Merge branch 'gchp/dev' into feature/FillValue_handling_fix

.github/workflows/changelog-enforcer.yml

@@ -1,21 +1,21 @@
-# name: "Enforce Changelog"
-# on:
-#   pull_request:
-#       types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+name: "Enforce Changelog"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
 
-# jobs:
-#   # Enforces the update of a changelog file on every pull request 
-#   changelog:
-#     runs-on: ubuntu-latest
-#     steps:
-#     - uses: dangoslen/changelog-enforcer@v3
-#       with:
-#         changeLogPath: 'CHANGELOG.md'
-#         skipLabels: 'Skip Changelog,0 diff trivial,automatic'
-#         missingUpdateErrorMessage: >
-#             No update to CHANGELOG.md found! Please add a changelog
-#             entry to it describing your change.  Please note that the
-#             keepachangelog (https://keepachangelog.com) format is
-#             used. If your change is very trivial not applicable for a
-#             changelog entry, add a 'Skip Changelog' label to the pull
-#             request to skip the changelog enforcer.
+#jobs:
+#  # Enforces the update of a changelog file on every pull request
+#  changelog:
+#    runs-on: ubuntu-latest
+#    steps:
+#    - uses: dangoslen/changelog-enforcer@v3
+#      with:
+#        changeLogPath: 'CHANGELOG.md'
+#        skipLabels: 'Skip Changelog,0 diff trivial,automatic'
+#        missingUpdateErrorMessage: >
+#            No update to CHANGELOG.md found! Please add a changelog
+#            entry to it describing your change.  Please note that the
+#            keepachangelog (https://keepachangelog.com) format is
+#            used. If your change is very trivial not applicable for a
+#            changelog entry, add a 'Skip Changelog' label to the pull
+#            request to skip the changelog enforcer.

.github/workflows/validate_yaml_files.yml

@@ -0,0 +1,31 @@
+---
+
+# Based on code from https://github.com/marketplace/actions/yaml-lint
+
+name: Yaml Lint
+
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+# This validation is equivalent to running on the command line:
+#   yamllint -d relaxed --no-warnings
+# and is controlled by the .yamllint.yml file
+jobs:
+  validate-YAML:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - id: yaml-lint
+        name: yaml-lint
+        uses: ibiqlik/action-yamllint@v3
+        with:
+          no_warnings: true
+          format: colored
+          config_file: .yamllint.yml
+
+      - uses: actions/upload-artifact@v2
+        if: always()
+        with:
+          name: yamllint-logfile
+          path: ${{ steps.yaml-lint.outputs.logfile }}

.gitignore

@@ -8,3 +8,10 @@
 /.mepo/
 *.py.bak
 CMakeUserPresets.json
+
+*.swp
+*.swo
+.DS_Store
+*#
+.#*
+**/CVS/

.yamllint.yml

@@ -0,0 +1,29 @@
+---
+
+extends: default
+
+rules:
+  braces:
+    level: warning
+    max-spaces-inside: 1
+  brackets:
+    level: warning
+    max-spaces-inside: 1
+  colons:
+    level: warning
+  commas:
+    level: warning
+  comments: disable
+  comments-indentation: disable
+  document-start: disable
+  empty-lines:
+    level: warning
+  hyphens:
+    level: warning
+  indentation:
+    level: warning
+    indent-sequences: consistent
+  line-length:
+    level: warning
+    allow-non-breakable-inline-mappings: true
+  truthy: disable

Apps/MAPL_GridCompSpecs_ACG.py

@@ -73,16 +73,11 @@ def get_rank(self):
 
     @staticmethod
     def internal_name(name):
-        if name[-1] == '*':
-            return name[:-1]
-        else:
-            return name
+        return name.replace('*','')
+
     @staticmethod
     def mangled_name(name):
-        if name[-1] == '*':
-            return "'" + name[:-1] + "'//trim(comp_name)"
-        else:
-            return "'" + name + "'"
+        return "'" + name.replace("*","'//trim(comp_name)//'") + "'"
 
     # Pointers must be declared regardless of COND status.  Deactivated
     # pointers should not be _referenced_ but such sections should still

CHANGELOG.md

@@ -17,6 +17,224 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.26.0] - 2022-09-16
+
+### Fixed
+
+- Change the logic to check if the field is already connected to a valid grid. If yes, we bypass the checks for tilegrid (issue #1654)
+- Removed unnecessary DSO extension assert
+- Fixed bug that required a /dev/null ExtData entry to still have a file variable name
+- Fixed bug with checking for duplicate alias in collection
+- Added protection in History to only allow `instantaneous` or `time-averaged` modes
+
+### Added
+
+- Added Ninja build of MAPL to CI tests
+
+### Changed
+
+- Have `MAPL_AddChildFromDSO` call `MAPL_AddChildFromDSOMeta` (#1598)
+
+### Removed
+
+- Removed unused code from History GridComp
+
+## [2.25.0] - 2022-09-01
+
+### Fixed
+
+- Fix setting stretched grid target latitude and longitude from restart file metadata
+
+### Added
+
+- Added member function get_global_var to FileMetadata
+- Added option to build source tarfile when building MAPL standalone. By default this is `OFF`, but can be enabled with
+  `-DINSTALL_SOURCE_TARFILE=ON`
+- Added `regrid_method` metadata to History output
+- Added an overloaded interface for MAPL_BalanceWork to handle both REAL32 and REAL64
+
+### Changed
+
+- Updated `components.yaml` to match GEOSgcm v10.22.5 (actually a bit beyond)
+  - ESMA_env v4.2.0 → v4.4.0 (Update to Intel 2022.1, Add TOSS4 Support at NAS)
+  - ESMA_cmake v3.17.0 → v3.18.0 (Updates to CPack and Provisional M2 Support)
+
+### Removed
+
+- Removed `LatLonGridFactory_basic` factory constructor (dead code)
+## [2.24.0] - 2022-08-08
+
+### Fixed
+
+- Fix error trapping in bundleio test
+
+### Added
+
+- Add tutorials
+- Check for duplicate entries in the History.rc file
+- Check that a user-provided chunking in the History.rc is compatible with the output grid
+- If a user requests CFIOasync in the History.rc, print warning and set to CFIO
+- Added option allow writing to pre-existing files with History
+
+### Changed
+
+- Replaced deprecated __RC__ macro with _RC and remove unused code in ExtData2G
+- Moved to `checkout@v3` action due to git safe directory issue
+- Added tutorials to CI
+
+## [2.23.1] - 2022-07-15
+
+### Fixed
+
+- Fixed the History file existence detection to only run for netCDF output. For still unknown reasons, this detection has an issue
+  with binary output (see https://github.com/GEOS-ESM/GEOSldas/pull/568)
+- Fix GitHub Actions
+
+## [2.23.0] - 2022-07-06
+
+### Added
+
+- Check return codes for YAML files when parsing in ExtData2G
+
+### Changed
+
+- Updated the ESMA_env version to v4.2.0 (Baselibs 7.5.0 → GFE v1.4.0)
+  - With this update, MAPL now **requires** these versions of GFE libraries
+    - yaFyaml v1.0.4 (if building with ExtData2G support)
+    - pFlogger v1.9.1 (if building with pFlogger support)
+- Update the CI for Baselibs 7.5.0, BCs version 10.22.3
+
+## [2.22.0] - 2022-06-24
+
+### Fixed
+
+- By pass the check of the missing value of Nan
+- Update CI to work with latest GEOSadas `develop` (Uses a special branch of GEOSadas)
+- Fix bundleio tests
+- HistoryGridComp now checks if a file exists already before writing and errors out if so
+- Minor updates for FORD documentation testing
+  - Add `program` statements to some test programs
+  - Remove `pfio/pfio_io_demo.F90` as dead code
+  - Fix redefinition of `_RETURN` in `pflogger_stub.F90`
+  - Removed unused `Test_SimpleClient.pf`
+- Update CMake to require NetCDF C components and add `NetCDF::NetCDF_C` to pfio CMake
+
+### Added
+
+- Updated MAPL_CapGridComp to mark fields going to ExtData to not be checkpointed by components
+- Add debug loggers for start/stop during stages in MAPL_Generic
+- Handling for double precision input when retrieving single precision attributes
+- Enable GCM run test in CircleCI (1-hour, no ExtData)
+- Added monotonic regridding option
+- Make availalbe to History and ExtData2G all supported regridding methods
+- Add test cases for ExtData
+- Add YAML validator GitHub Action
+  - This action makes sure all YAML files are valid (to a relaxed standard)
