…ck_args

…or it

…t name, add a simple check for using it

…t set, and a test for it that passes

…t it fails

…now passes

…black, check some of the values from setup_files

…when set

… args.out_surface is set

…currently done

…NEON_fates

…ed and the file exists

…ake it more clear in response to review

…not set

… error if the file does not exist

… echoed when the urban datasets are made

…bose option

…s always used, which will make it easier to remove the use of 16pft versions which we do want to do

…se the 78pft surface datasets

… list that also has specific resolutions

This set of changes allows CTSM to continue API compatability with changes to the FATES API. FATES has updated its nutrient dynamics routine, and required a modification to the test environment, some minor updates to variable dimensions in the history, and a call to a new FATES history routine.  Implicitly, the updating of the FATES tag introduces new content in the FATES model since the last API update (mostly bug fixes).

…surdat_4_1x1_from_subset

Fix issue ESCOMP#1864 in master documentation

…subset

…est fails

…ved if the test previously failed

…istently start with read_cfg_

Get single point surface datasets from subset_data rather than mksurfdata

NEON FATES capabilities

Resolved conflicts:
cime_config/SystemTests/fsurdatmodifyctsm.py
test/tools/test_driver.sh

Update ChangeLog and python tests

Have fsurdat_modifier system test use conda environment rather than ncar_pylib

ERP_D_Ld10.f09_f09_mg17.IHistClm50BgcCrop.cheyenne_gnu.clm-f09_dec1990Start
ran out of time at 40 minutes, so I bumped it up to 59 and it passed

 Params file sets the respiration fractions for CWD to zero:
 rf_cwdl2_bgc = 0
 rf_cwdl3_bgc = 0
 The model has no code to handle rf_cwd* > 0. So...
 - I have introduced cwdhr_col to track this HR the same way that we track
 lithr_col for litter.
 - I have removed if-statements that prevented CWD HR pools and decomposition
 from writing to history.
 - I have introduced a new test to the cheyenne test-suite that makes active
 seven history fields pertaining to CWD HR and points to a params file with
 rf_cwd* > 0. I have confirmed that the new test returns the new active
 variables as greater than 0 when pointing to the new params file and equal
 to 0 when pointing to the default params file.

Resolved conflicts:
bld/CLMBuildNamelist.pm
bld/unit_testers/build-namelist_test.pl
cime_config/testdefs/testlist_clm.xml
src/biogeochem/CNBalanceCheckMod.F90
src/biogeochem/CNDriverMod.F90
src/biogeochem/CNProductsMod.F90
src/biogeochem/CNVegCarbonFluxType.F90
src/dyn_subgrid/dynSubgridControlMod.F90
src/dyn_subgrid/dynSubgridDriverMod.F90

Cheyenne test-suite OK (against regenerated baselines for dev045)

Expand crop reproductive pools; remove some unused options

The main change in this tag is adding placeholder pools (and
corresponding fluxes) that will be needed to couple the AgSys crop
model: Rather than a single grain pool, AgSys has two different grain
pools (meal & oil) as well as two different reproductive structure pools
(pod & floret). This tag adds a dynamically-allocated second dimension to
the relevant variables to accommodate these new pools. The new
CropReprPoolsMod controls the allocation and naming of these pools, and
facilitates looping over the new dimension. Currently parameters in
there are hard-coded for the current crop model, but this will become
more dynamic with the coupling of AgSys.

This tag also removes experimental / untested options in
NutrientCompetitionFlexibleCNMod. Although this is mostly unrelated to
the main change, doing this simplified the changes needed for the main
change.

This tag also resolves ESCOMP#1666 (Isotopic values of grain_mr not
set correctly when use_grainproduct is false).

Finally, this tag removes or modifies some of the most expensive tests
in the aux_clm test suite to reduce the cost of running the test suite.

