Merge pull request NOAA-EMC#43 from climbfuji/update_gsd_develop_from…

…_develop

Update gsd/develop from NOAA-EMC develop

.github/CODEOWNERS

@@ -0,0 +1,7 @@
+# This is a comment.
+# Each line is a file pattern followed by one or more owners.
+# Order is important; the last matching pattern takes the most
+# precedence.
+
+# The components are owned by their respective teams
+/FV3/ @noaa-emc/fv3atm-team

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,56 @@
+---
+name: Bug report
+about: Create a report to fix bugs
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## Description
+Provide a clear and concise description of what the bug is.
+Also give a description of how to fix the bug.
+
+
+### To Reproduce:
+What compilers/machines are you seeing this with?
+Give explicit steps to reproduce the behavior.
+1. do this
+2. then that
+3. then, oops, look at the bug
+
+
+## Additional context
+Add any other context about the problem here.
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related. Example:
+- needs to be fixed also in noaa-emc/nems/issues/<issue_number>
+- needed for noaa-emc/fv3atm/pull/<pr_number>
+
+
+## Output
+
+**Screenshots**
+If applicable, drag and drop screenshots to help explain your problem.
+
+**output logs**
+If applicable, include relevant output logs.
+Either drag and drop the entire log file here (if a long log) or
+
+```
+paste the code here (if a short section of log)
+```
+
+## Testing:
+
+1. Have you tested the code changes? On what platforms?
+
+2. Have you run regression test in ufs-weather-model or ufs-s2s-model with code changes?
+- Will the baseline results change? 
+- If the baseline results change, is it expected? Please give brief explanation.
+
+## Dependent PRs:
+
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related. Example:
+- required to support noaa-emc/GFDL_atmos_cubed_sphere/issues/<issue_number>
+- ncar/ccpp-physics/pull/<pr_number>
+- associated ufs-weather-model/pull/<pr_number>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+## Description
+Provide a clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+## Solution
+Add a clear and concise description of what solution you provide.
+
+## Alternatives
+If applicable, add a description of any alternative solutions or features you've considered.
+
+## Testing:
+
+1. Have you tested the code changes? On what platforms?
+2. Have you run regression test in ufs-weather-model or ufs-s2s-model with code changes?
+- Will the baseline results change?
+- If yes, please give brief explanation of your code updates on the regression test.
+
+## Dependent PRs:
+
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related. Example:
+- required to support noaa-emc/GFDL_atmos_cubed_sphere/issues/<issue_number>
+- ncar/ccpp-physics/pull/<pr_number>
+- associated ufs-weather-model/pull/<pr_number>
+

.github/pull_request_template.md

@@ -0,0 +1,37 @@
+## Description
+
+(Instructions: this, and all subsequent sections of text should be removed and filled in as appropriate.)
+Provide a detailed description of what this PR does.  
+What bug does it fix, or what feature does it add?  
+Is a change of answers expected from this PR?  
+
+
+
+### Issue(s) addressed
+
+Link the issues to be closed with this PR, whether in this repository, or in another repository.
+(Remember, issues should always be created before starting work on a PR branch!)
+- fixes #<issue_number>
+- fixes noaa-emc/fv3atm/issues/<issue_number>
+
+
+
+## Testing
+
+How were these changes tested?  
+What compilers / HPCs was it tested with?  
+Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)  
+Have the ufs-weather-model regression test been run? On what platform?  
+- Will the code updates change regression test baseline? If yes, why? Please show the baseline directory below.
+- Please commit the regression test log files in your ufs-weather-model branch
+
+
+## Dependencies
+
+If testing this branch requires non-default branches in other repositories, list them.
+Those branches should have matching names (ideally)
+
+Do PRs in upstream repositories need to be merged first?
+If so add the "waiting for other repos" label and list the upstream PRs
+- waiting on noaa-emc/nems/pull/<pr_number>
+- waiting on noaa-emc/fv3atm/pull/<pr_number>

CMakeLists.txt

@@ -1,20 +1,21 @@
 if(CCPP)
-  add_definitions(-DCCPP)
+    add_definitions(-DCCPP)
 endif()
 
 add_subdirectory(cpl)
 add_subdirectory(gfsphysics)
 add_subdirectory(ipd)
 add_subdirectory(io)
 
-# fv3core library
-
+###############################################################################
+### fv3dycore
+###############################################################################
 if(NOT CCPP)
-set(FAST_PHYSICS_SRCS_F90 atmos_cubed_sphere/model/fv_cmp.F90)
+    set(FAST_PHYSICS_SRCS_F90 atmos_cubed_sphere/model/fv_cmp.F90)
 endif()
 
 add_library(
-    fv3core
+    fv3dycore
 
     atmos_cubed_sphere/model/a2b_edge.F90
     atmos_cubed_sphere/model/multi_gases.F90
@@ -61,37 +62,46 @@ add_library(
 set_property(SOURCE atmos_cubed_sphere/model/nh_utils.F90 APPEND_STRING PROPERTY COMPILE_FLAGS "${FAST}")
 set_property(SOURCE atmos_cubed_sphere/model/fv_mapz.F90  APPEND_STRING PROPERTY COMPILE_FLAGS "${FAST}")
 
-target_link_libraries(fv3core PRIVATE fms)
-target_link_libraries(fv3core PRIVATE gfsphysics)
-target_link_libraries(fv3core PRIVATE ipd)
+set_target_properties(fv3dycore PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
+target_include_directories(fv3dycore PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
 