+
+### Changed
+
+- Modified error messages in FileMetadataUtilities to be unique and print filename
+- Updated the ESMA_env version to v3.14.0
+- Updated the ESMA_cmake version to v3.17.0
+- Updated GitHub Actions MAPL build tests
+- Added assert for missing file with ExtData2G
+- Re-enable bundleio tests in CI
+- Updated CircleCI to use latest Baselibs
+- Updates for Spack support
+   - Add `find_package(MPI)` for non-Baselibs builds
+   - Add explicit interface dependence of `MPI` for `ESMF` target
+   - Add `esmf` alias library for `ESMF` for compatibility
+
+## [2.21.3] - 2022-06-07
+
+### Fixed
+
+- Fixed bug in non cubed-sphere grid path in MAPL_GetHorzIJIndex
+
+## [2.21.2] - 2022-05-31
+
+### Fixed
+
+- Initialize `cap%lperp` in `MAPL_CapGridComp.F90` (see Issue #1530)
+
+## [2.21.1] - 2022-05-24
+
+### Fixed
+
+- Adding missing _RETURN and _VERIFY macros in GriddedIO.F90
+- Update CircleCI to work with latest GEOSadas
+
+## [2.21.0] - 2022-05-05
+
+### Fixed
+
+- Fixed incorrect legend when using PRINTSPEC option in MAPL Cap
+- Fix ESMF errors exposed by monthly collections
+
+### Added
+
+- Added has_variable function to FileMetadata
+- Added information about the container type for each item in state when using PRINTSPEC option
+
+### Changed
+
+- Change many instances of `_ASSERT(.false.,"msg")` to `_FAIL("msg")`
+- Extended format width for exclusive and inclusive times in profiler from `f9.2` to `f10.2` (see #1420)
+
+## [2.20.0] - 2022-04-19
+
+### Fixed
+
+- Removed one redundant get_file_extension call
+- Fix issue where ACG was called when no file had changed
+- Add missing `rc=status` in `MAPL_GetResourceFromMAPL_scalar`
+- Fixed bugs with next generation ExtData
+- Fixed variable PTR40 declaration in GenericCplComp.F90
+
+### Added
+
+- Added support for 4d variables in the coupler. Intentionally decided not to support 4d in the coupler's ReadRestart and WriteRestart to catch errors
+- Added ability to use multiple rules for different time periods in next generation ExtData
+
+### Changed
+
+- Cleaned up a bit of old CMake
+- Updated CircleCI config to use new orb `build` job
+- Updated `components.yaml` to match GEOSgcm v10.22.1
+  - ESMA_env v3.13.0
+  - ESMA_cmake v3.12.0
+
+## [2.19.2] - 2022-03-28
+
+### Fixed
+
+-  Provided workaround for  GNU bug when defining file metadata in cubed-sphere grid factory (similar to Issue #1433 and its solution)
+
+## [2.19.1] - 2022-03-24
+
+### Fixed
+
+- Fix a bug deallocating a pointer potentially pointing to shared memory allocated by MAPL_Shmem
+
+## [2.19.0] - 2022-03-18
+
+### Fixed
+
+- Fixed duration of the clock to be the smaller of the user specified duration and (END_DATE - currTime)
+- Fixes for compiling on M1 Macs (remove REAL128)
+- Fix for CMake when `esmf` is already a target
+
+### Added
+
+- New cmake option USE_EXTDATA2G to enable the next generation of ExtData for development, by default uses 1st generation ExtData
+- MAPL_ESMFFieldBundleRead/Write modules are now available in when using MAPL
+
+### Changed
+
+- Replaced a wild card "*" in any position of a string in MAPL_GridCompSpecs_ACG.py
+- Updated `MAPL_SunGetSolarConstantFromNRLFile` to open NRL Solar Table file only on root and broadcast the tables to all processes.  Now all processes do interpolation.
+- Add voting interpolation method as optional argument to SimpleBundleRead method
+
 ## [2.18.3] - 2022-03-15
 
 ### Fixed
@@ -54,6 +272,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updates to CircleCI
   - Added GEOSadas CI ifort build test
   - Add "like-UFS" build to CI. This is no FLAP and pFlogger, and static build
+- Added new `_STAT` and `_IOSTAT` macros a la `_RC`
 
 ### Changed
 
@@ -66,6 +285,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated `components.yaml`. These changes are to support using Spack to build MAPL
   - ESMA_cmake v3.10.0 (add `FindESMF.cmake` from NOAA-EMC)
   - ecbuild geos/v1.2.0 (updat `FindNetCDF.cmake` to that from NOAA-EMC)
+- Improved file-not-found error handling in ExtData for non-templated filenames
 
 ## [2.17.2] - 2022-02-16