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add megan compatibility with fates #98

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aa3bda9
Update bassed on ctsm5.3.0
ekluzek Sep 18, 2024
eb8816e
Remove mkprocdata, rename README.filecopies to just under mksurfdata_…
ekluzek Sep 18, 2024
1f97cb1
Remove mention of mkprocdata_map from README files
ekluzek Sep 18, 2024
f045358
Remove mention of mkprocdata and the FORTRAN tool build from the user…
ekluzek Sep 18, 2024
d6a2047
Move how-to-make-mesh.md to the User's Guide; give extension .rst.
samsrabin Sep 18, 2024
f84c5b7
how-to-make-mesh: Markdown to RestructuredText.
samsrabin Sep 18, 2024
2a6ed6d
Improve mesh_maker instructions.
samsrabin Sep 18, 2024
1b99435
Fix typo in mesh_plotter arg description.
samsrabin Sep 18, 2024
fc261d4
mesh_plotter now stops if output file exists w/o --overwrite given.
samsrabin Sep 18, 2024
627940a
Add --dpi option to mesh_plotter.
samsrabin Sep 18, 2024
7ad5fd0
More reasonable marker sizes in mesh_plotter.
samsrabin Sep 18, 2024
4247294
Get working for 78 or 16 pft surface datasets, as well as 16 or 78 pf…
ekluzek Sep 19, 2024
23192c6
Apply last suggestion from @samrabin removing the npfts module variab…
ekluzek Sep 19, 2024
0eed033
Convert I1850 hillslope 5x5_amazon tests to I2000.
samsrabin Sep 19, 2024
08d0923
Add non-serial HillslopeC 5x5_amazon test to hillslope suite.
samsrabin Sep 19, 2024
7242a6b
Add issue reference to non-serial HillslopeC 5x5_amazon test.
samsrabin Sep 19, 2024
8361f8b
Fix HillslopeC test in expected fails list.
samsrabin Sep 19, 2024
edbef5f
Add mesh_plotter instructions.
samsrabin Sep 18, 2024
5fb68ac
UG: Fix path of example mksurfdata_esmf namelist.
samsrabin Sep 20, 2024
2d39418
Add double backticks in lots of places.
samsrabin Sep 20, 2024
ac01cb3
Add doc todo to replace missing figure.
samsrabin Sep 20, 2024
5c3ea51
Fix a title overline.
samsrabin Sep 20, 2024
6fca829
More formatting fixes.
samsrabin Sep 20, 2024
24354eb
Replace some :: with :.
samsrabin Sep 20, 2024
e368dd4
Formatting fixes in wrf-nesting.rst.
samsrabin Sep 20, 2024
d1a4552
Update finidat files picked up by LII* tests from namelist_defaults_ctsm
slevis-lmwg Sep 21, 2024
3cf93a9
Add --no-center-coords option.
samsrabin Sep 19, 2024
06fdc64
Properly handle --outdir.
samsrabin Sep 20, 2024
0de1673
Add tests to test_advanced_sys_mesh_plotter.py.
samsrabin Sep 20, 2024
f0c9f31
Use os.path.join in test_advanced_sys_mesh_plotter.py.
samsrabin Sep 20, 2024
badbc50
Add dpi test to test_advanced_sys_mesh_plotter.py.
samsrabin Sep 20, 2024
6d3bf8c
Format with black.
samsrabin Sep 20, 2024
e725759
Add previous commit to .git-blame-ignore-revs.
samsrabin Sep 20, 2024
92078e3
Fixes to finidat settings
ekluzek Sep 23, 2024
550442a
Merge branch 'new_rawpftlai' of github.com:slevis-lmwg/CTSM into new_…
ekluzek Sep 23, 2024
00b9f3a
Merge pull request #2772 from samsrabin/mesh-plotter-improvements
samsrabin Sep 23, 2024
6bdaef9
Adjust the failing test to include nofireemis
ekluzek Sep 24, 2024
21de9a2
Adjust init_interp_attributes for 1979 for f09 and f19 for clm6_0_cam…
ekluzek Sep 24, 2024
9166192
Merge pull request #14 from ekluzek/rmmkproc
ekluzek Sep 24, 2024
e761cd9
Merge branch 'new_rawpftlai' of github.com:slevis-lmwg/CTSM into new_…
ekluzek Sep 24, 2024
318a312
Update namelist_defaults_clm4_5.xml references.
samsrabin Sep 24, 2024
260c3c9
namelist_defaults_|version|_tools.xml files no longer exist.
samsrabin Sep 24, 2024
5d2ebe1
Fix namelist XML refs in what-are-the-clm-tools.rst.
samsrabin Sep 24, 2024
9ed3cca
Specify path to create_newcase.
samsrabin Sep 24, 2024
f22f227
Add TODOs to update refs to queryDefaultNamelist.pl.
samsrabin Sep 24, 2024
8304414
Add TODOs to update refs to mksurfdata.pl.
samsrabin Sep 24, 2024
5826608
Merge branch 'new_rawpftlai' into changelog_readme_update
ekluzek Sep 24, 2024
962a090
Fix compset and add TODO to "Running with historical CO2 forcing."
samsrabin Sep 24, 2024
8a31077
TODO added in "Running with irrigation".
samsrabin Sep 24, 2024
42ff69c
Add TODO about -bgc_spinup.
samsrabin Sep 24, 2024
2bf912f
Add TODOs about mkprocdata_map.
samsrabin Sep 24, 2024
6ac23b2
Add TODOs about domain files not being needed in nuopc.
samsrabin Sep 24, 2024
5e75f2e
Add TODO about updating "Observational Sites Datasets".
samsrabin Sep 24, 2024
79f50f4
Merge branch 'b4b-dev' into docs-fixes-202409
samsrabin Sep 24, 2024
38598da
Fix another namelist_definition_clm4_5.xml reference.
samsrabin Sep 24, 2024
a251582
More double-backticks in "Spinup of |version|-BGC-Crop".
samsrabin Sep 24, 2024
b5a82cc
Remove User's Guide section about running w/ transient hist CO2.
samsrabin Sep 24, 2024
edefa3c
Resolve a docs build warning.
samsrabin Sep 24, 2024
482d786
Fix typo in test in ExpectedTestFails.xml
slevis-lmwg Sep 25, 2024
a25bf74
Update doc/ChangeLog
ekluzek Sep 25, 2024
1e75db0
A few updates
ekluzek Sep 25, 2024
