GEOS-ESM/MAPL: MAPL 2.9.0

This is release of MAPL 2.9.0 tests as zero-diff to 2.8.10 in regards to GEOS. It contains many changes as detailed below including some bugfixes.

• Added option to flip vertical orientation of checkpoint files from the provided orientation which is assumed to be down (TOA -> surface) as index increases. User can provide a per grid comp INTERNAL_CHECKPOINT_POSITIVE: and IMPORT_CHECKPOINT_POSITIVE: option with the default as down. If this is set to up 3D fields that are vlocationedge or vlocationcenter will be flipped on writing and positive in the lev variable will be up. Likewise restarts with positive up will be flipped relative to the orientation in the file.
• Added GEOSldas CI build test
• Added option to regrid to a regional lat-lon grid in the Regrid_Util.x utility
• Added scc badges to README
• Added Service-Services functionality. Components could advertise services they can provide, they can request services to be done to a list of variables, and current components could connect services.
• Added EditorConfig file
  • 4 spaces for Python
  • 2 spaces for CMake and YAML
• Preload available macros in CMake package configuration file.

• Moved newcfio modules from base into new griddedio directory
  • Renamed newCFIO modules and routines to GriddedIO
• Refactored ExtData modules. Because of the dependencies, the following changes were also done:
  • Moved Collection ExtData modules into griddedio directory. Removed the Ext prefix for collection modules and subroutines and types
  • Moved BundleRead and BundleWrite modules from base to griddedio
  • Moved Regrid_Util.F90 from base to griddedio due to griddedio dependency on base. Executable still generated in install/bin
• Updated components.yaml
  • ESMA_cmake v3.6.5 (Bug fix for NAG, support for mepo styles, Release flags are now vectorized, Fix for BASEDIR)
  • ESMA_env v3.4.1 (Support for Cascade Lake, moves to Intel 2021.2)
• Refactored MAPL_IO by separating it into a Binary (BinIO.F90) and NetCDF (NCIO.F90) modules. Shared subroutines and types have been moved to FileIOShared.F90. MAPL_IO becomes a package module to hold these aforementioned three modules.

• Fixed #338. Added a workaround for a gfortran bug that handles end-of-file incorrectly (returns IOSTAT=5001).
• Fixed ESMF logging errors from MAPL_IO (#1032)
• Make BUILD_WITH_PFLOGGER a CMake option()
• MAPL finds yaFyaml in CMake through PFLOGGER::pflogger, so if you build the stub, specifically add it as a dependency
• Fix annoying misspelling of FLAP

• Feature/bmauer/#942 checkpoint positive handling by @bena-nasa in https://github.com/GEOS-ESM/MAPL/pull/1029
• Add GEOSldas CI Build Tests to MAPL by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1033
• Refactors remaining ExtData Modules by @Gvilla1000-nasa in https://github.com/GEOS-ESM/MAPL/pull/1031
• Closes #1034. Cleans up redundant CircleCI code by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1036
• Closes #1032. Fix logging error with FLIPPED AttributeGet by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1039
• Auto GitFlow - main → develop by @github-actions in https://github.com/GEOS-ESM/MAPL/pull/1043
• add options to regrid to regional lat-lon grid in Regrid_Util.x by @bena-nasa in https://github.com/GEOS-ESM/MAPL/pull/1041
• Bugfix/atrayno/#338 enf of file gfortran bug by @atrayano in https://github.com/GEOS-ESM/MAPL/pull/1038
• Auto GitFlow - main → develop by @github-actions in https://github.com/GEOS-ESM/MAPL/pull/1047
• Add scc badges by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1051
• Update to ESMA_cmake 3.5.7, ESMA_env 3.3.1 by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1053
• Refactors MAPL_IO to separate Binary and NetCDF subroutines. by @Gvilla1000-nasa in https://github.com/GEOS-ESM/MAPL/pull/1055
• Fixes #1032...again. by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1057
• Changes to prettify CircleCI by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1066
• AT: Very first --alpha-- version of service-services. The code compil… by @atrayano in https://github.com/GEOS-ESM/MAPL/pull/547
• Handmerge main into develop (2021-Oct-12) by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1072
• Handmerge main hotfix into develop 2021-Oct-13 by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1078
• Auto GitFlow - main → develop by @github-actions in https://github.com/GEOS-ESM/MAPL/pull/1076
• Update ESMA_cmake and ESMA_env, other fixes by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1062
• Add EditorConfig File by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1061
• Handmerge main to develop 2021-Oct-15 by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1086
• Handmerge main to develop 2021-Oct-18 by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1097
• Update to ESMA_cmake v3.6.5 and ESMA_env 3.4.1 by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1099
• Improve MAPL configuration for external projects by @rmontuoro in https://github.com/GEOS-ESM/MAPL/pull/1101
• Prepare for 2.9.0 Release by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1103
• Merge Develop into Main for 2.9.0 Release by @mathomp4 in https://github.com/GEOS-ESM/MAPL/pull/1105

Full Changelog: https://github.com/GEOS-ESM/MAPL/compare/v2.8.10...v2.9.0