Merge Pull Request #3014 from E3SM-Project/scream/bartgol/eamxx/atmmanip-any

Automatically Merged using E3SM Pull Request AutoTester
PR Title: Change handling of multiple matches in atmchange/atmquery
PR Author: bartgol
PR LABELS: enhancement, AT: AUTOMERGE, scripts

Author: E3SM-Bot

components/eamxx/cime_config/eamxx_buildnml.py

@@ -126,7 +126,7 @@ def perform_consistency_checks(case, xml):
     >>> case = MockCase({'ATM_NCPL':'24', 'REST_N':2, 'REST_OPTION':'nsteps'})
     >>> perform_consistency_checks(case,xml)
     Traceback (most recent call last):
-    CIME.utils.CIMEError: ERROR: rrtmgp::rad_frequency incompatible with restart frequency.
+    CIME.utils.CIMEError: ERROR: rrtmgp::rad_frequency (3 steps) incompatible with restart frequency (2 steps).
      Please, ensure restart happens on a step when rad is ON
     >>> case = MockCase({'ATM_NCPL':'24', 'REST_N':10800, 'REST_OPTION':'nseconds'})
     >>> perform_consistency_checks(case,xml)
@@ -970,7 +970,7 @@ def create_input_data_list_file(case,caseroot):
                             permissions = stat.filemode(file_stat.st_mode)
 
                         except Exception as e:
-                            raise RuntimeError(f"Error retrieving file info for '{file_path}': {e}")
+                            raise RuntimeError(f"Error retrieving file info for '{file_path}': {e}") from e
 
                         curr_user = getpass.getuser()
                         user_info = pwd.getpwnam(curr_user)

components/eamxx/cime_config/testdefs/testmods_dirs/scream/internal_diagnostics_level/shell_commands

@@ -1,2 +1,2 @@
-$CIMEROOT/../components/eamxx/scripts/atmchange --all internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
 ./xmlchange POSTRUN_SCRIPT="$CIMEROOT/../components/eamxx/scripts/check-hashes-ers"

components/eamxx/cime_config/testdefs/testmods_dirs/scream/small_kernels/shell_commands

@@ -1,2 +1,2 @@
 ./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_SMALL_KERNELS On'
-$CIMEROOT/../components/eamxx/scripts/atmchange --all internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b

components/eamxx/cime_config/testdefs/testmods_dirs/scream/small_kernels_p3/shell_commands

@@ -1,2 +1,2 @@
 ./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_P3_SMALL_KERNELS On'
-$CIMEROOT/../components/eamxx/scripts/atmchange --all internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b

components/eamxx/cime_config/testdefs/testmods_dirs/scream/small_kernels_shoc/shell_commands

@@ -1,2 +1,2 @@
 ./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_SHOC_SMALL_KERNELS On'
-$CIMEROOT/../components/eamxx/scripts/atmchange --all internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b

components/eamxx/docs/user/model_input.md

@@ -148,7 +148,7 @@ scoped name, which allows `atmchange` to uniquely identify the XML node to modif
 $ ./atmquery homme::number_of_subcycles
     namelist_defaults::atmosphere_processes::homme::number_of_subcycles: 1
 $ ./atmchange number_of_subcycles=10
-ERROR: number_of_subcycles is ambiguous (use --all to change all matches), matches:
+ERROR: internal_diagnostics_level is ambiguous. Use ANY in the node path to allow multiple matches. Matches:
   namelist_defaults::atmosphere_processes::number_of_subcycles
   namelist_defaults::atmosphere_processes::sc_import::number_of_subcycles
   namelist_defaults::atmosphere_processes::homme::number_of_subcycles
@@ -157,6 +157,7 @@ ERROR: number_of_subcycles is ambiguous (use --all to change all matches), match
   namelist_defaults::atmosphere_processes::physics::mac_aero_mic::tms::number_of_subcycles
   namelist_defaults::atmosphere_processes::physics::mac_aero_mic::shoc::number_of_subcycles
   namelist_defaults::atmosphere_processes::physics::mac_aero_mic::cldFraction::number_of_subcycles
+  namelist_defaults::atmosphere_processes::physics::mac_aero_mic::spa::internal_diagnostics_level
   namelist_defaults::atmosphere_processes::physics::mac_aero_mic::p3::number_of_subcycles
   namelist_defaults::atmosphere_processes::physics::rrtmgp::number_of_subcycles
   namelist_defaults::atmosphere_processes::sc_export::number_of_subcycles
@@ -167,7 +168,7 @@ $ ./atmquery homme::number_of_subcycles
 ```
 
 In some cases, the user may be interested in changing _all_ nodes with a given name. In that case,
-the `--all` flag can be used:
+you can use 'ANY' as a node name:
 
 ```shell
 $ ./atmquery --grep number_of_subcycles
@@ -183,7 +184,7 @@ $ ./atmquery --grep number_of_subcycles
     p3::number_of_subcycles: 1
     rrtmgp::number_of_subcycles: 1
     sc_export::number_of_subcycles: 1
-$ ./atmchange --all number_of_subcycles=3
+$ ./atmchange ANY::number_of_subcycles=3
 Regenerating /path/to/namelist_scream.xml. Manual edits will be lost.
 $ ./atmquery --grep number_of_subcycles
     atmosphere_processes::number_of_subcycles: 3
@@ -199,6 +200,24 @@ $ ./atmquery --grep number_of_subcycles
     rrtmgp::number_of_subcycles: 3
     sc_export::number_of_subcycles: 3
 ```
+In addition, "ANY" can be used in a "scoped" string, to limit the set of matches:
+```shell
+$ ./atmchange mac_aero_mic::ANY::number_of_subcycles=1
+Regenerating /path/to/namelist_scream.xml. Manual edits will be lost.
+$ ./atmquery --grep number_of_subcycles
+    atmosphere_processes::number_of_subcycles: 3
+    sc_import::number_of_subcycles: 3
+    homme::number_of_subcycles: 3
+    physics::number_of_subcycles: 3
+    mac_aero_mic::number_of_subcycles: 1
+    tms::number_of_subcycles: 1
+    shoc::number_of_subcycles: 1
+    cldFraction::number_of_subcycles: 1
+    spa::number_of_subcycles: 1
+    p3::number_of_subcycles: 1
+    rrtmgp::number_of_subcycles: 3
+    sc_export::number_of_subcycles: 3
+```
 
 Since the XML file stores constraints on the parameter value (like its type or valid values), attempting to use the
 wrong type will cause an error: