Update to API42 plus fixes for nbp

.gitattributes

@@ -5,16 +5,13 @@
 # This is primarily being implemented to allow users to develop code with any operating system (OS)
 # preferred and mitigates potential problems with end of line (eol) character differences.
 # -----------------------------------------------------------------------------------------------------
-
 ## Set the default end of line behavior (i.e. normalization to `lf` upon commit) for all files git recognizes as text
 * text=auto
-
 # Note that the above *only* applies to newly commited files.  If the file previously existed with a `crlf` end of file
 # and was checked out to local, then git will not change the eol character during check-in (i.e. commit).  For 
 # windows users they will see a warning like this:
 # warning: CRLF will be replaced by LF in functional_unit_testing/allometry/drive_allomtests.py.
 # The file will have its original line endings in your working directory
-
 ## Explicitly declare to git which files should be normalized (i.e. treated as text files)
 *.cdl text
 *.F90 text
@@ -23,6 +20,6 @@
 *.sh text
 *.txt text
 *.xml text
-
 ## Declare to git which file types are binary files and should not have end of line modified
-*.mod binary
+*.mod binary
+testing/test_data/*.nc filter=lfs diff=lfs merge=lfs -text

.github/PULL_REQUEST_TEMPLATE.md

@@ -28,6 +28,9 @@ All checklist items must be checked to enable merging this pull request:
 *Integrator*
 - [ ] FATES PASS/FAIL regression tests were run
 - [ ] Evaluation of test results for answer changes was performed and results provided
+- [ ] FATES-CLM6 Code Freeze: satellite phenology regression tests are b4b
+
+*If satellite phenology regressions are **not** b4b, please hold merge and notify the FATES development team.*
 
 ### Documentation
 <!--- If this pull requests warrants an update to the tech doc or user's guide, and said changes have been made paste a link to the documentation pull request below.  -->

.gitignore

@@ -24,6 +24,9 @@
 *.zip
 *.nc
 
+# Allow netcdf files in the test data directory
+!testing/test_data/*.nc
+
 # Logs and databases #
 ######################
 *.log
@@ -54,4 +57,4 @@ _run/
 # Old Files
 *~
 # Editor specific setting files
-*.vscode
+*.vscode

.gitmodules

@@ -11,3 +11,9 @@
 	fxrequired = AlwaysRequired
 	# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 	fxDONOTUSEurl = https://github.com/NGEET/tools-fates-landusedata
+[submodule "tools/xarray-functions"]
+	path = tools/xarray-functions
+	url = https://github.com/NGEET/tools-fates-xarray.git
+	fxtag = v0.0.0
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/NGEET/tools-fates-xarray

CMakeLists.txt

@@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 3.4)
 
 list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../share/cmake")
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../components/cmeps/cmake")
 
 FIND_PATH(NETCDFC_FOUND libnetcdf.a ${NETCDF_C_DIR}/lib)
 FIND_PATH(NETCDFF_FOUND libnetcdff.a ${NETCDF_FORTRAN_DIR}/lib)
@@ -19,6 +20,23 @@ include(CIME_utils)
 
 set(HLM_ROOT "../../")
 
+if (DEFINED ENV{ESMF_ROOT})
+  list(APPEND CMAKE_MODULE_PATH $ENV{ESMF_ROOT}/cmake)
+endif()
+find_package(ESMF REQUIRED)
+
+# This adds include directories needed for ESMF
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${ESMF_F90COMPILEPATHS} ")
+# This (which is *not* done in the share CMakeLists.txt) adds all directories and
+# libraries needed when linking ESMF, including any dependencies of ESMF. (But note that
+# this does *not* include the "-lesmf" itself). In particular, note that this includes any
+# link flags needed to link against PIO, which is needed on some systems (including
+# derecho); bringing in these PIO-related link flags via this ESMF mechanism allows us to
+# avoid explicitly including PIO as a link library, which wouldn't work on systems where
+# there is no separate PIO library and instead ESMF is built with its internal PIO
+# library.
+link_libraries(${ESMF_INTERFACE_LINK_LIBRARIES})
+
 # Add source directories from other share code (csm_share, etc.)
 add_subdirectory(${HLM_ROOT}/share/src csm_share)
 add_subdirectory(${HLM_ROOT}/share/unit_test_stubs/util csm_share_stubs)
@@ -90,6 +108,7 @@ include_directories(${CMAKE_CURRENT_BINARY_DIR})
 
 # Directories and libraries to include in the link step
 link_directories(${CMAKE_CURRENT_BINARY_DIR})
+link_libraries(esmf)
 
 # Add the main test directory
 add_subdirectory(${HLM_ROOT}/src/fates/testing)

CODE_OF_CONDUCT.md

@@ -53,4 +53,4 @@ This Code of Conduct is adapted from the [Contributor Covenant][homepage], versi
 
