Merge branch 'master' into expand_documentation

.github/CODEOWNERS

@@ -25,44 +25,47 @@
 # These owners will be the default owners for all the files in the
 # repository.  Unless a later match is found, these owners
 # will be requested for a review when a PR is opened.
-*          @wrongkindofdoctor @thomas-robinson @colingladueNOAA
+*          @wrongkindofdoctor @thomas-robinson @bensonr @rem1776
 
 # GNU autotools files
-Makefile.am      @underwoo @colingladueNOAA
-/configure.ac    @underwoo @colingladueNOAA
-/m4/             @underwoo @colingladueNOAA
-*.m4             @underwoo @colingladueNOAA
+Makefile.am      @uramirez8707 @rem1776
+/configure.ac    @uramirez8707 @rem1776
+/m4/             @uramirez8707 @rem1776
+*.m4             @uramirez8707 @rem1776
+
+# cmake files
+CM*              @mlee03 @ngs333
+cmake            @mlee03 @ngs333
 
 # Files specific to GitHub or GitLab
-/.github/        @underwoo @colingladueNOAA
-/.gitlab/        @underwoo @colingladueNOAA
+/.github/        @GFDL-Eric @rem1776
+/.gitlab/        @GFDL-Eric @rem1776
 
 # Testing files
-/.gitlab-ci.yml  @uramirez8707 @mlee03 @underwoo @bensonr @thomas-robinson @wrongkindofdoctor @colingladueNOAA
-/.travis.yml     @uramirez8707 @mlee03 @underwoo @bensonr @thomas-robinson @wrongkindofdoctor @colingladueNOAA
-/test_fms/       @uramirez8707 @mlee03 @underwoo @bensonr @thomas-robinson @wrongkindofdoctor @colingladueNOAA
+/.gitlab-ci.yml  @uramirez8707 @mlee03 @bensonr @thomas-robinson @wrongkindofdoctor @rem1776
+/test_fms/       @uramirez8707 @mlee03 @bensonr @thomas-robinson @wrongkindofdoctor @rem1776
 
 # Specific component directories
 /affinity/          @bensonr
-/test_fms/affinity/ @bensonr @colingladueNOAA
+/test_fms/affinity/ @bensonr @rem1776
 
 /block_control/          @bensonr
-/test_fms/block_control/ @bensonr @colingladueNOAA
+/test_fms/block_control/ @bensonr @rem1776
 
 /data_override/          @GFDL-Eric
-/test_fms/data_override/ @GFDL-Eric @colingladueNOAA
+/test_fms/data_override/ @GFDL-Eric @rem1776
 
-/diag_manager            @thomas-robinson @underwoo @ngs333
-/test_fms/diag_manager/  @thomas-robinson @underwoo @ngs333 @colingladueNOAA
+/diag_manager            @thomas-robinson @ngs333
+/test_fms/diag_manager/  @thomas-robinson @ngs333
 
 /fv3gfs/          @bensonr
 
-/fms/             @wrongkindofdoctor @thomas-robinson
-/test_fms/fms/    @wrongkindofdoctor @thomas-robinson @colingladueNOAA
-/fms2/            @wrongkindofdoctor @thomas-robinson
-/test_fms/fms2/   @wrongkindofdoctor @thomas-robinson @colingladueNOAA
+/fms/             @wrongkindofdoctor @thomas-robinson @rem1776
+/test_fms/fms/    @wrongkindofdoctor @thomas-robinson @rem1776
+/fms2/            @uramirez8707 @GFDL-Eric
+/test_fms/fms2/   @uramirez8707 @GFDL-Eric
 
-/libFMS/           @underwoo @colingladueNOAA
+/libFMS/           @thomas-robinson @rem1776
 
-/mpp/              @wrongkindofdoctor @thomas-robinson
-/test_fms/mpp/     @wrongkindofdoctor @thomas-robinson @colingladueNOAA
+/mpp/              @wrongkindofdoctor @thomas-robinson @bensonr
+/test_fms/mpp/     @wrongkindofdoctor @thomas-robinson @bensonr @rem1776