-target_include_directories(fv3core PRIVATE atmos_cubed_sphere ${ESMF_MOD})
+target_link_libraries(fv3dycore PRIVATE fms)
+target_link_libraries(fv3dycore PRIVATE gfsphysics)
+target_link_libraries(fv3dycore PRIVATE ipd)
+target_link_libraries(fv3dycore PRIVATE esmf)
 
-# end of fv3core
+target_include_directories(fv3dycore PRIVATE atmos_cubed_sphere ${ESMF_MOD})
 
 ###############################################################################
 ### ccpp
 ###############################################################################
 if(CCPP)
-  add_subdirectory(ccpp)
-  add_subdirectory(ccpp/driver)
-  add_dependencies(gfsphysics ccpp ccppphys)
-  add_dependencies(ccppdriver ccpp ccppphys)
-  add_dependencies(ccppphys ccpp)
-
-  target_include_directories(fv3core PRIVATE ${CMAKE_BINARY_DIR}/FV3/ccpp/framework/src)
-  target_include_directories(fv3core PRIVATE ${CMAKE_BINARY_DIR}/FV3/ccpp/driver)
-endif()
+    add_subdirectory(ccpp)
+    add_subdirectory(ccpp/driver)
+
+    add_dependencies(gfsphysics ccpp ccppphys)
+    add_dependencies(ccppdriver ccpp ccppphys)
+    add_dependencies(ccppphys ccpp)
 
-set_target_properties(fv3core PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(fv3core PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/mod)
+    target_include_directories(fv3dycore PRIVATE ${CMAKE_BINARY_DIR}/FV3/ccpp/framework/src)
+    target_include_directories(fv3dycore PRIVATE ${CMAKE_BINARY_DIR}/FV3/ccpp/driver)
 
+    target_link_libraries(ccppphys PRIVATE sp::sp_d)
+    target_link_libraries(ccppphys PRIVATE w3nco::w3nco_d)
+endif()
+
+###############################################################################
+### stochastic_physics
+###############################################################################
 # When specifying an out-of-tree source a binary directory must be explicitly specified.
 #add_subdirectory(../stochastic_physics stochastic_physics)
 add_subdirectory(stochastic_physics)
 
+###############################################################################
+### fv3atm
+###############################################################################
 add_library(
-    fv3cap
+    fv3atm
 
     atmos_model.F90
     fv3_cap.F90
@@ -100,21 +110,46 @@ add_library(
     time_utils.F90
 )
 
+set_target_properties(fv3atm PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
+target_include_directories(fv3atm PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+
 if(CCPP)
-target_include_directories(fv3cap PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/ccpp/driver/mod)
-add_dependencies(fv3cap ccppdriver ccppphys)
+    target_include_directories(fv3atm PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/ccpp/driver/mod)
+    set(CCPP_LIBRARIES ccppdriver ccppphys ccpp)
+    add_dependencies(fv3atm ccppdriver ccppphys ccpp)
+    target_link_libraries(fv3atm PUBLIC ccppdriver ccppphys ccpp)
+endif()
+target_include_directories(fv3atm PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/stochastic_physics)
+target_compile_definitions(fv3atm PRIVATE -DESMF_VERSION_MAJOR=${ESMF_VERSION_MAJOR})
+
+target_link_libraries(fv3atm PUBLIC fms)
+target_link_libraries(fv3atm PUBLIC cpl)
+target_link_libraries(fv3atm PUBLIC gfsphysics)
+target_link_libraries(fv3atm PUBLIC ipd)
+target_link_libraries(fv3atm PUBLIC io)
+target_link_libraries(fv3atm PUBLIC fv3dycore)
+target_link_libraries(fv3atm PUBLIC stochastic_physics)
+target_link_libraries(fv3atm PUBLIC stochastic_physics_wrapper)
+
+target_link_libraries(fv3atm PUBLIC
+                      nemsio::nemsio w3emc::w3emc_d w3nco::w3nco_d sp::sp_d bacio::bacio_4)
+if(INLINE_POST)
+  target_link_libraries(fv3atm PUBLIC nceppost::nceppost)
 endif()
-target_include_directories(fv3cap PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/stochastic_physics)
-target_compile_definitions(fv3cap PRIVATE -DESMF_VERSION_MAJOR=${ESMF_VERSION_MAJOR})
-target_include_directories(fv3cap PRIVATE ${ESMF_MOD})
-
-target_link_libraries(fv3cap PRIVATE fms)
-target_link_libraries(fv3cap PRIVATE fv3cpl)
-target_link_libraries(fv3cap PRIVATE gfsphysics)
-target_link_libraries(fv3cap PRIVATE ipd)
-target_link_libraries(fv3cap PRIVATE io)
-target_link_libraries(fv3cap PRIVATE fv3core)
-target_link_libraries(fv3cap PRIVATE stochastic_physics)
-
-set_target_properties(fv3cap PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(fv3cap PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/mod)
+
+target_link_libraries(fv3atm PUBLIC esmf)
+
+###############################################################################
+### Install
+###############################################################################
+install(
+  TARGETS fv3atm fv3dycore io ipd gfsphysics ${CCPP_LIBRARIES} cpl stochastic_physics stochastic_physics_wrapper
+  EXPORT fv3atm-config
+  LIBRARY DESTINATION lib
+  ARCHIVE DESTINATION lib)
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod DESTINATION ${CMAKE_INSTALL_PREFIX})
+
+install(EXPORT fv3atm-config
+  DESTINATION lib/cmake
+)
+