Resolved conflicts:
src/biogeochem/CNBalanceCheckMod.F90
src/biogeochem/CNCIsoFluxMod.F90
src/biogeochem/CNDriverMod.F90
src/biogeochem/CNProductsMod.F90
src/biogeochem/CNVegCarbonFluxType.F90
src/biogeochem/CNVegNitrogenFluxType.F90

Cheyenne test-suite in progress and looks promising this far.

First Commit of CN Matrix Solution:
Start bringing in the use_matrixcn and use_soil_matrixcn control options for the Carbon/Nitrogen BGC model using
the matrix solution methodology developed by Dr. Yiqi Luo and his EcoLab members: Drs. Xingjie Lu,
Yuanyuan Huang and Zhengguang Du, at Northern Arizona University

Work on Anomaly forcing for SSEP scenarios:
Do some work on anomoly forcing for SSP scenarios. Update the script in tools/contrib to work with the latest
data and replicate results of Keith Oleson and Sean Swenson. Add some test cases for it.

Python Environment Management using Conda:
More work on the manage_python_env script to setup the "ctsm_py" conda environment. This now works for UCAR machines
(such as cheyenne and casper) as well as CGD machines (like izumi). This script can also be called for tools, and
the test tools mechanism is now using it rather than ncar_pylib.

./manage_python_env

SCAM Fix:
Add checkimport method for CMEPS so that single-column case can work with SCAM, from Jim Edwards.

Black Formatter for Python Code:
Run "black" python code reformatter on all code under the "python" directory. Add the commits
to .git-blame-ignore-revs so they can be ignored when "git blame" is used, if you add this
to each clone where you want this to apply:

   git config blame.ignoreRevsFile .git-blame-ignore-revs

You can do it for your worktrees, but since the file only applies to CTSM for ctsm5.1.dev100 and
forward, you'll need to do it for each CTSM clone seperately. Also there is now a github action
that checks that python code under the "python" subdirectory is black clean. If it's not the action
will fail and send you an email about it.

Make Map Data Fix:
Simple fix from Sam Rabin.

Fix for DISPLA on History Output:
Fix from Keith Oleson to set history output for DISPLA (displa_patch) to zero when vegetation is buried by snow.

Resolved conflicts:
bld/CLMBuildNamelist.pm
src/biogeochem/CNDriverMod.F90
src/biogeochem/CNVegCarbonFluxType.F90

Cheyenne test-suite in progress and looks promising this far.

Use conda environment rather than ncar_pylib with the fsurdat_modifier system test

Reason: ncar_pylib is going away soon.

These changes pertain to GU_LULCC tests in this commit.

This was an unintentional line removal that Erik realized.
I also reordered the error checks that Erik recommended in
dynSubgridControlMod.

