GitHub Enterprise Crashes

[cement-head]

$ git clone https://github.cs.huji.ac.il/dina-lab/cryo-folding/tree/colab
Cloning into 'colab'...
fatal: unable to update url base from redirection:
asked for: https://github.cs.huji.ac.il/dina-lab/cryo-folding/tree/colab/info/refs?service=git-upload-pack
redirect: https://github.cs.huji.ac.il/login?return_to=https%3A%2F%2Fgithub.cs.huji.ac.il%2Fdina-lab%2Fcryo-folding%2Ftree%2Fcolab%2Finfo%2Frefs%3Fservice%3Dgit-upload-pack

[cement-head]

  Building wheels for collected packages: greenlet
    Building wheel for greenlet (pyproject.toml): started
    Building wheel for greenlet (pyproject.toml): finished with status 'error'
    error: subprocess-exited-with-error
  
    × Building wheel for greenlet (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [118 lines of output]
        running bdist_wheel
        running build
        running build_py
        creating build/lib.linux-x86_64-cpython-312/greenlet
        copying src/greenlet/__init__.py -> build/lib.linux-x86_64-cpython-312/greenlet
        creating build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/__init__.py -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        creating build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_tracing.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_greenlet.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_version.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_weakref.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_cpp.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_stack_saved.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_generator_nested.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_contextvars.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/__init__.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_throw.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_leaks.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_extension_interface.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_gc.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/test_generator.py -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        running egg_info
        writing src/greenlet.egg-info/PKG-INFO
        writing dependency_links to src/greenlet.egg-info/dependency_links.txt
        writing requirements to src/greenlet.egg-info/requires.txt
        writing top-level names to src/greenlet.egg-info/top_level.txt
        reading manifest file 'src/greenlet.egg-info/SOURCES.txt'
        reading manifest template 'MANIFEST.in'
        no previously-included directories found matching 'docs/_build'
        warning: no files found matching '*.py' under directory 'appveyor'
        warning: no previously-included files matching '*.pyc' found anywhere in distribution
        warning: no previously-included files matching '*.pyd' found anywhere in distribution
        warning: no previously-included files matching '*.so' found anywhere in distribution
        warning: no previously-included files matching '.coverage' found anywhere in distribution
        adding license file 'LICENSE'
        adding license file 'LICENSE.PSF'
        adding license file 'AUTHORS'
        writing manifest file 'src/greenlet.egg-info/SOURCES.txt'
        copying src/greenlet/greenlet.c -> build/lib.linux-x86_64-cpython-312/greenlet
        copying src/greenlet/greenlet.h -> build/lib.linux-x86_64-cpython-312/greenlet
        copying src/greenlet/slp_platformselect.h -> build/lib.linux-x86_64-cpython-312/greenlet
        copying src/greenlet/platform/setup_switch_x64_masm.cmd -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_aarch64_gcc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_alpha_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_amd64_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_arm32_gcc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_arm32_ios.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_csky_gcc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_m68k_gcc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_mips_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_ppc64_aix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_ppc64_linux.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_ppc_aix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_ppc_linux.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_ppc_macosx.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_ppc_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_riscv_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_s390_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_sparc_sun_gcc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_x32_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_x64_masm.asm -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_x64_masm.obj -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_x64_msvc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_x86_msvc.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/platform/switch_x86_unix.h -> build/lib.linux-x86_64-cpython-312/greenlet/platform
