Merge tag 'ctsm5.1.dev169' into masterdoc

Merge pull request ESCOMP#2382 from samsrabin/merge-b4bdev-20240222

Brings in 3 PRs from b4b-dev to master:
- Do not crash "make all" even if pylint isn't clean (ESCOMP#2353; Sam Rabin)
- Resolve pylint issues (ESCOMP#2354; Sam Rabin)
- Move FSURDATMODIFYCTSM test to Derecho (ESCOMP#2364; Sam Rabin)

.git-blame-ignore-revs

@@ -21,6 +21,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630
 025d5e7c2e80263717fb029101d65cbbf261c3c4
 a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
+0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

.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/assign-one-project-github-action@1.3.1
+      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'

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -484,9 +484,9 @@ 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="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240105.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240105.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240105.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240207b.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240207b.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240207b.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->

cime_config/testdefs/testlist_clm.xml

@@ -3308,8 +3308,8 @@
 
   <test name="FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1" grid="5x5_amazon" compset="I2000Clm50SpRs">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="intel" category="clm_pymods"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="clm_pymods"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3433,6 +3433,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm

@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240105.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240207b.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'

doc/ChangeLog

@@ -1,4 +1,290 @@
 ===============================================================
+Tag name: ctsm5.1.dev169
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Thu 22 Feb 2024 09:42:57 AM MST
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+Brings in 3 PRs from b4b-dev to master:
+- Do not crash "make all" even if pylint isn't clean (ESCOMP/CTSM#2353; Sam Rabin)
+- Resolve pylint issues (ESCOMP/CTSM#2354; Sam Rabin)
+- Move FSURDATMODIFYCTSM test to Derecho (ESCOMP/CTSM#2364; Sam Rabin)
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+CTSM issues fixed:
+- Fixes ESCOMP/CTSM#2255: make lint is not clean in ctsm5.1.dev152
+- Fixes ESCOMP/CTSM#2316: "make all" doesn't run black if lint fails
+- FIXES ESCOMP/CTSM#2362: FSURDATMODIFYCTSM test should be moved to Derecho or Izumi
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- FSURDATMODIFYCTSM test changed from derecho_intel (didn't work in debug mode) to derecho_gnu. I.e., from
+    FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.derecho_intel
+  to
+    FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.derecho_gnu
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  any other testing (give details below):
+  - "make all" in python/ is clean. 
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2353: Do not crash "make all" even if pylint isn't clean (https://github.com/ESCOMP/CTSM/pull/2353)
+- ESCOMP/CTSM#2354: Resolve pylint issues (https://github.com/ESCOMP/CTSM/pull/2354)
+- ESCOMP/CTSM#2364: Move FSURDATMODIFYCTSM test to Derecho (https://github.com/ESCOMP/CTSM/pull/2364)
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev168
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 16 Feb 2024 01:27:41 PM MST
+One-line Summary: Remove a source of negative snocan in CanopyFluxesMod
+
+Purpose and description of changes
+----------------------------------
+
+In ctsm5.2 testing, this test
+LWISO_Ld10.f10_f10_mg37.I2000Clm50BgcCrop.derecho_gnu.clm-coldStart
+complained of a tiny negative ice1_grc tracer not matching the bulk
+value. My troubleshooting led me to more than tiny negative snocan
+originating in a line of code that this PR now changes to prevent
+negative values.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+CTSM issues fixed (include CTSM Issue #):
+Fixes #2366
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ It was suggested at the ctsm software meeting yesterday that, in addition to
+ including "max(0._r8," in this line of code, that I reorder the code
+ by bringing "liqcan(p) =" before "snocan(p) =". I have decided against this
+ because the existing order repeats in a following paragraph of code right
+ after this one. It's likely that the group's suggestion would have worked, but
+ I did not want to delay this PR for a longer evaluation because CTSM5.2 is
+ waiting for this merge, in order to proceed with next steps.
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all
+    - what platforms/compilers: all
+    - nature of change: roundoff
+ A short test, e.g.
+ SMS_Ln9.ne30pg2_ne30pg2_mg17.I1850Clm50Sp.derecho_intel.clm-clm50cam6LndTuningMode
+ has these maximum differences:
+RMS H2OCAN 4.7359E-19            NORMALIZED  4.0163E-18
+RMS SNOCAN 4.4873E-19            NORMALIZED  9.1036E-18
+ while the differences grow in longer tests.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2371
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev167
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Thu 08 Feb 2024 01:56:05 PM MST
+One-line Summary: Delete _FillValue and history from parameter files
+
+Purpose and description of changes
+----------------------------------
+
+Updates parameter files to c240207b. These are the same as c240105 except:
+- Attribute _FillValue has been removed from all variables
+- Global attributes history, history_of_appended_files, and latest_git_log have been removed
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+CTSM issues fixed (include CTSM Issue #):
+- Fixes #2347
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- #2350: Delete _FillValue and history from parameter files (https://github.com/ESCOMP/CTSM/pull/2350)
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev166
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), tking (Teagan King), samrabin (Sam Rabin)
+Date: Wed 24 Jan 2024 05:39:41 PM MST
+One-line Summary: BFB merge tag
+
+Purpose and description of changes
+----------------------------------
+
+ #2315 @TeaganKing Refactoring run_neon for PLUMBER2 part1
+ #2213 @samsrabin Automatically assign high priority items to project 25
+ #2330 @samsrabin Add Izumi version of the aux_clm unit testing
+ #2326 @samsrabin run_sys_tests: Check Python environment for FatesColdTwoStream tests
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+CTSM issues fixed (include CTSM Issue #):
+ Fixes #2315
+ Fixes #2213
+ Fixes #2330
+ Fixes #2326
+
+Known bugs introduced in this tag (include issue #):
+ - New feature coming in with #2213 where user will receive email from
+ github when pushing to their remote:
+ "Run failed: .github/workflows/assign-to-project.yml"
+ - New feature that also affects older tags: The izumi FatesColdTwoStream
+ test submitted from ./run_sys_tests will fail at CREATE_NEWCASE unless users
+ introduce "module load lang/python/3.7.0" in their .bash_profile.
+ Longterm solution discussed in #2335. The test also works when submitted
+ manually with ./create_test.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ #2315 New unit tests for arg_parse and NeonSite
+ #2330 New test in aux_clm that does unit testing on izumi because unit
+       testing does not work on derecho, yet
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - OK, pylint gives long list of warnings (expected)
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+Changes answers relative to baseline: No
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2334
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev165
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), oleson (Keith Oleson), samrabin (Sam Rabin)
 Date: Fri 19 Jan 2024 06:40:36 PM MST

