Merge branch 'master' into btran

Author: adrifoster

.git-blame-ignore-revs

@@ -1,4 +1,4 @@
-# Ran python directory through black python formatter
+# Reformat with black
 d89c86e7776bbf7451860b60038b4725fe7a0560
 b429b63824e09f82e95d2982f14311cbbd8e4a37
 d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
@@ -29,7 +29,6 @@ e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
 fd5f177131d63d39e79a13918390bdfb642d781e
 a51816e0de380300b69db9fc3e2c7fa83b267b64
-# Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
 0bc3f00115d86d026a977918661c93779b3b19f9
@@ -59,3 +58,9 @@ bd535c710db78420b8e8b9d71d88d8339e899c59
 cf433215b58ba8776ec5edfb0b0d80c0836ed3a0
 16d57ff37859b34dab005693e3085d64e2bcd95a
 e8fc526e0d7818d45f171488c78392c4ff63902a
+30d2682a0893f5620bfe37ca6e2614fa60c99f51
+890b4633c5477dc074f79c69c40d650196337591
+1972cef6bba0d97169b30a53f540d56bcbd97281
+cdf40d265cc82775607a1bf25f5f527bacc97405
+251e389b361ba673b508e07d04ddcc06b2681989
+8ec50135eca1b99c8b903ecdaa1bd436644688bd

.github/workflows/black.yml

@@ -0,0 +1,31 @@
+name: git-fleximod test
+#
+# Test git-fleximod update and cleanliness
+# Based closely on workflow from CESM repo
+#
+on: [push, pull_request]
+
+jobs:
+  fleximod-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # oldest supported and latest supported
+        python-version: ["3.7", "3.x"]
+    steps:
+      - id: checkout-CTSM
+        uses: actions/checkout@v4
+      - id: run-fleximod
+        run: |
+          $GITHUB_WORKSPACE/bin/git-fleximod update
+          echo
+          echo "Update complete, checking status"
+          echo
+          $GITHUB_WORKSPACE/bin/git-fleximod test
+      - id: check-cleanliness
+        run: |
+          echo
+          echo "Checking if git fleximod matches expected externals"
+          echo
+          git diff --exit-code

.github/workflows/fleximod_test.yaml

@@ -0,0 +1,44 @@
+name: Check Python formatting
+
+on:
+  push:
+    paths:
+      - 'python/**'
+      - 'cime_config/SystemTests/**'
+      - 'cime_config/buildlib/**'
+      - 'cime_config/buildnml/**'
+  pull_request:
+    paths:
+      - 'python/**'
+      - 'cime_config/SystemTests/**'
+      - 'cime_config/buildlib/**'
+      - 'cime_config/buildnml/**'
+
+jobs:
+  lint-and-format-check:
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the code
+      - uses: actions/checkout@v4
+
+      # Set up the conda environment
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ctsm_pylib
+          environment-file: python/conda_env_ctsm_py.yml
+          channels: conda-forge
+          auto-activate-base: false
+
+      # Run pylint check
+      - name: Run pylint
+        run: |
+          cd python
+          conda run -n ctsm_pylib make lint
+
+      # Run black check
+      - name: Run black
+        # Run this step even if previous step(s) failed
+        if: success() || failure()
+        run: |
+          cd python
+          conda run -n ctsm_pylib make black

.github/workflows/formatting_python.yml

@@ -75,12 +75,11 @@ ctsm.input_data_list.previous
 /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
+/tools/mksurfdata_esmf/mpibind*.log
 
 # mksurfdata unit tests
 unit_test_build

.gitignore

@@ -28,10 +28,10 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.81.1_api.38.0.0
+fxtag = sci.1.82.3_api.39.0.0
 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
+fxDONOTUSEurl = https://github.com/NGEET/fates
 
 [submodule "cism"]
 path = components/cism
@@ -92,15 +92,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.61
+fxtag = cdeps1.0.70
 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 = share1.1.7
+fxtag = share1.1.8
 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

.gitmodules

@@ -2,7 +2,7 @@ $CTSMROOT/README                                          09/05/2024
 
 Community Terrestrial Systems Model (CTSM) science version 5.3 series -- source code, tools, 
 offline-build and test scripts. This gives you everything you need
-to run CTSM with CESM with the CMEPS driver and CDEPS data models to provide CRU NCEP or GSWP3 forcing data in 
+to run CTSM with CESM with the CMEPS driver and CDEPS data models to provide CRUJRA or GSWP3 forcing data (some older options also available) in
 place of a modeled atmosphere.
 
 CMEPS is the Community Mediator for Earth Prediction Systems. And CDEPS is the

README

@@ -37,7 +37,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <lnd_tuning_mode phys="clm4_5" >clm4_5_CRUv7</lnd_tuning_mode>
 <lnd_tuning_mode phys="clm5_0" >clm5_0_cam6.0</lnd_tuning_mode>
-<lnd_tuning_mode phys="clm6_0" >clm6_0_GSWP3v1</lnd_tuning_mode>
+<lnd_tuning_mode phys="clm6_0" >clm6_0_CRUJRA2024</lnd_tuning_mode>
 
 <!-- Component name for output files (could depdend on the physics version) -->
 <compname >clm2</compname>
@@ -524,9 +524,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params_nfix.c241119.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params_nfix.c241119.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params_nfix.c241119.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c250311.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c250311.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c250311.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -848,8 +848,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </init_interp_attributes>
 
 <!-- 1850 for CLM6.0 -->
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm6_0_GSWP3v1"
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. phys=clm6_0 use_excess_ice=.true.
+</init_interp_attributes>
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
->hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_GSWP3v1 use_excess_ice=.true.
+>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nex=10 do_transient_pfts=.false. lnd_tuning_mode=clm6_0_CRUJRA2024 use_excess_ice=.true.
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false." phys="clm6_0"
@@ -1267,7 +1270,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >lnd/clm2/initdata_map/clmi.I1850Clm50SpCru.1706-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc
 </finidat>
 
-<!-- CTSM6_0 - use clm6_0_GSWP3v1 BgcCrop at f09 for all clm6_0 options -->
+<!-- CTSM6_0 - use clm6_0_CRUJRA2024 BgcCrop at f09 for all clm6_0 options -->
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." use_excess_ice=".true."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
@@ -2363,6 +2366,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_GSWP3v1"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
+<stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm6_0_CRUJRA2024"
+>lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
 
 <stream_meshfile_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd"
 >lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c230730.nc</stream_meshfile_zendersoilerod>