Fix minor typos

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+---
+exclude: doc/attic/|doc/author_*|AUTHORS|COPYING|example/linksc/COPYING|iniparser/LICENSE|libb64/README|config/ax_prefix_config_h.m4
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.36.2
+    hooks:
+      - id: typos

AUTHORS

@@ -58,7 +58,7 @@
   Advanced Computing Center (TACC) for providing them with access to the Ranger
   supercomputer under NSF TeraGrid award MCA04N026, and the National Center for
   Computational Science (NCCS) for early-user access to the Jaguar Cray XT5
-  supercomputer.  Any opinions, findings and conclusions or recomendations
+  supercomputer.  Any opinions, findings and conclusions or recommendations
   expressed in the source code and documentation are those of the authors and
   do not necessarily reflect the views of the National Science Foundation
   (NSF).
@@ -85,7 +85,7 @@
   domain software, see the LICENSE and AUTHORS files in that directory.
 
   The files under iniparser are derived from iniparser3.0b.  iniparser is
-  licensed unter the MIT license, see the LICENSE and AUTHORS files in
+  licensed under the MIT license, see the LICENSE and AUTHORS files in
   that directory.
 
   Several scripts under config are released under GNU GPL versions.

INSTALL

@@ -288,4 +288,3 @@ operates.
 
 `configure' also accepts some other, not widely useful, options.  Run
 `configure --help' for more details.
-

NEWS

@@ -3,7 +3,7 @@ NEWS
 
  * The current stable version 2 of the libsc code is maintained in branches
    v2.2--v2.5.  It will be backwards compatible as much as possible.
-   The code will remain usable and bugfixed for the forseeable future.
+   The code will remain usable and bugfixed for the foreseeable future.
    The branches master (official) and develop (fairly stable) live here.
  * We have introduced a new development branch leading up to v3.0.
    The initial version is v2.8.  The branch is called prev3-develop.  On

_typos.toml

@@ -0,0 +1,8 @@
+#[default.extend-words]
+
+[default.extend-identifiers]
+sc_MPI_MODE_WRONLY = "sc_MPI_MODE_WRONLY"
+MPI_MODE_WRONLY = "MPI_MODE_WRONLY"
+PNGs = "PNGs"
+asend = "asend"
+nce = "nce"

config/sc_include.m4

@@ -127,7 +127,7 @@ dnl its INVOCATION is one valid statement of a C/C++ program.
 dnl It may require INCLUDE statements to compile and link ok.
 dnl On the inside we call AC_LANG_PROGRAM(INCLUDE, INVOCATION).
 dnl The SEARCH_LIBS are a white-space separated list or empty.
-dnl The OTHER_LIBS may be empty or a list of depency libraries.
+dnl The OTHER_LIBS may be empty or a list of dependency libraries.
 dnl
 dnl This macro is modified from AC_SEARCH_LIBS.  In particular,
 dnl we use a separate cache variable ac_cv_sc_search_FUNCTION.

config/sc_mpi.m4

@@ -495,7 +495,7 @@ dnl This was only used for our lint code, which needs to be replaced.
 dnl
 dnl dnl SC_MPI_INCLUDES
 dnl dnl Call the compiler with various --show* options
-dnl dnl to figure out the MPI_INCLUDES and MPI_INCLUDE_PATH varables
+dnl dnl to figure out the MPI_INCLUDES and MPI_INCLUDE_PATH variables
 dnl dnl
 dnl AC_DEFUN([SC_MPI_INCLUDES],
 dnl [

config/sc_package.m4

@@ -107,7 +107,7 @@ $1_$3_RPATH=
 $1_DISTCLEAN="$$1_DISTCLEAN $1_$3_SOURCE.log"
 
 SC_ARG_WITH_PREFIX([$4],
-  [specifiy how to depend on package $4 (optional).
+  [specify how to depend on package $4 (optional).
    If the option value is literal no or the option is not present, use the
    source subdirectory.  If the option value is the literal external, expect
    all necessary environment variables to be set to compile and link against

doc/Doxyfile.in

@@ -457,7 +457,7 @@ LOOKUP_CACHE_SIZE      = 0
 # than 0 to get more control over the balance between CPU load and processing
 # speed. At this moment only the input processing can be done using multiple
 # threads. Since this is still an experimental feature the default is set to 1,
-# which efficively disables parallel processing. Please report any issues you
+# which effectively disables parallel processing. Please report any issues you
 # encounter. Generating dot graphs in parallel is controlled by the
 # DOT_NUM_THREADS setting.
 # Minimum value: 0, maximum value: 32, default value: 1.

doc/coding_standards.txt

@@ -62,7 +62,7 @@ tries to adhere to.
 
        printf ("%jd %ju", (intmax_t) i, (uintmax_t) u);
 
