TKY2 Result failure with gather

/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:207: RuntimeWarning: divide by zero encountered in scalar power
  F_matrix[i, j] = -df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:208: RuntimeWarning: divide by zero encountered in scalar power
  F_matrix[j, i] = -df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:228: RuntimeWarning: divide by zero encountered in scalar power
  z[i] += f_ij[i, j] * df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:229: RuntimeWarning: divide by zero encountered in scalar power
  z[j] += f_ij[j, i] * df_ij[j, i] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:228: RuntimeWarning: invalid value encountered in scalar add
  z[i] += f_ij[i, j] * df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:229: RuntimeWarning: invalid value encountered in scalar add
  z[j] += f_ij[j, i] * df_ij[j, i] ** (-2)
Traceback (most recent call last):
  File "/usr/local/bin/openfe", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/openfecli/commands/gather.py", line 376, in gather
    writing_func(legs, writer, allow_partial)
  File "/usr/local/lib/python3.10/site-packages/openfecli/commands/gather.py", line 259, in _write_dg_mle
    f_i, df_i = mle(g, factor='calc_DDG')
  File "/usr/local/lib/python3.10/site-packages/cinnabar/stats.py", line 232, in mle
    Finv = np.linalg.pinv(F_matrix)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 2022, in pinv
    u, s, vt = svd(a, full_matrices=False, hermitian=hermitian)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 1681, in svd
    u, s, vh = gufunc(a, signature=signature, extobj=extobj)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 121, in _raise_linalgerror_svd_nonconvergence
    raise LinAlgError("SVD did not converge")
numpy.linalg.LinAlgError: SVD did not converge

This is with https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2024/results_tyk2_transformations_openfe_1.0.0rc0_uc_2.tar.gz

Tái hiện lỗi bằng kho lưu trữ kết quả được liên kết, sau đó bắt đầu từ openfecli/commands/gather.py trong _write_dg_mle và theo dõi lời gọi đến cinnabar/stats.py:mle. Điều tra các cảnh báo chia cho không và lỗi SVD; hoàn tất khi đường dẫn gather xử lý được đầu vào này hoặc báo cáo rõ ràng về nó mà không phát sinh ngoại lệ chưa được xử lý hiện tại.