Thanks to visit codestin.com
Credit goes to github.com

Skip to content

sklearn.externals._lobpcg.lobpcg throws ValueError in test_function_docstring #23596

Closed
@Diadochokinetic

Description

@Diadochokinetic

Describe the bug

I cloned and installed the current main branch from the repository and ran pytest sklearn out of curiosity and encountered a ValueError for the function sklearn.externals._lobpcg.lobpcg. Further examination revealed that it occured in 'pytest -vl sklearn/tests/test_docstrings.py -k test_docstring'.

I suggest to either fix the docstring or temporarly add it to FUNCTION_DOCSTRING_IGNORE_LIST

Steps/Code to Reproduce

pytest -vl sklearn/tests/test_docstrings.py -k test_docstring

Expected Results

No error is thrown.

Actual Results

========================================================== FAILURES ===========================================================
__________________________________ test_function_docstring[sklearn.externals._lobpcg.lobpcg] __________________________________

function_name = 'sklearn.externals._lobpcg.lobpcg'
request = <FixtureRequest for <Function test_function_docstring[sklearn.externals._lobpcg.lobpcg]>>

    @pytest.mark.parametrize("function_name", get_all_functions_names())
    def test_function_docstring(function_name, request):
        """Check function docstrings using numpydoc."""
        if function_name in FUNCTION_DOCSTRING_IGNORE_LIST:
            request.applymarker(
                pytest.mark.xfail(run=False, reason="TODO pass numpydoc validation")
            )
    
        res = numpydoc_validation.validate(function_name)
    
        res["errors"] = list(filter_errors(res["errors"], method="function"))
    
        if res["errors"]:
            msg = repr_errors(res, method=f"Tested function: {function_name}")
    
