AnnData warnings

[Zethson]

There's quite a few of them, especially when the tests are executed. Let's collect them:

/home/zeth/PycharmProjects/ehrapy/ehrapy/preprocessing/encoding/_encode.py:324: FutureWarning: X.dtype being converted to np.float32 from object. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
  encoded_ann_data = AnnData(

then

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/h5ad.py:238: OldFormatWarning: Element '/X' was written without encoding metadata.
    d[k] = read_elem(f[k])

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/h5ad.py:238: OldFormatWarning: Element '/layers' was written without encoding metadata.
    d[k] = read_elem(f[k])

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/layers/original' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:590: OldFormatWarning: Element '/obs/_index' was written without encoding metadata.
    return read_elem(dataset)

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/h5ad.py:238: OldFormatWarning: Element '/uns' was written without encoding metadata.
    d[k] = read_elem(f[k])

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/columns_obs_only' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/ehrapy_dummy_encoding' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/non_numerical_columns' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/numerical_columns' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:590: OldFormatWarning: Element '/var/_index' was written without encoding metadata.
    return read_elem(dataset)

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:584: OldFormatWarning: Element '/obs/__categories/datetime' was written without encoding metadata.
    categories = read_elem(categories_dset)

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:587: OldFormatWarning: Element '/obs/datetime' was written without encoding metadata.
    read_elem(dataset), categories, ordered=ordered

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:584: OldFormatWarning: Element '/obs/__categories/strcol' was written without encoding metadata.
    categories = read_elem(categories_dset)

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:587: OldFormatWarning: Element '/obs/strcol' was written without encoding metadata.
    read_elem(dataset), categories, ordered=ordered

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:590: OldFormatWarning: Element '/obs/boolcol' was written without encoding metadata.
    return read_elem(dataset)

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:590: OldFormatWarning: Element '/obs/binary_col' was written without encoding metadata.
    return read_elem(dataset)

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/encoding_to_var' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/encoding_to_var/label_encoding' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/original_values_categoricals' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/original_values_categoricals/binary_col' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/original_values_categoricals/boolcol' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/original_values_categoricals/strcol' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/var_to_encoding' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/var_to_encoding/binary_col' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/var_to_encoding/boolcol' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

tests/io/test_read.py::TestRead::test_read_multiple_h5ad
  /home/zeth/PycharmProjects/ehrapy/.nox/tests-3-8/lib/python3.8/site-packages/anndata/_io/specs/methods.py:92: OldFormatWarning: Element '/uns/var_to_encoding/strcol' was written without encoding metadata.
    return {k: read_elem(v) for k, v in elem.items()}

[namsaraeva]

When moving non-numerical and numerical columns (e.g. ['age', 'gender_num'] for MIMIC-II dataset) from X to obs and backwards.

[Zethson]

@Imipenem could it be that you're reading old h5ad files here and these trigger the AnnData warnings?

[Zethson]

Also

tests/anndata/test_anndata_ext.py::TestAnndataExt::test_move_to_x_move_to_obs
tests/anndata/test_anndata_ext.py::TestAnndataExt::test_move_to_x_move_to_obs
  /home/zeth/miniconda3/envs/ehrapy/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
    warnings.warn(

must be resolved.

Edit: I did this.

[Zethson]

I got rid of quite many of them. Let's have another pass in the future.