Merge pull request #2982 from samsrabin/ctsm_pylib_3.13.2

ctsm5.3.040: Update ctsm_pylib to 3.13.2

Author: samsrabin

.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
@@ -59,4 +58,7 @@ bd535c710db78420b8e8b9d71d88d8339e899c59
 cf433215b58ba8776ec5edfb0b0d80c0836ed3a0
 16d57ff37859b34dab005693e3085d64e2bcd95a
 e8fc526e0d7818d45f171488c78392c4ff63902a
+30d2682a0893f5620bfe37ca6e2614fa60c99f51
+890b4633c5477dc074f79c69c40d650196337591
+1972cef6bba0d97169b30a53f540d56bcbd97281
 cdf40d265cc82775607a1bf25f5f527bacc97405

.github/workflows/black.yml

@@ -18,20 +18,20 @@ jobs:
              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"
+             version: "25.1.0"
           # 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"
+             version: "25.1.0"
         - uses: psf/black@stable
           with:
              options: "--check --config python/pyproject.toml"
              src: "./cime_config/buildlib"
-             version: "22.3.0"
+             version: "25.1.0"
         - uses: psf/black@stable
           with:
              options: "--check --config python/pyproject.toml"
              src: "./cime_config/buildnml"
-             version: "22.3.0"
+             version: "25.1.0"

cime_config/SystemTests/mksurfdataesmf.py

@@ -10,6 +10,7 @@
 I added -C to the `git describe` in gen_mksurfdata_namelist for this
 system test to work.
 """
+
 import os
 import sys
 import subprocess

cime_config/SystemTests/pvt.py

@@ -9,6 +9,7 @@
 2) run a transient landuse case with use_fates_lupft
     - start from the restart file generated in (1)
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files

cime_config/SystemTests/ssp.py

@@ -12,6 +12,7 @@
     - start from the restart files generated in (1)
     - turn MOSART off
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 import shutil, glob, os

cime_config/SystemTests/sspmatrixcn.py

@@ -12,6 +12,7 @@
 Step 3: Run a slow-mode spinup
 Step 4: matrix Spinup off
 """
+
 import shutil, glob, os, sys
 from datetime import datetime
 

cime_config/buildlib

@@ -20,6 +20,7 @@ from CIME.utils import run_cmd, expect
 
 logger = logging.getLogger(__name__)
 
+
 ###############################################################################
 def _write_ctsm_mk(gmake, gmake_opts, makefile, exeroot, libroot):
     """Writes a ctsm.mk file in exeroot.

cime_config/testdefs/testlist_clm.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
      CTSM test list. Test suites included:
-        ctsm_pymods: System tests for the python codes that also run CTSM cases (subset of aux_clm tests)
+        clm_pymods: System tests for the python code that also run CTSM cases (subset of aux_clm tests)
         clm_short: The short CLM test for basic testing of a few configurations
         aux_clm: Main workhorse test list to be run on main machines before most tags are made
         fates: The FATES testlist, run when FATES is updated

doc/ChangeLog

@@ -1,4 +1,78 @@
 ===============================================================
+Tag name: ctsm5.3.040
+Originator(s): samrabin (Sam Rabin, UCAR/TSS)
+Date: Tue 15 Apr 2025 10:15:39 AM MDT
+One-line Summary: Update ctsm_pylib to 3.13.2
+
+Purpose and description of changes
+----------------------------------
+
+This tag updates the ctsm_pylib conda environment, installed with py_env_create, to use Python 3.13.2 instead of 3.7.9. There are also some improvements to how py_env_create works.
+
+
+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.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description):
+- Resolves ESCOMP/CTSM#2625 (Move ctsm_pylib to something beyond 3.7)
+- Resolves ESCOMP/CTSM#2771 (Add User's Guide section about ctsm_pylib)
+
+Notes of particular relevance for users
+---------------------------------------
+
+The new ctsm_pylib conda environment will be incompatible with the CTSM Python tools from before this tag (ctsm5.3.040) and vice versa. If you already have a copy of the ctsm_pylib conda environment installed, we thus suggest keeping that around under a different name. Here is the suggested command for doing this:
+    ./py_env_create -r ctsm_pylib_old
+This will (1) rename your existing ctsm_pylib to ctsm_pylib_old and (2) install the Python 3.13.2 version as ctsm_pylib.
+
+Information about additional py_env_create options---including how to install a fresh copy of the old conda environment---can be found like so:
+  ./py_env_create --help
+
+Changes to documentation:
+- User's Guide: Adds "Installing the CTSM Python environment" page
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- New Python system test module: test_sys_py_env_create.py
+- That module will install a bunch of empty conda envs with the prefix pec_test. It should clean those up on exit, but if not, you can safely delete them afterward.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  python testing:
+
+    derecho - PASS
+
+    clm_pymods test suite on derecho - PASS
+
+Other details
+-------------
+
+Pull Requests that document the changes:
+- [CTSM PR #2982: Update ctsm_pylib to 3.13.2](https://github.com/ESCOMP/CTSM/pull/2982)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.039
 Originator(s): afoster (Adrianna Foster,UCAR/TSS,303-497-1728)
 Date: Mon 14 Apr 2025 07:22:22 PM MDT

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.040 samrabin 04/15/2025 Update ctsm_pylib to 3.13.2
        ctsm5.3.039  afoster 04/14/2025 Create driver data structure for SP mode
        ctsm5.3.038 samrabin 04/10/2025 Merge b4b-dev
        ctsm5.3.037     erik 04/02/2025 Add calculations for GSSUN and GSSHA at night in both subroutine Photosynthesis and PhotosynthesisHydraulicStress