Merge tag 'ctsm5.1.dev142' into tillage-mike-merge142

b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)

# Conflicts:
#	src/biogeochem/CNBalanceCheckMod.F90
#	src/biogeochem/CNCIsoFluxMod.F90
#	src/biogeochem/CNDriverMod.F90
#	src/biogeochem/CNPhenologyMod.F90
#	src/biogeochem/CNProductsMod.F90
#	src/biogeochem/CNVegCarbonFluxType.F90
#	src/biogeochem/CNVegNitrogenFluxType.F90
#	src/biogeochem/EDBGCDynMod.F90
#	src/main/clm_initializeMod.F90
#	src/main/controlMod.F90
#	src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

.config_files.xml

@@ -5,27 +5,31 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for clm:
-       In a standalone clm checkout, COMP_ROOT_DIR_LND is $SRCROOT
+       cime/config/cesm/config_files.xml except for the value for CLM:
+       In a standalone CLM checkout, COMP_ROOT_DIR_LND is $SRCROOT
        rather than $SRCROOT/components/clm.
 
        However, because of the way overrides are handled, we need to
        re-specify the full information here rather than just overriding
-       the value for clm.
+       the value for CLM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"      >$SRCROOT</value>
-      <value component="dlnd"      >$CIMEROOT/src/components/data_comps/dlnd</value>
-      <value component="slnd"      >$CIMEROOT/src/components/stub_comps/slnd</value>
-      <value component="xlnd"      >$CIMEROOT/src/components/xcpl_comps/xlnd</value>
+      <value component="clm"                         >$SRCROOT</value>
+      <value component="slim"                        >$SRCROOT/components/slim/</value>
+      <value component="dlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc" >$SRCROOT/components/cdeps/dlnd</value>
+      <value component="slnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="slnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="xlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
+      <value component="xlnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>
     <desc>Root directory of the case land model component  </desc>
-    <schema>$CIMEROOT/config/xml_schemas/config_compsets.xsd</schema>
+    <schema>$CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd</schema>
   </entry>
 
 </entry_id>

.git-blame-ignore-revs

@@ -0,0 +1,21 @@
+# Ran python directory through black python formatter
+d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
+4cd83cb3ee6d85eb909403487abf5eeaf4d98911
+0aa2957c1f8603c63fa30b11295c06cfddff44a5
+2cdb380febb274478e84cd90945aee93f29fa2e6
+e44dc469439e02e9ee582dab274d890ebdfab104
+565e7bcacbb0bba20ff80d680d8ad769676641c6
+b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
+51c102c5df2e0ef971b5f8eeeb477567899af63a
+7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7
+b771971e3299c4fa56534b93421f7a2b9c7282fd
+9de88bb57ea9855da408cbec1dc8acb9079eda47
+8bc4688e52ea23ef688e283698f70a44388373eb
+0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
+810cb346f05ac1aabfff931ab1a2b7b584add241
+5933b0018f8e29413e30dda9b906370d147bad45
+# Ran SystemTests and python/ctsm through black python formatter
+5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
+8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+540b256d1f3382f4619d7b0877c32d54ce5c40b6
+8a168bb0895f4f2421608dd2589398e13a6663e6

.gitattributes

@@ -0,0 +1,7 @@
+*.svg filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+*.nc filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: CESM forums
+    url: https://bb.cgd.ucar.edu/cesm/forums/ctsm-clm-mosart-rtm.134/
+    about: For support with model use, troubleshooting, etc., please use the CTSM forum

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,5 +16,7 @@ Testing performed, if any:
 (Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
 (aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master)
 
-**NOTE: Be sure to check your Coding style against the standard:**
-https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines
+**NOTE: Be sure to check your coding style against the standard
+(https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review
+the list of common problems to watch out for
+(https://github.com/ESCOMP/CTSM/wiki/List-of-common-problems).**