-   since that would be a nice way to accomodate 128 bit integers without
+   since that would be a nice way to accommodate 128 bit integers without
    changing the `printf` code.
    This also holds for `size_t` since support for the following is still
    incomplete:

doc/mainpage.dox

@@ -100,7 +100,7 @@
  *
  * This file contains routines for parallel I/O format.
  * In particular there are functions to write and read data in parallel according
- * to a user prescribed partition of contigously indexed potentially
+ * to a user prescribed partition of contiguously indexed potentially
  * variable-sized elements. In addition, the user can also write and read
  * data in serial and the data can be stored element-wise compressed.
  *

doc/portability/portitm4.sh

@@ -18,4 +18,3 @@ perl -p -i \
 	-e 's,test\s+"\$,test "x\$,;' \
 	-e 's,=\s+"?x?(yes|no|unknown|disable)"?,= x\1,;' \
 	"$FILE"
-

example/openmp/juqueen_job.js

@@ -1,6 +1,6 @@
-# This jobscript can be submitted to the juqueen 
+# This jobscript can be submitted to the juqueen
 # job queue via llsubmit [script]
-# Do not forget to put your email adress in the 
+# Do not forget to put your email address in the
 # notify_user field.
 #
 # This script has to be executed within the folder of

iniparser/dictionary.c

@@ -6,7 +6,7 @@
 
    This module implements a simple dictionary object, i.e. a list
    of string/string associations. This object is useful to store e.g.
-   informations retrieved from a configuration file (ini files).
+   information retrieved from a configuration file (ini files).
 */
 /*--------------------------------------------------------------------------*/
 
@@ -107,7 +107,7 @@ unsigned dictionary_hash(const char * key)
 /**
   @brief    Create a new dictionary object.
   @param    size    Optional initial size of the dictionary.
-  @return   1 newly allocated dictionary objet.
+  @return   1 newly allocated dictionary object.
 
   This function allocates a new dictionary object of given size and returns
   it. If you do not know in advance (roughly) the number of entries in the

iniparser/dictionary.h

@@ -7,7 +7,7 @@
 
    This module implements a simple dictionary object, i.e. a list
    of string/string associations. This object is useful to store e.g.
-   informations retrieved from a configuration file (ini files).
+   information retrieved from a configuration file (ini files).
 */
 /*--------------------------------------------------------------------------*/
 
@@ -89,7 +89,7 @@ unsigned dictionary_hash(const char * key);
 /**
   @brief    Create a new dictionary object.
   @param    size    Optional initial size of the dictionary.
-  @return   1 newly allocated dictionary objet.
+  @return   1 newly allocated dictionary object.
 
   This function allocates a new dictionary object of given size and returns
   it. If you do not know in advance (roughly) the number of entries in the

iniparser/iniexample.c

@@ -79,18 +79,16 @@ static int parse_ini_file(const char * ini_name)
     printf("Wine:\n");
     s = iniparser_getstring(ini, "wine:grape", NULL);
     printf("Grape:     [%s]\n", s ? s : "UNDEF");
-    
+
     i = iniparser_getint(ini, "wine:year", -1);
     printf("Year:      [%d]\n", i);
 
     s = iniparser_getstring(ini, "wine:country", NULL);
     printf("Country:   [%s]\n", s ? s : "UNDEF");
-    
+
     d = iniparser_getdouble(ini, "wine:alcohol", -1.0);
     printf("Alcohol:   [%g]\n", d);
 
     iniparser_freedict(ini);
     return 0 ;
 }
-
-

iniparser/iniparser.c

@@ -78,9 +78,9 @@ static char * strstrip(const char * s)
 {
     static char l[ASCIILINESZ+1];
     char * last ;
-    
+
     if (s==NULL) return NULL ;
-    
+
     while (isspace((int)*s) && *s) s++;
     memset(l, 0, ASCIILINESZ+1);
     sc3_strcopy (l, ASCIILINESZ + 1, s);
@@ -295,7 +295,7 @@ int iniparser_getsecnkeys(dictionary * d, char * s)
     for (j=0 ; j<d->size ; j++) {
         if (d->key[j]==NULL)
             continue ;
-        if (!strncmp(d->key[j], keym, seclen+1)) 
+        if (!strncmp(d->key[j], keym, seclen+1))
             nkeys++;
     }
 