1379ddd
Merge branch 'changelog_readme_update' of github.com:ekluzek/CTSM int…
ekluzek Sep 25, 2024
f120fcd
Update contributors and more in the change files
ekluzek Sep 25, 2024
e86c33a
Finish descriptions on updates in the Change files
ekluzek Sep 25, 2024
508a966
Add the WhatsNew markdown file
ekluzek Sep 25, 2024
4f7f8a0
Merge pull request #11 from ekluzek/changelog_readme_update
ekluzek Sep 25, 2024
cc34cc4
Update changelog date
ekluzek Sep 25, 2024
a3459c5
Merge pull request #2500 from slevis-lmwg/new_rawpftlai
ekluzek Sep 25, 2024
2b1fedf
Merge remote-tracking branch 'upstream/master' into 5-3-update
mvdebolskiy Sep 25, 2024
8357df5
update ccs
mvdebolskiy Sep 25, 2024
9db6f8d
fix url
mvdebolskiy Sep 25, 2024
6b1d846
upd ccs
mvdebolskiy Sep 25, 2024
6c7ecf6
PPE change to sa_leaf
olyson Sep 25, 2024
a9cd52f
Error in Hillslope/shell_commands if running on grid w/o a hillslope_…
samsrabin Sep 20, 2024
d837838
Hillslope testmod: Add hillslope_file for 5x5_amazon.
samsrabin Sep 25, 2024
5e99159
add 60 to components
mvdebolskiy Sep 26, 2024
da386fe
Merge pull request #2770 from samsrabin/docs-fixes-202409
samsrabin Sep 26, 2024
12d9329
Merge tag 'ctsm5.2.029' into fates-api36.1
glemieux Sep 26, 2024
31a5cc7
Merge tag 'ctsm5.3.0' into merge-b4bdev-20240926
slevis-lmwg Sep 26, 2024
615224a
Updated number of tests
slevis-lmwg Sep 26, 2024
cb7e922
Don't manually set meshfile in Hillslope tests.
samsrabin Sep 26, 2024
ed5d17b
First draft ChangeLog/ChangeSum
slevis-lmwg Sep 26, 2024
830e675
Updated EXPECTED FAILUREs (I should have done this in ctsm5.3.0)
slevis-lmwg Sep 26, 2024
c393123
correct clm_demand option typo
glemieux Sep 27, 2024
e591a1a
Remove parallel 5x5_amazon test from expected fails.
samsrabin Sep 27, 2024
4f2129f
Rename 10x15 synthetic hillslope_file to include 10x15.
samsrabin Sep 27, 2024
ad0ab60
Add/edit comments about 5x5_amazon hillslope tests.
samsrabin Sep 27, 2024
061b1c9
Remove parallel 5x5_amazon hillslope test from aux_clm.
samsrabin Sep 27, 2024
792abd1
Adding one more EXPECTED FAILURE
slevis-lmwg Sep 27, 2024
e6d58ec
Merge pull request #2792 from slevis-lmwg/merge-b4bdev-20240926
slevis-lmwg Sep 27, 2024
eed2d73
Merge tag 'ctsm5.3.001' into merge-master-20240927
slevis-lmwg Sep 27, 2024
cb19c43
Merge pull request #2795 from slevis-lmwg/merge-master-20240927
slevis-lmwg Sep 27, 2024
adecc67
Revert "Merge tag 'ctsm5.3.001' into b4b-dev"
slevis-lmwg Sep 27, 2024
16cf4ac
Merge pull request #2796 from ESCOMP/revert-2795-merge-master-20240927
slevis-lmwg Sep 27, 2024
9604614
Merge tag 'ctsm5.3.002' into merge-master-20240927
slevis-lmwg Sep 27, 2024
a1d0ef4
Merge pull request #2797 from slevis-lmwg/merge-master-20240927
slevis-lmwg Sep 27, 2024
039626c
Fix clm-basic tests
slevis-lmwg Sep 27, 2024
70c9f8b
Updates for my fix to take effect correctly
slevis-lmwg Sep 28, 2024
698902d
Small important correction
slevis-lmwg Sep 28, 2024
0a06a62
Merge branch 'b4b-dev' into shr_file_to_shr_log
samsrabin Sep 30, 2024
bcbc462
Change testlist_clm ne30pg3_t061 tests to ne30pg3_t232
slevis-lmwg Sep 30, 2024
f312b8a
First commit for CESM3 tuning of the dust emission module by dmleung.…
dmleung Sep 30, 2024
20b81c1
Merge branch 'b4b-dev' into fix_clm-basic_tests
slevis-lmwg Sep 30, 2024
f88d050
Merge pull request #2798 from slevis-lmwg/fix_clm-basic_tests
slevis-lmwg Sep 30, 2024
d3d4e2e
Allocate elevclass_o before use in mkglcmecMod.F90
slevis-lmwg Sep 30, 2024
f40ee1a
Change testlist_clm C96_t061 test to C96_t232
slevis-lmwg Sep 30, 2024
b15640f
Remove elevclass_o altogether because it is NOT used
slevis-lmwg Oct 1, 2024
191a399
dmleung deleted a few unused parameters and variables. 30 Sep 2024
dmleung Oct 1, 2024
efbeafc
Revert change to C96 test; will do later, when ccs_config gets updated
slevis-lmwg Oct 1, 2024
40fc188
Merge pull request #2799 from slevis-lmwg/change_t061_to_t232
slevis-lmwg Oct 1, 2024
62ca130
Merge branch 'b4b-dev' into alloc_elevclass_o
slevis-lmwg Oct 1, 2024
79811dd
Add domain check for hillslope file.
samsrabin Sep 30, 2024
ea9228c
Update 10x15 hillslope_file (now has LATIXY/LONGXY).
samsrabin Oct 1, 2024
4b032be
Improve use_init_interp+use_hillslope namelist warning.
samsrabin Oct 1, 2024
3bc5eed
Merge tag 'ctsm5.3.002' into hillslopes-off-fsurdat
samsrabin Oct 1, 2024
ca4caa7
Merge pull request #2804 from slevis-lmwg/alloc_elevclass_o
slevis-lmwg Oct 1, 2024
5c74ff4
Call domain_clean() at end of check_domain_attributes().
samsrabin Oct 1, 2024
1a93690
Remove outdated comment/TODO.
samsrabin Oct 1, 2024
5e71b7d
Rename surfdata_domain to inputdata_domain.
samsrabin Oct 1, 2024
c2c99dd
Merge branch 'fix-namelist-tester' of github.com:mvdebolskiy/CTSM int…
ekluzek Oct 1, 2024
5173018
Merge remote-tracking branch 'escomp/b4b-dev' into fix-namelist-tester
ekluzek Oct 1, 2024
3295adb
Correct the name of the hash to use in the checks that hash values ar…
ekluzek Oct 1, 2024
