Unable to import hail due to Numpy Scipy dependency mismatch

Hail Query & hailctl
1

Hi,
I am currently trying to import hail(0.2.72). However, I get the following error.


Traceback (most recent call last): 
  File "/usr/local/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 70, in import_module
    return importlib.import_module(modname)
  File "/usr/local/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/jupyter/notebooks/piranha/__init__.py", line 11, in <module>
    module = import_module(f"{__name__}.{module_name}")
  File "/usr/local/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/jupyter/notebooks/piranha/utils.py", line 19, in <module>
    import hail as hl
  File "/usr/local/lib/python3.7/site-packages/hail/__init__.py", line 48, in <module>
    from .methods import *  # noqa: F401,F403,E402
  File "/usr/local/lib/python3.7/site-packages/hail/methods/__init__.py", line 8, in <module>
    from .statgen import (skat, impute_sex, genetic_relatedness_matrix, realized_relationship_matrix,
  File "/usr/local/lib/python3.7/site-packages/hail/methods/statgen.py", line 16, in <module>
    from hail.linalg import BlockMatrix
  File "/usr/local/lib/python3.7/site-packages/hail/linalg/__init__.py", line 1, in <module>
    from .blockmatrix import BlockMatrix, _jarray_from_ndarray, _breeze_from_ndarray, _svd, _eigh
  File "/usr/local/lib/python3.7/site-packages/hail/linalg/blockmatrix.py", line 7, in <module>
    import scipy.linalg as spla
  File "/usr/local/lib/python3.7/site-packages/scipy/__init__.py", line 77, in <module>
    _fun = _deprecated(_msg.format(_key))(_fun)
  File "/usr/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 16, in wrap
    @functools.wraps(fun)
  File "/home/jupyter/notebooks/ref_docs/source/conf.py", line 27, in no_op_wraps
    if func.__module__ is None or module_name not in func.__module__:
AttributeError: 'numpy.ufunc' object has no attribute '__module__'

The versions are as follows:

pandas==1.1.4
scipy==1.6.3
numpy==1.21.1

PS: I installed hail(0.2.72) on a fresh system using pip.

2

Hi @Abhishek !

I’m sorry to hear you’re having trouble with Hail. This appears to be a conflict between skimage and numpy. You should either update skimage to 0.14.2 or later:

pip install -U 'skimage>=0.14.2'

or downgrade numpy to 1.15:

pip install -U 'numpy<=1.15'
3

Hi @danking,

These are the solutions I tried,

  1. Upgrading skimage
    pip install -U 'skimage>=0.14.2'
    It didn’t work

  2. Downgrading numpy
    pip install -U 'numpy<=1.15'
    It didn’t work and each time process ended up getting killed due to pip trying to figure out dependencies.

Screenshot 2021-10-08 at 12.32.10 PM
Screenshot 2021-10-08 at 12.32.10 PM826×652 31.6 KB

PS: To give you overall context, I have written wrapper over hail for our custom pipelines. I am trying to generate sphinx documentation. However, whenever I try to generate sphinx documentation(which requires importing hail), I get the following error.

AttributeError: 'numpy.ufunc' object has no attribute '__module__'
4

I tried installing hail 0.2.72 in a virtual environment from scratch with python 3.7 and it worked fine.
But whenever I try to do the same in our CI/CD gitlab runner, it seems to break. I will check the gitlab runner docker base image installed packages.

5

Hmm. After running

pip install -U 'skimage>=0.14.2'

did you get this error again:

AttributeError: 'numpy.ufunc' object has no attribute '__module__'

?

Hmm, OK. After a closer look, it seems that you might have changed functools.wraps to be a function on line 27 of ref_docs/source/conf.py:

  File "/home/jupyter/notebooks/ref_docs/source/conf.py", line 27, in no_op_wraps
    if func.__module__ is None or module_name not in func.__module__:

It sounds like the issue might be that numpy.ufunc has no attribute __module__. Can you try changing your no_op_wraps code to be:

if not hasattr(func, '__module__') or func.__module__ is None or module_name not in func.__module__:
6

I tried updating no_wraps_code as you suggested

import functools
def no_op_wraps(func):

    if hasattr(func, '__module__'):
        if func.__module__ is None or module_name not in func.__module__:
            return functools.orig_wraps(func)
        
    def wrapper(decorator):
        return func
    return wrapper

functools.orig_wraps = functools.wraps 
functools.wraps = no_op_wraps

However, I got a new error.(You can see the full stack trace at the bottom)

call.__doc__ = msg
AttributeError: attribute '__doc__' of 'numpy.ufunc' objects is not writable

PS: The no op wraps code replaces functools.wraps in order to undo wrapping. It is used to preserve the decorated function’s signature in the documentation generated by Sphinx.

Stack trace 
Traceback (most recent call last): 
  File "/usr/local/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 70, in import_module
    return importlib.import_module(modname)
  File "/usr/local/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/jupyter/notebooks/piranha/__init__.py", line 11, in <module>
    module = import_module(f"{__name__}.{module_name}")
  File "/usr/local/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/jupyter/notebooks/piranha/utils.py", line 19, in <module>
    import hail as hl
  File "/usr/local/lib/python3.7/site-packages/hail/__init__.py", line 48, in <module>
    from .methods import *  # noqa: F401,F403,E402
  File "/usr/local/lib/python3.7/site-packages/hail/methods/__init__.py", line 8, in <module>
    from .statgen import (skat, impute_sex, genetic_relatedness_matrix, realized_relationship_matrix,
  File "/usr/local/lib/python3.7/site-packages/hail/methods/statgen.py", line 16, in <module>
    from hail.linalg import BlockMatrix
  File "/usr/local/lib/python3.7/site-packages/hail/linalg/__init__.py", line 1, in <module>
    from .blockmatrix import BlockMatrix, _jarray_from_ndarray, _breeze_from_ndarray, _svd, _eigh
  File "/usr/local/lib/python3.7/site-packages/hail/linalg/blockmatrix.py", line 7, in <module>
    import scipy.linalg as spla
  File "/usr/local/lib/python3.7/site-packages/scipy/__init__.py", line 77, in <module>
    _fun = _deprecated(_msg.format(_key))(_fun)
  File "/usr/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 21, in wrap
    call.__doc__ = msg
AttributeError: attribute '__doc__' of 'numpy.ufunc' objects is not writable

WARNING: autodoc: failed to import module 'setup'; the module executes module level statement and it might call sys.exit().
7

It seems like the issue is this: Link

Numpy functions were deprecated in Scipy after 1.14

8

I agree. It appears there’s some issue between scipy and numpy. I don’t think hail is involved except that hail imports scipy. If you remove hail entirely from your utils.py file, add import scipy.linalg and try to generate docs, does that also fail? I’m not sure what’s wrong, but I think you’ll need to find compatible versions of scipy, numpy, and skimage.