.github/workflows/black.yml

@@ -0,0 +1,37 @@
+name: black check on push and PR
+#
+# Run the python formatting in check mode
+#
+on: [push, pull_request]
+
+jobs:
+  black-check:
+     runs-on: ubuntu-latest
+     steps:
+        # Checkout the code
+        - uses: actions/checkout@v2
+        # Use the latest stable version of the github action
+        - uses: psf/black@stable
+          with:
+             # Use options and version identical to the conda environment
+             # Using pyproject.toml makes sure this testing is consistent with our python directory testing
+             options: "--check --config python/pyproject.toml"
+             src: "./python"
+             # Version should be coordinated with the ctsm_pylib conda environment under the python directory
+             version: "22.3.0"
+          # Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field)
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/SystemTests"
+             version: "22.3.0"
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/buildlib"
+             version: "22.3.0"
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/buildnml"
+             version: "22.3.0"

.gitignore

@@ -1,21 +1,44 @@
 # directories checked out by manage_externals, and other files created
 # by manage_externals
 manage_externals.log
+ccs_config
 /src/fates/
-/tools/PTCLM/
 /cime/
 /components/
+/libraries/
+/share/
+/doc/doc-builder/
 
 # ignore svn directories
 **/.svn/**
 .svn/
 
-# binary files
+# netcdf files
 *.nc
+# but don't ignore netcdf files here:
+!/python/ctsm/test/testinputs/*.nc
 
 # editor files
 *.swp
 *~
+.vscode/
+
+# vim files (from https://github.com/github/gitignore/blob/master/Global/Vim.gitignore)
+# Swap
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+# Session
+Session.vim
+# Temporary
+.netrwhist
+# (removed *~ because it is listed above)
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
 
 # mac files
 .DS_Store
@@ -30,16 +53,6 @@ CMakeFiles/
 # unit testing directories
 /src/unit_tests.*
 
-# files generated by the unit test build
-/src/dyn_subgrid/dynVarMod.F90
-/src/dyn_subgrid/dynVarTimeInterpMod.F90
-/src/dyn_subgrid/dynVarTimeUninterpMod.F90
-/src/utils/array_utils.F90
-/src/unit_test_stubs/utils/restUtilMod_stub.F90
-/src/unit_test_stubs/main/ncdio_pio_fake.F90
-/src/unit_test_stubs/main/ncdio_var.F90
-/src/unit_test_shr/unittestArrayMod.F90
-
 # cime_config
 buildnmlc
 
@@ -55,6 +68,7 @@ buildnmlc
 /bld/unit_testers/drv_flds_in*
 /bld/unit_testers/temp_file.txt*
 /bld/unit_testers/user_nl_clm_real_parameters*
+/bld/unit_testers/user_nl_ctsm_real_parameters*
 /bld/unit_testers/env_run.xml
 
 # tools testing output
@@ -69,10 +83,13 @@ surfdata_*.namelist
 landuse.timeseries_*.namelist
 landuse.timeseries_*.log
 landuse_timeseries_*.txt
-clm.input_data_list
-clm.input_data_list.previous
+ctsm.input_data_list
+ctsm.input_data_list.previous
 *.stdout.txt.o*
 
+# mksurfdata unit tests
+unit_test_build
+
 # Tools executables
 /tools/mksurfdata_map/mksurfdata_map
 /tools/mkprocdata_map/mkprocdata_map
@@ -88,6 +105,13 @@ clm.input_data_list.previous
 /tools/mkmapdata/regrid.o*
 /tools/mkmapdata/map*.nc
 
+# run_neon output directories
+/tools/site_and_regional/listing.csv
+/tools/site_and_regional/????/
+/tools/site_and_regional/????.ad/
+/tools/site_and_regional/????.postad/
+/tools/site_and_regional/????.transient/
+
 # build output
 *.o
 *.mod

.lfsconfig

@@ -0,0 +1,7 @@
+[lfs]
+	# We auto-fetch any netCDF files, because they are needed for
+	# running tests; however, we do NOT auto-fetch other binary
+	# files, in particular image files that are part of the
+	# documentation source (these are fetched as part of the
+	# documentation build process).
+	fetchinclude = *.nc

.zenodo.json

@@ -0,0 +1,7 @@
+{
+    "creators": [
+        {
+            "name": "CTSM Development Team"
+        }
+    ]
+}