@@ -313,7 +313,7 @@ int iniparser_getsecnkeys(dictionary * d, char * s)
   This function queries a dictionary and finds all keys in a given section.
   Each pointer in the returned char pointer-to-pointer is pointing to
   a string allocated in the dictionary; do not free or modify them.
-  
+
   This function returns NULL in case of error.
  */
 /*--------------------------------------------------------------------------*/
@@ -337,7 +337,7 @@ char ** iniparser_getseckeys(dictionary * d, char * s)
 
     seclen  = (int)strlen(s);
     sc3_snprintf (keym, ASCIILINESZ + 1, "%s:", s);
-    
+
     i = 0;
 
     for (j=0 ; j<d->size ; j++) {
@@ -563,7 +563,7 @@ static line_status iniparser_line(
     char * section,
     char * key,
     char * value)
-{   
+{
     line_status sta ;
     char        line[ASCIILINESZ+1];
     int         len ;
@@ -577,7 +577,7 @@ static line_status iniparser_line(
         sta = LINE_EMPTY ;
     } else if (line[0]=='#' || line[0]==';') {
         /* Comment line */
-        sta = LINE_COMMENT ; 
+        sta = LINE_COMMENT ;
     } else if (line[0]=='[' && line[len-1]==']') {
         /* Section name */
         sscanf(line, "[%[^]]", section);

src/sc.c

@@ -1046,7 +1046,7 @@ void
 sc_abort (void)
 {
   sc_default_abort_handler ();
-  abort ();                     /* if the user supplied callback incorrecty returns, abort */
+  abort ();                     /* if the user supplied callback incorrectly returns, abort */
 }
 
 static void

src/sc.h

@@ -467,7 +467,7 @@ void                SC_CHECK_ABORTF (int success, SC_PRINTF_FMT const char *fmt,
 #define SC_LP_SILENT      9     /**< Never log anything.  Instead suggesting \ref SC_LP_ERROR. */
 /** @} */
 
-/* The default log priority may be overridded by this preprocessor define. */
+/* The default log priority may be overridden by this preprocessor define. */
 #ifdef SC_LOG_PRIORITY
 #define SC_LP_THRESHOLD SC_LOG_PRIORITY
 #define SC_LP_APPLICATION SC_LOG_PRIORITY

src/sc_builtin/getopt_int.h

@@ -26,7 +26,7 @@ extern int _getopt_internal (int ___argc, char *const *___argv,
 		             const struct option *__longopts, int *__longind,
 			     int __long_only);
 
-
+
 /* Reentrant versions which can handle parsing multiple argument
    vectors at the same time.  */
 

src/sc_camera.h

@@ -362,7 +362,7 @@ void                sc_camera_get_view_mat (const sc_camera_t * camera,
  * device coordinates (NDC).
  *
  * 1. Switch from right-handed to left-handed coordinate system by negating the z-axis.
- * 2. Apply the perpective projection into the cuboid
+ * 2. Apply the perspective projection into the cuboid
  *    [-2/s_x, 2/s_x] x [-2/s_y, 2/s_y] x [n,f] with use of homogeneous coordinates.
  *    Here s_x and s_y are width and height of the visible picture on the near plane.
  * 3. Map the cuboid to the NDC cube [-1, 1]^3.

src/sc_io.c

@@ -1485,7 +1485,7 @@ sc_io_error_class (int errorcode, int *errorclass)
 
   if (errorcode == 0) {
     /* This is the errno for no error or
-     * possibly also the sc_MPI_SUCESS value.
+     * possibly also the sc_MPI_SUCCESS value.
      * In both cases, we want to set errorclass to
      * sc_MPI_SUCCESS.
      */

src/sc_scda.c

@@ -93,9 +93,9 @@
 #define SC_SCDA_CHECK_VERBOSE_NONCOLL(lp, errcode, msg) SC_SCDA_CHECK_VERBOSE_GEN (\
                                     errcode, msg, SC_LOGF, lp)
 
-/** Collectivly check a given errorcode.
+/** Collectively check a given errorcode.
  * This macro assumes that errcode is a collective
- * variable and that the macro is called collectivly.
+ * variable and that the macro is called collectively.
  * The calling function must return NULL in case of an error.
  */
 #define SC_SCDA_CHECK_COLL_ERR(errcode, fc, user_msg) do {                   \
@@ -395,7 +395,7 @@ sc_scda_pad_to_fix_len_inplace (const char *input_data, size_t input_len,
  * \param [out] raw_len       The length of \b raw_data in number of bytes.
  *                            Undefined if the function returns true.
  * \return                    True if \b padded_data does not satisfy the
- *                            scda padding convention for fixed-length paddding.
+ *                            scda padding convention for fixed-length padding.
  *                            False, otherwise.
  */
 static int
@@ -449,7 +449,7 @@ sc_scda_check_pad_to_fix_len (const char *padded_data, size_t pad_len,
  * \param [out] raw_len       The length of \b raw_data in number of bytes.
  *                            Undefined if the function returns true.
  * \return                    True if \b padded_data does not satisfy the
- *                            scda padding convention for fixed-length paddding.
+ *                            scda padding convention for fixed-length padding.
  *                            False, otherwise.
  */
 static int
@@ -1214,7 +1214,7 @@ sc_scda_params_init (sc_scda_params_t *params)
 #endif
 }
 
