Non-bats testing and repo structure update

.gitignore

@@ -63,6 +63,7 @@ t/Test26/
 
 # Other build generated files
 config.h
+*.mod
 postprocessing/land_utils/combine-ncc
 postprocessing/land_utils/decompress-ncc
 postprocessing/land_utils/is-compressed

.vscode/c_cpp_properties.json

@@ -1,21 +1,34 @@
 {
     "configurations": [
         {
-            "name": "Mac",
+            "name": "Mac (Arm)",
             "includePath": [
                 "${workspaceFolder}/**",
-                "/opt/homebrew/Cellar/netcdf/4.9.0/include"
-            ],
-            "defines": [
-
+                "/opt/homebrew/include"
             ],
+            "defines": [],
             "macFrameworkPath": [
                 "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks"
             ],
             "compilerPath": "/usr/bin/clang",
             "cStandard": "c17",
             "cppStandard": "c++17",
             "intelliSenseMode": "macos-clang-arm64"
+        },
+        {
+            "name": "Mac (Intel)",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${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",
+            "intelliSenseMode": "macos-clang-x64"
         }
     ],
     "version": 4

.vscode/settings.json

@@ -0,0 +1,37 @@
+{
+    "cSpell.words": [
+        "Balaji",
+        "Forrestal",
+        "hght",
+        "Malyshev",
+        "Mohan",
+        "mppnccombine",
+        "NCEP",
+        "plevel",
+        "plevs",
+        "reananalysis",
+        "Sergey",
+        "sphum",
+        "Tauber",
+        "Tushar",
+        "Vahlenkamp",
+        "zsurf"
+    ],
+    "cSpell.languageSettings": [
+        {
+            // use with cpp or c files
+            "languageId": "cpp,c",
+            // turn off compound words, because it is only checking strings.
+            "allowCompoundWords": false,
+            // Only check comments and strings
+            "includeRegExpList": [
+                "CStyleComment",
+                "string"
+            ],
+            // Exclude includes, because they are also strings.
+            "ignoreRegExpList": [
+                "/#include.*/",
+            ]
+        }
+    ]
+}

.vscode/tasks.json

@@ -0,0 +1,86 @@
+{
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "type": "shell",
+            "label": "make",
+            "command": "make",
+            "args": [],
+            "options": {
+                "cwd": "${workspaceFolder}/build"
+            },
+            "problemMatcher": [
+                "$gcc"
+            ],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            }
+        },
+        {
+            "type": "shell",
+            "label": "clean build dir",
+            "command": "rm",
+            "args": ["-rf", "${workspaceFolder}/build"],
+            "options": {
+                "cwd": "${workspaceFolder}",
+            },
+            "group": {
+                "kind": "build",
+                "isDefault": false
+            }
+        },
+        {
+            "type": "shell",
+            "label": "mk build dir",
+            "command": "mkdir",
+            "args": ["-p", "${workspaceFolder}/build"],
+            "options": {
+                "cwd": "${workspaceFolder}",
+            },
+            "group": {
+                "kind": "build",
+                "isDefault": false
+            },
+            "dependsOn": ["clean build dir"]
+        },
+        {
+            "type": "shell",
+            "label": "configure",
+            "command": "../configure",
+            "args": ["--prefix=${workspaceFolder}/build/opt"],
+            "options": {
+                "cwd": "${workspaceFolder}/build"
+            },
+            "group": {
+                "kind": "build",
+                "isDefault": false
+            },
+            "dependsOn": ["mk build dir"]
+        },
+        {
+            "type": "shell",
+            "label": "autoreconf",
+            "command": "autoreconf",
+            "args": ["-if"],
+            "options": {
+                "cwd": "${workspaceFolder}"
+            },
+            "group": {
+                "kind": "none",
+                "isDefault": false
+            },
+            "problemMatcher": {
+                "owner": "autoconf",
+                "fileLocation": "relative",
+                "pattern": {
+                    "regexp": "^(\\S+):(\\d+):\\s+(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "severity": 3,
+                    "message": 4
+                }
+            }
+        }
+    ]
+}

Makefile.am

@@ -19,14 +19,9 @@
 #***********************************************************************
 ACLOCAL_AMFLAGS = -I m4
 
-SUBDIRS = postprocessing/combine_restarts \
-          postprocessing/iceberg_comb \
-          postprocessing/land_utils \
-          postprocessing/list_ncvars \
-          postprocessing/mppnccombine \
-          postprocessing/plevel \
+SUBDIRS = lib/libnfu \
+          src \
           postprocessing/split_ncvars \
-          postprocessing/timavg \
           tools/libfrencutils \
           tools/check_mask \
           tools/cubic_utils \
@@ -52,6 +47,9 @@ SUBDIRS = postprocessing/combine_restarts \
           tools/simple_hydrog/rmvpr \
           tools/nc_null_check
 