98e42fb
Merge pull request #2678 from mvdebolskiy/fix-namelist-tester
ekluzek Oct 1, 2024
6c35216
dmleung changed the values of the tuning parameters and added a new t…
dmleung Oct 1, 2024
f2f7535
add shell call to generate fates hydro parameter file on the fly
glemieux Oct 1, 2024
52e5801
dmleung renamed the tuning parameter for Okin's vegetation drag parti…
dmleung Oct 1, 2024
97d1657
fix typo in fates hydro user_nl_clm
glemieux Oct 1, 2024
52389c0
correct call typo to clm_demand for fateslanduse test mod
glemieux Oct 2, 2024
69b815b
update default fates parameter files
glemieux Oct 2, 2024
2639750
Merge tag 'ctsm5.3.002' into fates-api36.1
glemieux Oct 2, 2024
4e0197b
update the gitmodules tag for fates
glemieux Oct 2, 2024
1f851c4
Getting a new set of tuning parameters for dust. dmleung 2 Oct 2024
dmleung Oct 3, 2024
65d26e6
add expected failure for FatesColdLandUse test mod
glemieux Oct 3, 2024
1045e1b
add new changelog entry
glemieux Oct 3, 2024
9abbb70
minor changelog update
glemieux Oct 3, 2024
b12f6ff
update filename
glemieux Oct 3, 2024
99124de
Merge branch 'b4b-dev' into shr_file_to_shr_log-ssr
samsrabin Oct 4, 2024
b9fde41
update fates tag to api36.1
glemieux Oct 4, 2024
c3ddc48
update testing results for ctsm5.3.003
glemieux Oct 7, 2024
29f9ac8
update changelog and changesum date/time for ctsm5.3.003
glemieux Oct 7, 2024
f80f4c4
Merge pull request #2700 from rgknox/fates-api36.1
samsrabin Oct 7, 2024
1fbe88a
Revert this change as it changed answers for SMS_Ln9.ne30pg2_ne30pg2_…
ekluzek Oct 7, 2024
8819fdf
Merge branch 'dustemis_tune4cesm3' of github.com:dmleung/CTSM into du…
ekluzek Oct 7, 2024
3f5aa0f
Bump up wallclock time for one test.
samsrabin Oct 7, 2024
f2c5d37
Merge tag 'ctsm5.3.003' into hillslopes-off-fsurdat
samsrabin Oct 7, 2024
3ec9215
Remove include_user_mods from matrixcnOn testmod.
samsrabin Oct 7, 2024
7964509
Merge branch 'shr_file_to_shr_log-ssr' into shr_file_to_shr_log
samsrabin Oct 8, 2024
ae6b188
Change a test wallclock time to ensure it's what we want.
samsrabin Oct 8, 2024
f95d192
Merge pull request #2434 from samsrabin/hillslopes-off-fsurdat
samsrabin Oct 8, 2024
6ae3719
Update ChangeLog and ChangeSum.
samsrabin Oct 8, 2024
4c9631b
Make dust_moist_fact different for Leung and Zender, even though both…
ekluzek Oct 8, 2024
c98600b
Merge pull request #2820 from samsrabin/hillslopes-off-fsurdat
samsrabin Oct 8, 2024
146dba4
Fix issue #2793
olyson Oct 2, 2024
cbea138
Merge pull request #2627 from jedwards4b/shr_file_to_shr_log
samsrabin Oct 8, 2024
86fbf18
Merge pull request #2806 from olyson/eflxbuild
olyson Oct 8, 2024
ac2aec1
Merge tag 'ctsm5.3.004' into dustemis_tune4cesm3
ekluzek Oct 8, 2024
c1fe258
Clm60 finidat updates for ne30, f09, f19 grids
slevis-lmwg Oct 8, 2024
058320d
Fix hillslope with use_init_interp warning test, by specifying the hi…
ekluzek Oct 9, 2024
0814274
ne30 updates in response to Keith Oleson's review
slevis-lmwg Oct 9, 2024
e47ffab
f19 updates for test to pick up the correct finidat
slevis-lmwg Oct 9, 2024
10ff404
Add more expected fails
ekluzek Oct 10, 2024
af587a0
Merge commit '10ff40411' into dustemis_tune4cesm3
ekluzek Oct 10, 2024
8777879
Update change files
ekluzek Oct 10, 2024
899c32c
Merge pull request #2803 from dmleung/dustemis_tune4cesm3
ekluzek Oct 10, 2024
7f35823
Merge remote-tracking branch 'escomp/master' into ne30_f09_f19_IC
slevis-lmwg Oct 10, 2024
3e9f02a
Merge tag 'ctsm5.3.005' into merge-b4bdev-20241010
samsrabin Oct 10, 2024
33c8d55
Updates after Erik's reviewr; ne30 1979 does not work, yet
slevis-lmwg Oct 10, 2024
ab9bdf9
Draft ChangeLog/Sum
slevis-lmwg Oct 10, 2024
cfcd041
Update ChangeLog/ChangeSum.
samsrabin Oct 11, 2024
b330990
Merge pull request #2829 from samsrabin/merge-b4bdev-20241010
samsrabin Oct 11, 2024
bb97fb3
Updates from review with Erik and subsequent testing
slevis-lmwg Oct 11, 2024
2c078bb
Merge remote-tracking branch 'escomp/master' into ne30_f09_f19_IC
slevis-lmwg Oct 11, 2024
38e6fb1
Correct mask for ne30pg3 1979 finidat file
ekluzek Oct 11, 2024
7874521
Remove 2003 finidat settings for clm5_1/clm6_0 so will use 2000 files…
ekluzek Oct 12, 2024
29023fb
Updated ChangeLog/Sum
slevis-lmwg Oct 13, 2024
941ec71
Remove redundant lines
slevis-lmwg Oct 13, 2024
5f9d597
Add matrixcn test suite.
samsrabin Oct 14, 2024
4797fd2
Final update to ChangeLog
slevis-lmwg Oct 14, 2024
6d8dad8
Merge pull request #2821 from slevis-lmwg/ne30_f09_f19_IC
slevis-lmwg Oct 14, 2024
0464237
Merge remote-tracking branch 'escomp/master' into saleaf
slevis-lmwg Oct 14, 2024
9f4844c
Draft ChangeLog/Sum
slevis-lmwg Oct 14, 2024
77fdb8d
Updated ChangeLog from Keith Oleson's review
slevis-lmwg Oct 14, 2024
ea0dadd
Final ChangeLog
slevis-lmwg Oct 14, 2024
f726adb
Merge pull request #2788 from olyson/saleaf
slevis-lmwg Oct 14, 2024
207364f
Merge tag 'ctsm5.3.008' into matrixcnon-no-include
samsrabin Oct 15, 2024
b846e2b
