +307,11 @@ IF(NOT CYCLUS_DOC_ONLY)
     #
     # Use new Python library finder
     find_package (Python3 COMPONENTS Interpreter Development NumPy)
-
-    execute_process(COMMAND "${Python3_EXECUTABLE}" -m site --user-site
-                    OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
-                    OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT DEFINED PYTHON_SITE_PACKAGES)
+        execute_process(COMMAND "${Python3_EXECUTABLE}" -m site --user-site
+                        OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
+                        OUTPUT_STRIP_TRAILING_WHITESPACE)
+    endif()
     message("-- PYTHON_EXECUTABLE: ${Python3_EXECUTABLE}")
     message("-- PYTHON_SITE_PACKAGES: ${PYTHON_SITE_PACKAGES}")
 
@@ -437,9 +438,17 @@ IF(NOT CYCLUS_DOC_ONLY)
         )
 
     if(Cython_FOUND)
-        set(pyinstallscript "${CMAKE_CURRENT_BINARY_DIR}/cmake/SetupPyInstall.cmake")
-        configure_file(cmake/SetupPyInstall.cmake.in ${pyinstallscript} @ONLY)
-        install(SCRIPT ${pyinstallscript})
+        install(CODE "
+            message(\"############### Begin Python Install ###############\")
+            set(ENV{CYCLUS_PROJECT_VERSION} \"${CMAKE_PROJECT_VERSION}\")
+            execute_process(COMMAND ${Python3_EXECUTABLE} -m pip install --target=${PYTHON_SITE_PACKAGES} --force-reinstall --upgrade --no-deps .
+                    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                    RESULT_VARIABLE res_var)
+            Message(\"res var is ${res_var}\")
+            if(NOT \"${res_var}\" STREQUAL \"\")
+                message(FATAL_ERROR \"Process python -m pip install failed, res_var = '${res_var}'\")
+            endif()
+        ")
     endif(Cython_FOUND)
     ##############################################################################################
     ################################## begin uninstall target ####################################
diff --git a/cyclus/CMakeLists.txt b/cyclus/CMakeLists.txt
index 4177e08b42..82edcfc88c 100644
--- a/cyclus/CMakeLists.txt
+++ b/cyclus/CMakeLists.txt
@@ -42,6 +42,3 @@ foreach(file ${CYCLUS_CYTHON_FILES})
     # by setup.py, along with the pure python files.
     install(TARGETS ${targ} LIBRARY DESTINATION "${PYTHON_SITE_PACKAGES}/cyclus")
 endforeach()
-
-FILE(GLOB CYCLUS_PYTHON_FILES "${CYCLUS_PYSOURCE_DIR}/*.py")
-INSTALL(FILES ${CYCLUS_PYTHON_FILES} DESTINATION "${PYTHON_SITE_PACKAGES}/cyclus")

From cfb2ea718d3042f01b03457558ad37441c9ae4dd Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Tue, 16 Apr 2024 20:13:44 -0500
Subject: [PATCH 2/9] Minor changes

---
 CMakeLists.txt                |  1 -
 cmake/SetupPyInstall.cmake.in | 26 --------------------------
 docker/Dockerfile             |  1 -
 3 files changed, 28 deletions(-)
 delete mode 100644 cmake/SetupPyInstall.cmake.in