-/** This function peforms the start up for both scda fopen functions.
+/** This function performs the start up for both scda fopen functions.
  *
  * \param [in]   params     The sc_scda_params_t structure that is
  *                          passed to the scda fopen function. \b params may be
@@ -1452,7 +1452,7 @@ sc_scda_fopen_write (sc_MPI_Comm mpicomm,
   mpiret =
     sc_io_open (mpicomm, filename, SC_IO_WRITE_CREATE, info, &fc->file);
   sc_scda_mpiret_to_errcode (mpiret, errcode, fc);
-  /* We call a macro for checking an error that occurs collectivly.
+  /* We call a macro for checking an error that occurs collectively.
    * In case of an error the macro prints an error message using \ref
    * SC_GLOBAL_LERRORF, closes the file and frees fc.
    */

src/sc_scda.h

@@ -54,7 +54,7 @@
  * the process count can differ between writing and reading.
  *
  * The main purpose of \b scda is to enable the user to implement parallel I/O
- * for numerical appliations, e.g. simulation checkpoint/restart.
+ * for numerical applications, e.g. simulation checkpoint/restart.
  *
  * We elaborate further on the workflow in \ref scda_workflow.
  *
@@ -271,7 +271,7 @@ sc_scda_ret_t;
  * The parsing logic of \ref sc_scda_ferror_t is that first \b scdaret is examined
  * and if \b scdaret != \ref SC_SCDA_FERR_MPI, we know that \b mpiret = 0.
  * If \b scdaret = \ref SC_SCDA_FERR_MPI, we know that an MPI error occurred and
- * we can examine \b mpiret for more informartion.
+ * we can examine \b mpiret for more information.
  *
  * Moreover, a valid sc_scda_ferror always satisfy that if \b scdaret = 0 then
  * \b mpiret = 0 and if \b scdaret = \ref SC_SCDA_FERR_MPI then \b mpiret !=0.
@@ -550,7 +550,7 @@ sc_scda_fcontext_t *sc_scda_fwrite_block (sc_scda_fcontext_t * fc,
  * \param [in]      indirect    A Boolean to determine whether \b array_data
  *                              must be a sc_array of sc_arrays to write
  *                              indirectly and in particular from potentially
- *                              non-contigous memory. In the remaining case of
+ *                              non-contiguous memory. In the remaining case of
  *                              \b indirect being false \b array_data must be
  *                              a sc_array with element size equals to
  *                              \b elem_size that contains the actual array
@@ -682,7 +682,7 @@ int                 sc_scda_proc_sizes (sc_array_t * elem_sizes,
  * \param [in]      indirect    A Boolean to determine whether \b array_data
  *                              must be a sc_array of sc_arrays to write
  *                              indirectly and in particular from potentially
- *                              non-contigous memory. In the remaining case of
+ *                              non-contiguous memory. In the remaining case of
  *                              \b indirect being false \b array_data must be
  *                              a sc_array with the actual array elements as
  *                              data as further explained in the documentation
@@ -810,7 +810,7 @@ sc_scda_fcontext_t *sc_scda_fopen_read (sc_MPI_Comm mpicomm,
  *                              true. For \b decode true as input the file
  *                              section is interpreted as a compressed file
  *                              section if the type and user string of the first
- *                              raw file section satisfiy the compression
+ *                              raw file section satisfy the compression
  *                              convention. If the compression convention is not
  *                              satisfied the data is read raw. For false as
  *                              input the data will be read raw by the
@@ -969,7 +969,7 @@ sc_scda_fcontext_t *sc_scda_fread_block_data (sc_scda_fcontext_t * fc,
  * \param [in]      indirect    A Boolean to determine whether \b array_data
  *                              must be a sc_array of sc_arrays to read
  *                              indirectly and in particular to potentially
- *                              non-contigous memory. See the documentation of
+ *                              non-contiguous memory. See the documentation of
  *                              the parameter \b array_data for more information.
  * \param [out]     errcode     An errcode that can be interpreted by \ref
  *                              sc_scda_ferror_string or mapped to an error class
@@ -1102,7 +1102,7 @@ sc_scda_fcontext_t *sc_scda_fread_varray_sizes (sc_scda_fcontext_t * fc,
  * \param [in]      indirect    A Boolean to determine whether \b array_data
  *                              must be a sc_array of sc_arrays to read
  *                              indirectly and in particular to potentially
- *                              non-contigous memory. See the documentation of
+ *                              non-contiguous memory. See the documentation of
  *                              the parameter \b array_data for more information.
  * \param [out]     errcode     An errcode that can be interpreted by \ref
  *                              sc_scda_ferror_string or mapped to an error class