Roll back change of one cnmatrix test length.
samsrabin Oct 15, 2024
82a0952
Update ChangeLog and ChangeSum.
samsrabin Oct 15, 2024
26b9aa7
Merge pull request #2815 from samsrabin/matrixcnon-no-include
samsrabin Oct 15, 2024
694333f
Transfer the following parameters from namelist to parameter file:
olyson Oct 20, 2024
be134d8
Merge tag 'ctsm5.3.009' into merge-master-20241021
samsrabin Oct 21, 2024
9f44365
Merge pull request #2842 from samsrabin/merge-master-20241021
samsrabin Oct 21, 2024
77b8e80
Make jmaxb0, wc2wjb0, r_mort pft-dimensioned
olyson Oct 22, 2024
b7121a6
ncd_io not needed after all
olyson Oct 22, 2024
3f4936c
Other variables not needed after all
olyson Oct 22, 2024
bc3d518
Consistent naming of units
olyson Oct 22, 2024
e5100a4
New versions of specialized parameter files
olyson Oct 23, 2024
28d552e
Reinstate SMS_Lm1.f10_f10_mg37.I1850Clm60Bgc.derecho_intel.clm-clm60_…
olyson Oct 24, 2024
f91cd8a
Merge branch 'b4b-dev' into b4b-dev_PPE2830-2831
olyson Oct 24, 2024
1571076
Move read of jmaxb0,jmaxb1,wc2wjb0 from pftcon to LunaMod and r_mort …
olyson Oct 26, 2024
0fd1a04
Final paths for parameter files
olyson Oct 27, 2024
f0566a6
Merge pull request #2845 from olyson/b4b-dev_PPE2830-2831
olyson Oct 28, 2024
152f5d6
Remove/replace refs to DATM_C*_YR_* variables
slevis-lmwg Oct 30, 2024
f2a8ce0
Remove some more DATM_C..._YR_...
slevis-lmwg Oct 30, 2024
c697c76
Remove additional DATM_C..._YR_...
slevis-lmwg Oct 30, 2024
862739b
Replace outdated DATM_CPL_CASE with DATM_CPLHIST_CASE
slevis-lmwg Oct 30, 2024
16d83c1
Add warning box to MOAR User's Guide page.
samsrabin Nov 1, 2024
33607a0
Merge pull request #2852 from slevis-lmwg/rm_refs_to_datm_vars
slevis-lmwg Nov 6, 2024
b32c775
Merge branch 'b4b-dev' into hist_doc_bc
ekluzek Nov 6, 2024
b50d65b
Merge pull request #2866 from johnpaulalex/hist_doc_bc
ekluzek Nov 7, 2024
bd85656
build-namelist_test: Ensure cold starts w/ finidat are handled properly.
samsrabin Nov 8, 2024
f8f3a6f
Ignore finidat for cold-start FATES runs.
samsrabin Nov 8, 2024
33fd95d
Don't allow users to supply finidat for cold-start non-FATES runs.
samsrabin Nov 8, 2024
000b70d
adding izumi nag fails
adrifoster Nov 9, 2024
bbe061d
changelog
adrifoster Nov 9, 2024
e07c66a
Merge pull request #2872 from adrifoster/merge-b4bdev-20241108
adrifoster Nov 9, 2024
3a74fe0
added CTSM side variables for MEGAN_pft_index
rosiealice Apr 2, 2024
3d6f907
spelling corrections
rosiealice Apr 8, 2024
1513e80
use FATES voc index in MEGAN calculations (implied mapping between FA…
rosiealice Apr 8, 2024
e860387
debugging
rosiealice Apr 8, 2024
076b3c4
turn off the -megan cant run with FATES- statement in bldnamelist
rosiealice Oct 28, 2024
494b326
passing ci from FATES into MEGAN
rosiealice Oct 28, 2024
eee49a6
Merge tag 'ctsm5.3.010' into fix-fates-cold-finidat
samsrabin Nov 11, 2024
a5bb5c4
updates to testlist
mvertens Nov 11, 2024
e187c80
Merge branch 'feature/update_testlist' into rosiealice_CTSM/megan_che…
mvertens Nov 11, 2024
c60fe19
Add some tests to expected fail list.
samsrabin Nov 12, 2024
ebcd4fb
Update ChangeLog and ChangeSum.
samsrabin Nov 12, 2024
931b425
Merge pull request #2870 from samsrabin/fix-fates-cold-finidat
samsrabin Nov 12, 2024
7363a3d
updated with new tests
mvertens Nov 12, 2024
5533548
updated fates megan tests
mvertens Nov 13, 2024
6508c01
Merge branch 'rosiealice_CTSM/megan_cherrypick_ctsm' into feature/meg…
mvertens Nov 13, 2024
dbab48c
Merge tag 'ctsm5.3.011' into feature/megan_cherrypick_ctsm_mvertens
mvertens Nov 13, 2024
c685a27
updated several files to ctsm5.3.011
mvertens Nov 13, 2024
b7d29df
fixed some testing problems
mvertens Nov 14, 2024
5d00740
updated fates pointer in .gitmodules
mvertens Nov 14, 2024
884a402
updated fates to have megan functionality
mvertens Nov 14, 2024
427cdd2
updates for megan functionality
mvertens Nov 14, 2024
7c583d4
added masterproc if for log output
mvertens Nov 18, 2024
ee5ecca
updating cdeps to cdeps1.0.58
mvertens Nov 20, 2024
e4f386f
updated ccs_config to ccs_config_noresm0.0.38
mvertens Nov 20, 2024
0b847a1
updated submodule cmeps
mvertens Nov 20, 2024
c4c3473
updated share submodule
mvertens Nov 20, 2024
d1211d1
updated externals
mvertens Nov 20, 2024
c9de28c
updated testlists to remove months
mvertens Nov 20, 2024
aba53d2
removed ctsm5_1 settings
mvertens Nov 20, 2024
f884b85
updated mizuRoute submodule
mvertens Nov 20, 2024
40aefe6
updated .gitmodules
mvertens Nov 20, 2024
b2e7367
updated submodule cime
mvertens Nov 20, 2024
1be2d2f
udpated cime in .gitmodules
mvertens Nov 20, 2024
eb0d436
changed cdeps to cdeps1.0.53 since you need rpointer changes across t…
mvertens Nov 20, 2024
594b4a0
updated .gitmodules
mvertens Nov 20, 2024
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21 changes: 9 additions & 12 deletions .config_files.xml
Original file line number Diff line number Diff line change
Expand Up @@ -5,31 +5,28 @@
<entry_id>

