Error inflating stream

[gudlaugu]

I am getting a logic error, "Error inflating stream", when reading larger arrays from an npz archive. After a lot of debugging I found out that by increasing the size of CHUNK in zip.cpp so that the file could be read in a single pass everything worked as expected.

Here is the solution I came up with. Basically replacing the npy_inflate() call in the read_file function in npz.cpp with a single pass inflation. Everything is anyway in memory all the time and there is no need to split the inflation step up into chunks.

   //Use one step inflation, we anyway need to hold everything in memory at some point
   std::vector<std::uint8_t> compressed_bytes(uncompressed_bytes);
   uncompressed_bytes.resize(entry.uncompressed_size);

   //Initialize miniz
   z_stream strm;
   strm.zalloc = Z_NULL;
   strm.zfree = Z_NULL;
   strm.opaque = Z_NULL;
   strm.avail_in = 0;
   strm.next_in = Z_NULL;
   const int WINDOW_BITS = -15;
   auto ret = inflateInit2(&strm, WINDOW_BITS);
   if (ret != Z_OK)
   {
      throw std::logic_error("Unable to initialize inflate algorithm");
   }

   //Inflate in one step
   strm.next_in = &compressed_bytes[0];
   strm.avail_in = compressed_bytes.size();
   strm.next_out = &uncompressed_bytes[0];
   strm.avail_out = uncompressed_bytes.size();

   ret = inflate(&strm, Z_FINISH);
   if (ret != Z_STREAM_END) {
      std::cerr<<strm.msg<<std::endl;
      (void)inflateEnd(&strm);
      throw std::logic_error("Error inflating stream");
   }
   (void)inflateEnd(&strm);

[matajoh]

I've not seen this issue in testing, but I'll see if I can reproduce it. That said, the solution seems fine. If it checks out on my end, I'll make the change.