 [homepage]: http://contributor-covenant.org
 [version]: http://contributor-covenant.org/version/1/4/
-[wiki_ref_page]: https://github.com/NGEET/fates/wiki/Relevant-References
+[references]: https://fates-users-guide.readthedocs.io/en/latest/user/Relevant-References.html

CONTRIBUTING.md

@@ -12,11 +12,11 @@ https://github.com/NGEET/fates/blob/master/CODE_OF_CONDUCT.md
 
 ## Getting Started
 
-Those who wish to contribute code to FATES must have those changes integrated through the developer repository NGEET/fates.  Changes that make it to public releases must go through this repository first, as well.  Here are some basic first steps.
+Those who wish to contribute code to FATES must have those changes integrated through the developer repository NGEET/fates.  Changes that make it to public releases must go through this repository first, as well.  Please refer to the [developer section](hhttps://fates-users-guide.readthedocs.io/en/latest/developer/developer-guide.html) of the [User's Guide](https://fates-users-guide.readthedocs.io/en/latest/index.html) for more details.  Here are some basic first steps:
 
 * All developers should create a fork of the NGEET/fates repository into their personal space on github
-* Follow the developer work-flow described here: https://github.com/NGEET/fates/wiki/FATES-Development-Workflow
-* Each set of changes should have its own feature branch that encapsulates your desired changes, following the conventions outlined here: https://github.com/NGEET/fates/wiki/Feature-Branch-Naming-Convention
+* Follow the [developer work-flow](https://fates-users-guide.readthedocs.io/en/latest/developer/FATES-Development-Workflow.html) 
+* Each set of changes should have its own [feature branch](https://fates-users-guide.readthedocs.io/en/latest/developer/Feature-Branch-Naming-Convention.html) that encapsulates your desired changes.
 * The work-flow will lead you eventually to submit a Pull-Request to NGEET/fates:master, please follow the template in the Pull Request and communicate as best you can if you are unsure how to fill out the text
 * It is best to create an issue to describe the work you are undertaking prior to starting.  This helps the community sync with your efforts, prevents duplication of efforts, and science is not done in a vaccuum!
 * Expect peers to interact, help, discuss and eventually approve your submission (pull-request)
@@ -31,11 +31,11 @@ In addition to the github discussions, we hold a roughly biweekly call, which co
 * Changes that are submitted should be limited to 1 single feature (i.e. don't submit changes to the radiation code and the nutrient cycle simultaneous, pick one thing)
 * Check for unnecessary whitespace with `git diff --check` before committing
 * We have no standard protocol for commit messages, but try to make them meaningful, concise and succinct.
-* You will most likely have to test (see workflow above), see: https://github.com/NGEET/fates/wiki/Testing-Protocols
+* You will most likely have to test (see workflow above), see the [testing protocols](https://fates-users-guide.readthedocs.io/en/latest/developer/Testing-Protocols.html) for more details.
 
 ## Coding Practices and Style
 
-Please refer to the FATES style guide: https://github.com/NGEET/fates/wiki/Coding-Practices-and-Style-Guide
+Please refer to the FATES [style guide](https://fates-users-guide.readthedocs.io/en/latest/developer/style.html)
 
 ## Trivial Changes
 

README.md

@@ -18,7 +18,7 @@ To receive email updates about forthcoming release tags, regular meeting notific
 
 [How to Contribute](https://github.com/NGEET/fates/blob/master/CONTRIBUTING.md)
 
-[Table of FATES and Host Land Model API compatability](https://fates-users-guide.readthedocs.io/en/latest/user/Table-of-FATES-API-and-HLM-STATUS.html)
+[Table of FATES and Host Land Model API compatability](https://fates-users-guide.readthedocs.io/en/latest/user/release-tags-compat-table.html)
 
 [List of Unsupported or Broken Features](https://fates-users-guide.readthedocs.io/en/latest/user/Current-Unsupported-or-Broken-Features.html)
 
@@ -35,4 +35,4 @@ https://github.com/E3SM-Project/E3SM
 
 https://github.com/ESCOMP/cesm
 
-The FATES, E3SM and CTSM teams maintain compatability of the NGEET/FATES master branch with the E3SM master and CTSM master branches respectively. There may be some modest lag time in which the latest commit on the FATES master branch is available to these host land models (HLM) by default.  This is typically correlated with FATES development updates forcing necessary changes to the FATES API.  See the table of [FATES API/HLM compatibility](https://fates-users-guide.readthedocs.io/en/latest/user/Table-of-FATES-API-and-HLM-STATUS.html) for information on which fates tag corresponds to which HLM tag or commit.  
+The FATES, E3SM and CTSM teams maintain compatability of the NGEET/FATES master branch with the E3SM master and CTSM master branches respectively. There may be some modest lag time in which the latest commit on the FATES master branch is available to these host land models (HLM) by default.  This is typically correlated with FATES development updates forcing necessary changes to the FATES API.  See the table of [FATES API/HLM compatibility](https://fates-users-guide.readthedocs.io/en/latest/user/release-tags-compat-table.html) for information on which fates tag corresponds to which HLM tag or commit.