<!-- This is the same as the default entry in
cime/config/cesm/config_files.xml except for the value for CTSM:
In a standalone CTSM checkout, COMP_ROOT_DIR_LND is $SRCROOT
cime/config/cesm/config_files.xml except for the value for CLM:
In a standalone CLM checkout, COMP_ROOT_DIR_LND is $SRCROOT
rather than $SRCROOT/components/clm.

However, because of the way overrides are handled, we need to
re-specify the full information here rather than just overriding
the value for CTSM.
the value for CLM.
-->
<entry id="COMP_ROOT_DIR_LND">
<type>char</type>
<default_value>unset</default_value>
<values>
<value component="clm" >$SRCROOT</value>
<value component="ctsm" >$SRCROOT</value>
<value component="dlnd" comp_interface="mct">$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
<value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
<value component="slnd" comp_interface="mct" >$SRCROOT/components/cpl7/components/stub_comps_mct/slnd</value>
<value component="xlnd" comp_interface="mct" >$SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd</value>
<value component="slnd" comp_interface="nuopc" >$CIMEROOT/src/components/stub_comps_nuopc/slnd</value>
<value component="xlnd" comp_interface="nuopc" >$CIMEROOT/src/components/xcpl_comps_nuopc/xlnd</value>
<value component="clm" >$SRCROOT</value>
<value component="slim" >$SRCROOT/components/slim/</value>
<value component="dlnd" comp_interface="nuopc" >$SRCROOT/components/cdeps/dlnd</value>
<value component="slnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
<value component="xlnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
</values>
<group>case_comps</group>
<file>env_case.xml</file>
<desc>Root directory of the case land model component </desc>
<schema>$CIMEROOT/config/xml_schemas/config_compsets.xsd</schema>
<schema>$CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd</schema>
</entry>

