ctsm5.3.040: Update ctsm_pylib to 3.13.2

.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
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@@ -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/source/users_guide/running-single-points/running-single-point-subset-data.rst

@@ -13,7 +13,7 @@ Subset the data
 
 For single-point cases, you need to subset a surface dataset and (optionally) DATM data. The Python script to subset this data can be found in the CTSM repository at ``tools/site_and_regional/subset_data``.
 
-Note that you will need to have a python environment set up that includes the packages ``scipy``, ``xarray``, and ``numpy``. If you have conda or miniconda installed, you can create a conda environment for this and other CTSM python tools using the script ``py_env_create`` at the top level of your CTSM checkout.
+Note that you will need to have a python environment set up that includes the packages ``scipy``, ``xarray``, and ``numpy``. If you have conda or miniconda installed, you can create a conda environment for this and other CTSM python tools using the script ``py_env_create`` at the top level of your CTSM checkout. See :ref:`using-ctsm-pylib` for more information.
 
 To subset surface data and climate forcings (DATM) for a single point, use the command:
 

doc/source/users_guide/using-clm-tools/index.rst

@@ -16,6 +16,7 @@ Using CLM tools
 
    what-are-the-clm-tools.rst
    building-the-clm-tools.rst
+   using-ctsm-pylib.rst
    creating-input-for-surface-dataset-generation.rst
    creating-surface-datasets.rst
    creating-domain-files.rst

doc/source/users_guide/using-clm-tools/using-ctsm-pylib.rst

@@ -0,0 +1,14 @@
+
+.. include:: ../substitutions.rst
+.. _using-ctsm-pylib:
+
+Installing the CTSM Python environment
+======================================
+
+Many of our Python-based tools require non-standard Python modules to be installed. To facilitate this, you can install a CTSM-specific `Conda <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`__ environment with the exact version of everything needed. From the top level of your CTSM checkout, simply do
+
+.. code:: shell
+
+   ./py_env_create
+
+and that script will install the ``ctsm_pylib`` environment for you. If ``ctsm_pylib`` already exists, it will give you options on how to handle that.