search

jeromekelleher / sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
4 stars 3 forks source link

Issue with zarr 2.18.2 #191

Closed szhan closed 3 days ago

szhan commented 3 days ago

I'm encounter the following error when running sc2ts using zarr 2.18.2.

File "/Users/shingzhan/Projects/sc2ts/sc2ts/inference.py", line 996, in convert_tsinfer_sample_data
    resize_copy(data["sites/metadata"], ts.num_sites)
  File "/Users/shingzhan/Projects/sc2ts/sc2ts/inference.py", line 988, in resize_copy
    array[:] = [x] * new_size
    ~~~~~^^^
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 1452, in __setitem__
    self.set_basic_selection(pure_selection, value, fields=fields)
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 1548, in set_basic_selection
    return self._set_basic_selection_nd(selection, value, fields=fields)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 1938, in _set_basic_selection_nd
    self._set_selection(indexer, value, fields=fields)
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 1991, in _set_selection
    self._chunk_setitem(chunk_coords, chunk_selection, chunk_value, fields=fields)
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 2259, in _chunk_setitem
    self._chunk_setitem_nosync(chunk_coords, chunk_selection, value, fields=fields)
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 2263, in _chunk_setitem_nosync
    cdata = self._process_for_setitem(ckey, chunk_selection, value, fields=fields)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/shingzhan/micromamba/envs/ts/lib/python3.12/site-packages/zarr/core.py", line 2324, in _process_for_setitem
    chunk[chunk_selection] = value
    ~~~~~^^^^^^^^^^^^^^^^^
ValueError: could not broadcast input array from shape (29422,) into shape (750,)

It works fine when I install zarr 2.18.0. I haven't looked into exactly why.

jeromekelleher commented 3 days ago

Good to know, thanks. Let's pin on < 2.18 for now.