</entry_id>
45 changes: 45 additions & 0 deletions .git-blame-ignore-revs
Original file line number Diff line number Diff line change
@@ -1,9 +1,54 @@
# Ran python directory through black python formatter
b429b63824e09f82e95d2982f14311cbbd8e4a37
d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
4cd83cb3ee6d85eb909403487abf5eeaf4d98911
d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
0aa2957c1f8603c63fa30b11295c06cfddff44a5
2cdb380febb274478e84cd90945aee93f29fa2e6
e44dc469439e02e9ee582dab274d890ebdfab104
565e7bcacbb0bba20ff80d680d8ad769676641c6
b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
51c102c5df2e0ef971b5f8eeeb477567899af63a
7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7
b771971e3299c4fa56534b93421f7a2b9c7282fd
9de88bb57ea9855da408cbec1dc8acb9079eda47
8bc4688e52ea23ef688e283698f70a44388373eb
c8bd4c6f98c0b411391b4355da449507db3aab4e
4ee49e3e516ca7dee5df378f65664f93a7db4415
0207bc98dd5c75cd69a0e788bc53e41093712f5c
e4d38681df23ccca0ae29581a45f8362574e0630
0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
810cb346f05ac1aabfff931ab1a2b7b584add241
5933b0018f8e29413e30dda9b906370d147bad45
025d5e7c2e80263717fb029101d65cbbf261c3c4
a9d96219902cf609636886c7073a84407f450d9a
d866510188d26d51bcd6d37239283db690af7e82
0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
e096358c832ab292ddfd22dd5878826c7c788968
475831f0fb0e31e97f630eac4e078c886558b61c
fd5f177131d63d39e79a13918390bdfb642d781e
# Ran SystemTests and python/ctsm through black python formatter
5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
8056ae649c1b37f5e10aaaac79005d6e3a8b2380
0bc3f00115d86d026a977918661c93779b3b19f9
540b256d1f3382f4619d7b0877c32d54ce5c40b6
8a168bb0895f4f2421608dd2589398e13a6663e6
183fc26a6691bbdf87f515dc47924a64be3ced9b
6fccf682eaf718615407d9bacdd3903b8786a03d
2500534eb0a83cc3aff94b30fb62e915054030bf
78d05967c2b027dc9776a884716597db6ef7f57c
47839a77229c61555e3b8932927bb54cdc511b27
a0d014fae9550dd9ffbc934abd29ef16176f8208
c7b7ca1d94ac19abb9ecea9fb5b712ddbdd6645d
b565b55ce7a9f8d812a573d716a5fd3d78cfea81
fdf72cd011e2ba318987a1e100efc5a1847c9d04
de9a30bfbbec36f9dcacc4380005ab596da47af4
cda0cf1412212e6f4363e6e8eb39f74c944b454d
aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
6c6f57e948bfa31e60b383536cc21663fedb8b70
9660667b1267dcd4150889f5f39db540158be74a
665cf86102e09b4c4c5a140700676dca23bc55a9
1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
753fda3ff0147837231a73c9c728dd9ce47b5997
f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c
4 changes: 3 additions & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,13 @@ Are answers expected to change (and if so in what way)?

