From 58afd361a578fc6f44fb35700abb09b2362ecfb1 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Fri, 22 Mar 2024 16:47:09 -0500
Subject: [PATCH 01/12] new interface

---
 musica/micm/micm.F90            |  8 ++----
 test/CMakeLists.txt             |  8 +++---
 test/docker/Dockerfile.musica   | 46 +++++++++++----------------------
 test/musica/micm/CMakeLists.txt | 16 +++++-------
 4 files changed, 28 insertions(+), 50 deletions(-)

diff --git a/musica/micm/micm.F90 b/musica/micm/micm.F90
index cbc94caf..988df9d2 100644
--- a/musica/micm/micm.F90
+++ b/musica/micm/micm.F90
@@ -11,7 +11,7 @@ module micm
   public :: micm_init, micm_run, micm_final
   private :: convert_to_mol_per_cubic_meter, convert_to_mass_mixing_ratio
 
-  type(micm_t), allocatable :: micm_obj
+  type(micm_t), pointer         :: micm_obj
 
 contains
 
@@ -26,10 +26,7 @@ subroutine micm_init(config_path, iulog, errcode, errmsg)
     errcode = 0
     errmsg = ''
 
-    allocate(micm_obj)
-    micm_obj = micm_t(config_path)
-
-    errcode = micm_obj%create_solver()
+    micm_obj => micm_t(config_path, errcode)
 
     if (errcode /= 0) then
       errmsg = "[fatal] [micm] Failed to create MICM solver. Parsing configuration failed. &
@@ -136,7 +133,6 @@ subroutine micm_final(iulog, errcode, errmsg)
     errmsg = ''
 
     write(iulog,*) "[debug] [micm] Deallocating MICM object..."
-    if (allocated(micm_obj)) deallocate(micm_obj)
 
   end subroutine micm_final
 
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 74db2091..5b02cc8c 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -11,15 +11,15 @@ set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 # --------------------------------------------------------------------------------
-# NOTE: If 'ENABLE_MICM_TEST' on, this is not a stand-alone cmake project anymore. 
+# NOTE: If 'CCPP_ENABLE_MUSICA_TESTS' on, this is not a stand-alone cmake project anymore. 
 #       MICM CCPP wrapper needs MUSICA library and ccpp-framework/src.
-#       To 'ENABLE_MICM_TEST', you either build a cmake project through
+#       To 'CCPP_ENABLE_MUSICA_TESTS', you either build a cmake project through
 #       'docker/Dockerfile.musica' or follow the build instructions in the file.
 #       The following '$ENV' variables are set by the docker file.
 # --------------------------------------------------------------------------------
-option(ENABLE_MICM_TEST "Build the micm test" OFF)
+option(CCPP_ENABLE_MUSICA_TESTS "Build the micm test" OFF)
 
-if (ENABLE_MICM_TEST)
+if (CCPP_ENABLE_MUSICA_TESTS)
   set(MUSICA_VERSION $ENV{MUSICA_VERSION})
   set(MICM_SRC_PATH ${CMAKE_SOURCE_DIR}/../musica/micm)
   set(CCPP_SRC_PATH ${CMAKE_SOURCE_DIR}/$ENV{CCPP_SRC_PATH})
diff --git a/test/docker/Dockerfile.musica b/test/docker/Dockerfile.musica
index 27bb7cef..5a0e6139 100644
--- a/test/docker/Dockerfile.musica
+++ b/test/docker/Dockerfile.musica
@@ -5,53 +5,37 @@ RUN apt update \
     cmake \
     cmake-curses-gui \
     curl \
+    g++ \
+    gcc \
+    gfortran \
+    git \
+    lcov \
     libcurl4-openssl-dev \
     libhdf5-dev \
+    libnetcdff-dev \
     m4 \
+    make \
     nlohmann-json3-dev \
+    tree \
+    valgrind \
     vim \
     zlib1g-dev \
-    git \
-    lcov \
-    make \
-    libnetcdff-dev \
-    valgrind \
-    gcc \
-    gfortran \
-    g++ \
-    tree \
     && apt clean
 