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e8203738ae..bcdc2fc6f7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -444,7 +444,6 @@ IF(NOT CYCLUS_DOC_ONLY)
             execute_process(COMMAND ${Python3_EXECUTABLE} -m pip install --target=${PYTHON_SITE_PACKAGES} --force-reinstall --upgrade --no-deps .
                     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                     RESULT_VARIABLE res_var)
-            Message(\"res var is ${res_var}\")
             if(NOT \"${res_var}\" STREQUAL \"\")
                 message(FATAL_ERROR \"Process python -m pip install failed, res_var = '${res_var}'\")
             endif()
diff --git a/cmake/SetupPyInstall.cmake.in b/cmake/SetupPyInstall.cmake.in
deleted file mode 100644
index 78800d2c6e..0000000000
--- a/cmake/SetupPyInstall.cmake.in
+++ /dev/null
@@ -1,26 +0,0 @@
-#
-# Runs setup.py install
-#
-set(PYTHON_EXECUTABLE @Python3_EXECUTABLE@)
-set(CYCLUS_PROJECT_VERSION @CMAKE_PROJECT_VERSION@)
-set(ENV{CYCLUS_PROJECT_VERSION} "${CYCLUS_PROJECT_VERSION}")
-message("############### Begin Python Install ###############")
-message("-- Python installer:")
-message("  PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
-message("  CYCLUS_PROJECT_VERSION: ${CYCLUS_PROJECT_VERSION}")
-message("  CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
-set(CMAKE_CURRENT_BINARY_DIR @CMAKE_CURRENT_BINARY_DIR@)
-message("  CMAKE_CURRENT_BINARY_DIR: ${CMAKE_CURRENT_BINARY_DIR}")
-execute_process(COMMAND ${PYTHON_EXECUTABLE} -m site --user-site
-                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                OUTPUT_VARIABLE site_packages
-                OUTPUT_STRIP_TRAILING_WHITESPACE
-                RESULT_VARIABLE res_var)
-message("  PYTHON_SITE_PACKAGES: ${site_packages}")
-execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pip install --target=${site_packages} --force-reinstall --upgrade --no-deps .
-                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                RESULT_VARIABLE res_var)
-if(NOT "${res_var}" STREQUAL "0")
-  message(FATAL_ERROR "Process python -m pip install failed, res_var = '${res_var}'")
-endif()
-message("###############  End Python Install  ###############")
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 40d411378d..69be5a1e63 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -150,7 +150,6 @@ WORKDIR /cyclus
 # for further CMake debugging.
 RUN python install.py -j ${make_cores} --build-type=Release --allow-milps
 ENV PATH /root/.local/bin:$PATH
-ENV LD_LIBRARY_PATH /root/.local/lib:/root/.local/lib/cyclus
 
 FROM cyclus as deb-generation
 WORKDIR /cyclus/build

From 9e64e29dd84733da562a231edaeccd7ec64ebcb2 Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Tue, 16 Apr 2024 21:32:28 -0500
Subject: [PATCH 3/9] change references to cycpp in tests

---
 tests/cycpp_test.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/cycpp_test.py b/tests/cycpp_test.py
index ca853582f3..4dc932af36 100644
--- a/tests/cycpp_test.py
+++ b/tests/cycpp_test.py
@@ -13,20 +13,20 @@
 sys.path.insert(0, os.path.join(cycdir, 'cli'))
 
 # pass 1 Filters
-from cycpp import NamespaceFilter, TypedefFilter, UsingFilter,\
+from cyclus.cycpp import NamespaceFilter, TypedefFilter, UsingFilter,\
         UsingNamespaceFilter, NamespaceAliasFilter, ClassFilter, \
         AccessFilter, PragmaCyclusErrorFilter
 
 # pass 2 Filters
-from cycpp import VarDecorationFilter, VarDeclarationFilter, ExecFilter, \
+from cyclus.cycpp import VarDecorationFilter, VarDeclarationFilter, ExecFilter, \
     NoteDecorationFilter, StateAccumulator
 
 # pass 3 Filters
-from cycpp import CloneFilter, InitFromCopyFilter, \
+from cyclus.cycpp import CloneFilter, InitFromCopyFilter, \
         InitFromDbFilter, InfileToDbFilter, SchemaFilter, SnapshotFilter, \
         SnapshotInvFilter, InitInvFilter, DefaultPragmaFilter, AnnotationsFilter
 
-import cycpp
+import cyclus.cycpp as cycpp
 
 class MockMachine(object):
     def __init__(self):

From c24b088957839ab6255ddb4c1f64d41e073b3f60 Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Wed, 17 Apr 2024 08:30:13 -0500
Subject: [PATCH 4/9] add ending message to python install

---
 CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index bcdc2fc6f7..ae6a6b36d0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -447,6 +447,7 @@ IF(NOT CYCLUS_DOC_ONLY)
             if(NOT \"${res_var}\" STREQUAL \"\")
                 message(FATAL_ERROR \"Process python -m pip install failed, res_var = '${res_var}'\")
             endif()
+            message(\"Cyclus Python package successfully installed in ${PYTHON_SITE_PACKAGES}\")
         ")
     endif(Cython_FOUND)
     ##############################################################################################

From 11a031951a83678d7b97dfc348c748d396863076 Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Wed, 17 Apr 2024 08:53:12 -0500
Subject: [PATCH 5/9] use suggeseted boost package

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

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 69be5a1e63..96d94a63ff 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -85,7 +85,7 @@ RUN conda update -y --all && \
                liblapack \
                pkg-config \
                coincbc \
-               boost-cpp \
+               libboost-devel \
                hdf5 \
                sqlite \
                pcre \

