Move libraries and applications from the tools directory to src

.github/workflows/distcheck.yml

@@ -0,0 +1,42 @@
+# Github actions CI file
+# Ryan Mulhall 2020
+# CI testing for the FRE-NCtools repo, builds and runs unit tests
+# image dockerfile is maintained here:
+# https://gitlab.gfdl.noaa.gov/fre/hpc-me
+name: FRE-NCtools CI
+on:
+  workflow_run:
+    workflows: ["FRE-NCtools Check Expensive"]
+    types:
+      - completed
+jobs:
+  CI:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        with_mpi: ['','--with-mpi']
+        enable_quad_precision: ['', '--enable-quad-precision']
+    container:
+      image: ghcr.io/noaa-gfdl/fre-nctools-ci-rocky-gnu:14.2.0_v2
+      env:
+        MPI: ${{ matrix.with_mpi }}
+        QUAD_P: ${{ matrix.enable_quad_precision }}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Configure
+      run: |
+        mkdir build && cd build
+        autoreconf -i ../configure.ac
+        ../configure $MPI $QUAD_P || cat config.log
+    - name: Build distribution with check
+      run: make DISTCHECK_CONFIGURE_FLAGS="$MPI $QUAD_P" -C build -j
+    - name: Save log file on failure
+      uses: actions/[email protected]
+      if: failure()
+      with:
+        name: test-suites
+        path: |
+          build/tests/test-suite.log

.github/workflows/main.yml

@@ -27,21 +27,14 @@ jobs:
         mkdir build && cd build
         autoreconf -i ../configure.ac
         ../configure $MPI $QUAD_P || cat config.log
-    - name: Build tools
+    - name: Build
       run: make -C build -j
-    - name: Run all tests
-      if: matrix.with_mpi == ''
-      run: make -C build -j check SH_LOG_DRIVER_FLAGS=--comments
     - name: Run most tests (skip the slow ones)
-      if: matrix.with_mpi == '--with-mpi'
-      env:
-        SKIP_TESTS: 4
-      run: make -C build -j check SH_LOG_DRIVER_FLAGS=--comments
+      run: make -C build -j check
     - name: Save log file on failure
       uses: actions/[email protected]
       if: failure()
       with:
         name: test-suites
         path: |
-          build/t/test-suite.log
           build/tests/test-suite.log

.github/workflows/main_expensive.yml

@@ -0,0 +1,44 @@
+# Github actions CI file
+# Ryan Mulhall 2020
+# CI testing for the FRE-NCtools repo, builds and runs unit tests
+# image dockerfile is maintained here:
+# https://gitlab.gfdl.noaa.gov/fre/hpc-me
+name: FRE-NCtools Check Expensive
+on:
+  workflow_run:
+    workflows: ["FRE-NCtools CI"]
+    types:
+      - completed
+jobs:
+  CI:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        with_mpi: ['','--with-mpi']
+        enable_quad_precision: ['', '--enable-quad-precision']
+    container:
+      image: ghcr.io/noaa-gfdl/fre-nctools-ci-rocky-gnu:14.2.0_v2
+      env:
+        MPI: ${{ matrix.with_mpi }}
+        QUAD_P: ${{ matrix.enable_quad_precision }}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Configure
+      run: |
+        mkdir build && cd build
+        autoreconf -i ../configure.ac
+        ../configure $MPI $QUAD_P || cat config.log
+    - name: Build
+      run: make -C build -j
+    - name: Run most tests (skip the slow ones)
+      run: make -C build check-very-expensive
+    - name: Save log file on failure
+      uses: actions/[email protected]
+      if: failure()
+      with:
+        name: test-suites
+        path: |
+          build/tests/test-suite.log

.gitignore

@@ -4,6 +4,7 @@
 *.gz
 build.fre-nctools*
 build
+_build
 *.exe
 *.1
 .DS_Store
@@ -22,6 +23,7 @@ Makefile.in
 # http://www.gnu.org/software/autoconf
 
 .deps
+.dirstamp
 autom4te.cache
 /autoscan.log
 /autoscan-*.log
@@ -64,36 +66,62 @@ t/Test26/
 *.nc
 