+SUBDIRS += man \
+           tests
+
 if WITH_CHECK_PROGS
 SUBDIRS += t
 endif

configure.ac

@@ -21,26 +21,30 @@
 # Prelude
 AC_PREREQ([2.63])
 AC_INIT(
-  [FRE NC Tools],
+  [FRE NCTools],
   [2024.04],
-  [[email protected]],
+  [https://github.com/NOAA-GFDL/FRE-NCtools/issues],
   [fre-nctools],
   [https://github.com/NOAA-GFDL/FRE-NCtools])
 
 # Place the git description informatin in the configure script
 m4_define([git_revision],
-  [m4_esyscmd_s([git describe --always --dirty 2> /dev/null || echo "unknown version"])])
-AC_REVISION([$git_revision])
-
+  [m4_esyscmd_s([git describe --tags --always --dirty 2> /dev/null || echo "unknown version"])])
+AC_REVISION([git_revision])
 m4_define([git_hashval],
   [m4_esyscmd_s([git rev-parse HEAD 2> /dev/null || echo "unknown githash"])])
-AC_REVISION([$git_hashval])
+AC_REVISION([git_hashval])
+m4_define([git_date],
+  [m4_esyscmd_s([git show --no-patch --format=%as HEAD 2> /dev/null || date +%Y-%m-%d])])
+AC_REVISION([git_date])
+m4_define([copyright_year],
+  [m4_substr(git_date, 0, 4)])
 
-AC_CONFIG_SRCDIR([postprocessing/land_utils/combine-ncc.F90])
+AC_CONFIG_SRCDIR([src/land_utils/combine-ncc.F90])
 AC_CONFIG_MACRO_DIR([m4])
 AC_REQUIRE_AUX_FILE([tap-driver.sh])
 
-AM_INIT_AUTOMAKE([foreign -Wall -Werror -Woverride tar-ustar])
+AM_INIT_AUTOMAKE([foreign -Wall -Werror -Woverride tar-pax subdir-objects])
 AM_EXTRA_RECURSIVE_TARGETS([docs install-docs])
 
 # Check for programs
@@ -69,6 +73,8 @@ AC_FC_SRCEXT([F90])
 AC_FC_LINE_LENGTH([unlimited])
 AC_FC_FREEFORM()
 AC_FC_MODULE_EXTENSION()
+AC_FC_MODULE_FLAG()
+AC_FC_MODULE_OUTPUT_FLAG()
 GX_FC_DEFAULT_REAL_KIND8_FLAG()
 GX_FC_DEFAULT_REAL_KIND4_FLAG()
 
@@ -107,6 +113,10 @@ if test ! -z "$FC_CRAY_POINTER_FLAG"; then
    FCFLAGS="$FCFLAGS $FC_CRAY_POINTER_FLAG"
 fi
 
+# Check for programs
+AC_PROG_GREP
+AC_PROG_EGREP
+AC_PROG_SED
 
 AC_CHECK_PROGS(ASCIIDOC, [asciidoc])
 if test -n "$ASCIIDOC"; then
@@ -127,7 +137,29 @@ AC_CHECK_PROGS(BATS, [bats])
 AC_CHECK_PROGS(PROVE, [prove])
 AM_CONDITIONAL([WITH_CHECK_PROGS], [test -n "$PROVE" -a -n "$BATS"])
 
-AC_PYTHON_MODULE(xarray, [], python3)
+# Although these are supplied with the NetCDF C library, we'll double
+# check that ncgen and ncdump are available
+AC_ARG_VAR([NCGEN], [Path to ncgen])
+AC_PATH_PROG(NCGEN, [ncgen])
+AS_IF([test -z "$NCGEN"],
+  [AC_MSG_ERROR([Cannot find ncgen.  Please ensure ncgen is in PATH or set the environment variable NCGEN to the full path to ncgen.])])
+
+AC_ARG_VAR([NCDUMP], [Path to ncdump])
+AC_PATH_PROG(NCDUMP, [ncdump])
+AS_IF([test -z "$NCDUMP"],
+  [AC_MSG_ERROR([Cannot find ncdump.  Please ensure ncdump is in PATH or set the environment variable NCDUMP to the full path to ncgen.])])
+
+AC_ARG_VAR([NCRCAT], [Path to ncrcat])
+AC_PATH_PROG(NCRCAT, [ncrcat])
+AS_IF([test -z "$NCRCAT"],
+  [AC_MSG_ERROR([Cannot find ncrcat.  Please ensure ncrcat is in PATH or set the environment variable NCRCAT to the full path to ncgen.])])
+
+AC_ARG_VAR([NCATTED], [Path to ncatted])
+AC_PATH_PROG(NCATTED, [ncatted])
+AS_IF([test -z "$NCATTED"],
+  [AC_MSG_ERROR([Cannot find ncatted.  Please ensure ncatted is in PATH or set the environment variable NCATTED to the full path to ncgen.])])
+
+AX_PYTHON_MODULE([xarray],[],[python3])
 if test ${HAVE_PYMOD_XARRAY} = yes; then
   AM_CONDITIONAL([SKIP_XARRAY_TESTS], false )
 else
@@ -171,13 +203,21 @@ AS_IF([test $ac_cv_type_long_double_wider = no],
 # Check if Test25-input link points to an existing directory
 AM_CONDITIONAL([HAVE_TEST25_INPUT], [test -e ${srcdir}/t/Test25-input/grid_spec.nc])
 