From 2a4d293efa5fe18d6a01e34cd6bc80531fea405f Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Wed, 17 Apr 2024 09:23:04 -0500
Subject: [PATCH 6/9] update changelog

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

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e0e316ff1e..fb6683f0eb 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -38,7 +38,7 @@ Since last release
 **Changed:**
 
 * Moved to unified CHANGELOG Entry and check them with GithubAction (#1571)
-* Major update and modernization of build (#1587, #1632, #1734)
+* Major update and modernization of build (#1587, #1632, #1734, #1737)
 * Changed Json formatting for compatibility with current python standards (#1587)
 * Changed README.rst installation instructions, tested on fresh Ubuntu-22.04 system with Python 3.11 (#1617, #1644)
 * Resolved various compilation warnings due to use of deprecated APIs (#1671)

From e50ccf5298aa813aecbc53b3fb4b5c0ff9163ab2 Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Wed, 17 Apr 2024 19:39:11 -0500
Subject: [PATCH 7/9] update FindCyclus.cmake to find the cython modules

---
 cmake/FindCyclus.cmake | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/cmake/FindCyclus.cmake b/cmake/FindCyclus.cmake
index 873c317d24..2a2fecea59 100644
--- a/cmake/FindCyclus.cmake
+++ b/cmake/FindCyclus.cmake
@@ -88,6 +88,30 @@ FIND_LIBRARY(CYCLUS_CORE_LIBRARY NAMES cyclus
     /opt/local /opt/local/cyclus
     PATH_SUFFIXES cyclus/lib lib)
 
+# Look for the library
+FIND_LIBRARY(CYCLUS_EVENTHOOKS_LIBRARY NAMES eventhooks.so
+    HINTS "${CYCLUS_ROOT_DIR}" "${CYCLUS_ROOT_DIR}/cyclus"
+    ${DEPS_CYCLUS}
+    /usr/local/cyclus/lib /usr/local/cyclus
+    /opt/local /opt/local/cyclus
+    PATH_SUFFIXES cyclus/lib lib)
+    
+# Look for the library
+FIND_LIBRARY(CYCLUS_PYINFILE_LIBRARY NAMES pyinfile.so
+    HINTS "${CYCLUS_ROOT_DIR}" "${CYCLUS_ROOT_DIR}/cyclus"
+    ${DEPS_CYCLUS}
+    /usr/local/cyclus/lib /usr/local/cyclus
+    /opt/local /opt/local/cyclus
+    PATH_SUFFIXES cyclus/lib lib)  
+
+# Look for the library
+FIND_LIBRARY(CYCLUS_PYMODULE_LIBRARY NAMES pymodule.so
+    HINTS "${CYCLUS_ROOT_DIR}" "${CYCLUS_ROOT_DIR}/cyclus"
+    ${DEPS_CYCLUS}
+    /usr/local/cyclus/lib /usr/local/cyclus
+    /opt/local /opt/local/cyclus
+    PATH_SUFFIXES cyclus/lib lib)  
+
 # Look for the library
 FIND_LIBRARY(CYCLUS_AGENT_TEST_LIBRARY NAMES baseagentunittests
     HINTS "${CYCLUS_ROOT_DIR}" "${CYCLUS_ROOT_DIR}/cyclus"
@@ -112,6 +136,17 @@ IF(CYCLUS_CORE_INCLUDE_DIR AND CYCLUS_CORE_TEST_INCLUDE_DIR
         AND CYCLUS_AGENT_TEST_LIBRARY)
     SET(CYCLUS_CORE_FOUND 1)
     SET(CYCLUS_CORE_LIBRARIES "${CYCLUS_CORE_LIBRARY}")
+    # if Cyclus was installed without Cython these three libraries won't be found because they don't exist
+    # if Cyclus was installed WITH Cython we need to link against them
+    if(NOT ${CYCLUS_EVENTHOOKS_LIBRARY} STREQUAL "CYCLUS_EVENTHOOKS_LIBRARY-NOTFOUND")
+        SET(CYCLUS_CORE_LIBRARIES "${CYCLUS_CORE_LIBRARIES}" "${CYCLUS_EVENTHOOKS_LIBRARY}")
+    endif()
+    if(NOT ${CYCLUS_PYINFILE_LIBRARY} STREQUAL "CYCLUS_PYINFILE_LIBRARY-NOTFOUND")
+        SET(CYCLUS_CORE_LIBRARIES "${CYCLUS_CORE_LIBRARIES}" "${CYCLUS_PYINFILE_LIBRARY}")
+    endif()
+    if(NOT ${CYCLUS_PYMODULE_LIBRARY} STREQUAL "CYCLUS_PYMODULE_LIBRARY-NOTFOUND")
+        SET(CYCLUS_CORE_LIBRARIES "${CYCLUS_CORE_LIBRARIES}" "${CYCLUS_PYMODULE_LIBRARY}")
+    endif()
     SET(CYCLUS_TEST_LIBRARIES "${CYCLUS_GTEST_LIBRARY}" "${CYCLUS_AGENT_TEST_LIBRARY}")
     SET(CYCLUS_AGENT_TEST_LIBRARIES "${CYCLUS_AGENT_TEST_LIBRARY}")
     SET(CYCLUS_CORE_INCLUDE_DIRS "${CYCLUS_CORE_INCLUDE_DIR}")

