[Bug 2002660] [NEW] networkx incompatible with numpy 1.24

[Simon Chopin]

Public bug reported:

The nipype autopkgtests have started failing with the following stack
trace:

____________ ERROR collecting pipeline/plugins/tests/test_tools.py _____________
/usr/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1050: in _gcd_import
    ???
<frozen importlib._bootstrap>:1027: in _find_and_load
    ???
<frozen importlib._bootstrap>:992: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1050: in _gcd_import
    ???
<frozen importlib._bootstrap>:1027: in _find_and_load
    ???
<frozen importlib._bootstrap>:992: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1050: in _gcd_import
    ???
<frozen importlib._bootstrap>:1027: in _find_and_load
    ???
<frozen importlib._bootstrap>:1006: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:688: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:883: in exec_module
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
nipype/pipeline/plugins/__init__.py:5: in <module>
    from .debug import DebugPlugin
nipype/pipeline/plugins/debug.py:7: in <module>
    import networkx as nx
/usr/lib/python3/dist-packages/networkx/__init__.py:115: in <module>
    import networkx.readwrite
/usr/lib/python3/dist-packages/networkx/readwrite/__init__.py:15: in <module>
    from networkx.readwrite.graphml import *
/usr/lib/python3/dist-packages/networkx/readwrite/graphml.py:314: in <module>
    class GraphML(object):
/usr/lib/python3/dist-packages/networkx/readwrite/graphml.py:346: in GraphML
    (np.int, "int"), (np.int8, "int"),
/usr/lib/python3/dist-packages/numpy/__init__.py:284: in __getattr__
    raise AttributeError("module {!r} has no attribute "
E   AttributeError: module 'numpy' has no attribute 'int'

The problematic code is in the networkx package, and seems to have been
fixed in
https://github.com/networkx/networkx/commit/207147ee179554a33f10f25032054d3e01f96188
(which is in 2.5 onwards).

Debian currently ships with 2.8.8, we might want to merge?

This is currently blocking the python3-defaults transition.

** Affects: networkx (Ubuntu)
     Importance: Undecided
         Status: New

** Affects: nipype (Ubuntu)
     Importance: Undecided
         Status: Invalid

** Affects: python3-defaults (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: update-excuse

** Tags added: update-excuse

** Also affects: nipype (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: nipype (Ubuntu)
       Status: New => Invalid

** Also affects: python3-defaults (Ubuntu)
   Importance: Undecided
       Status: New

-- 
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https://bugs.launchpad.net/bugs/2002660

Title:
  networkx incompatible with numpy 1.24

Status in networkx package in Ubuntu:
  New
Status in nipype package in Ubuntu:
  Invalid
Status in python3-defaults package in Ubuntu:
  New

Bug description:
  The nipype autopkgtests have started failing with the following stack
  trace:

  ____________ ERROR collecting pipeline/plugins/tests/test_tools.py _____________
  /usr/lib/python3.10/importlib/__init__.py:126: in import_module
      return _bootstrap._gcd_import(name[level:], package, level)
  <frozen importlib._bootstrap>:1050: in _gcd_import
      ???
  <frozen importlib._bootstrap>:1027: in _find_and_load
      ???
  <frozen importlib._bootstrap>:992: in _find_and_load_unlocked
      ???
  <frozen importlib._bootstrap>:241: in _call_with_frames_removed
      ???
  <frozen importlib._bootstrap>:1050: in _gcd_import
      ???
  <frozen importlib._bootstrap>:1027: in _find_and_load
      ???
  <frozen importlib._bootstrap>:992: in _find_and_load_unlocked
      ???
  <frozen importlib._bootstrap>:241: in _call_with_frames_removed
      ???
  <frozen importlib._bootstrap>:1050: in _gcd_import
      ???
  <frozen importlib._bootstrap>:1027: in _find_and_load
      ???
  <frozen importlib._bootstrap>:1006: in _find_and_load_unlocked
      ???
  <frozen importlib._bootstrap>:688: in _load_unlocked
      ???
  <frozen importlib._bootstrap_external>:883: in exec_module
      ???
  <frozen importlib._bootstrap>:241: in _call_with_frames_removed
      ???
  nipype/pipeline/plugins/__init__.py:5: in <module>
      from .debug import DebugPlugin
  nipype/pipeline/plugins/debug.py:7: in <module>
      import networkx as nx
  /usr/lib/python3/dist-packages/networkx/__init__.py:115: in <module>
      import networkx.readwrite
  /usr/lib/python3/dist-packages/networkx/readwrite/__init__.py:15: in <module>
      from networkx.readwrite.graphml import *
  /usr/lib/python3/dist-packages/networkx/readwrite/graphml.py:314: in <module>
      class GraphML(object):
  /usr/lib/python3/dist-packages/networkx/readwrite/graphml.py:346: in GraphML
      (np.int, "int"), (np.int8, "int"),
  /usr/lib/python3/dist-packages/numpy/__init__.py:284: in __getattr__
      raise AttributeError("module {!r} has no attribute "
  E   AttributeError: module 'numpy' has no attribute 'int'

  The problematic code is in the networkx package, and seems to have
  been fixed in
  https://github.com/networkx/networkx/commit/207147ee179554a33f10f25032054d3e01f96188
  (which is in 2.5 onwards).

  Debian currently ships with 2.8.8, we might want to merge?

  This is currently blocking the python3-defaults transition.

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