.github/workflows/build_ubuntu_gnu.yml

@@ -0,0 +1,32 @@
+name: Build libFMS test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        distcheck-conf-flags: [--enable-openmp, --disable-openmp, --enable-mixed-mode, --disable-setting-flags]
+        fcflags: ["-I/usr/include", "-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include"]
+        exclude:
+          - distcheck-conf-flags: --disable-setting-flags
+            fcflags: -I/usr/include
+          - distcheck-conf-flags: --enable-mixed-mode
+            fcflags: "-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include"
+    container:
+      image: underwoo/ubuntu_libfms_gnu
+      env:
+        FCFLAGS: "${{ matrix.fcflags }}"
+        VERBOSE: 1
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+    - name: Prepare GNU autoconf for build
+      run: autoreconf -if
+    - name: Configure the build
+      run: ./configure ${{ matrix.distcheck-conf-flags }}
+      env:
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.distcheck-conf-flags }}"
+    - name: Build the library
+      run: make -j distcheck

.github/workflows/lint_fms.yml

@@ -0,0 +1,12 @@
+name: libFMS lint tests
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Run Lint
+        uses: NOAA-GFDL/simple_lint@v1

CHANGELOG.md

@@ -5,6 +5,72 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0),
 and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is released,
 `rr` is a sequential release number (starting from `01`), and an optional two-digit
 sequential patch number (starting from `01`).
+## [2020.04] - 2020-12-07
+### Added
+- DIAG_MANAGER: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
+- DIAG_MANAGER: A check is added before a time axis is registered to check if the time axis is registered as a variable
+- DIAG_MANAGER: A unit test was added to test the optional `new_file_freq` functionality
+- XGRID: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io.  The default is .false. and will use fms2_io.
+- INTERPOLATOR: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
+- AMIP_INTERP: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
+- TOPOGRAPHY: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
+- DATA_OVERRIDE: A namelist flag called `use_mpp_bug` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
+- DATA_OVERRIDE: A namelist flag called `reproduce_null_char_bug_flag` if set to .true. and fms2_io is being used, it will reproduce the mpp_io bug where the axis bounds were calculated instead of read. The default is .false.
+A unit test was added to test the functionality of `get_grid_version_1`
+- FMS2_IO: A unit test was added to test the functionality of `get_valid` and `is_valid`
+### Changed
+- The autotools build has been changed to copy each subdirectory module (.mod) files to a common .mod directory located at the top of the source directory.  This change simplifies the include path specifications.
+- Use F90 module files for external libraries (MPI and NetCDF) for improved interface checking, thereby removing the reliance on library header include files.
+### Removed
+- LIBFMS: The flag -Duse_mpp_io should not be used and will cause a crash
+- LIBFMS: Macros and logic for interfacing to the Flexible File I/O library
+- LIBFMS: Macros for SGI MIPSpro compilers, including: mpp_node function and SGI Irix specific high resolution timer
+- LIBFMS: Macros for IBM AIX compilers
+- LIBFMS: Files in mpp supporting the CRAY SHMEM communications library
+- LIBFMS: Files in mpp for the SGI PSET approach for communication via GSM
+### Fixed
+- DATA_OVERRIDE: Fixed a bug in `get_grid_version_1` where the variable_size calls were not correct
+- FMS2_IO: Fixed a bug in `get_valid` where the mpp_broadcast calls were done inside `if (root_pe)` blocks
+The fms2_io unit tests were modified so they can work with the AOCC compiler
