[gnuastro-commits] master fd51c80 050/113: Imported recent work from master, no conflicts

[Mohammad Akhlaghi]

branch: master
commit fd51c806553ce9865ec6535e73528c650606118f
Merge: 45bd003 2ccd136
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Imported recent work from master, no conflicts
    
    The recent bug fixes in the master branch are now incorported here also.
---
 NEWS                               |   4 +
 doc/gnuastro.fr.html               |  34 +++++++++
 lib/gnuastro-internal/commonopts.h |  10 +--
 lib/gnuastro-internal/options.h    |   1 +
 lib/options.c                      | 150 +++++++++++++++++++++++--------------
 5 files changed, 139 insertions(+), 60 deletions(-)

diff --git a/NEWS b/NEWS
index f0c4a7b..7f3782f 100644
--- a/NEWS
+++ b/NEWS
@@ -15,6 +15,10 @@ GNU Astronomy Utilities NEWS                          -*- 
outline -*-
 
   Configure time CPPFLAGS and LDFLAGS don't pass to BuildProgram (bug #53122).
 
+  Crash when printing values with the `--onlyversion' option (bug #53142).
+
+  NULL value of onlyversion option causing a crash (bug #53147).
+
 
 
 
diff --git a/doc/gnuastro.fr.html b/doc/gnuastro.fr.html
index 93750b0..26b7785 100644
--- a/doc/gnuastro.fr.html
+++ b/doc/gnuastro.fr.html
@@ -45,6 +45,7 @@ h3 { clear: both; }
   <li><a href="#mail">Listes de diffusion</a></li>
   <li><a href="#bug">Signalement de bogues</a></li>
   <li><a href="#contribute">Participer</a></li>
+  <li><a href="#cite">Citations</a></li>
   <li><a href="#license">Licence</a></li>
 </ul>
 <hr class="no-display"/>
@@ -325,6 +326,39 @@ git clone http://git.sv.gnu.org/r/gnuastro.git</pre>
 </dl>
 
 
+<h3 id="cite">Citations</h3>
+
+<p>Les citations sont vitales pour la continuité du travail sur Gnuastro. Tous
+  les programmes ont une option commune, <code>--cite</code>, qui vous
+  indiquera comment citer et reconnaître correctement le travail qu'a nécessité
+  la création et la maintenance de chacun d'entre eux ainsi que, plus
+  généralement, celles de Gnuastro. Si vous vous servez dans votre recherche
+  de l'un des programmes ou de l'une des bibliothèques proposées par Gnuastro,
+  merci d'utiliser ce qu'affiche cette option pour citer le programme et
+  Gnuastro dans votre publication. Notez que les différents programmes peuvent
+  demander des références à différents articles qui leur sont plus
+  particulièrement consacrés.</p>
+
+<p>Gnuastro est encore jeune, sa présentation et la description de ses
+  fonctionnalités n'ont pas encore fait l'objet d'un article complet. Tant que
+  cet article n'est pas paru, la référence à donner pour Gnuastro dans son
+  ensemble est la présentation de NoiseChisel (<a
+  href="http://adsabs.harvard.edu/abs/2015ApJS..220....1A";>ApJS 220, 1</a>). Il
+  s'agit de la première publication utilisant Gnuastro. Lorsque ce dernier aura
+  atteint une maturité suffisante, une publication lui sera entièrement dédiée.
+  Voir <a
+  
href="https://www.gnu.org/software/gnuastro/manual/html_node/GNU-Astronomy-Utilities-1_002e0.html";>
+  GNU Astronomy Utilities 1.0</a>.</p>
+
+<p>Gnuastro est également répertorié dans la Bibliothèque de code source pour
+  l'astrophysique (<a href="http://ascl.net";>ASCL</a> — <cite>Astrophysics
+  Source Code Library</cite>) sous le numéro <a
+  href="http://ascl.net/1801.009";>ascl.net/1801.009</a>. Veuillez utiliser cet
+  identifiant quelque part dans votre article (par exemple dans les
+  remerciements ou lorsque vous mentionnerez Gnuastro pour la première fois).
+  Dans la bibliographie ou la liste de références en fin d'article, utilisez
+  seulement les publications affichées par l'option <code>--cite</code>.</p>
+
 <h3 id="license">Licence</h3>
 