 ENV FC=gfortran
 ENV FFLAGS="-I/usr/include/"
 
-RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
-    && tar -zxvf 8.2.0.tar.gz \
-    && cd json-fortran-8.2.0 \
-    && mkdir build \
-    && cd build \
-    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
-    && make install
-
-ENV JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0"
-
 # Install MUSICA (MUSICA-C)
-RUN git clone --depth 1 https://github.com/NCAR/musica.git
+RUN git clone https://github.com/NCAR/musica.git
 RUN cd musica \
+    && git fetch \
+    && git checkout atmo_fixes \
     && cmake \
         -S . \
         -B build \
-        -D USE_MUSICA=ON \
-        -D USE_MUSICA_FORTRAN=OFF \
-        -D MAKE_MUSICA_FORTRAN_INSTALLABLE=ON \
-        -D ENABLE_MICM=ON \
-        -D ENABLE_TESTS=OFF \
-        -D ENABLE_TUVX=OFF \
+        -D MUSICA_ENABLE_TESTS=OFF \
     && cd build \
-    && make install -j 8
-
-RUN ln -s /usr/local/musica-0.5.0/lib/libmusica.a /usr/local/lib/libmusica.a
-ENV MUSICA_VERSION="0.5.0"
+    && make install
 
 COPY . atmospheric_physics
 
@@ -64,7 +48,7 @@ ENV CCPP_SRC_PATH="lib/ccpp-framework/src"
 RUN cd atmospheric_physics/test \
     && cmake -S. \
              -B build \
-             -D ENABLE_MICM_TEST=ON \
+             -D CCPP_ENABLE_MUSICA_TESTS=ON \
     && cmake --build ./build
 
 RUN cd atmospheric_physics \
diff --git a/test/musica/micm/CMakeLists.txt b/test/musica/micm/CMakeLists.txt
index 65c65d53..95e339e1 100644
--- a/test/musica/micm/CMakeLists.txt
+++ b/test/musica/micm/CMakeLists.txt
@@ -1,6 +1,3 @@
-find_package(PkgConfig REQUIRED)
-pkg_check_modules(netcdff IMPORTED_TARGET REQUIRED netcdf-fortran)
-
 find_package(musica ${MUSICA_VERSION} REQUIRED)
 message(STATUS "  MUSICA version ${MUSICA_VERSION}")
 
@@ -8,14 +5,14 @@ include(FetchContent)
 
 FetchContent_Declare(musica
   GIT_REPOSITORY https://github.com/NCAR/musica.git
-  GIT_TAG        8ab0aa0
+  GIT_TAG        atmo_fixes
+  GIT_SUBMODULES
 )
 
-set(USE_MUSICA OFF)
-set(USE_MUSICA_FORTRAN ON)
-set(MAKE_MUSICA_FORTRAN_INSTALLABLE OFF)
-set(ENABLE_TUVX OFF)
-set(ENABLE_TESTS OFF)
+set(MUSICA_ENABLE_TESTS OFF)
+set(MUSICA_BUILD_C_CXX_INTERFACE OFF)
+set(MUSICA_BUILD_FORTRAN_INTERFACE ON)
+set(MUSICA_ENABLE_TUVX OFF)
 
 FetchContent_MakeAvailable(musica)
 
@@ -38,6 +35,7 @@ target_sources(test_micm_api
 
 target_link_libraries(test_micm_api
   PRIVATE
+    musica::musica
     musica::musica-fortran
 )
 

From 52e1bb5bfa94960b09958f61676f927766ac9ab4 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Fri, 22 Mar 2024 17:04:59 -0500
Subject: [PATCH 02/12] using better linkage

---
 test/musica/micm/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/musica/micm/CMakeLists.txt b/test/musica/micm/CMakeLists.txt
index 95e339e1..5ce58fee 100644
--- a/test/musica/micm/CMakeLists.txt
+++ b/test/musica/micm/CMakeLists.txt
@@ -35,7 +35,6 @@ target_sources(test_micm_api
 
 target_link_libraries(test_micm_api
   PRIVATE
-    musica::musica
     musica::musica-fortran
 )
 