 # Other build generated files
+gt-*/
 config.h
 *.mod
-postprocessing/land_utils/combine-ncc
-postprocessing/land_utils/decompress-ncc
-postprocessing/land_utils/is-compressed
-postprocessing/land_utils/nfu_compress_mod.mod
-postprocessing/land_utils/nfu_mod.mod
-postprocessing/land_utils/scatter-ncc
-postprocessing/mppnccombine/mppnccombine
-postprocessing/plevel/moisture_convert_mod.mod
-postprocessing/plevel/pinterp_utilities_mod.mod
-postprocessing/plevel/plev_constants_mod.mod
-postprocessing/plevel/pressure_interp_mod.mod
+src/combine_restarts
+src/combine-ncc
+src/decompress-ncc
+src/iceberg_comb.sh
+src/is-compressed
+src/list_ncvars
+src/list_ncvars.csh
+src/list_ncvars.sh
+src/scatter-ncc
+src/mppnccombine
+src/plevel-interp
+src/plevel.sh
+src/print_version
+src/split_ncvars.pl
+src/timavg
+src/timavg.csh
+src/time_average
+src/version.h
+src/version.inc
+tests/c_test_version
+tests/create_5degree_topog
+tests/create_daily_tile_files
+tests/create_land_remap_files
+tests/create_mask_topog
+tests/create_ocean_mask_grid
+tests/create_plevel_test_ncfile
+tests/create_regional_file
+tests/create_runoff_file
+tests/create_temp_salt_file
+tests/create_timeavg_test_ncfiles
+tests/f_test_version
 tools/check_mask/check_mask
 tools/cubic_utils/make_remap_file
 tools/fregrid/fregrid
+tools/fregrid/fregrid_parallel
 tools/make_coupler_mosaic/make_coupler_mosaic
+tools/make_coupler_mosaic/make_coupler_mosaic_parallel
 tools/make_hgrid/make_hgrid
 tools/make_land_domain/make_land_domain
 tools/make_quick_mosaic/make_quick_mosaic
 tools/make_regional_mosaic/make_regional_mosaic
 tools/make_solo_mosaic/make_solo_mosaic
 tools/make_topog/make_topog
+tools/make_topog/make_topog_parallel
 tools/make_vgrid/make_vgrid
 tools/mppncscatter/mppncscatter
 tools/nc_null_check/nc_null_check
 tools/ncexists/ncexists
 tools/remap_land/remap_land
+tools/remap_land/remap_land_parallel
 tools/river_regrid/river_regrid
 tools/runoff_regrid/runoff_regrid
+tools/runoff_regrid/runoff_regrid_parallel
 tools/simple_hydrog/lakes/cr_lake_files
 tools/simple_hydrog/libfmslite/constants_mod.mod
 tools/simple_hydrog/libfmslite/horiz_interp_bilinear_mod.mod
@@ -104,3 +132,13 @@ tools/simple_hydrog/postp/cp_river_vars
 tools/simple_hydrog/rmvpr/rmv_parallel_rivers
 tools/transfer_to_mosaic_grid/transfer_to_mosaic_grid
 
+# Ignore generated files from vscode makefile extension
+defines.awk
+subs*.awk
+conftest
+conftest.*
+confdefs.*
+confinc.*
+confmf.*
+conf*/
+conf*.file

.vscode/c_cpp_properties.json

@@ -7,9 +7,6 @@
                 "/opt/homebrew/include"
             ],
             "defines": [],
-            "macFrameworkPath": [
-                "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks"
-            ],
             "compilerPath": "/usr/bin/clang",
             "cStandard": "c17",
             "cppStandard": "c++17",
@@ -22,9 +19,6 @@
                 "${HOME}/opt/homebrew/include"
             ],
             "defines": [],
-            "macFrameworkPath": [
-                "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks"
-            ],
             "compilerPath": "/usr/bin/clang",
             "cStandard": "c17",
             "cppStandard": "c++17",

.vscode/settings.json

@@ -36,5 +36,29 @@
                 "/#include.*/",
             ]
         }
-    ]
+    ],
+    "makefile.dryrunSwitches": [
+        "--always-make",
+        "--print-directory",
+        "--dry-run",
+        "--assume-old=Makefile",
+        "Makefile",
+        "all",
+        "AM_MAKEFLAGS=--assume-old=Makefile Makefile"
+    ],
+    "fortran.linter.includePaths": [
+        "/opt/homebrew/include",
+        "${workspaceFolder}/**"
+    ],
+    "fortran.fortls.preprocessor.directories": [
+        "/opt/homebrew/include",
+        "./lib"
+    ],
+    "fortran.fortls.suffixes": [
+        "inc"
+    ],
+    "fortran.fortls.directories": [
+        "./**",
+        "/opt/homebrew/include"
+    ],
 }