Any User Interface Changes (namelist or namelist defaults changes)?

Does this create a need to change or add documentation? Did you do so?

Testing performed, if any:
(List what testing you did to show your changes worked as expected)
(This can be manual testing or running of the different test suites)
(Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
(aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master)
(aux_clm on derecho for intel/gnu and izumi for intel/gnu/nag/nvhpc is the standard for tags on master)

**NOTE: Be sure to check your coding style against the standard
(https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review
Expand Down
20 changes: 18 additions & 2 deletions .github/workflows/black.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,22 @@ jobs:
# Use options and version identical to the conda environment
# Using pyproject.toml makes sure this testing is consistent with our python directory testing
options: "--check --config python/pyproject.toml"
src: "./python"
# Version should be coordinated with the ctsm_py conda environment under the python directory
src: "./python"
# Version should be coordinated with the ctsm_pylib conda environment under the python directory
version: "22.3.0"
# 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"
- uses: psf/black@stable
with:
options: "--check --config python/pyproject.toml"
src: "./cime_config/buildlib"
version: "22.3.0"
- uses: psf/black@stable
with:
options: "--check --config python/pyproject.toml"
src: "./cime_config/buildnml"
version: "22.3.0"
52 changes: 20 additions & 32 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,18 +1,3 @@
# directories checked out by manage_externals, and other files created
# by manage_externals
manage_externals.log
ccs_config
/src/fates/
/cime/
/components/
/libraries/
/share/
/doc/doc-builder/

# ignore svn directories
**/.svn/**
.svn/

# netcdf files
*.nc
# but don't ignore netcdf files here:
Expand Down Expand Up @@ -75,35 +60,38 @@ buildnmlc
td.*.status
td.*.log
td.*.status.xFail
test_driver_*.sh

