Merge tag 'ctsm5.1.dev142' into hist-anomalies

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)

.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>

.git-blame-ignore-revs

@@ -1,5 +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

.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"
-             # Version should be coordinated with the ctsm_py conda environment under the python directory
+             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

@@ -105,6 +105,13 @@ unit_test_build
 /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

Externals.cfg

@@ -23,7 +23,7 @@ required = True
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_45
+tag = mosart1_0_48
 required = True
 
 [mizuRoute]
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.38
+tag = ccs_config_cesm0.0.65
 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 = cime6.0.40
+tag = cime6.0.125
 required = True
 
 [cmeps]
-tag = cmeps0.13.68
+tag = cmeps0.14.21
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.41
+tag = cdeps1.0.13
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl7.0.13
+tag = cpl77.0.5
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.12
+tag = share1.0.17
 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_5_10
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.58.1_api.24.1.0
+tag = sci.1.67.2_api.27.0.0
 required = True
 
 [externals_description]

README.md

@@ -43,15 +43,19 @@ CTSM code management is provided primarily by:
 Software engineering team:
 - [Erik Kluzek](https://github.com/ekluzek)
 - [Bill Sacks](https://github.com/billsacks)
-- [Mariana Vertenstein](https://github.com/mvertens)
-- [Negin Sobhani](https://github.com/negin513)
 - [Sam Levis](https://github.com/slevisconsulting)
+- [Adrianna Foster](https://github.com/adrifoster)
+- [Sam Rabin](https://github.com/samsrabin)
+- [Greg Lemieux](https://github.com/glemieux)
+- [Ryan Knox](https://github.com/rgknox)
 
 Science team:
 - [Dave Lawrence](https://github.com/dlawrenncar)
 - [Will Wieder](https://github.com/wwieder)
 - [Danica Lombardozzi](https://github.com/danicalombardozzi)
 - [Keith Oleson](https://github.com/olyson)
 - [Sean Swenson](https://github.com/swensosc)
-- [Mike Barlage](https://github.com/barlage)
+- [Jackie Shuman](https://github.com/jkshuman)
+- [Peter Lawrence](https://github.com/lawrencepj1)
 - [Rosie Fisher](https://github.com/rosiealice)
+- Gordon Bonan