 <p><cite>GNU Astronomy Utilities</cite> (Gnuastro) est un logiciel
diff --git a/lib/gnuastro-internal/commonopts.h 
b/lib/gnuastro-internal/commonopts.h
index 06421e4..1e41a03 100644
--- a/lib/gnuastro-internal/commonopts.h
+++ b/lib/gnuastro-internal/commonopts.h
@@ -227,10 +227,10 @@ struct argp_option gal_commonopts_options[] =
       0,
       "Type of output: e.g., int16, float32, etc...",
       GAL_OPTIONS_GROUP_OUTPUT,
-      &cp->type,
-      GAL_TYPE_STRING,
-      GAL_OPTIONS_RANGE_GT_0,
-      GAL_OPTIONS_NOT_MANDATORY,
+      &cp->type,                /* Internally, `cp->type' is actually an   */
+      GAL_TYPE_STRING,          /* `uint8_t', but the user gives a string. */
+      GAL_OPTIONS_RANGE_GT_0,   /* So for the sanity checks to pass, we    */
+      GAL_OPTIONS_NOT_MANDATORY,/* use `GAL_TYPE_STRING' for this option.  */
       GAL_OPTIONS_NOT_SET,
       gal_options_read_type
     },
@@ -427,7 +427,7 @@ struct argp_option gal_commonopts_options[] =
       0,
       "Only run if the program version is STR.",
       GAL_OPTIONS_GROUP_OPERATING_MODE,
-      NULL,
+      &cp->onlyversion,
       GAL_TYPE_STRING,
       GAL_OPTIONS_RANGE_0_OR_1,
       GAL_OPTIONS_NOT_MANDATORY,
diff --git a/lib/gnuastro-internal/options.h b/lib/gnuastro-internal/options.h
index a3f8ea3..599702b 100644
--- a/lib/gnuastro-internal/options.h
+++ b/lib/gnuastro-internal/options.h
@@ -196,6 +196,7 @@ struct gal_options_common_params
   size_t            numthreads; /* Number of threads to use.              */
   size_t            minmapsize; /* Minimum bytes necessary to use mmap.   */
   uint8_t                  log; /* Make a log file.                       */
+  char            *onlyversion; /* Redundant, kept/set for generality.    */
 
   /* Configuration files. */
   uint8_t          printparams; /* To print the full list of parameters.  */
diff --git a/lib/options.c b/lib/options.c
index 8b2f89e..c1df2fb 100644
--- a/lib/options.c
+++ b/lib/options.c
@@ -179,35 +179,60 @@ void *
 gal_options_check_version(struct argp_option *option, char *arg,
                           char *filename, size_t lineno, void *junk)
 {
+  char *str;
+
+  /* First see if we are reading or writing. */
+  if(lineno==-1)
+    {
+      /* `PACKAGE_VERSION' is a static/literal string, but the pointer
+         returned by this function will be freed, so we must allocate space
+         for it.
+
+         We didn't allocate and give this option a value when we read it
+         because it is redundant and much more likely for the option to
+         just be present (for a check in a reproduction pipeline for
+         example) than for it to be printed. So we don't want to waste
+         resources in allocating a redundant value. */
+      gal_checkset_allocate_copy(PACKAGE_VERSION, &str);
+      return str;
+    }
+
   /* Check if the given value is different from this version. */
-  if( strcmp(arg, PACKAGE_VERSION) )
+  else
     {
-      /* Print an error message and abort.  */
-      error_at_line(EXIT_FAILURE, 0, filename, lineno, "version mis-match: "
-                    "you are running GNU Astronomy Utilities (Gnuastro) "
-                    "version `%s'. However, the `onlyversion' option is set "
-                    "to version `%s'.\n\n"
-                    "This was probably done for reproducibility. Therefore, "
-                    "manually removing, or changing, the option value might "
-                    "produce errors or unexpected results. It is thus "
-                    "strongly advised to build Gnuastro %s and re-run this "
-                    "command/script.\n\n"
-                    "You can download previously released tar-balls from the "
-                    "following URLs respectively:\n\n"
-                    "    Stable (version format: X.Y):      "
-                    "http://ftpmirror.gnu.org/gnuastro\n";
-                    "    Alpha  (version format: X.Y.A-B):  "
-                    "http://alpha.gnu.org/gnu/gnuastro\n\n";
-                    "Alternatively, you can clone Gnuastro, checkout the "
-                    "respective commit (from the version number), then "
-                    "bootstrap and build it. Please run the following "
-                    "command for more information:\n\n"
-                    "    $ info gnuastro \"Version controlled source\"\n",
-                    PACKAGE_VERSION, arg, arg);
-
-      /* Just to avoid compiler warnings for unused variables. The program
-         will never reach this point! */
-      arg=filename=NULL; lineno=0; option=NULL; junk=NULL;
+      if(arg==NULL)
+        error(EXIT_FAILURE, 0, "%s: a bug! Please contact us at %s to fix "
+              "the problem. The value to `arg' is NULL", __func__,
+              PACKAGE_BUGREPORT);
+      else if( strcmp(arg, PACKAGE_VERSION) )
+        {
+          /* Print an error message and abort.  */
+          error_at_line(EXIT_FAILURE, 0, filename, lineno, "version "
+                        "mis-match: you are running GNU Astronomy Utilities "
+                        "(Gnuastro) version `%s'. However, the `onlyversion' "
+                        "option is set to version `%s'.\n\n"
+                        "This was probably done for reproducibility. "
+                        "Therefore, manually removing, or changing, the "
+                        "option value might produce errors or unexpected "
+                        "results. It is thus strongly advised to build "
+                        "Gnuastro %s and re-run this command/script.\n\n"
+                        "You can download previously released tar-balls "
+                        "from the following URLs respectively:\n\n"
+                        "    Stable (version format: X.Y):      "
+                        "http://ftpmirror.gnu.org/gnuastro\n";
+                        "    Alpha  (version format: X.Y.A-B):  "
+                        "http://alpha.gnu.org/gnu/gnuastro\n\n";
+                        "Alternatively, you can clone Gnuastro, checkout the "
+                        "respective commit (from the version number), then "
+                        "bootstrap and build it. Please run the following "
+                        "command for more information:\n\n"
+                        "    $ info gnuastro \"Version controlled source\"\n",
+                        PACKAGE_VERSION, arg, arg);
+
+          /* Just to avoid compiler warnings for unused variables. The program
+             will never reach this point! */
+          arg=filename=NULL; lineno=0; option=NULL; junk=NULL;
+        }
     }
   return NULL;
 }
@@ -2118,37 +2143,52 @@ gal_options_print_state(struct 
gal_options_common_params *cp)
         case GAL_OPTIONS_KEY_PRINTPARAMS:
         case GAL_OPTIONS_KEY_SETDIRCONF:
         case GAL_OPTIONS_KEY_SETUSRCONF:
+
+          /* Note that these options can have a value of 1 (enabled) or 0
+             (explicitly disabled). Therefore the printing should only be
+             done if they have a value of 1. This is why we have defined
+             the `OPTIONS_UINT8VAL' macro above. */
           sum += OPTIONS_UINT8VAL;
         }
-  if(sum>1)
-    error(EXIT_FAILURE, 0, "only one of the `printparams', `setdirconf' "
-          "and `setusrconf' options can be called in each run");
 