From ba7c419c4250166023b4b11dc3fc2c56bd3eb3b4 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Sat, 23 Mar 2024 16:10:08 -0500
Subject: [PATCH 03/12] using main

---
 test/musica/micm/CMakeLists.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/musica/micm/CMakeLists.txt b/test/musica/micm/CMakeLists.txt
index 5ce58fee..467a9a87 100644
--- a/test/musica/micm/CMakeLists.txt
+++ b/test/musica/micm/CMakeLists.txt
@@ -5,8 +5,7 @@ include(FetchContent)
 
 FetchContent_Declare(musica
   GIT_REPOSITORY https://github.com/NCAR/musica.git
-  GIT_TAG        atmo_fixes
-  GIT_SUBMODULES
+  GIT_TAG        main
 )
 
 set(MUSICA_ENABLE_TESTS OFF)

From 75e4e0d8510550c8f21c47da875b27a3bf592c17 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Sat, 23 Mar 2024 16:14:38 -0500
Subject: [PATCH 04/12] branch

---
 .github/workflows/test.yaml   | 5 +----
 test/docker/Dockerfile.musica | 1 -
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index fef84aea..998a668d 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -1,9 +1,6 @@
 name: build
 
-on:
-  push:
-  pull_request:
-    types: [opened, reopened]
+on: [pull_request,workflow_dispatch]
 
 jobs:
   test_micm_api:
diff --git a/test/docker/Dockerfile.musica b/test/docker/Dockerfile.musica
index 5a0e6139..49c196bb 100644
--- a/test/docker/Dockerfile.musica
+++ b/test/docker/Dockerfile.musica
@@ -29,7 +29,6 @@ ENV FFLAGS="-I/usr/include/"
 RUN git clone https://github.com/NCAR/musica.git
 RUN cd musica \
     && git fetch \
-    && git checkout atmo_fixes \
     && cmake \
         -S . \
         -B build \

From 2f6b2559d0e2052c0deab0e458307fb07f2f330e Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Tue, 26 Mar 2024 13:58:30 -0500
Subject: [PATCH 05/12] using a musica tag

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

diff --git a/test/musica/micm/CMakeLists.txt b/test/musica/micm/CMakeLists.txt
index 467a9a87..487041b7 100644
--- a/test/musica/micm/CMakeLists.txt
+++ b/test/musica/micm/CMakeLists.txt
@@ -5,7 +5,7 @@ include(FetchContent)
 
 FetchContent_Declare(musica
   GIT_REPOSITORY https://github.com/NCAR/musica.git
-  GIT_TAG        main
+  GIT_TAG        v0.6.1
 )
 
 set(MUSICA_ENABLE_TESTS OFF)

From b3f6f99994211cc9c2768eb9ff7463fa110c3de4 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Tue, 26 Mar 2024 14:25:56 -0500
Subject: [PATCH 06/12] updating changelog

---
 doc/ChangeLog | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index f315694e..df365cb8 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,5 +1,32 @@
 ===============================================================
 
+Tag name:atmos_phys0_02_004
+Originator(s): kshores
+Date: 12 Mar 2024
+One-line Summary: Update MUSICA git tag
+Github PR URL: https://github.com/ESCOMP/atmospheric_physics/pull/89
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+- Update the MUSICA git tag
+
+This PR fixes the following NCAR/atmospheric_physics Github issues:
+
+- [Update MUSICA tag](https://github.com/NCAR/musica/issues/72)
+
+Code reviewed by: cacraigucar, boulderdaze
+
+List all existing files that have been added (A), modified (M), or deleted (D),
+and describe the changes:
+
+See [https://github.com/ESCOMP/atmospheric_physics/pull/89](https://github.com/ESCOMP/atmospheric_physics/pull/89)
+for a list of changed files and what changed.
+
+List and Describe any test failures: No known test failures.
+
+Summarize any changes to answers: None
+
+===============================================================
+
 Tag name:atmos_phys0_02_004
 Originator(s): boulderdaze
 Date: 12 Mar 2024

