Update CI workflows (#28)

* Update CI workflows and grib_index_rewind fix

Update actions to latest versions and check newest eccodes. Fix for grib_index_rewind being removed from public API.

.github/workflows/check-latest.yaml

@@ -30,10 +30,10 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      ECCODES_VERSION: 2.29.0
+      ECCODES_VERSION: 2.36.0
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/check-minimum.yaml

@@ -33,7 +33,7 @@ jobs:
       ECCODES_VERSION: 2.19.0
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -62,7 +62,7 @@ jobs:
       - name: Build eccodes from source (macOS)
         if: runner.os == 'macOS'
         env:
-          OPENJPEG_INCLUDE_DIR: /usr/local/include/openjpeg-2.5
+          OPENJPEG_INCLUDE_DIR: /opt/homebrew/include/openjpeg-2.5
         run: ./install_eccodes.sh
         shell: bash          
 

.github/workflows/check-standard.yaml

@@ -33,7 +33,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/lint.yaml

@@ -19,7 +19,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/test-coverage.yaml

@@ -20,7 +20,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gribr
 Type: Package
 Title: Read GRIB Files
-Version: 1.2.6
-Date: 2023-07-10
+Version: 1.2.7
+Date: 2024-07-12
 Author: Nathan Wendt <nathan.wendt@noaa.gov>
 Maintainer: Nathan Wendt <nathan.wendt@noaa.gov>
 BugReports: https://github.com/nawendt/gribr/issues

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for gribr 1.2.6.
+# Generated by GNU Autoconf 2.71 for gribr 1.2.7.
 #
 # Report bugs to <nathan.wendt@noaa.gov>.
 #
@@ -610,8 +610,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gribr'
 PACKAGE_TARNAME='gribr'
-PACKAGE_VERSION='1.2.6'
-PACKAGE_STRING='gribr 1.2.6'
+PACKAGE_VERSION='1.2.7'
+PACKAGE_STRING='gribr 1.2.7'
 PACKAGE_BUGREPORT='nathan.wendt@noaa.gov'
 PACKAGE_URL=''
 
@@ -1260,7 +1260,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gribr 1.2.6 to adapt to many kinds of systems.
+\`configure' configures gribr 1.2.7 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1322,7 +1322,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of gribr 1.2.6:";;
+     short | recursive ) echo "Configuration of gribr 1.2.7:";;
    esac
   cat <<\_ACEOF
 
@@ -1406,7 +1406,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-gribr configure 1.2.6
+gribr configure 1.2.7
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1624,7 +1624,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by gribr $as_me 1.2.6, which was
+It was created by gribr $as_me 1.2.7, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -4235,7 +4235,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gribr $as_me 1.2.6, which was
+This file was extended by gribr $as_me 1.2.7, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4290,7 +4290,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-gribr config.status 1.2.6
+gribr config.status 1.2.7
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([gribr],[1.2.6],[nathan.wendt@noaa.gov])
+AC_INIT([gribr],[1.2.7],[nathan.wendt@noaa.gov])
 
 AC_CONFIG_MACRO_DIR([tools/m4])
 

src/grib_select.c

@@ -4,7 +4,6 @@
 #include <string.h>
 
 #include "gribr.h"
-#include "grib_api_extra.h"
 
 SEXP gribr_select(SEXP gribr_filePath, SEXP gribr_fileHandle, SEXP gribr_keyList, SEXP gribr_isMulti) {
   int err;
@@ -87,16 +86,10 @@ SEXP gribr_select(SEXP gribr_filePath, SEXP gribr_fileHandle, SEXP gribr_keyList
     codes_grib_multi_support_on(DEFAULT_CONTEXT);
   }
 
-  index = codes_index_new(DEFAULT_CONTEXT, keyString, &err);
+  index = codes_index_new_from_file(DEFAULT_CONTEXT, filePath, keyString, &err);
   if (err) {
     gerror("unable to create index", err);
   }
-  nfree(keyString);
-
-  err = codes_index_add_file(index, filePath);
-  if (err) {
-    gerror("unable to add file to index", err);
-  }
 