 
-  /* Print the required configuration files. Note that simply having a
-     non-NULL value is not enough. They can have a value of 1 or 0, and the
-     respective file should only be created if we have a value of 1. */
-  for(i=0; !gal_options_is_last(&cp->coptions[i]); ++i)
-    if(cp->coptions[i].set && OPTIONS_UINT8VAL)
-      switch(cp->coptions[i].key)
-        {
-        case GAL_OPTIONS_KEY_PRINTPARAMS:
-          options_print_all(cp, NULL, NULL);
-          break;
-
-        case GAL_OPTIONS_KEY_SETDIRCONF:
-          if( asprintf(&dirname, ".%s", PACKAGE)<0 )
-            error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
-          options_print_all(cp, dirname, cp->coptions[i].name);
-          free(dirname);
-          break;
+  /* See if the values should be printed and if so, where. */
+  switch(sum)
+    {
+    /* No printing option has been called, so just return. */
+    case 0:  return;
+
+    /* (Only) one of the printing options has been called, so we'll need to
+       print the values in the proper place. */
+    case 1:
+      for(i=0; !gal_options_is_last(&cp->coptions[i]); ++i)
+        if(cp->coptions[i].set && OPTIONS_UINT8VAL)
+          switch(cp->coptions[i].key)
+            {
+            case GAL_OPTIONS_KEY_PRINTPARAMS:
+              options_print_all(cp, NULL, NULL);
+              break;
+
+            case GAL_OPTIONS_KEY_SETDIRCONF:
+              if( asprintf(&dirname, ".%s", PACKAGE)<0 )
+                error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
+              options_print_all(cp, dirname, cp->coptions[i].name);
+              free(dirname);
+              break;
+
+            case GAL_OPTIONS_KEY_SETUSRCONF:
+              home=options_get_home();
+              if( asprintf(&dirname, "%s/%s", home, USERCONFIG_DIR)<0 )
+                error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
+              options_print_all(cp, dirname, cp->coptions[i].name);
+              free(dirname);
+              break;
+            }
+      break;
 
-        case GAL_OPTIONS_KEY_SETUSRCONF:
-          home=options_get_home();
-          if( asprintf(&dirname, "%s/%s", home, USERCONFIG_DIR)<0 )
-            error(EXIT_FAILURE, 0, "%s: asprintf allocation", __func__);
-          options_print_all(cp, dirname, cp->coptions[i].name);
-          free(dirname);
-          break;
-        }
+    /* More than one of the printing options has been called. */
+    default:
+      error(EXIT_FAILURE, 0, "only one of the `printparams', `setdirconf' "
+            "and `setusrconf' options can be called in each run");
+    }
 }