Merge tag 'ctsm5.3.009' into hist_all-ssr

Reduce outputs from matrixcnOn tests

.config_files.xml

@@ -19,11 +19,8 @@
     <values>
       <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>

.git-blame-ignore-revs

@@ -1,9 +1,54 @@
 # Ran python directory through black python formatter
+b429b63824e09f82e95d2982f14311cbbd8e4a37
+d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911
+d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 0aa2957c1f8603c63fa30b11295c06cfddff44a5
 2cdb380febb274478e84cd90945aee93f29fa2e6
 e44dc469439e02e9ee582dab274d890ebdfab104
 565e7bcacbb0bba20ff80d680d8ad769676641c6
 b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 51c102c5df2e0ef971b5f8eeeb477567899af63a
 7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7
+b771971e3299c4fa56534b93421f7a2b9c7282fd
+9de88bb57ea9855da408cbec1dc8acb9079eda47
+8bc4688e52ea23ef688e283698f70a44388373eb
+c8bd4c6f98c0b411391b4355da449507db3aab4e
+4ee49e3e516ca7dee5df378f65664f93a7db4415
+0207bc98dd5c75cd69a0e788bc53e41093712f5c
+e4d38681df23ccca0ae29581a45f8362574e0630
+0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
+810cb346f05ac1aabfff931ab1a2b7b584add241
+5933b0018f8e29413e30dda9b906370d147bad45
+025d5e7c2e80263717fb029101d65cbbf261c3c4
+a9d96219902cf609636886c7073a84407f450d9a
+d866510188d26d51bcd6d37239283db690af7e82
+0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
+e096358c832ab292ddfd22dd5878826c7c788968
+475831f0fb0e31e97f630eac4e078c886558b61c
+fd5f177131d63d39e79a13918390bdfb642d781e
+# Ran SystemTests and python/ctsm through black python formatter
+5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
+8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+0bc3f00115d86d026a977918661c93779b3b19f9
+540b256d1f3382f4619d7b0877c32d54ce5c40b6
+8a168bb0895f4f2421608dd2589398e13a6663e6
+183fc26a6691bbdf87f515dc47924a64be3ced9b
+6fccf682eaf718615407d9bacdd3903b8786a03d
+2500534eb0a83cc3aff94b30fb62e915054030bf
+78d05967c2b027dc9776a884716597db6ef7f57c
+47839a77229c61555e3b8932927bb54cdc511b27
+a0d014fae9550dd9ffbc934abd29ef16176f8208
+c7b7ca1d94ac19abb9ecea9fb5b712ddbdd6645d
+b565b55ce7a9f8d812a573d716a5fd3d78cfea81
+fdf72cd011e2ba318987a1e100efc5a1847c9d04
+de9a30bfbbec36f9dcacc4380005ab596da47af4
+cda0cf1412212e6f4363e6e8eb39f74c944b454d
+aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
+6c6f57e948bfa31e60b383536cc21663fedb8b70
+9660667b1267dcd4150889f5f39db540158be74a
+665cf86102e09b4c4c5a140700676dca23bc55a9
+1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
+045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
+753fda3ff0147837231a73c9c728dd9ce47b5997
+f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,11 +10,13 @@ Are answers expected to change (and if so in what way)?
 
 Any User Interface Changes (namelist or namelist defaults changes)?
 
+Does this create a need to change or add documentation? Did you do so?
+
 Testing performed, if any:
 (List what testing you did to show your changes worked as expected)
 (This can be manual testing or running of the different test suites)
 (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)
+(aux_clm on derecho for intel/gnu and izumi for intel/gnu/nag/nvhpc 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) and review

.github/workflows/black.yml

@@ -16,6 +16,22 @@ jobs:
              # 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"
+             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

@@ -1,18 +1,3 @@
-# directories checked out by manage_externals, and other files created
-# by manage_externals
-manage_externals.log
-ccs_config
-/src/fates/
-/cime/
-/components/
-/libraries/
-/share/
-/doc/doc-builder/
-
-# ignore svn directories
-**/.svn/**
-.svn/
-
 # netcdf files
 *.nc
 # but don't ignore netcdf files here:
@@ -75,42 +60,38 @@ buildnmlc
 td.*.status
 td.*.log
 td.*.status.xFail
-test_driver_*.sh
 
 # mksurfdata output
 surfdata_*.log
-surfdata_*.namelist
-landuse.timeseries_*.namelist
+*.namelist
+mksurfdata.o*
 landuse.timeseries_*.log
 landuse_timeseries_*.txt
 ctsm.input_data_list
 ctsm.input_data_list.previous
 *.stdout.txt.o*
+/tools/mksurfdata_esmf/PET*
+/tools/mksurfdata_esmf/job_name.o*
+/tools/mksurfdata_esmf/mksurfdata_in
+/tools/mksurfdata_esmf/surfdata_*.nc
+/tools/mksurfdata_esmf/landuse.timeseries_*.nc
+/tools/mksurfdata_esmf/mksurfdata_jobscript_multi.sh
+/tools/mksurfdata_esmf/mksurfdata_jobscript_single.sh
+/tools/mksurfdata_esmf/pio_iotype.txt
+/tools/mksurfdata_esmf/*.sh
+/tools/mksurfdata_esmf/tool_bld
+/tools/mksurfdata_esmf/pio_iotype.txt
 
