Fix codespell issues (#5256)

.codespellrc

@@ -1,6 +1,6 @@
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
 [codespell]
-skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5import/testfiles/*.conf,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp
+skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5import/testfiles/*.conf,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp,./release_docs/HISTORY-*.txt
 check-hidden = true
 # ignore-regex = 
-ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos,TEXTIN,FLE
+ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos,TEXTIN,indx,FLE

doxygen/dox/ImageSpec.dox

@@ -430,7 +430,7 @@ and blue components that make up each color.
 <table>
 <tr>
 <td>
-\image html Palettes.fm.anc.gif
+\image html Palettes_fm_anc.gif
 </td>
 </tr>
 </table>

hl/test/test_ld.c

@@ -33,7 +33,7 @@
 #define DSET_SCALAR      "DSET_SCALAR"
 
 /* Selected compound field members for testing */
-#define VALID_FIELDS1 "field1,field2.a,field3,field4" /* TEMPORORAY */
+#define VALID_FIELDS1 "field1,field2.a,field3,field4" /* TEMPORARY */
 #define VALID_FIELDS2 "field2.b.a,field2.c,field4.b"
 
 #define INVALID_FIELDS1 "field2.k.a,field2.c,field4.k"

src/H5B2test.c

@@ -599,7 +599,7 @@ H5B2__get_node_depth_test(H5B2_t *bt2, void *udata)
     /* Check arguments. */
     assert(bt2);
 
-    /* Get information abou the node */
+    /* Get information about the node */
     if (H5B2__get_node_info_test(bt2, udata, &ninfo) < 0)
         HGOTO_ERROR(H5E_BTREE, H5E_NOTFOUND, (-1), "error looking up node info");
 

src/H5Dbtree.c

@@ -466,7 +466,7 @@ H5D__chunk_disjoint(unsigned n, const hsize_t *scaled1, const hsize_t *scaled2)
     assert(scaled1);
     assert(scaled2);
 
-    /* Loop over two chunks, detecting disjointness and getting out quickly */
+    /* Loop over two chunks, detecting disjointedness and getting out quickly */
     for (u = 0; u < n; u++)
         if ((scaled1[u] + 1) <= scaled2[u] || (scaled2[u] + 1) <= scaled1[u])
             HGOTO_DONE(true);

src/H5Dchunk.c

@@ -5029,7 +5029,7 @@ H5D__chunk_allocate(const H5D_t *dset, bool full_overwrite, const hsize_t old_di
         fill_buf = &fb_info.fill_buf;
 
         /* Check if there are filters which need to be applied to the chunk */
-        /* (only do this in advance when the chunk info can be re-used (i.e.
+        /* (only do this in advance when the chunk info can be reused (i.e.
          *      it doesn't contain any non-default VL datatype fill values)
          */
         if (!fb_info.has_vlen_fill_type && pline->nused > 0) {

src/H5FDonion_index.c

@@ -437,7 +437,7 @@ H5FD__onion_revision_index_resize(H5FD_onion_revision_index_t *rix)
  *              checksum value will change.
  *
  *              Entry data is copied into separate memory region; user pointer
- *              can be safley re-used or discarded after operation.
+ *              can be safley reused or discarded after operation.
  *
  * Return:      SUCCEED/FAIL
  *-----------------------------------------------------------------------------

src/H5FDs3comms.c

@@ -861,7 +861,7 @@ H5FD__s3comms_s3r_configure_aws(s3r_t *handle, const H5FD_ros3_fapl_t *fa, const
     if (H5FD__s3comms_make_iso_8661_string(time(NULL), iso8601) < 0)
         HGOTO_ERROR(H5E_VFL, H5E_BADVALUE, FAIL, "could not construct ISO-8601 string");
 
