HiDiHlabs / ovrl.py

A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.
https://ovrlpy.readthedocs.io
MIT License
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Numpy recursion loop on import #36

Closed pakiessling closed 5 hours ago

pakiessling commented 21 hours ago

Hi I get

File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 143, in _scalar_str
    elif np.issubdtype(dtype, np.number):
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
    arg1 = dtype(arg1).type
           ^^^^^^^^^^^
  File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 46, in __repr__
    arg_str = _construction_repr(dtype, include_align=False)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 100, in _construction_repr
    return _scalar_str(dtype, short=short)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 143, in _scalar_str
    elif np.issubdtype(dtype, np.number):
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
    arg1 = dtype(arg1).type
           ^^^^^^^^^^^
RecursionError: maximum recursion depth exceeded while calling a Python object

When importing ovrl 50c1d6c29c1b35f2a9ceca63793e975b308ca1fa with both Numpy 2.1.3 and 1.26.4

Any ideas?

sebastiantiesmeyer commented 17 hours ago

Hi Paul,

Danke für die Rüclmeldung : ) Es kann sein, dass das Notebook noch ein veraltetes Import-Statement hat; Gibt es eine Zeile die das sys-package verwendet um einen Systempfad zu erweitern? Dann müsstest du diese Zeilen löschen und einfach durch 'import ovrlpy' ersetzen. thx & LG --Sebastian

On Thu, 21 Nov 2024 at 18:24, pakiessling @.***> wrote:

Hi I get

File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 143, in _scalar_str elif np.issubdtype(dtype, np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 46, in repr arg_str = _construction_repr(dtype, include_align=False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 100, in _construction_repr return _scalar_str(dtype, short=short) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/_dtype.py", line 143, in _scalar_str elif np.issubdtype(dtype, np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpcwork/p0020567/enviroments/overlpy/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ RecursionError: maximum recursion depth exceeded while calling a Python object

When importing ovrl with both Numpy 2.1.3 and 1.26.4

Any ideas?

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pakiessling commented 5 hours ago

Mhh ne das war per pip installiert.

Aber eine frische Installation in python 3.12.7 funktioniert