* update to include a 'high_Sierra' machine with gnu compilers,
only marginally modified from the travisCI env and Macros.

* Syncing theia and upstream/master branch

* theia execution

* intel compiler version tests -- 15.0.0 or greater

* working on variations for round robin test

* syncing to main

* sync

* testing

* end test

* successful on phase2 for all regression tests

* start on phase3 execution

* add phase3 system

* syncing and phase3 modules

* update configs manually from master

* env edit

* builds on phase3 now

* test

* trying to pull/merge cice master

* theia

* successful theia build

* garbage

* update theia intel env

* mods for running in NOAA

* start towards hera

* tmp

* theia passes with most recent of all modules

* moving to hera

* clean regression run on hera

* cleanup

* phase3 work

* minor manual move towards master copy

* re-fix phase3 script

* nearing full phase3

* update path for data

* actual final version of phase3

* from master

* cicecore updating from master

* from consortium/master

* more from master

* retry sync

* manual add/subtrace

* script perms and large diff files

* retrieve hera

* docs and cicecore sync to master

* machine syncing

* couple more

* some more

* finally the right template

* finally correct template

* typography in master

* restore working batch.csh

* towards matching consortium master

* last? add for syncing

* Revert icepack to 1.1.2

Co-authored-by: Tony Craig <[email protected]>

* Add history_precision option for history files.

* Update to work with pio2

* Precision updates

* Fix missing value precision

* Add documentation

* revert the Macros and env

* revert cice.build

* Move abort statement for history_precision

* add pio standalone capability on cheyenne, add cheyenne_gnu, cheyenne_pgi, fix several bugs in history implementation, add histall setting, add io_suite

* add history_format, add support for pio1.10.1 and pio2.4.2 testing on cheyenne, add support for pio netcdf and pnetcdf testing, clean up Macros files pio settings, clean up some log output

* clean up restart_format

* fix bug in drivers/mct/cesm1/CICE_RunMod.F90 and update documentation

* rebase to current master, fix a couple of minor precision8 bugs, update test suites, update io_pio

* add set_nml.cdf64

* fix error in mct/cesm1 code

* fix nfsd default value and remove io_pio

* update documentation and add nfsd error check

…448)

* cice.setup: remove deprecated variables from cice.settings.mods

Let's not keep these commented variables in cice.settings.mods,
they've been in the namelist for a while now.

* cice.batch.csh: uniformize script output with other scripts

Other scripts called by cice.setup output "running <script name>",
but this convention was not respected by cice.batch.csh.

Uniformize the output to respect the convention.

* parse_namelist.sh: don't use `sed -i` without a backup

Some `sed` implementations (notably, on macOS) do not handle using
the `-i` option without a backup file. As such, the following argument
('-e') is used as an extension for the backup file, resulting in a
file named ${filename}.check-e  which does not get
deleted and stays in the case directory.

Add a backup extension and remove the backup file at the end of the
script.

* doc: remove executable bit from non-script files

* scripts: add support for setting `ICE_CPPDEFS` in set_env.* options

Allow using the present case/test configuration mechanism
(set_env.* in configuration/scripts/options/) to add preprocessor macros.

cice.setup already allows for modifying cice.setttings using set_env.*
options, so the only change needed is to add a default value for
`ICE_CPPDEFS` in the default cice.settings file, and not resetting
this variable in cice.build.

Note that contrary to what was proposed in #445, we
do not implement a similar ICE_SLIBS variable, that could be used to add
linker flags (such as optional libraries), because the way in which
libraries are made accessible and linked with an executable vary
depending on the machine in use, so such modifications are best made in
the Macros.<machine>_<compiler> and env.<machine>_<compiler> files.

Closes #445

* update hera port

* remove phase2 and theia machines

* initial orion port

…#450)

* rename l_conservation_check to conserv_check and move to namelist, copy cice.settings to run directory, update error messages, modify alt03 and alt04 configurations to extend test coverage

* update documentation

* copy env file to run directory

* update documentation

* update documentation

* update documentation

* update documentation

* update icepack and conserv_check setting in icepack

* Remove vector directives

* Remove diag disable in Macros