From 0005bea441839fd2f12ebe09436c7b3e81152aef Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Sat, 20 Apr 2024 13:35:29 -0500
Subject: [PATCH 8/9] require python components

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

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ae6a6b36d0..2f2f63ee97 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -306,7 +306,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     # Cython & Python Bindings
     #
     # Use new Python library finder
-    find_package (Python3 COMPONENTS Interpreter Development NumPy)
+    find_package (Python3 REQUIRED COMPONENTS Interpreter Development NumPy)
     if(NOT DEFINED PYTHON_SITE_PACKAGES)
         execute_process(COMMAND "${Python3_EXECUTABLE}" -m site --user-site
                         OUTPUT_VARIABLE PYTHON_SITE_PACKAGES

From 80023338b034a053d8a797b1b4ac055c5c92ffa0 Mon Sep 17 00:00:00 2001
From: bennibbelink <79653949+bennibbelink@users.noreply.github.com>
Date: Sat, 20 Apr 2024 13:50:18 -0500
Subject: [PATCH 9/9] change repository back to cyclus in publish_release.yml

---
 .github/workflows/publish_release.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/publish_release.yml b/.github/workflows/publish_release.yml
index 95a00b82f4..4800fded31 100644
--- a/.github/workflows/publish_release.yml
+++ b/.github/workflows/publish_release.yml
@@ -34,7 +34,7 @@ jobs:
           echo "stable_tag=ci-image-cache" >> "$GITHUB_ENV"
 
       - name: Tag as stable
-        if: ${{ github.repository_owner == 'bennibbelink' && github.event_name == 'release' }}
+        if: ${{ github.repository_owner == 'cyclus' && github.event_name == 'release' }}
         run: |
           echo "version_tag=${{ github.event.release.tag_name }}" >> "$GITHUB_ENV"
           echo "stable_tag=stable" >> "$GITHUB_ENV"
@@ -60,8 +60,8 @@ jobs:
           push: true
           target: cyclus
           tags: |
-            ghcr.io/bennibbelink/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cyclus:${{ env.version_tag }}
-            ghcr.io/bennibbelink/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cyclus:${{ env.stable_tag }}
+            ghcr.io/cyclus/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cyclus:${{ env.version_tag }}
+            ghcr.io/cyclus/cyclus_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cyclus:${{ env.stable_tag }}
           build-args: |
             pkg_mgr=${{ matrix.pkg_mgr }}
             ubuntu_version=${{ matrix.ubuntu_versions }}
@@ -108,7 +108,7 @@ jobs:
           echo "stable_tag=ci-image-cache" >> "$GITHUB_ENV"
 
       - name: Tag as stable
-        if: ${{ github.repository_owner == 'bennibbelink' && github.event_name == 'release' }}
+        if: ${{ github.repository_owner == 'cyclus' && github.event_name == 'release' }}
         run: |
           echo "version_tag=${{ github.event.release.tag_name }}" >> "$GITHUB_ENV"
           echo "stable_tag=stable" >> "$GITHUB_ENV"
@@ -133,7 +133,7 @@ jobs:
           file: docker/Rocky.dockerfile
           push: true
           tags: |
-            ghcr.io/bennibbelink/cyclus_rocky_${{ matrix.rocky_versions }}/cyclus:${{ env.version_tag }}
-            ghcr.io/bennibbelink/cyclus_rocky_${{ matrix.rocky_versions }}/cyclus:${{ env.stable_tag }}
+            ghcr.io/cyclus/cyclus_rocky_${{ matrix.rocky_versions }}/cyclus:${{ env.version_tag }}
+            ghcr.io/cyclus/cyclus_rocky_${{ matrix.rocky_versions }}/cyclus:${{ env.stable_tag }}
           build-args: |
             rocky_version=${{ matrix.rocky_versions }}