-# Other defs
-AC_DEFINE([GIT_REVISION], "git_revision",
-          [Holds the 'git describe' information if configure ran within a git working directory])
-AC_DEFINE([GIT_HEADHASH], "git_hashval",
-          [Holds the 'git rev-parse HEAD' information if configure ran within a git working directory])
+# Set macros
+AS_VAR_SET([GIT_REVISION], ["git_revision"])dnl
+AC_DEFINE([GIT_REVISION], ["git_revision"],
+          [Holds the 'git describe' information if configure ran within a git working directory])dnl
+AC_SUBST(GIT_REVISION)dnl
+AS_VAR_SET([GIT_HEADHASH], ["git_hashval"])dnl
+AC_DEFINE([GIT_HEADHASH], ["git_hashval"],
+          [Holds the 'git rev-parse HEAD' information if configure ran within a git working directory])dnl
+AC_SUBST(GIT_HEADHASH)dnl
+AS_VAR_SET([COPYRIGHT_YEAR], ["copyright_year"])dnl
+AC_DEFINE([COPYRIGHT_YEAR], ["copyright_year"],
+          [Year to place in Copyright notices printed with --version information])dnl
+AC_SUBST(COPYRIGHT_YEAR)dnl
 
-#Code for setting rpath based ncview's configure.in code.
+# Code for setting rpath based ncview's configure.in code.
 AS_IF([test x$ac_compiler_gnu = xyes], [RPATH_FLAGS=""
   for word in $NETCDF_LDFLAGS $NETCDF_FCLDFLAGS
   do
@@ -197,14 +237,10 @@ AC_SUBST(RPATH_FLAGS) dnl
 # Output files
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([Makefile
-                 postprocessing/combine_restarts/Makefile
-                 postprocessing/iceberg_comb/Makefile
-                 postprocessing/land_utils/Makefile
-                 postprocessing/list_ncvars/Makefile
-                 postprocessing/mppnccombine/Makefile
-                 postprocessing/plevel/Makefile
+                 lib/libnfu/Makefile
+                 man/Makefile
+                 src/Makefile
                  postprocessing/split_ncvars/Makefile
-                 postprocessing/timavg/Makefile
                  tools/libfrencutils/Makefile
                  tools/libfrencutils_acc/Makefile
                  tools/check_mask/Makefile
@@ -237,7 +273,7 @@ AC_CONFIG_FILES([Makefile
                  t_acc/test_get_grid_cell_struct/Makefile
                  t_acc/test_get_upbound_nxcells_2dx2d/Makefile
                  t_acc/test_get_interp_order1/Makefile
-
+                 tests/Makefile
 ])
 
 AC_OUTPUT

postprocessing/list_ncvars/Makefile.am → lib/libnfu/Makefile.am

@@ -17,12 +17,18 @@
 # License along with FRE-NCTools.  If not, see
 # <http://www.gnu.org/licenses/>.
 #***********************************************************************
-bin_PROGRAMS = list_ncvars.exe
-dist_bin_SCRIPTS = list_ncvars.csh
 
-list_ncvars_exe_SOURCES = list_ncvars.f90
-list_ncvars_exe_FCFLAGS = $(NETCDF_FCFLAGS) $(FC_DEFAULT_REAL_KIND8_FLAG) $(AM_FCFLAGS)
-list_ncvars_exe_LDADD = $(NETCDF_FCLDFLAGS) $(NETCDF_FCLIBS) $(RPATH_FLAGS)
+noinst_LIBRARIES = libnfu.a
+
+AM_FCFLAGS =  $(FC_DEFAULT_REAL_KIND8_FLAG) $(NETCDF_FCFLAGS)
+LDADD = $(NETCDF_LDFLAGS) $(NETCDF_LIBS) $(RPATH_FLAGS)
+
+libnfu_a_SOURCES = nfu.F90 nfu_compress.F90
+
+nfu_mod.$(FC_MODEXT): nfu.$(OBJEXT)
+nfu_compress_mod.$(FC_MODEXT): nfu_compress.$(OBJEXT)
+
+nfu_compress.$(OBJEXT): nfu_mod.$(FC_MODEXT)
 
 clean-local:
-	$(RM) *.mod
+	$(RM) *.$(FC_MODEXT)