Getting error with Numpy

[carolinasisco]

hello,

Code used: memote report snapshot --filename "report_model.html" ~/Desktop//model.xml Error: Traceback (most recent call last): File "/home/carol/miniconda3/envs/metabolic_model_env/bin/memote", line 5, in from memote.suite.cli.runner import cli File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/memote/suite/cli/runner.py", line 42, in import memote.suite.cli.callbacks as callbacks File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/memote/suite/cli/callbacks.py", line 30, in from memote.experimental import ExperimentConfiguration File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/memote/experimental/init.py", line 22, in from memote.experimental.config import File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/memote/experimental/config.py", line 39, in from memote.experimental.essentiality import EssentialityExperiment File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/memote/experimental/essentiality.py", line 25, in import pandera as pa File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/init.py", line 5, in import pandera.backends File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/backends/init.py", line 4, in import pandera.backends.base.builtin_checks File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/backends/base/builtin_checks.py", line 14, in from pandera.api.checks import Check File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/api/checks.py", line 17, in from pandera.strategies.base_strategies import SearchStrategy File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/strategies/init.py", line 3, in from pandera.strategies.pandas_strategies import File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/strategies/pandas_strategies.py", line 42, in from pandera.engines import numpy_engine, pandas_engine File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/pandera/engines/pandasengine.py", line 757, in np.string, ^^^^^^^^^^ File "/home/carol/miniconda3/envs/metabolic_model_env/lib/python3.11/site-packages/numpy/init.py", line 397, in getattr raise AttributeError(

Any suggestions?

Thanks!

[Midnighter]

Hi,

Thanks for the report. You have cut off the most important part of the error message, i.e., what comes after AttributeError. Also, please provide version information like we ask for in the bug report template.

[jjkoehorst]

I might have the same issue after a pip install in a clean venv

memote report snapshot --filename "test_report.html" ~/Documents/protein_model_carve 
Traceback (most recent call last):
  File "/home/peiyi/venv_memote/bin/memote", line 5, in <module>
    from memote.suite.cli.runner import cli
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/memote/suite/cli/runner.py", line 42, in <module>
    import memote.suite.cli.callbacks as callbacks
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/memote/suite/cli/callbacks.py", line 30, in <module>
    from memote.experimental import ExperimentConfiguration
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/memote/experimental/__init__.py", line 22, in <module>
    from memote.experimental.config import *
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/memote/experimental/config.py", line 39, in <module>
    from memote.experimental.essentiality import EssentialityExperiment
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/memote/experimental/essentiality.py", line 25, in <module>
    import pandera as pa
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/__init__.py", line 5, in <module>
    import pandera.backends
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/backends/__init__.py", line 4, in <module>
    import pandera.backends.base.builtin_checks
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/backends/base/builtin_checks.py", line 14, in <module>
    from pandera.api.checks import Check
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/api/checks.py", line 17, in <module>
    from pandera.strategies.base_strategies import SearchStrategy
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/strategies/__init__.py", line 3, in <module>
    from pandera.strategies.pandas_strategies import *
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/strategies/pandas_strategies.py", line 42, in <module>
    from pandera.engines import numpy_engine, pandas_engine
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/pandera/engines/pandas_engine.py", line 757, in <module>
    np.string_,
    ^^^^^^^^^^
  File "/home/peiyi/venv_memote/lib/python3.12/site-packages/numpy/__init__.py", line 397, in __getattr__
    raise AttributeError(
AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'?

[jjkoehorst]

pip install 'numpy<2.0.0' did the trick as this major release made some breaking changes (probably why its a major release).

[Midnighter]

This is coming from the pandera dependency and has already been addressed there. Hopefully, they will release the fix soon.

https://github.com/unionai-oss/pandera/issues/1656