-    /* Compute signing key (part of AWS/S3 REST API). Can be re-used by
+    /* Compute signing key (part of AWS/S3 REST API). Can be reused by
      * user/key for 7 days after creation.
      */
     if (H5FD__s3comms_make_aws_signing_key(signing_key, (const char *)fa->secret_key,

src/H5FDs3comms.h

@@ -320,7 +320,7 @@ typedef struct {
  *
  * Instantiated through `H5FD__s3comms_s3r_open()`, copies data into self.
  *
- * Intended to be re-used for operations on a remote object.
+ * Intended to be reused for operations on a remote object.
  *
  * Cleaned up through `H5FD__s3comms_s3r_close()`.
  *
@@ -373,7 +373,7 @@ typedef struct {
  *     key, generated via
  *     `HMAC-SHA256(HMAC-SHA256(HMAC-SHA256(HMAC-SHA256("AWS4<secret_key>",
  *         "<yyyyMMDD"), "<aws-region>"), "<aws-service>"), "aws4_request")`
- *     which may be re-used for several (up to seven (7)) days from creation
+ *     which may be reused for several (up to seven (7)) days from creation
  *
  *     Computed once upon file open from the secret key string in the fapl
  *

src/H5FDsubfiling/H5FDioc_int.c

@@ -396,7 +396,7 @@ H5FD__ioc_async_completion(MPI_Request *mpi_reqs, size_t num_reqs)
 
     H5_CHECK_OVERFLOW(num_reqs, size_t, int);
 
-    /* Have to supppress gcc warnings regarding MPI_STATUSES_IGNORE
+    /* Have to suppress gcc warnings regarding MPI_STATUSES_IGNORE
      * with MPICH (https://github.com/pmodels/mpich/issues/5687)
      */
     H5_GCC_DIAG_OFF("stringop-overflow")

src/H5Fmodule.h

@@ -2156,7 +2156,7 @@
  * image> \endcode
  *
  * If we can further arrange matters so that only the contents of the datasets in the HDF5 file image change,
- * but not the structure of the file itself, we can optimize still further by re-using the image and changing
+ * but not the structure of the file itself, we can optimize still further by reusing the image and changing
  * only the contents of the datasets after the initial write to the buffer. The following pseudo code shows
  * how this might be done. Note that the code assumes that buf already contains the image of the HDF5 file
  * whose dataset contents are to be overwritten. Again, much error checking is omitted for clarity. Also,

src/H5Pfapl.c

@@ -2388,7 +2388,7 @@ H5Pget_mdc_config(hid_t plist_id, H5AC_cache_config_t *config /*out*/)
  *        probably) use space in the file heap.  If garbage collection
  *        is on and the user passes in an uninitialized value in a
  *        reference structure, the heap might get corrupted.  When
- *        garbage collection is off however and the user re-uses a
+ *        garbage collection is off however and the user reuses a
  *        reference, the previous heap block will be orphaned and not
  *        returned to the free heap space.  When garbage collection is
  *        on, the user must initialize the reference structures to 0 or

src/H5Ppublic.h

@@ -4910,7 +4910,7 @@ H5_DLL herr_t H5Pset_file_locking(hid_t fapl_id, hbool_t use_file_locking, hbool
  *          HDF5 file's global heap. If garbage collection is on and the user
  *          passes in an uninitialized value in a reference structure, the heap
  *          might get corrupted. When garbage collection is off, however, and
- *          the user re-uses a reference, the previous heap block will be
+ *          the user reuses a reference, the previous heap block will be
  *          orphaned and not returned to the free heap space.
  *
  *          When garbage collection is on, the user must initialize the

src/H5Rdeprec.c

@@ -191,7 +191,7 @@ H5R__encode_token_region_compat(H5F_t *f, const H5O_token_t *obj_token, size_t t
          * file libver bounds, this is later retrieved in H5S hyper encode */
         H5CX_set_libver_bounds(f);
 
-        /* Zero the heap ID out, may leak heap space if user is re-using
+        /* Zero the heap ID out, may leak heap space if user is reusing
          * reference and doesn't have garbage collection turned on
          */
         memset(buf, 0, buf_size);

src/H5Sselect.c

@@ -2575,11 +2575,11 @@ H5S_select_project_intersection(H5S_t *src_space, H5S_t *dst_space, H5S_t *src_i
                     /* Advance iterators */
                     if (H5S_SELECT_ITER_NEXT(ss_iter, 1) < 0)
                         HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL,
-                                    "can't advacne source selection iterator");
+                                    "can't advance source selection iterator");
                     ss_iter->elmt_left--;
                     if (H5S_SELECT_ITER_NEXT(ds_iter, 1) < 0)
                         HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL,
-                                    "can't advacne destination selection iterator");
+                                    "can't advance destination selection iterator");
                     ds_iter->elmt_left--;
                 } while (ss_iter->elmt_left > 0);
                 assert(H5S_SELECT_ITER_NELMTS(ds_iter) == 0);

src/H5TSbarrier.h

@@ -57,7 +57,7 @@
  *
  * Purpose:     Wait at a barrier.
  *
- * Note:     	Similar to pthread_barrier_wait, a barrier may be re-used
+ * Note:     	Similar to pthread_barrier_wait, a barrier may be reused
  *		multiple times without intervening calls to H5TS_barrier_init.
  *
  * Return:      Non-negative on success / Negative on failure

test/mirror_vfd.c

@@ -2445,7 +2445,7 @@ main(int argc, char **argv)
     /* TESTS */
 
     if (nerrors == 0) {
-        H5FD_mirror_xmit_t xmit_mock; /* Re-used header in various xmit tests */
+        H5FD_mirror_xmit_t xmit_mock; /* Reused header in various xmit tests */
 
         /* Set bogus values matching expected; encoding doesn't care
          * Use sequential values to easily generate the expected buffer with a

test/swmr.c

@@ -5625,7 +5625,7 @@ static int
 test_file_lock_swmr_concur(hid_t H5_ATTR_UNUSED in_fapl)
 {
     /* Output message about test being performed */
-    TESTING("File open with different combintations of flags + SWMR flags--concurrent access");
+    TESTING("File open with different combinations of flags + SWMR flags--concurrent access");
     SKIPPED();
     puts("    Test skipped due to fork or waitpid not defined.");
     return 0;
@@ -5647,7 +5647,7 @@ test_file_lock_swmr_concur(hid_t in_fapl)
     int   notify = 0;
 
     /* Output message about test being performed */
-    TESTING("File open with different combintations of flags + SWMR flags--concurrent access");
+    TESTING("File open with different combinations of flags + SWMR flags--concurrent access");
 
     /* Set locking in the fapl */
     if ((fapl = H5Pcopy(in_fapl)) < 0)

test/tmisc.c

@@ -354,7 +354,7 @@ typedef struct {
 /****************************************************************
 **
 **  test_misc1(): test unlinking a dataset from a group and immediately
-**                      re-using the dataset name
+**                      reusing the dataset name
 **
 ****************************************************************/
 static void
@@ -7132,7 +7132,7 @@ test_misc(void H5_ATTR_UNUSED *params)
     /* Output message about test being performed */
     MESSAGE(5, ("Testing Miscellaneous Routines\n"));
 
-    test_misc1();  /* Test unlinking a dataset & immediately re-using name */
+    test_misc1();  /* Test unlinking a dataset & immediately reusing name */
     test_misc2();  /* Test storing a VL-derived datatype in two different files */
     test_misc3();  /* Test reading from chunked dataset with non-zero fill value */
     test_misc4();  /* Test retrieving the fileno for various objects with H5Oget_info() */

test/ttsafe_thread_id.c

@@ -62,7 +62,7 @@ thread_main(void H5_ATTR_UNUSED *arg)
         goto pre_barrier_error;
     }
 
-    /* Verify that the thread ID hasn't been re-used */
+    /* Verify that the thread ID hasn't been reused */
     if (used[tid - 2]) {
         TestErrPrintf("reused tid %" PRIu64 " FAIL\n", tid);
         H5TS_mutex_unlock(&used_lock);