>           raise ValueError(msg)
E           ValueError: 
E           
E           /home/fabian/Projects/scikit-learn/sklearn/externals/_lobpcg.py
E           
E           Tested function: sklearn.externals._lobpcg.lobpcg
E           
E           Locally Optimal Block Preconditioned Conjugate Gradient Method (LOBPCG)
E           
E           LOBPCG is a preconditioned eigensolver for large symmetric positive
E           definite (SPD) generalized eigenproblems.
E           
E           Parameters
E           ----------
E           A : {sparse matrix, dense matrix, LinearOperator}
E               The symmetric linear operator of the problem, usually a
E               sparse matrix.  Often called the "stiffness matrix".
E           X : ndarray, float32 or float64
E               Initial approximation to the ``k`` eigenvectors (non-sparse). If `A`
E               has ``shape=(n,n)`` then `X` should have shape ``shape=(n,k)``.
E           B : {dense matrix, sparse matrix, LinearOperator}, optional
E               The right hand side operator in a generalized eigenproblem.
E               By default, ``B = Identity``.  Often called the "mass matrix".
E           M : {dense matrix, sparse matrix, LinearOperator}, optional
E               Preconditioner to `A`; by default ``M = Identity``.
E               `M` should approximate the inverse of `A`.
E           Y : ndarray, float32 or float64, optional
E               n-by-sizeY matrix of constraints (non-sparse), sizeY < n
E               The iterations will be performed in the B-orthogonal complement
E               of the column-space of Y. Y must be full rank.
E           tol : scalar, optional
E               Solver tolerance (stopping criterion).
E               The default is ``tol=n*sqrt(eps)``.
E           maxiter : int, optional
E               Maximum number of iterations.  The default is ``maxiter = 20``.
E           largest : bool, optional
E               When True, solve for the largest eigenvalues, otherwise the smallest.
E           verbosityLevel : int, optional
E               Controls solver output.  The default is ``verbosityLevel=0``.
E           retLambdaHistory : bool, optional
E               Whether to return eigenvalue history.  Default is False.
E           retResidualNormsHistory : bool, optional
E               Whether to return history of residual norms.  Default is False.
E           
E           Returns
E           -------
E           w : ndarray
E               Array of ``k`` eigenvalues
E           v : ndarray
E               An array of ``k`` eigenvectors.  `v` has the same shape as `X`.
E           lambdas : list of ndarray, optional
E               The eigenvalue history, if `retLambdaHistory` is True.
E           rnorms : list of ndarray, optional
E               The history of residual norms, if `retResidualNormsHistory` is True.
E           
E           Notes
E           -----
E           If both ``retLambdaHistory`` and ``retResidualNormsHistory`` are True,
E           the return tuple has the following format
E           ``(lambda, V, lambda history, residual norms history)``.
E           
E           In the following ``n`` denotes the matrix size and ``m`` the number
E           of required eigenvalues (smallest or largest).
E           
E           The LOBPCG code internally solves eigenproblems of the size ``3m`` on every
E           iteration by calling the "standard" dense eigensolver, so if ``m`` is not
E           small enough compared to ``n``, it does not make sense to call the LOBPCG
E           code, but rather one should use the "standard" eigensolver, e.g. numpy or
E           scipy function in this case.
E           If one calls the LOBPCG algorithm for ``5m > n``, it will most likely break
E           internally, so the code tries to call the standard function instead.
E           
E           It is not that ``n`` should be large for the LOBPCG to work, but rather the
E           ratio ``n / m`` should be large. It you call LOBPCG with ``m=1``
E           and ``n=10``, it works though ``n`` is small. The method is intended
E           for extremely large ``n / m``.
E           
E           The convergence speed depends basically on two factors:
E           
E           1. How well relatively separated the seeking eigenvalues are from the rest
E              of the eigenvalues. One can try to vary ``m`` to make this better.
E           
E           2. How well conditioned the problem is. This can be changed by using proper
E              preconditioning. For example, a rod vibration test problem (under tests
E              directory) is ill-conditioned for large ``n``, so convergence will be
E              slow, unless efficient preconditioning is used. For this specific
E              problem, a good simple preconditioner function would be a linear solve
E              for `A`, which is easy to code since A is tridiagonal.
E           
E           References
E           ----------
E           .. [1] A. V. Knyazev (2001),
E                  Toward the Optimal Preconditioned Eigensolver: Locally Optimal
E                  Block Preconditioned Conjugate Gradient Method.
E                  SIAM Journal on Scientific Computing 23, no. 2,
E                  pp. 517-541. :doi:`10.1137/S1064827500366124`
E           
E           .. [2] A. V. Knyazev, I. Lashuk, M. E. Argentati, and E. Ovchinnikov
E                  (2007), Block Locally Optimal Preconditioned Eigenvalue Xolvers
E                  (BLOPEX) in hypre and PETSc. :arxiv:`0705.2626`
E           
E           .. [3] A. V. Knyazev's C and MATLAB implementations:
E                  https://github.com/lobpcg/blopex
E           
E           Examples
E           --------
E           
E           Solve ``A x = lambda x`` with constraints and preconditioning.
E           
E           >>> import numpy as np
E           >>> from scipy.sparse import spdiags, issparse
E           >>> from scipy.sparse.linalg import lobpcg, LinearOperator
E           >>> n = 100
E           >>> vals = np.arange(1, n + 1)
E           >>> A = spdiags(vals, 0, n, n)
E           >>> A.toarray()
E           array([[  1.,   0.,   0., ...,   0.,   0.,   0.],
E                  [  0.,   2.,   0., ...,   0.,   0.,   0.],
E                  [  0.,   0.,   3., ...,   0.,   0.,   0.],
E                  ...,
E                  [  0.,   0.,   0., ...,  98.,   0.,   0.],
E                  [  0.,   0.,   0., ...,   0.,  99.,   0.],
E                  [  0.,   0.,   0., ...,   0.,   0., 100.]])
E           
E           Constraints:
E           
E           >>> Y = np.eye(n, 3)
E           
E           Initial guess for eigenvectors, should have linearly independent
E           columns. Column dimension = number of requested eigenvalues.
E           
E           >>> rng = np.random.default_rng()
E           >>> X = rng.random((n, 3))
E           
E           Preconditioner in the inverse of A in this example:
E           
E           >>> invA = spdiags([1./vals], 0, n, n)
E           
E           The preconditiner must be defined by a function:
E           
E           >>> def precond( x ):
E           ...     return invA @ x
E           
E           The argument x of the preconditioner function is a matrix inside `lobpcg`,
E           thus the use of matrix-matrix product ``@``.
E           
E           The preconditioner function is passed to lobpcg as a `LinearOperator`:
E           
E           >>> M = LinearOperator(matvec=precond, matmat=precond,
E           ...                    shape=(n, n), dtype=np.float64)
E           
E           Let us now solve the eigenvalue problem for the matrix A:
E           
E           >>> eigenvalues, _ = lobpcg(A, X, Y=Y, M=M, largest=False)
E           >>> eigenvalues
E           array([4., 5., 6.])
E           
E           Note that the vectors passed in Y are the eigenvectors of the 3 smallest
E           eigenvalues. The results returned are orthogonal to those.
E           
E           # Errors
E           
E            - GL03: Double line break found; please use only one blank line to separate sections or paragraphs, and do not leave blank lines at the end of docstrings
E            - SS03: Summary does not end with a period
E            - PR08: Parameter "Y" description should start with a capital letter
E            - RT05: Return value description should finish with "."