# mksurfdata output
surfdata_*.log
surfdata_*.namelist
landuse.timeseries_*.namelist
*.namelist
mksurfdata.o*
landuse.timeseries_*.log
landuse_timeseries_*.txt
ctsm.input_data_list
ctsm.input_data_list.previous
*.stdout.txt.o*
/tools/mksurfdata_esmf/PET*
/tools/mksurfdata_esmf/job_name.o*
/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

# mksurfdata unit tests
unit_test_build

# Tools executables
/tools/mksurfdata_map/mksurfdata_map
/tools/mkprocdata_map/mkprocdata_map

# mksurfdata output files
/tools/mksurfdata_map/surfdata_*.nc
/tools/mksurfdata_map/landuse.timeseries_*.nc

# mkmapdata output files
/tools/mkmapdata/PET*.RegridWeightGen.Log
/tools/mkmapdata/regrid.*.out
/tools/mkmapdata/regrid.*.err
/tools/mkmapdata/regrid.o*
/tools/mkmapdata/map*.nc
# run_neon output directories
/tools/site_and_regional/listing.csv
/tools/site_and_regional/????/
/tools/site_and_regional/????.ad/
/tools/site_and_regional/????.postad/
/tools/site_and_regional/????.transient/
/tools/site_and_regional/archive/

# build output
*.o
Expand Down
130 changes: 130 additions & 0 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -0,0 +1,130 @@
# This is a git submodule file with additional support for
# git-fleximod (https://github.com/ESMCI/git-fleximod)
#
# The additional flags supported by git-fleximod are
# fxtag - the tag associated with the submodule, this tag can be tested for
# consistancy with the submodule hash using git-fleximod status
# the hash can be updated to the tag using git-fleximod update
#
# fxrequired - indicates if a given submodule should be checked out on install
# submoudules can be toplevel or internal and required or optional
# toplevel means that the submodule should only be checked out if the
# module is the toplevel of the git repo (is not a submodule itself)
# internal means that the submodule is needed by the component whether
# the component is toplevel or the submodule of another repo
# required means that the submodule should always be checked out
# optional means that the submodule should only be checked out if the
# optional flag is provided to git-fleximod or the submodule name is
# explicitly listed on the git-fleximod command line.
#
# fxsparse - this is a path to a git sparse checkout file indicating that the
# submodule should be checked out in sparse mode
#
# fxDONOTUSEurl - this field is used by git-fleximod test to insure that the url is pointing
# to the official url of the repo and not to an unofficial fork.
# It is intended for use of github workflows to test commits to protected
# repository branches.
#
[submodule "fates"]
path = src/fates
url = https://github.com/NorESMhub/fates
fxtag = sci.1.78.3_api.36.1.0_noresm_v1
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

[submodule "cism"]
path = components/cism
url = https://github.com/ESCOMP/CISM-wrapper
fxtag = cismwrap_2_2_002
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper

[submodule "rtm"]
path = components/rtm
url = https://github.com/ESCOMP/RTM
fxtag = rtm1_0_80
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/RTM

[submodule "mosart"]
path = components/mosart
url = https://github.com/ESCOMP/MOSART
fxtag = mosart1.1.02
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/MOSART

[submodule "mizuRoute"]
path = components/mizuRoute
url = https://github.com/ESCOMP/mizuRoute
fxtag = cesm-coupling.n02_v2.1.3
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute

[submodule "ccs_config"]
path = ccs_config
url = https://github.com/NorESMhub/ccs_config_noresm.git
fxtag = ccs_config_noresm0.0.38
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/NorESMhub/ccs_config_noresm

[submodule "cime"]
path = cime
url = https://github.com/NorESMhub/cime.git
fxtag = cime6.1.28_noresm_v0
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESMCI/cime

[submodule "cmeps"]
path = components/cmeps
url = https://github.com/NorESMhub/cmeps
fxtag = cmeps1.0.20_noresm_v0
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git

[submodule "cdeps"]
path = components/cdeps
url = https://github.com/ESCOMP/CDEPS.git
fxtag = cdeps1.0.53
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/NorESMHub/NorESM_share
fxtag = share1.1.2_noresm_v0
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

[submodule "mct"]
path = libraries/mct
url = https://github.com/MCSclimate/MCT
fxtag = MCT_2.11.0
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/MCSclimate/MCT

[submodule "parallelio"]
path = libraries/parallelio
url = https://github.com/NCAR/ParallelIO
fxtag = pio2_6_2
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/NCAR/ParallelIO

[submodule "doc-builder"]
path = doc/doc-builder
url = https://github.com/ESMCI/doc-builder
fxtag = v1.0.8
fxrequired = ToplevelOptional
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESMCI/doc-builder
13 changes: 13 additions & 0 deletions .lib/git-fleximod/.github/workflows/pre-commit
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
name: pre-commit
on:
pull_request:
push:
branches: [main]

jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v3
- uses: pre-commit/[email protected]
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