merging changes

negin513 · May 8, 2024 · 5b596a9 · 5b596a9
2 parents 36344de + 9a28e2a
commit 5b596a9
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diff --git a/.config_files.xml b/.config_files.xml
@@ -5,31 +5,31 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for CTSM:
-       In a standalone CTSM 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 CTSM.
+       the value for CLM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"       >$SRCROOT</value>
-      <value component="ctsm"      >$SRCROOT</value>
-      <value component="dlnd" comp_interface="mct">$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
-      <value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
-      <value component="slnd"  comp_interface="mct"     >$SRCROOT/components/cpl7/components/stub_comps_mct/slnd</value>
-      <value component="xlnd" comp_interface="mct"      >$SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd</value>
-      <value component="slnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/stub_comps_nuopc/slnd</value>
-      <value component="xlnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/xcpl_comps_nuopc/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>
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,48 @@
+# 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
+# Ran SystemTests and python/ctsm through black python formatter
+5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
+8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+0bc3f00115d86d026a977918661c93779b3b19f9
+540b256d1f3382f4619d7b0877c32d54ce5c40b6
+8a168bb0895f4f2421608dd2589398e13a6663e6
+183fc26a6691bbdf87f515dc47924a64be3ced9b
+6fccf682eaf718615407d9bacdd3903b8786a03d
+2500534eb0a83cc3aff94b30fb62e915054030bf
+78d05967c2b027dc9776a884716597db6ef7f57c
+a0d014fae9550dd9ffbc934abd29ef16176f8208
+c7b7ca1d94ac19abb9ecea9fb5b712ddbdd6645d
+b565b55ce7a9f8d812a573d716a5fd3d78cfea81
+fdf72cd011e2ba318987a1e100efc5a1847c9d04
+de9a30bfbbec36f9dcacc4380005ab596da47af4
+cda0cf1412212e6f4363e6e8eb39f74c944b454d
+aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
+6c6f57e948bfa31e60b383536cc21663fedb8b70
+9660667b1267dcd4150889f5f39db540158be74a
+665cf86102e09b4c4c5a140700676dca23bc55a9
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -10,6 +10,8 @@ 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)

diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml
@@ -0,0 +1,23 @@
+name: Auto Assign to Project(s)
+
+on:
+  issues:
+    types: [opened, labeled]
+  pull_request:
+    types: [opened, labeled]
+  issue_comment:
+    types: [created]
+
+jobs:
+  assign_high_priority:
+    runs-on: ubuntu-latest
+    name: Assign to High Priority project
+    steps:
+    - name: Assign issues and pull requests with priority-high label to project 25
+      uses: srggrs/[email protected]
+      if: |
+        contains(github.event.issue.labels.*.name, 'priority: high') ||
+        contains(github.event.pull_request.labels.*.name, 'priority: high')
+      with:
+        project: 'https://github.com/ESCOMP/CTSM/projects/25'
+        column_name: 'Needs triage'
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -1,2 +1,37 @@
-- name: Black Code Formatter
-  uses: lgeiger/[email protected]
+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"
diff --git a/.gitignore b/.gitignore
@@ -79,31 +79,38 @@ 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

diff --git a/Externals.cfg b/Externals.cfg
@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_95
+tag = cismwrap_2_1_99
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_78
+tag = rtm1_0_79
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_45
+tag = mosart1_0_49
 required = True
 
 [mizuRoute]
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.36
+tag = ccs_config_cesm0.0.92
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,33 +44,33 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.27
+tag = cime6.0.217_httpsbranch03
 required = True
 
 [cmeps]
-tag = cmeps0.13.63
+tag = cmeps0.14.50
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.41
+tag = cdeps1.0.28
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl7.0.12
+tag = cpl77.0.7
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.11
+tag = share1.0.18
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -84,7 +84,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_7
+tag = pio2_6_2
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.56.0_api.23.0.0
+tag = sci.1.73.0_api.35.0.0
 required = True
 
 [externals_description]