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Potentially broken cython dep #55

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mortonjt opened this issue Oct 20, 2023 · 4 comments
Open

Potentially broken cython dep #55

mortonjt opened this issue Oct 20, 2023 · 4 comments

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@mortonjt
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We're running into issues install iow with cython=3.0.4, but can confirm that it installs with cython=0.29.36

Below is the full error message

      /usr/share/miniconda/envs/dynomics/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-5754f7ae/iow_5366f21e62044cd79a8c9be2f6701f3e/bp/GPL/_insert.pyx
        tree = Parsing.p_module(s, pxd, full_module_name)
      /usr/share/miniconda/envs/dynomics/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-5754f7ae/iow_5366f21e62044cd79a8c9be2f6701f3e/bp/_ba.pxd
        tree = Parsing.p_module(s, pxd, full_module_name)
      /usr/share/miniconda/envs/dynomics/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-5754f7ae/iow_5366f21e62044cd79a8c9be2f6701f3e/bp/_binary_tree.pxd
        tree = Parsing.p_module(s, pxd, full_module_name)
      /usr/share/miniconda/envs/dynomics/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-5754f7ae/iow_5366f21e62044cd79a8c9be2f6701f3e/bp/_bp.pxd
        tree = Parsing.p_module(s, pxd, full_module_name)
      performance hint: bp/_bp.pyx:349:29: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:362:29: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:371:29: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:376:33: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:378:33: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:387:27: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:389:31: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:402:27: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:404:31: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:450:25: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:453:31: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:468:26: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:473:40: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:473:30: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:484:26: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:487:43: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:487:32: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:489:40: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:489:30: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:517:28: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:519:41: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:519:31: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:542:27: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:544:41: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:544:31: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:567:28: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:569:42: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:569:32: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:584:26: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:600:42: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:600:28: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:602:28: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:617:36: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:617:24: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:642:25: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:644:34: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:660:25: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:662:26: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:684:25: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:686:29: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:700:40: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:700:29: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:717:26: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:719:28: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:722:39: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:722:30: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      performance hint: bp/_bp.pyx:737:33: Exception check will always require the GIL to be acquired. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: bp/tests/test_bp_cy.pyx
      Compiling bp/_bp.pyx because it changed.
      Compiling bp/_io.pyx because it changed.
      Compiling bp/_conv.pyx because it changed.
      Compiling bp/_binary_tree.pyx because it changed.
      Compiling bp/_insert.pyx because it changed.
      Compiling bp/GPL/_insert.pyx because it changed.
      Compiling bp/tests/test_bp_cy.pyx because it changed.
      Compiling bp/_ba.pyx because it changed.
      [1/8] Cythonizing bp/GPL/_insert.pyx
      [2/8] Cythonizing bp/_ba.pyx
      [3/8] Cythonizing bp/_binary_tree.pyx
      [4/8] Cythonizing bp/_bp.pyx
      [5/8] Cythonizing bp/_conv.pyx
      [6/8] Cythonizing bp/_insert.pyx
      [7/8] Cythonizing bp/_io.pyx
      [8/8] Cythonizing bp/tests/test_bp_cy.pyx
      [end of output]
@wasade
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wasade commented Oct 20, 2023 via email

@mortonjt
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Maybe I shouldn't have pasted the full output (the key components were accidentally excluded)

Below it the relevant error

Error compiling Cython file:
      ------------------------------------------------------------
      ...
          assert exp.shape[0] == obs.mM.shape[0]
          assert exp.shape[1] == obs.mM.shape[1]
      
          for i in range(exp.shape[0]):
              for j in range(exp.shape[1]):
                  assert obs.mM[i, j] == exp[i, j]
                               ^
      ------------------------------------------------------------
      
      bp/tests/test_bp_cy.pyx:350:25: Compiler crash in AnalyseExpressionsTransform
      
      ModuleNode.body = StatListNode(test_bp_cy.pyx:1:0)
      StatListNode.stats[28] = StatListNode(test_bp_cy.pyx:329:0)
      StatListNode.stats[0] = DefNode(test_bp_cy.pyx:329:0,
          is_cyfunction = True,
          modifiers = [...]/0,
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: bp/tests/test_bp_cy.pyx
      Compiling bp/_bp.pyx because it changed.
      Compiling bp/_io.pyx because it changed.
      Compiling bp/_conv.pyx because it changed.
      Compiling bp/_binary_tree.pyx because it changed.
      Compiling bp/_insert.pyx because it changed.
      Compiling bp/GPL/_insert.pyx because it changed.
      Compiling bp/tests/test_bp_cy.pyx because it changed.
      Compiling bp/_ba.pyx because it changed.
      [1/8] Cythonizing bp/GPL/_insert.pyx
      [2/8] Cythonizing bp/_ba.pyx
      [3/8] Cythonizing bp/_binary_tree.pyx
      [4/8] Cythonizing bp/_bp.pyx
      [5/8] Cythonizing bp/_conv.pyx
      [6/8] Cythonizing bp/_insert.pyx
      [7/8] Cythonizing bp/_io.pyx
      [8/8] Cythonizing bp/tests/test_bp_cy.pyx
      [end of output]

@wasade
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wasade commented Oct 20, 2023

Thanks, clearly something is diff with the new version of Cython...

@mortonjt
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Forgot to mention, the same error gets thrown with cython=0.29.36 on github actions -- not sure what is going on there, since cython=0.29.36 works with my machine.

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@wasade @mortonjt