function_name = 'sklearn.externals._lobpcg.lobpcg'
msg        = '\n\n/home/fabian/Projects/scikit-learn/sklearn/externals/_lobpcg.py\n\nTested function: sklearn.externals._lobpcg.lob...Parameter "Y" description should start with a capital letter\n - RT05: Return value description should finish with "."'
request    = <FixtureRequest for <Function test_function_docstring[sklearn.externals._lobpcg.lobpcg]>>
res        = {'deprecated': False, 'docstring': 'Locally Optimal Block Preconditioned Conjugate Gradient Method (LOBPCG)\n\nLOBPCG ... description should finish with "."')], 'file': '/home/fabian/Projects/scikit-learn/sklearn/externals/_lobpcg.py', ...}

sklearn/tests/test_docstrings.py:296: ValueError
================================ 1 failed, 2032 passed, 97 xfailed, 4 xpassed in 11.19 seconds ================================

Versions

System:
    python: 3.8.13 (default, Mar 28 2022, 11:38:47)  [GCC 7.5.0]
executable: /home/fabian/anaconda3/envs/sklearn-dev/bin/python3
   machine: Linux-5.13.0-48-generic-x86_64-with-glibc2.17

Python dependencies:
      sklearn: 1.2.dev0
          pip: 21.2.4
   setuptools: 61.2.0
        numpy: 1.17.3
        scipy: 1.3.2
       Cython: None
       pandas: None
   matplotlib: None
       joblib: 1.0.0
threadpoolctl: 2.0.0

Built with OpenMP: True

threadpoolctl info:
       filepath: /home/fabian/anaconda3/envs/sklearn-dev/lib/libgomp.so.1.0.0
         prefix: libgomp
       user_api: openmp
   internal_api: openmp
        version: None
    num_threads: 12

       filepath: /home/fabian/anaconda3/envs/sklearn-dev/lib/python3.8/site-packages/numpy/.libs/libopenblasp-r0-34a18dc3.3.7.so
         prefix: libopenblas
       user_api: blas
   internal_api: openblas
        version: 0.3.7
    num_threads: 12
threading_layer: pthreads

       filepath: /home/fabian/anaconda3/envs/sklearn-dev/lib/python3.8/site-packages/scipy/.libs/libopenblasp-r0-2ecf47d5.3.7.dev.so
         prefix: libopenblas
       user_api: blas
   internal_api: openblas
        version: 0.3.7.dev
    num_threads: 12
threading_layer: pthreads

Metadata

Metadata

Assignees

No one assigned

    Labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions