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Merge branch 'b4b-dev' into subsetdata-systemtest-rebase2
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‎.github/workflows/check-clm6-aliases.sh‎

Lines changed: 25 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,25 @@
1+
#!/usr/bin/env bash
2+
set -e
3+
4+
# Check that clm6* compset aliases return CLM6* longnames
5+
6+
# Change to top level of clone
7+
cd "$(git rev-parse --show-toplevel)"
8+
9+
# Check that query_config can run without error
10+
cime/scripts/query_config --compsets 1>/dev/null
11+
12+
# Find bad compsets
13+
OLD_IFS=$IFS
14+
IFS='\n'
15+
set +e
16+
# Relies on case sensitivity here: Alias should have Clm6 and longname should have CLM6
17+
bad_compsets="$(cime/scripts/query_config --compsets | sort | uniq | grep Clm6 | grep -v CLM6)"
18+
set -e
19+
if [[ "${bad_compsets}" != "" ]]; then
20+
echo "One or more compsets with Clm6 alias but not CLM6 longname:" >&2
21+
echo $bad_compsets >&2
22+
exit 1
23+
fi
24+
25+
exit 0

‎.github/workflows/check-clm6-aliases.yml‎

Lines changed: 40 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,40 @@
1+
name: Check that clm6* compset aliases return CLM6* longnames
2+
# Only check files in our repo that AREN'T in submodules
3+
# Use a Python command to check each file because xmllint isn't available on GH runners
4+
5+
on:
6+
push:
7+
# Run when a change to these files is pushed to any branch. Without the "branches:" line, for some reason this will be run whenever a tag is pushed, even if the listed files aren't changed.
8+
branches: ['*']
9+
paths:
10+
- '.github/workflows/check-clm6-aliases.sh'
11+
- 'cime/**'
12+
- 'cime_config/config_compsets.xml'
13+
14+
pull_request:
15+
# Run on pull requests that change the listed files
16+
paths:
17+
- '.github/workflows/check-clm6-aliases.sh'
18+
- 'cime/**'
19+
- 'cime_config/config_compsets.xml'
20+
21+
workflow_dispatch:
22+
23+
jobs:
24+
check-clm6-aliases:
25+
runs-on: ubuntu-latest
26+
steps:
27+
- name: Checkout repository
28+
uses: actions/checkout@v4
29+
30+
- name: Checkout submodules
31+
run: |
32+
bin/git-fleximod update
33+
34+
- name: Install xmllint for CIME
35+
run: |
36+
sudo apt-get update && sudo apt-get install --no-install-recommends -y libxml2-utils
37+
38+
- name: Check aliases
39+
run: |
40+
.github/workflows/check-clm6-aliases.sh

‎.github/workflows/formatting_python.yml‎ renamed to ‎.github/workflows/python-tests.yml‎

Lines changed: 22 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
name: Check Python formatting
1+
name: Run Python tests
22

33
on:
44
push:
@@ -18,7 +18,27 @@ on:
1818
- 'cime_config/buildnml/**'
1919

2020
jobs:
21-
lint-and-format-check:
21+
python-unit-tests:
22+
runs-on: ubuntu-latest
23+
steps:
24+
# Checkout the code
25+
- uses: actions/checkout@v4
26+
27+
# Set up the conda environment
28+
- uses: conda-incubator/setup-miniconda@v3
29+
with:
30+
activate-environment: ctsm_pylib
31+
environment-file: python/conda_env_ctsm_py.yml
32+
channels: conda-forge
33+
auto-activate-base: false
34+
35+
# Run Python unit tests check
36+
- name: Run Python unit tests
37+
run: |
38+
cd python
39+
conda run -n ctsm_pylib ./run_ctsm_py_tests -u
40+
41+
python-lint-and-black:
2242
runs-on: ubuntu-latest
2343
steps:
2444
# Checkout the code

‎.gitmodules‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -58,8 +58,8 @@ fxrequired = ToplevelRequired
5858
fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
5959

6060
[submodule "mizuRoute"]
61-
path = components/mizuRoute
62-
url = https://github.com/ESCOMP/mizuRoute
61+
path = components/mizuroute
62+
url = https://github.com/ESCOMP/mizuRoute
6363
fxtag = cesm-coupling.n03_v2.2.0
6464
fxrequired = ToplevelRequired
6565
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed

‎README‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ components/cmeps -------------------- CESM top level driver (for NUOPC driver [w
6666
components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver).
6767
components/cism --------------------- CESM Community land Ice Sheet Model.
6868
components/mosart ------------------- Model for Scale Adaptive River Transport
69-
components/mizuRoute ---------------- Reached based river transport model for water routing
69+
components/mizuroute ---------------- Reached based river transport model for water routing
7070
(allows both gridded river and Hydrologic Responce Unit river grids)
7171
components/rtm ---------------------- CESM River Transport Model.
7272

‎bld/CLMBuildNamelist.pm‎

Lines changed: 64 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -1688,6 +1688,7 @@ sub process_namelist_inline_logic {
16881688
setup_logic_cnmatrix($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
16891689
setup_logic_spinup($opts, $nl_flags, $definition, $defaults, $nl);
16901690
setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
1691+
setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl);
16911692
setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl);
16921693
setup_logic_fates($opts, $nl_flags, $definition, $defaults, $nl);
16931694
setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl);
@@ -1737,7 +1738,6 @@ sub process_namelist_inline_logic {
17371738
# namelist group: ch4par_in #
17381739
###############################
17391740
setup_logic_methane($opts, $nl_flags, $definition, $defaults, $nl);
1740-
setup_logic_c_isotope($opts, $nl_flags, $definition, $defaults, $nl);
17411741

17421742
###############################
17431743
# namelist group: ndepdyn_nml #
@@ -3175,10 +3175,11 @@ sub setup_logic_do_grossunrep {
31753175

31763176
my $var = 'do_grossunrep';
31773177

3178-
# Start by assuming a default value of '.true.'. Then check a number of
3178+
# Start by assuming a default value of '.false.'. Then check a number of
31793179
# conditions under which do_grossunrep cannot be true. Under these
3180-
# conditions: (1) set default value to '.false.'; (2) make sure that the
3180+
# conditions: (1) set default value to '.false.' again; (2) make sure that the
31813181
# value is indeed false (e.g., that the user didn't try to set it to true).
3182+
# Ideally the default value would be set in namelist_defaults
31823183

31833184
my $default_val = ".false.";
31843185

@@ -3703,63 +3704,53 @@ sub setup_logic_c_isotope {
37033704
#
37043705
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
37053706

3707+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
3708+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
37063709
my $use_c13 = $nl->get_value('use_c13');
37073710
my $use_c14 = $nl->get_value('use_c14');
37083711
if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" ) {
37093712
if ( $nl_flags->{'bgc_mode'} ne "bgc" ) {
3710-
if ( defined($use_c13) && &value_is_true($use_c13) ) {
3713+
if ( &value_is_true($use_c13) ) {
37113714
$log->warning("use_c13 is ONLY scientifically validated with the bgc=BGC configuration" );
37123715
}
3713-
if ( defined($use_c14) && &value_is_true($use_c14) ) {
3716+
if ( &value_is_true($use_c14) ) {
37143717
$log->warning("use_c14 is ONLY scientifically validated with the bgc=BGC configuration" );
37153718
}
37163719
}
3717-
if ( defined($use_c14) ) {
3718-
if ( &value_is_true($use_c14) ) {
3719-
my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
3720-
if ( defined($use_c14_bombspike) && &value_is_true($use_c14_bombspike) ) {
3721-
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
3722-
'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
3723-
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
3724-
}
3725-
} else {
3726-
if ( defined($nl->get_value('use_c14_bombspike')) ||
3727-
defined($nl->get_value('atm_c14_filename')) ) {
3728-
$log->fatal_error("use_c14 is FALSE and use_c14_bombspike or atm_c14_filename set");
3729-
}
3720+
if ( &value_is_true($use_c14) ) {
3721+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
3722+
my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
3723+
if ( &value_is_true($use_c14_bombspike) ) {
3724+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
3725+
'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
3726+
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
37303727
}
37313728
} else {
37323729
if ( defined($nl->get_value('use_c14_bombspike')) ||
37333730
defined($nl->get_value('atm_c14_filename')) ) {
3734-
$log->fatal_error("use_c14 NOT set to .true., but use_c14_bompspike/atm_c14_filename defined.");
3731+
$log->fatal_error("use_c14 is FALSE and use_c14_bombspike or atm_c14_filename set");
37353732
}
37363733
}
3737-
if ( defined($use_c13) ) {
3738-
if ( &value_is_true($use_c13) ) {
3739-
my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
3740-
if ( defined($use_c13_timeseries) && &value_is_true($use_c13_timeseries) ) {
3741-
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
3742-
'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
3743-
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
3744-
}
3745-
} else {
3746-
if ( defined($nl->get_value('use_c13_timeseries')) ||
3747-
defined($nl->get_value('atm_c13_filename')) ) {
3748-
$log->fatal_error("use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set");
3749-
}
3734+
if ( &value_is_true($use_c13) ) {
3735+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
3736+
my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
3737+
if ( &value_is_true($use_c13_timeseries) ) {
3738+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
3739+
'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
3740+
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
37503741
}
37513742
} else {
37523743
if ( defined($nl->get_value('use_c13_timeseries')) ||
37533744
defined($nl->get_value('atm_c13_filename')) ) {
3754-
$log->fatal_error("use_c13 NOT set to .true., but use_c13_bompspike/atm_c13_filename defined.");
3745+
$log->fatal_error("use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set");
37553746
}
37563747
}
37573748
} else {
3758-
if ( defined($use_c13) ||
3759-
defined($use_c14) ||
3760-
defined($nl->get_value('use_c14_bombspike')) ||
3749+
if ( &value_is_true($use_c13) ||
3750+
&value_is_true($use_c14) ||
3751+
&value_is_true($nl->get_value('use_c14_bombspike')) ||
37613752
defined($nl->get_value('atm_c14_filename')) ||
3762-
defined($nl->get_value('use_c13_timeseries')) ||
3753+
&value_is_true($nl->get_value('use_c13_timeseries')) ||
37633754
defined($nl->get_value('atm_c13_filename')) ) {
37643755
$log->fatal_error("bgc=sp and C isotope namelist variables were set, both can't be used at the same time");
37653756
}
@@ -4071,7 +4062,16 @@ sub setup_logic_fire_emis {
40714062
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
40724063
$log->warning("Fire emission option $var can NOT be on when FATES is also on.\n" .
40734064
" DON'T use the '--fire_emis' option when '--bgc fates' is activated");
4074-
}
4065+
} elsif ( ! &value_is_true( $nl_flags->{'use_cn'} ) ) {
4066+
$log->fatal_error("Fire emission option $var can NOT be on when BGC SP (i.e. Satellite Phenology) is also on.\n" .
4067+
" DON'T use the '--fire_emis' option when '--bgc sp' is activated");
4068+
} elsif ( &value_is_true( $nl_flags->{'use_cn'}) ) {
4069+
my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') );
4070+
if ( $fire_method eq "nofire" ) {
4071+
$log->fatal_error("Fire emission option $var can NOT be on with BGC and fire_method=='nofire'.\n" .
4072+
" DON'T use the '--fire_emis' option when fire_method is nofire");
4073+
}
4074+
}
40754075
}
40764076
}
40774077
}
@@ -4235,7 +4235,7 @@ sub setup_logic_lai_streams {
42354235
if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) {
42364236
$log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
42374237
}
4238-
if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) {
4238+
if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl_flags->{'use_fates_sp'}) )) {
42394239
if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
42404240
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
42414241
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
@@ -4749,29 +4749,26 @@ sub setup_logic_fates {
47494749
# For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
47504750
# And also check for other settings that can't be trigged on as well
47514751
#
4752-
my $var = "use_fates_sp";
4753-
if ( defined($nl->get_value($var)) ) {
4754-
if ( &value_is_true($nl->get_value($var)) ) {
4755-
my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
4756-
foreach my $var ( @list ) {
4757-
if ( ! &value_is_true($nl->get_value($var)) ) {
4758-
$log->fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
4759-
}
4760-
}
4761-
# spit-fire can't be on with FATES SP mode is active
4762-
if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
4763-
$log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
4764-
}
4752+
if ( &value_is_true($nl_flags->{'use_fates_sp'}) ) {
4753+
my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
4754+
foreach my $var ( @list ) {
4755+
if ( ! &value_is_true($nl->get_value($var)) ) {
4756+
$log->fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
4757+
}
4758+
}
4759+
# spit-fire can't be on with FATES SP mode is active
4760+
if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
4761+
$log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
4762+
}
47654763

4766-
# fates landuse can't be on with FATES SP mode is active
4767-
if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
4768-
$log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
4769-
}
4764+
# fates landuse can't be on with FATES SP mode is active
4765+
if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
4766+
$log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
4767+
}
47704768

4771-
# hydro isn't currently supported to work when FATES SP mode is active
4772-
if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
4773-
$log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
4774-
}
4769+
# hydro isn't currently supported to work when FATES SP mode is active
4770+
if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
4771+
$log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
47754772
}
47764773
}
47774774
my $var = "use_fates_inventory_init";
@@ -4796,6 +4793,13 @@ sub setup_logic_fates {
47964793
}
47974794
}
47984795
}
4796+
# Check that both FaTES-SP and FATES ST3 aren't both on
4797+
my $var = "use_fates_ed_st3";
4798+
if ( defined($nl->get_value($var)) ) {
4799+
if ( &value_is_true($nl->get_value($var)) && &value_is_true($nl_flags->{'use_fates_sp'}) ) {
4800+
$log->fatal_error("$var can NOT also be true with use_fates_sp true" );
4801+
}
4802+
}
47994803
# check that fates landuse change mode has the necessary luh2 landuse timeseries data
48004804
# and add the default if not defined. Do not add default if use_fates_potentialveg is true.
48014805
# If fixed biogeography is on, make sure that flandusepftdat is avilable.

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