[BUG] New installs of PySCENIC will fail due to no longer supported np.object alias in current Numpy

[pcm32]

Describe the bug

Fresh installations over pip will fail because current version installed of numpy no longer supports:

.venv_pyscenic/lib/python3.11/site-packages/pyscenic/transform.py", line 42, in <module>
    ("Enrichment", COLUMN_NAME_ANNOTATION): np.object,
                                            ^^^^^^^^^
  File ".venv_pyscenic/lib/python3.11/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'object'.
`np.object` was a deprecated alias for the builtin `object`. To avoid this error in existing code, use `object` by itself. Doing this will not modify any behavior and is safe. 
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'object_'?

Mote that most errors are due to the input from the user, and therefore should be treated as questions in the Discussions. Please, only report them as bugs if you are quite certain that they are not behaving as expected.

This is not parameter depenedent, but a dependency issue.

Steps to reproduce the behavior

1. Command run when the error occurred:

# in a fresh venv
pip install pyscenic
# run grn with some data from the cli

2. Error encountered:

.venv_pyscenic/lib/python3.11/site-packages/pyscenic/transform.py:42: FutureWarning: In the future `np.object` will be defined as the corresponding NumPy scalar.
  ("Enrichment", COLUMN_NAME_ANNOTATION): np.object,
Traceback (most recent call last):
  File ".venv_pyscenic/bin/pyscenic", line 5, in <module>
    from pyscenic.cli.pyscenic import main
  File ".venv_pyscenic/lib/python3.11/site-packages/pyscenic/cli/pyscenic.py", line 26, in <module>
    from pyscenic.prune import _prepare_client, find_features, prune2df
  File ".venv_pyscenic/lib/python3.11/site-packages/pyscenic/prune.py", line 27, in <module>
    from .transform import (
  File ".venv_pyscenic/lib/python3.11/site-packages/pyscenic/transform.py", line 42, in <module>
    ("Enrichment", COLUMN_NAME_ANNOTATION): np.object,
                                            ^^^^^^^^^
  File ".venv_pyscenic/lib/python3.11/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'object'.
`np.object` was a deprecated alias for the builtin `object`. To avoid this error in existing code, use `object` by itself. Doing this will not modify any behavior and is safe. 
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'object_'?

Expected behavior

The command to run without complaining about the numpy issue.

Please complete the following information:

• pySCENIC version: even -h throws the error, 0.12.1 I think
• Installation method: pip
• Run environment: bash and Jupyter
• OS: macOS
• Package versions: [obtain using pip freeze, conda list, or skip this if using Docker/Singularity]:

aiohttp==3.8.4
aiosignal==1.3.1
arboreto==0.1.6
async-timeout==4.0.2
attrs==23.1.0
bokeh==3.1.1
boltons==23.0.0
certifi==2023.5.7
charset-normalizer==3.1.0
click==8.1.3
cloudpickle==2.2.1
contourpy==1.0.7
ctxcore==0.2.0
cytoolz==0.12.1
dask==2023.5.0
dill==0.3.6
distributed==2023.5.0
frozendict==2.3.8
frozenlist==1.3.3
fsspec==2023.5.0
h5py==3.8.0
idna==3.4
importlib-metadata==6.6.0
interlap==0.2.7
Jinja2==3.1.2
joblib==1.2.0
llvmlite==0.40.0
locket==1.0.0
loompy==3.0.7
lz4==4.3.2
MarkupSafe==2.1.2
msgpack==1.0.5
multidict==6.0.4
multiprocessing-on-dill==3.5.0a4
networkx==3.1
numba==0.57.0
numexpr==2.8.4
numpy==1.24.3
numpy-groupies==0.9.22
packaging==23.1
pandas==2.0.1
partd==1.4.0
Pillow==9.5.0
psutil==5.9.5
pyarrow==12.0.0
pynndescent==0.5.10
pyscenic==0.12.1
python-dateutil==2.8.2
pytz==2023.3
PyYAML==6.0
requests==2.31.0
scikit-learn==1.2.2
scipy==1.10.1
six==1.16.0
sortedcontainers==2.4.0
tblib==1.7.0
threadpoolctl==3.1.0
toolz==0.12.0
tornado==6.3.2
tqdm==4.65.0
tzdata==2023.3
umap-learn==0.5.3
urllib3==2.0.2
xyzservices==2023.5.0
yarl==1.9.2
zict==3.0.0
zipp==3.15.0

Thanks!

[pcm32]

Pining to Numpy 1.23.5 seems to get rid of this, leaving me again in the dask issues, but that is a different story.

[wbrett87]

Had same issue, using numpy1.23.5 worked... Thanks!

[ghuls]

Thanks for reporting this.

Solved in master:
eaf23eb