 # mksurfdata unit tests
 unit_test_build
 
-# Tools executables
-/tools/mksurfdata_map/mksurfdata_map
-/tools/mkprocdata_map/mkprocdata_map
-
-# mksurfdata output files
-/tools/mksurfdata_map/surfdata_*.nc
-/tools/mksurfdata_map/landuse.timeseries_*.nc
-
-# mkmapdata output files
-/tools/mkmapdata/PET*.RegridWeightGen.Log
-/tools/mkmapdata/regrid.*.out
-/tools/mkmapdata/regrid.*.err
-/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/
+/tools/site_and_regional/archive/
 
 # build output
 *.o

.gitmodules

@@ -0,0 +1,130 @@
+# This is a git submodule file with additional support for
+# git-fleximod (https://github.com/ESMCI/git-fleximod)
+#
+# The additional flags supported by git-fleximod are
+# fxtag - the tag associated with the submodule, this tag can be tested for
+#         consistancy with the submodule hash using git-fleximod status
+#         the hash can be updated to the tag using git-fleximod update
+#
+# fxrequired - indicates if a given submodule should be checked out on install
+#              submoudules can be toplevel or internal and required or optional
+#              toplevel means that the submodule should only be checked out if the
+#              module is the toplevel of the git repo (is not a submodule itself)
+#              internal means that the submodule is needed by the component whether
+#              the component is toplevel or the submodule of another repo
+#              required means that the submodule should always be checked out
+#              optional means that the submodule should only be checked out if the
+#              optional flag is provided to git-fleximod or the submodule name is
+#              explicitly listed on the git-fleximod command line.
+#
+# fxsparse -   this is a path to a git sparse checkout file indicating that the
+#              submodule should be checked out in sparse mode
+#
+# fxDONOTUSEurl    -   this field is used by git-fleximod test to insure that the url is pointing
+#              to the official url of the repo and not to an unofficial fork.
+#              It is intended for use of github workflows to test commits to protected
+#              repository branches.
+#
+[submodule "fates"]
+path = src/fates
+url = https://github.com/NGEET/fates
+fxtag = sci.1.78.3_api.36.1.0
+fxrequired = AlwaysRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/NCAR/fates-release
+
+[submodule "cism"]
+path = components/cism
+url = https://github.com/ESCOMP/CISM-wrapper
+fxtag = cismwrap_2_2_002
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+
+[submodule "rtm"]
+path = components/rtm
+url = https://github.com/ESCOMP/RTM
+fxtag = rtm1_0_80
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/RTM
+
+[submodule "mosart"]
+path = components/mosart
+url = https://github.com/ESCOMP/MOSART
+fxtag = mosart1.1.02
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
+
+[submodule "mizuRoute"]
+path = components/mizuRoute
+url = https://github.com/ESCOMP/mizuRoute
+fxtag = cesm-coupling.n02_v2.1.2
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
+
+[submodule "ccs_config"]
+path = ccs_config
+url = https://github.com/ESMCI/ccs_config_cesm.git
+fxtag = ccs_config_cesm1.0.0
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
+
+[submodule "cime"]
+path = cime
+url = https://github.com/ESMCI/cime
+fxtag = cime6.0.246
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESMCI/cime
+
+[submodule "cmeps"]
+path = components/cmeps
+url = https://github.com/ESCOMP/CMEPS.git
+fxtag = cmeps0.14.77
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
+
+[submodule "cdeps"]
+path = components/cdeps
+url = https://github.com/ESCOMP/CDEPS.git
+fxtag = cdeps1.0.48
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+
+[submodule "share"]
+path = share
+url = https://github.com/ESCOMP/CESM_share
+fxtag = share1.0.19
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
+
+[submodule "mct"]
+path = libraries/mct
+url = https://github.com/MCSclimate/MCT
+fxtag = MCT_2.11.0
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/MCSclimate/MCT
+
+[submodule "parallelio"]
+path = libraries/parallelio
+url = https://github.com/NCAR/ParallelIO
+fxtag = pio2_6_2
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+
+[submodule "doc-builder"]
+path = doc/doc-builder
+url = https://github.com/ESMCI/doc-builder
+fxtag = v1.0.8
+fxrequired = ToplevelOptional
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESMCI/doc-builder

.lib/git-fleximod/.github/workflows/pre-commit

@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/[email protected]