ValueError: Only CSR and CSC matrices are supported.

[yuhuyoyo]

Describe the bug
unexpected error going through getting started (scipy dependency pin not strict?)

To Reproduce
Steps to reproduce the behavior:

i followed the getting started instruction

pip install cirrocumulus
download the pbmc3k package
cirro launch pbmc3k.h5ad --markers markers.json

Expected behavior
launch cirro app and load the data

Screenshots
Unable to retrieve data. Please try again.

Additional context

[2025-08-04 16:50:38,302] ERROR in app: Exception on /api/data [POST]
Traceback (most recent call last):
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/flask/app.py", line 1511, in wsgi_app
    response = self.full_dispatch_request()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/flask/app.py", line 919, in full_dispatch_request
    rv = self.handle_user_exception(e)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/flask/app.py", line 917, in full_dispatch_request
    rv = self.dispatch_request()
         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/flask/app.py", line 902, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/cirrocumulus/api.py", line 413, in handle_data
    data_processing.handle_data(
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/cirrocumulus/data_processing.py", line 308, in handle_data
    adata = dataset_api.read_dataset(dataset=dataset, keys=keys)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/cirrocumulus/dataset_api.py", line 64, in read_dataset
    return provider.read_dataset(get_fs(path), path, keys=keys, dataset=dataset)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/cirrocumulus/anndata_dataset.py", line 241, in read_dataset
    adata = AnnData(X=X, obs=obs, var=var, obsm=obsm)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/anndata/_core/anndata.py", line 242, in __init__
    self._init_as_actual(
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/anndata/_core/anndata.py", line 388, in _init_as_actual
    X = coerce_array(X, name="X")
        ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yuhuyoyo/Library/Python/3.12/lib/python/site-packages/anndata/_core/storage.py", line 57, in coerce_array
    raise ValueError(msg)
ValueError: Only CSR and CSC matrices are supported.

[joshua-gould]

Fixed in #222