   /* Have to grab handle from file first in order to get
    * native key types. Will not work with handle from
@@ -112,37 +105,42 @@ SEXP gribr_select(SEXP gribr_filePath, SEXP gribr_fileHandle, SEXP gribr_keyList
     if (i % INTERRUPT_FREQ == 0) {
       R_CheckUserInterrupt();
     }
+
     lenKeys = xlength(VECTOR_ELT(gribr_keyList, i));
+
     for (j = 0; j < lenKeys; j++) {
       keyName = CHAR(STRING_ELT(getAttrib(VECTOR_ELT(gribr_keyList, i), R_NamesSymbol), j));
       err = codes_get_native_type(h, keyName, &keyType);
+
       if (err) {
         gerror("unable to get native type", err);
       }
+
       switch (keyType) {
-      case CODES_TYPE_DOUBLE:
-        kd = asReal(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j));
-        codes_index_select_double(index, keyName, kd);
-        break;
-      case CODES_TYPE_LONG:
-        /* Need to coerce vector to integer as R list components entered
-         * as integers really end up being numeric (double in C). Doing
-         * corecion here makes the most sense as the type gets deciced in
-         * the get_naitve_type call. The C routines know more about the
-         * typing than the R routines.
-         */
-        ki = (long)asReal(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j));
-        codes_index_select_long(index, keyName, ki);
-        break;
-      case CODES_TYPE_STRING:
-        ks = CHAR(asChar(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j)));
-        codes_index_select_string(index, keyName, ks);
-        break;
-      default:
-        /* Skip other key types with no codes_select_* methods to handle them */
-        break;
-      }
+        case CODES_TYPE_DOUBLE:
+          kd = asReal(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j));
+          codes_index_select_double(index, keyName, kd);
+          break;
+        case CODES_TYPE_LONG:
+          /* Need to coerce vector to integer as R list components entered
+          * as integers really end up being numeric (double in C). Doing
+          * corecion here makes the most sense as the type gets deciced in
+          * the get_naitve_type call. The C routines know more about the
+          * typing than the R routines.
+          */
+          ki = (long)asReal(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j));
+          codes_index_select_long(index, keyName, ki);
+          break;
+        case CODES_TYPE_STRING:
+          ks = CHAR(asChar(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j)));
+          codes_index_select_string(index, keyName, ks);
+          break;
+        default:
+          /* Skip other key types with no codes_select_* methods to handle them */
+          break;
+        }
     }
+
     index_count = 0;
     while((hi = codes_handle_new_from_index(index, &err))) {
       if (err) {
@@ -156,10 +154,41 @@ SEXP gribr_select(SEXP gribr_filePath, SEXP gribr_fileHandle, SEXP gribr_keyList
       error("gribr: no messages matched");
     }
 
-    grib_index_rewind(index);
-
     REPROTECT(gribr_temp = allocVector(VECSXP, index_count), pro_temp);
 
+    /* Recreate index and redo selections. This is done as the index will have been
+     * consumed to figure out the size of the vector needed. grib_index_rewind is no
+     * longer available to do this efficiently. This will suffice until a better
+     * approach is developed or exposed in the public API.
+     */
+    index = codes_index_new_from_file(DEFAULT_CONTEXT, filePath, keyString, &err);
+
+    for (j = 0; j < lenKeys; j++) {
+      keyName = CHAR(STRING_ELT(getAttrib(VECTOR_ELT(gribr_keyList, i), R_NamesSymbol), j));
+      err = codes_get_native_type(h, keyName, &keyType);
+
+      if (err) {
+        gerror("unable to get native type", err);
+      }
+
+      switch (keyType) {
+        case CODES_TYPE_DOUBLE:
+          kd = asReal(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j));
+          codes_index_select_double(index, keyName, kd);
+          break;
+        case CODES_TYPE_LONG:
+          ki = (long)asReal(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j));
+          codes_index_select_long(index, keyName, ki);
+          break;
+        case CODES_TYPE_STRING:
+          ks = CHAR(asChar(VECTOR_ELT(VECTOR_ELT(gribr_keyList, i), j)));
+          codes_index_select_string(index, keyName, ks);
+          break;
+        default:
+          break;
+        }
+    }
+
     m = 0;
     while((hi = codes_handle_new_from_index(index, &err)) && m < index_count) {
       if (err) {
@@ -174,6 +203,7 @@ SEXP gribr_select(SEXP gribr_filePath, SEXP gribr_fileHandle, SEXP gribr_keyList
 
   codes_handle_delete(h);
   codes_index_delete(index);
+  nfree(keyString);
 
   grewind(file);
 

src/gribr.h

@@ -14,7 +14,7 @@ SEXP gribr_grib_open(SEXP gribr_fileName);
 SEXP gribr_grib_list(SEXP gribr_fileHandle, SEXP gribr_filter,
                      SEXP gribr_namespace, SEXP gribr_isMulti);
 SEXP gribr_grib_df(SEXP gribr_fileHandle, SEXP gribr_filter,
-                     SEXP gribr_namespace, SEXP gribr_isMulti);
+                   SEXP gribr_namespace, SEXP gribr_isMulti);
 
 SEXP gribr_grib_length(SEXP gribr_fileHandle);
 SEXP gribr_is_null_ptr (SEXP gribr_ptr);

tests/testthat/test-messages.R

@@ -1,6 +1,6 @@
 context("GRIB message retrieval and attributes")
 
-test_that("Incorrect message requests are handled correctly", {
+test_that("Message requests are handled correctly", {
   g <- grib_open(system.file("extdata", "lfpw.grib1", package = "gribr"))
 
 #   grib_get_message