From c8db49f3815ee1bc4a339b72087879106cc8dc35 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Tue, 26 Mar 2024 14:27:39 -0500
Subject: [PATCH 07/12] updating tag number

---
 doc/ChangeLog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index df365cb8..14a6cf5e 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,6 +1,6 @@
 ===============================================================
 
-Tag name:atmos_phys0_02_004
+Tag name:atmos_phys0_02_005
 Originator(s): kshores
 Date: 12 Mar 2024
 One-line Summary: Update MUSICA git tag

From f9d3e33ebb906d7dc9407a313d11ae42894c27e7 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Tue, 26 Mar 2024 14:27:57 -0500
Subject: [PATCH 08/12] updating date

---
 doc/ChangeLog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 14a6cf5e..95224967 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -2,7 +2,7 @@
 
 Tag name:atmos_phys0_02_005
 Originator(s): kshores
-Date: 12 Mar 2024
+Date: 26 Mar 2024
 One-line Summary: Update MUSICA git tag
 Github PR URL: https://github.com/ESCOMP/atmospheric_physics/pull/89
 

From 6272fd0379d54038190c5c3904d78e17928848f7 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Mon, 15 Apr 2024 15:05:31 -0500
Subject: [PATCH 09/12] writing changelog by hand rather than pointing to a PR
 link

---
 doc/ChangeLog | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 95224967..426c8f91 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -18,8 +18,14 @@ Code reviewed by: cacraigucar, boulderdaze
 List all existing files that have been added (A), modified (M), or deleted (D),
 and describe the changes:
 
-See [https://github.com/ESCOMP/atmospheric_physics/pull/89](https://github.com/ESCOMP/atmospheric_physics/pull/89)
-for a list of changed files and what changed.
+M       .github/workflows/test.yaml
+          - Clean-up Github Action workflow
+         
+M       musica/micm/micm.F90
+M       test/CMakeLists.txt
+M       test/docker/Dockerfile.musica
+M       test/musica/micm/CMakeLists.txt
+           - Update MICM interface
 
 List and Describe any test failures: No known test failures.
 

From fabe391ac538ac8cbe52b6af6728d1d5c1b0bafd Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Mon, 15 Apr 2024 16:01:14 -0500
Subject: [PATCH 10/12] reruning on failed to see more errors

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

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 998a668d..b26d2664 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -12,4 +12,4 @@ jobs:
     - name: build Docker image
       run: docker build -t musica -f test/docker/Dockerfile.musica .
     - name: run tests in container
-      run: docker run --name test-container -t musica bash -c 'ctest'
\ No newline at end of file
+      run: docker run --name test-container -t musica bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
\ No newline at end of file

From 7a76c13d09f145a1036485e6a7304098f2f1d826 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Mon, 15 Apr 2024 16:40:07 -0500
Subject: [PATCH 11/12] checking out tag

---
 test/docker/Dockerfile.musica | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/docker/Dockerfile.musica b/test/docker/Dockerfile.musica
index 49c196bb..247878d1 100644
--- a/test/docker/Dockerfile.musica
+++ b/test/docker/Dockerfile.musica
@@ -29,6 +29,7 @@ ENV FFLAGS="-I/usr/include/"
 RUN git clone https://github.com/NCAR/musica.git
 RUN cd musica \
     && git fetch \
+    && git checkout 0.6.0 \
     && cmake \
         -S . \
         -B build \

From 7d9f5e574898910e9a7588768b6f3aa72694def1 Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Mon, 15 Apr 2024 16:44:56 -0500
Subject: [PATCH 12/12] correcting tag

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

diff --git a/test/docker/Dockerfile.musica b/test/docker/Dockerfile.musica
index 247878d1..7d14fc13 100644
--- a/test/docker/Dockerfile.musica
+++ b/test/docker/Dockerfile.musica
@@ -29,7 +29,7 @@ ENV FFLAGS="-I/usr/include/"
 RUN git clone https://github.com/NCAR/musica.git
 RUN cd musica \
     && git fetch \
-    && git checkout 0.6.0 \
+    && git checkout v0.6.0 \
     && cmake \
         -S . \
         -B build \