doc/ChangeSum

@@ -1,5 +1,9 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev169 samrabin 02/22/2024 Merge b4b-dev
+    ctsm5.1.dev168   slevis 02/16/2024 Remove a source of negative snocan in CanopyFluxesMod
+    ctsm5.1.dev167 samrabin 02/08/2024 Delete _FillValue and history from parameter files
+    ctsm5.1.dev166 multiple 01/24/2024 BFB merge tag
     ctsm5.1.dev165   slevis 01/19/2024 Turn Meier2022, tillage, residue removal on for ctsm5.1, fix #2212
     ctsm5.1.dev164   rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream
     ctsm5.1.dev163 samrabin 01/10/2024 Add tillage and residue removal

python/Makefile

@@ -19,15 +19,15 @@ ifneq ($(verbose), not-set)
 endif
 
 PYLINT=pylint
-PYLINT_ARGS=-j 4 --rcfile=ctsm/.pylintrc
+PYLINT_ARGS=-j 4 --rcfile=ctsm/.pylintrc --fail-under=0
 PYLINT_SRC = \
 	ctsm
 #  NOTE: These don't pass pylint checking and should be added when we put into effort to get them to pass
 #       ../cime_config/SystemTests \
 #       ../cime_config/buildlib \
 #       ../cime_config/buildnml
 
-all: test lint black
+all: test black lint
 	@echo
 	@echo
 	@echo "Successfully ran all standard tests"

python/ctsm/.pylintrc

@@ -436,7 +436,10 @@ good-names=i,
            _,
 # --- default list is above here, our own list is below here ---
 # Allow logger as a global name in each module, because this seems to follow general recommended convention:
-           logger
+           logger,
+# Allow these names, which are commonly used in matplotlib instructions
+           ax,
+           im
 
 # Include a hint for the correct naming format with invalid-name.
 include-naming-hint=no