+- XGRID: Fixed a bug in `load_xgrid` by checking if a dimension exists before calling `get_dimension_size` to avoid `FATAL: NetCDF: Invalid dimension ID or name` crashes
+### Tag Commit Hashes
+- 2020.04-alpha1 (2428bb182133b8062432ee1b15974739753ca470)
+- 2020.04-alpha2 (ad9915d83a2f34610cd748fd85889ba1f0f1fc02)
+- 2020.04-alpha3 (e7e48839ab25cc9405abe5d8418e1b6ee6fb2d69)
+- 2020.04-beta1 (6d3ac620423e7ede412e4bb1b36c338775d95193)
+
+## [2020.03] - 2020-10-08
+### Added
+- FMS2_IO: Adds header_buffer_val to the fms2io namelist which sets the netcdf header size in bytes. The default value is 16kb
+- FMS2_IO: Adds netcdf_default_format to the fms2io namelist which allows the user to change the netcdf file type. The default value is 64bit.
+- FMS2_IO: Adds support to read netcdf string global attributes
+- FMS2_IO: Adds an optional argument to open_file, `dont_add_res_to_filename`, which indicates that the filename should not be modified (default adds .res to restart file name)
+- FMS2_IO: Modifies the `register_variable_attribute` and `register_global_attribute` interfaces by adding str_len as an argument. This is a workaround to get fms2io to work with PGI because they don't support class (*) with len=*.
+- FMS2_IO: Adds unit test that tests `write_data` and `read_data` when using a domain with a mask table
+- FMS2_IO: Adds fms2io’s version of get_mosaic_tile_grid
+- MPP_IO: Adds `-Duse_mpp_io` compile option for data_override, interpolator, amip_interp, diag_manager, topography, and xgrid to select using mpp_io instead of fms2_io
+- MPP_INIT: Adds unit tests for routines/functions that are called in mpp_init
+- CMAKE: A cmake build system has been added with a CI build using cmake
+### Changed
+- FMS2_IO: Improves performance of previous release by gathering the domain decomposed data into one global buffer and doing one write rather than doing multiple reads
+- DATA_OVERRIDE: Changes line in time_interp_external2 to enable 3D overrides
+
+### Fixed
+- DATA_OVERRIDE[2]: Fixes a crash when doing ongrid data_override calls with a domain with halos
+- DIAG_MANAGER[2]: Fixes an issue where time_bnds were written incorrectly for the last time stamp
+- DIAG_MANAGER: Regional diagnostics with a mask table now work
+- FMS2_IO: Unit test includes fms2io_init call to improve functionality
+- MPP: BOZ literals that are used in variable declaration are converted to integers using the int() function.
+- MPP_DOMAINS2: Fixed unit test
+- FMS_IO: Changes the logic in get_tile_string to fix bug where tile numbers 9 and 99 produce an inappropriate error
+
+### Tag Commit Hashes
+- 2020.03-beta4 (4d38679c1e18e920feb03d69f8a9762eb6a047aa)
+- 2020.03-beta3 (521a15135a99d1f2da7d82f238353945f82ce1dd)
+- 2020.03-beta2 (3dae0dfa405d555ecc09bbd2d60a1be24461f69e)
+- 2020.03-beta1 (f7f1c1c73c1f478a53e84caee6aff2fa840ad086)
+- 2020.03-alpha1 (2dd30b7ca0ac75a4a38b969e4a6d446eb395b4dd)
+
 
 ## [2020.02] - 2020-05-01
 ### Added
@@ -20,7 +86,7 @@ sequential patch number (starting from `01`).
 
 ### Removed
 - GENERAL:  References to the macro _ALLOCATABLE have been replaced with “allocatable”, _ALLOCATED has been replaced with “allocated”, and _NULL has been removed.  It is now assumed that all compilers support the Fortran 2003 standard.  The macros still exist in fms_platforms.h for compatibility within other components.
-- DIAG_MANAGER:  “fms_platform.h” is no longer included in any of the diag_manager routines.  Instead, fms_platform_mod is now being use-associated where necessary.  This fixes an issue for debuggers not providing correct line numbers. 
+- DIAG_MANAGER:  “fms_platform.h” is no longer included in any of the diag_manager routines.  Instead, fms_platform_mod is now being use-associated where necessary.  This fixes an issue for debuggers not providing correct line numbers.
 
 ### Tag Commit Hashes
 - 2020.02-beta1 (bbc6f8d33cfb75a411bbcd3f8423fa74b8b7cdfd)