        copying src/greenlet/tests/_test_extension.c -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        copying src/greenlet/tests/_test_extension_cpp.cpp -> build/lib.linux-x86_64-cpython-312/greenlet/tests
        running build_ext
        building 'greenlet._greenlet' extension
        creating build/temp.linux-x86_64-cpython-312/src/greenlet
        x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/home/cbfgws6/Programs/OpsiGen/include -I/usr/include/python3.12 -c src/greenlet/greenlet.c -o build/temp.linux-x86_64-cpython-312/src/greenlet/greenlet.o
        src/greenlet/greenlet.c: In function ‘g_switchstack’:
        src/greenlet/greenlet.c:531:45: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_limit’; did you mean ‘py_recursion_limit’?
          531 |         current->recursion_depth = (tstate->recursion_limit
              |                                             ^~~~~~~~~~~~~~~
              |                                             py_recursion_limit
        src/greenlet/greenlet.c:532:47: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
          532 |                                     - tstate->recursion_remaining);
              |                                               ^~~~~~~~~~~~~~~~~~~
              |                                               c_recursion_remaining
        src/greenlet/greenlet.c:560:55: error: ‘_PyCFrame’ has no member named ‘use_tracing’
          560 |         ts__g_switchstack_use_tracing = tstate->cframe->use_tracing;
              |                                                       ^~
        src/greenlet/greenlet.c:621:23: error: ‘_PyCFrame’ has no member named ‘use_tracing’
          621 |         tstate->cframe->use_tracing = ts__g_switchstack_use_tracing;
              |                       ^~
        src/greenlet/greenlet.c:624:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
          624 |         tstate->recursion_remaining = (tstate->recursion_limit
              |                 ^~~~~~~~~~~~~~~~~~~
              |                 c_recursion_remaining
        src/greenlet/greenlet.c:624:48: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_limit’; did you mean ‘py_recursion_limit’?
          624 |         tstate->recursion_remaining = (tstate->recursion_limit
              |                                                ^~~~~~~~~~~~~~~
              |                                                py_recursion_limit
        src/greenlet/greenlet.c: In function ‘g_calltrace’:
        src/greenlet/greenlet.c:105:51: error: ‘_PyCFrame’ has no member named ‘use_tracing’
          105 | #define TSTATE_USE_TRACING(tstate) (tstate->cframe->use_tracing)
              |                                                   ^~
        src/greenlet/greenlet.c:654:5: note: in expansion of macro ‘TSTATE_USE_TRACING’
          654 |     TSTATE_USE_TRACING(tstate) = 0;
              |     ^~~~~~~~~~~~~~~~~~
        src/greenlet/greenlet.c:105:51: error: ‘_PyCFrame’ has no member named ‘use_tracing’
          105 | #define TSTATE_USE_TRACING(tstate) (tstate->cframe->use_tracing)
              |                                                   ^~
        src/greenlet/greenlet.c:657:5: note: in expansion of macro ‘TSTATE_USE_TRACING’
          657 |     TSTATE_USE_TRACING(tstate) =
              |     ^~~~~~~~~~~~~~~~~~
        src/greenlet/greenlet.c: In function ‘g_initialstub’:
        src/greenlet/greenlet.c:903:51: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_limit’; did you mean ‘py_recursion_limit’?
          903 |     self->recursion_depth = (PyThreadState_GET()->recursion_limit
              |                                                   ^~~~~~~~~~~~~~~
              |                                                   py_recursion_limit
        src/greenlet/greenlet.c:904:53: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
          904 |                              - PyThreadState_GET()->recursion_remaining);
              |                                                     ^~~~~~~~~~~~~~~~~~~
              |                                                     c_recursion_remaining
        error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
        [end of output]
  
    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for greenlet
  Failed to build greenlet
  ERROR: Could not build wheels for greenlet, which is required to install pyproject.toml-based projects
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[alephreish]

See the colab notebook which mentions the link to the archive (https://github.com/dina-lab3D/OpsiGen/archive/refs/heads/colab.zip) and the dependencies. This is my environment definition (can be simplified further but I did not bother):

channels:
 - conda-forge
 - bioconda
dependencies:
 - python=3.10.8
 - mafft=7.525
 - pip
 - pip:
   - --find-links https://data.pyg.org/whl/torch-1.13.0%2Bcu116.html
   - numpy==1.26.4
   - openpyxl
   - Bio
   - torch==1.13.0
   - torch-geometric==2.2.0
   - torch-scatter==2.1.0
   - torch-scatter==2.1.0
   - torch-sparse==0.6.16
   - torch-spline-conv==1.2.1