Attempt to write to vlen dataset

vlen_h5py_bug.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import h5py\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "dtvlen = h5py.special_dtype(vlen=np.float64)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "f = h5py.File(\"vlen_test.h5\", \"w\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "e0 = np.array([1.1, 2.2, 3.3], dtype=np.float64)\n",
    "e1 = np.array([1.9, 2.8, 3.7], dtype=np.float64) \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(2, 3)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "arr = np.array([e0, e1], dtype=dtvlen)\n",
    "arr.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(2,)"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "arr = np.empty((2,), dtype=dtvlen)\n",
    "arr[...] = [e0, e1]\n",
    "arr.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "dset = f.create_dataset(\"vlen_dset\", (2,), dtype=dtvlen)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "Can't broadcast (2, 3) -> (2,)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[0;32mIn [12], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m dset[\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m arr\n",
      "File \u001b[0;32mh5py/_objects.pyx:54\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
      "File \u001b[0;32mh5py/_objects.pyx:55\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
      "File \u001b[0;32m~/anaconda3/envs/py39/lib/python3.9/site-packages/h5py/_hl/dataset.py:1007\u001b[0m, in \u001b[0;36mDataset.__setitem__\u001b[0;34m(self, args, val)\u001b[0m\n\u001b[1;32m   1004\u001b[0m     mshape \u001b[38;5;241m=\u001b[39m val\u001b[38;5;241m.\u001b[39mshape\n\u001b[1;32m   1006\u001b[0m \u001b[38;5;66;03m# Perform the write, with broadcasting\u001b[39;00m\n\u001b[0;32m-> 1007\u001b[0m mspace \u001b[38;5;241m=\u001b[39m h5s\u001b[38;5;241m.\u001b[39mcreate_simple(\u001b[43mselection\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexpand_shape\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmshape\u001b[49m\u001b[43m)\u001b[49m)\n\u001b[1;32m   1008\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m fspace \u001b[38;5;129;01min\u001b[39;00m selection\u001b[38;5;241m.\u001b[39mbroadcast(mshape):\n\u001b[1;32m   1009\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mid\u001b[38;5;241m.\u001b[39mwrite(mspace, fspace, val, mtype, dxpl\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_dxpl)\n",
      "File \u001b[0;32m~/anaconda3/envs/py39/lib/python3.9/site-packages/h5py/_hl/selections.py:264\u001b[0m, in \u001b[0;36mSimpleSelection.expand_shape\u001b[0;34m(self, source_shape)\u001b[0m\n\u001b[1;32m    262\u001b[0m             eshape\u001b[38;5;241m.\u001b[39mappend(t)\n\u001b[1;32m    263\u001b[0m         \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 264\u001b[0m             \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCan\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt broadcast \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m -> \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m%\u001b[39m (source_shape, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39marray_shape))  \u001b[38;5;66;03m# array shape\u001b[39;00m\n\u001b[1;32m    266\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28many\u001b[39m([n \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m n \u001b[38;5;129;01min\u001b[39;00m remaining_src_dims]):\n\u001b[1;32m    267\u001b[0m     \u001b[38;5;66;03m# All dimensions from target_shape should either have been popped\u001b[39;00m\n\u001b[1;32m    268\u001b[0m     \u001b[38;5;66;03m# to match the selection shape, or be 1.\u001b[39;00m\n\u001b[1;32m    269\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCan\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt broadcast \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m -> \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m%\u001b[39m (source_shape, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39marray_shape))  \u001b[38;5;66;03m# array shape\u001b[39;00m\n",
      "\u001b[0;31mTypeError\u001b[0m: Can't broadcast (2, 3) -> (2,)"
     ]
    }
   ],
   "source": [
    "dset[...] = arr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(2,)"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dset.shape"
   ]
  }
 ],
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