Merge branch 'jgfouca/update_to_cime_5.3.0.34' into next (PR #1788)

New user interface features:
option --skip-preview-namelist to case.submit to skip calling preview_namelist during case.run
option -M MAIL_USER, --mail-user MAIL_USER to case.submit to set an email for batch system notification
option -m {never,all,begin,end,fail}, --mail-type {never,all,begin,end,fail} to case.submit for when the batch system should send email.
manage_case renamed to more accurate query_config and usage/arguments made easier and output more informative.
Add --pesfile option to create_test
New case.qstatus tool
Allow user to adjust ulimits
Add message at end of successful build
Add new user-mods option to create_clone
New ways to select queue in config_batch.xml
scripts_regression_tests.py now has --compiler and --mpilibs option
new case variables controlling spare nodes (for failing nodes workaround)

User interface bug fixes:
xmlquery options --file and --listall now work together.
xmlquery options clarified and help message improved.
Improve error message for passing incorrect grid alias to create_newcase.
Improve error messages from xmlchange

Removed user features:
Remove long term archiving support. "case.lt_archive" no longer in caseroot.

Other changes to case control system:
Improve ERR test.
New ERS2 test
Add IRT test
Implement NCR with SystemTestsCompareTwo
Rewrite ERP with SystemTestsCompareTwo
Convert the ERR and ERRI test to the compare2 framework
Fix SEQ test on skybridge
new case.test --reset option to manually reset a test to initial conditions.
TOTAL_CORES was inaccurate so remove it.
Only create rest directories if they are going to be populated
get_timing.py should use largest ncpl value, not assume it's the atm value
Improve comment for BASELINE status in TestStatus
Better handling of fails in the build (don't print a python stacktrace)
Add a new directory testmod that creates cpl history files on a daily basis and thereby permits answer changes to be compared more easily.
Add ability for create_test to infer non-default machine from testname
Change all python2 style strings to python3 style strings
Improve handling of hist comparisons in TestStatus.log
version 3.0 schema for entry_id files
Downscale build parallelism on small machines (so we don't overload it)
Bring bless_test_results behavior into an exact match with create_test -g
lcdf4 flag does apply to pnetcdf.
Replace cdf64 logical with PIO_NETCDF_FORMAT character variable
Refactor how spare nodes get computed
Preserve test order in test_scheduler
Allow queue selection by node count instead of task count
Improve error check for non-python sub processes

Data model changes:
Refactored data models
Use %CPLHIST for DATM coupler hist forcing
Add support for data model to read multiple time slices at once
New aquaplanet capability: adds aquaplanet capability to DOCN where the input is from a file rather than analytic; adds new A compsets to the driver config_compsets.xml that have different DOCN functionality: ADSOM - DOCN SOM, ADSOMAQP - DOCN aquaplanet SOM, ADAQP3 - DOCN analytic aquaplanet (mode 3), ADAQFILE - DOCN aquaplanet from file
DATM updates for clm
Change SIAF compset name in dice to IAF to be consistent with other components

Coupler/driver changes:
Map SMB from lnd to glc using bilinear mapping with a conservation correction
Remove more cesm refs in filenames.
seq_comm_mct code cleanup
Implementation of multiple couplers within multi-instance runs.

Other:
User's guide rst files now in cime/doc directory
Get PFUnit working on melvin
Homebrew generic mac port

Fixes #1255
Fixes #1424
Fixes #1426
Fixes #1573
Fixes #1576
Fixes #1585

* jgfouca/update_to_cime_5.3.0.34: (932 commits)
  One more short term archiver fix
  Fix merge conflicts, should mostly work
  cetus xml fix
  Hack to get PET test to work on chama
  Fix HOMME Cmake pointing to wrong cime area
  Update run_acme version
  Fixes for AQUAP
  Removes long term archiving from run_acme
  Move xml compiler and mpilib tags from env and command elements This is required for the new xml schema requirements; compiler and mpilib tags should be in the modules and environment_variables elements rather than their members
  Cherry-pick fixes from older merge branch
  cime_developer now working on melvin
  new git pelayout doc
  Update ChangeLog
  Change atm_grid "48x96" to T31 to match the model_grid_alias that is actually being used.
  Minor fix
  Fix mistake
  Better encapsulation of common calls (create_test, wait_for_tests)
  Add a timeout option to wait_for_tests
  update to sphinx documentation
  Restore task_count
  ...

cime/.github/PULL_REQUEST_TEMPLATE

@@ -1,6 +1,8 @@
 [ Description of the changes in this Pull Request. It should be enough
 information for someone not following this development to understand.
-Lines should be wrapped at about 72 characters. ]
+Lines should be wrapped at about 72 characters. Please also update
+the CIME documentation, if necessary, in doc/source/rst and indicate
+below if you need to have the gh-pages html regenerated.]
 
 Test suite: 
 Test baseline: 
@@ -11,4 +13,6 @@ Fixes [CIME Github issue #]
 
 User interface changes?: 
 
+Update gh-pages html (Y/N)?:
+
 Code review: 

cime/.gitignore

@@ -4,3 +4,9 @@ buildnmlc
 
 # Ignore emacs backup files
 *~
+
+# Ignore doc/build/doctrees
+##doc/build/doctrees 
+# ignore for the merge to master and orphaning of the gh-pages branch
+doc/build
+

cime/CMakeLists.txt

@@ -84,6 +84,7 @@ endif()
 # by different tests?)
 set(SHARE_ROOT "${CIME_ROOT}/src/share")
 add_subdirectory(${SHARE_ROOT}/util csm_share)
+add_subdirectory(${SHARE_ROOT}/unit_test_stubs/util csm_share_stubs)
 include_directories(${SHARE_ROOT}/include)
 
 # esmf_wrf_timemgr not built here because it depends on csm_share.