Update embedded PyTables code to v3.10.1

doc/information.rst

@@ -65,11 +65,11 @@ HDF5 compression filters and compression libraries sources were obtained from:
   (commit `49e3b65 <https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/49e3b65eca772bca77af13ba047d8b577673afba>`_)
   using LZ4.
 * `bitshuffle plugin <https://github.com/kiyo-masui/bitshuffle>`_ (v0.5.1) using LZ4 and ZStd.
-* bzip2 plugin (from `PyTables <https://github.com/PyTables/PyTables/>`_ v3.9.2)
+* bzip2 plugin (from `PyTables <https://github.com/PyTables/PyTables/>`_ v3.10.1)
   using `BZip2 <https://sourceware.org/git/bzip2.git>`_ (v1.0.8).
 * `hdf5-blosc plugin <https://github.com/Blosc/hdf5-blosc>`_ (v1.0.1)
   using `c-blosc <https://github.com/Blosc/c-blosc>`_ (v1.21.5), LZ4, Snappy, ZLib and ZStd.
-* hdf5-blosc2 plugin (from `PyTables <https://github.com/PyTables/PyTables/>`_ v3.9.2)
+* hdf5-blosc2 plugin (from `PyTables <https://github.com/PyTables/PyTables/>`_ v3.10.1)
   using `c-blosc2 <https://github.com/Blosc/c-blosc2>`_ (v2.15.0), LZ4, ZLib and ZStd.
 * `FCIDECOMP plugin <https://gitlab.eumetsat.int/open-source/data-tailor-plugins/fcidecomp>`_
   (`v2.0.1 <https://gitlab.eumetsat.int/open-source/data-tailor-plugins/fcidecomp/-/tree/e88f83c03bafcd0769c167dca14aa7aabf728e1b>`_)

src/PyTables/hdf5-blosc2/src/blosc2_filter.c

@@ -298,6 +298,7 @@ size_t blosc2_filter_function(unsigned flags, size_t cd_nelmts,
   /* Filter params that are only set for B2ND */
   int ndim = -1;
   int32_t chunkshape[BLOSC2_MAX_DIM];
+  size_t chunksize = typesize;
   if (cd_nelmts >= 8) {
     /* Get chunk shape for B2ND */
     ndim = cd_values[7];
@@ -321,6 +322,7 @@ size_t blosc2_filter_function(unsigned flags, size_t cd_nelmts,
     }
     for (int i = 0; i < ndim; i++) {
       chunkshape[i] = cd_values[8 + i];
+      chunksize *= (size_t) cd_values[8 + i];
     }
   }
 
@@ -367,6 +369,14 @@ size_t blosc2_filter_function(unsigned flags, size_t cd_nelmts,
 
     blosc2_storage storage = {.cparams=&cparams, .contiguous=false};
 
+    if (ndim > 1 && nbytes != chunksize) {
+      BLOSC_TRACE_INFO("Filter input size %lu does not match chunk data size %lu "
+                       "(e.g. Fletcher32 checksum added before compression step), "
+                       "using plain Blosc2 instead of B2ND",
+                       nbytes, chunksize);
+      ndim = -1;
+    }
+
     if (ndim > 1) {
 
       b2nd_context_t *ctx = NULL;
@@ -453,6 +463,15 @@ size_t blosc2_filter_function(unsigned flags, size_t cd_nelmts,
     /* declare dummy variables */
     int32_t cbytes;
 
+    /* It would be cool to have a check to detect whether the buffer contains
+     * an unexpected amout of bytes because of the application of a previous
+     * filter (e.g. a Fletcher32 checksum), thus disabling B2ND optimizations.
+     * However, we cannot know before parsing the super-chunk, and that
+     * operation accepts trailing bytes without reporting their presence.
+     * Thus such a test can only happen outside of the filter, with more
+     * information available about the whole pipeline setup.
+     */
+
     blosc2_schunk* schunk = blosc2_schunk_from_buffer(*buf, (int64_t)nbytes, false);
     if (schunk == NULL) {
       PUSH_ERR("blosc2_filter", H5E_CALLBACK, "Cannot get super-chunk from buffer");
@@ -549,6 +568,7 @@ size_t blosc2_filter_function(unsigned flags, size_t cd_nelmts,
       }
 
       blosc2_dparams dparams = BLOSC2_DPARAMS_DEFAULTS;
+      dparams.schunk = schunk;
       dctx = blosc2_create_dctx(dparams);
       status = blosc2_decompress_ctx(dctx, chunk, cbytes, outbuf, (int32_t) outbuf_size);
       if (status <= 0) {