…than the CN one for it

…M into clm5_shiftingcultivation

7b6d92ef6 Merge pull request ESCOMP#198 from johnpaulalex/gitdir
927ce3a98 Merge pull request ESCOMP#197 from johnpaulalex/testpath
a04f1148f Merge pull request ESCOMP#196 from johnpaulalex/readmod
d9c14bf25 Change the rest of the methods to use -C. Still some usage of getcwd in test_unit_repository_git.
332b10640 Fix incorrect logged path of checkout_externals in test_sys_checkout: it was basically the parent of the current directory, which varies throughout the test. (it called abspath with '{0}/../../', which adds arbitrary and not-interpolated subdir '{0}' to the path, then removes it and removes one more level).
932a7499b Remove printlog from read_gitmodules_file since read_externals_description_file() already has a nearly-the-same printlog (but add it to the other caller).
5d13719ed Merge pull request ESCOMP#195 from johnpaulalex/check_repo
423395449 Update utest to mock _git_remote_verbose in a new way, since it is now called via the GitRepository class rather than on the specific GitRepository instance.
d7a42ae96 Check that desired repo was actually checked out.
71596bbc1 Merge pull request ESCOMP#194 from johnpaulalex/manic2
4c96e824e Make the MANIC_TEST_BARE_REPO_ROOT env var special - give it a constant for easy tracking, and automatically tear it down after each test.
259bfc04d test_sys_checkout: use actual paths in on-the-fly configs rather than MANIC_TEST_BARE_REPO_ROOT env var. This will make it easier to test (in the near future) that checkout_externals actually checked out the desired repo dir.
557bbd6eb Merge pull request ESCOMP#193 from johnpaulalex/manic
5314eede1 Remove MANIC_TEST_TMP_REPO_ROOT environment variable in favor of module-level variable.
345fc1e14 Merge pull request ESCOMP#191 from johnpaulalex/test_doc12
2117b843c test_sys_checkout: verify that basic by-tag/branch/hash tests actually take us to the correct git tag/branch/hash.
94d6e5f2b Merge pull request ESCOMP#190 from johnpaulalex/test_doc11
3ff33a6a8 Inline local-path-creation methods
47dea7f64 Merge pull request ESCOMP#189 from johnpaulalex/test_doc10
9ea75cbf8 Grab-bag of renamings: Remove redundant _NAME from repo constants, and consistently add _REPO suffix (This causes the majority of diffs).
c0c847ec8 Merge pull request ESCOMP#188 from johnpaulalex/test_doc9
2dd5ce0f7 test_sys_checkout.py: only check for correct 'required' or 'optional' state in the test that exercises required vs optional behavior. Removed a lot of boilerplate.
eb3085984 Merge pull request ESCOMP#187 from johnpaulalex/test_doc8
1832e1f84 test_sys_checkout: Simplify many tests to only use a single external.
8689d61ec Merge pull request ESCOMP#186 from johnpaulalex/test_doc7
fbee4253e Grab bag of test_sys_checkout cleanups:    Doc inside of each test more clearly/consistently.    TestSysCheckoutSVN didn’t get the inlining-of-helper-methods treatment, now it has that.    Move various standalone repo helper methods (like create_branch) into a RepoUtils class.    README.md was missing newlines when rendered as markdown.    Doc the return value of checkout.main    Fix test_container_exclude_component - it was looking for the wrong key (which is never present); now it looks for the correct key.
f0ed44a6e Merge pull request ESCOMP#185 from johnpaulalex/test_doc6
a3d59f5f2 Merge pull request ESCOMP#184 from johnpaulalex/test_doc5
5329c8ba7 test_sys_checkout: Inline config generation functions that are only called once.
464f2c7a7 test_sys_checkout: Inline another layer (per-config-file checks). Rename the 4 methods that are used multiple times, to reflect what they do rather than what they're called.
8872c0df6 Merge pull request ESCOMP#183 from johnpaulalex/doc_test4
c045335f6 Merge pull request ESCOMP#182 from johnpaulalex/doc_test3
c583b956e Merge pull request ESCOMP#181 from johnpaulalex/doc_test2
e01cfe278 test_sys_checkout: less confusing handling of return values from checkout_externals. Specifically, when doing a checkout, don't return tree_status from _before_ the checkout. Make a new wrapper to call checkout_externals a second time, to calculate the new status after a checkout (very frequent pattern).
23286818c test_sys_checkout: Remove another layer (which generates test component names)
c3717b6bc Merge pull request ESCOMP#180 from johnpaulalex/doc_test
36d7a4434 test_sys_checkout.py: remove one layer of functions (that check for local status enums). No-op.
2c4584bf7 More documentation about tests: * contents of test repositories (n a new README.md) * various constants in test_sys_checkout.py that point to those contents, and terminology like container/simple/mixed. * in each test method, the scenarios being tested. * The coupling between test methods.
55e74bd0a Merge pull request ESCOMP#179 from johnpaulalex/circ
66be84290 Remove circular dependency by making _External stop doing tricky things with sourcetrees.

git-subtree-dir: manage_externals
git-subtree-split: 7b6d92ef689e2f65733e27f8635ab91fb341356b

… if use_fates