Code maintenance (#104)

Code maintenance: sorted imports, opened up CoLA ops for go to, pytest
incorporates defaults marks, and took out unsued files.

cola/annotations.py

@@ -1,12 +1,24 @@
+from collections.abc import Iterable
 from functools import reduce
 from typing import Set, Union
-from collections.abc import Iterable
+
 from plum import dispatch
-from cola.ops import LinearOperator, Array
-from cola.ops import Kronecker, Product, Sum
-from cola.ops import Transpose, Adjoint
-from cola.ops import BlockDiag, Identity, ScalarMul
-from cola.ops import Hessian, Permutation, Sliced
+
+from cola.ops import (
+    Adjoint,
+    Array,
+    BlockDiag,
+    Hessian,
+    Identity,
+    Kronecker,
+    LinearOperator,
+    Permutation,
+    Product,
+    ScalarMul,
+    Sliced,
+    Sum,
+    Transpose,
+)
 from cola.utils import export
 
 Scalar = Array

cola/linalg/__init__.py

@@ -1,5 +1,6 @@
 """ High level linear algebra functions, """
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/algorithm_base.py

@@ -1,7 +1,10 @@
+from types import SimpleNamespace
+
 from plum import parametric
+
 from cola.ops import LinearOperator
 from cola.utils import export
-from types import SimpleNamespace
+
 # import pytreeclass as tc
 
 

cola/linalg/decompositions/__init__.py

@@ -1,4 +1,5 @@
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/decompositions/arnoldi.py

@@ -1,10 +1,8 @@
 from typing import Tuple
-from cola import Stiefel
-from cola.ops import LinearOperator
-from cola.ops import Array, Dense
-from cola.ops import Householder, Product
+
 # from cola.utils import export
-from cola import lazify
+from cola import Stiefel, lazify
+from cola.ops import Array, Dense, Householder, LinearOperator, Product
 
 # def arnoldi_eigs_bwd(res, grads, unflatten, *args, **kwargs):
 #     val_grads, eig_grads, _ = grads

cola/linalg/decompositions/lanczos.py

@@ -1,7 +1,7 @@
+import cola
 from cola import SelfAdjoint, Unitary
 from cola.fns import lazify
-from cola.ops import Array, LinearOperator, Dense, Tridiagonal
-import cola
+from cola.ops import Array, Dense, LinearOperator, Tridiagonal
 
 
 def lanczos_eig_bwd(res, grads, unflatten, *args, **kwargs):

cola/linalg/eig/__init__.py

@@ -1,4 +1,5 @@
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/eig/iram.py

@@ -1,9 +1,8 @@
 import numpy as np
 from scipy.sparse.linalg import LinearOperator as LO
 from scipy.sparse.linalg import eigs
-from cola.ops import LinearOperator
-from cola.ops import Array
-from cola.ops import Dense
+
+from cola.ops import Array, Dense, LinearOperator
 from cola.utils import export
 from cola.utils.utils_linalg import get_numpy_dtype
 

cola/linalg/eig/lobpcg.py

@@ -1,10 +1,11 @@
-import numpy as np
 from dataclasses import dataclass
-from cola.linalg.algorithm_base import Algorithm
+
+import numpy as np
 from scipy.sparse.linalg import LinearOperator as LO
 from scipy.sparse.linalg import lobpcg as lobpcg_sp
-from cola.ops import LinearOperator
-from cola.ops import Dense
+
+from cola.linalg.algorithm_base import Algorithm
+from cola.ops import Dense, LinearOperator
 from cola.utils import export
 
 

cola/linalg/eig/power_iteration.py

@@ -1,8 +1,9 @@
-from cola.utils import export
-from cola.ops import LinearOperator
-from cola.linalg.algorithm_base import Algorithm
 from dataclasses import dataclass
-from typing import Optional, Any
+from typing import Any, Optional
+
+from cola.linalg.algorithm_base import Algorithm
+from cola.ops import LinearOperator
+from cola.utils import export
 
 PRNGKey = Any
 

cola/linalg/inverse/__init__.py

@@ -1,4 +1,5 @@
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/inverse/pinv.py

@@ -1,11 +1,10 @@
 import numpy as np
 from plum import dispatch
 
-import cola
+from cola.annotations import PSD
 from cola.linalg.algorithm_base import Algorithm, Auto, IterativeOperatorWInfo
 from cola.linalg.inverse.cg import CG
-from cola.ops.operators import Diagonal, Identity, LinearOperator, Permutation, ScalarMul, I_like
-from cola.annotations import PSD
+from cola.ops.operators import Diagonal, I_like, Identity, LinearOperator, Permutation, ScalarMul
 from cola.utils import export
 from cola.utils.utils_linalg import get_precision
 
@@ -43,7 +42,7 @@ def pinv(A: LinearOperator, alg: Algorithm = Auto()):
 
     Example:
         >>> A = MyLinearOperator()
-        >>> x = cola.pseudo(A) @ b
+        >>> x = cola.pinv(A) @ b
 
     """
 
@@ -67,7 +66,7 @@ def pinv(A: LinearOperator, alg: Auto):
 def pinv(A: LinearOperator, alg: CG):
     xnp = A.xnp
     M = A.H @ A
-    cons = get_precision(xnp, A.dtype) * xnp.sqrt(cola.eigmax(M))
+    cons = get_precision(xnp, A.dtype) * max(A.shape)
     Op = IterativeOperatorWInfo(M, alg)
     return PSD(Op + cons * I_like(M)) @ A.H
 

cola/linalg/logdet/__init__.py

@@ -1,4 +1,5 @@
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/logdet/logdet.py

@@ -1,15 +1,25 @@
-import numpy as np
 from functools import reduce
+
+import numpy as np
 from plum import dispatch
+
 from cola.annotations import PSD
-from cola.ops.operators import LinearOperator, Triangular, Permutation, Identity, ScalarMul
-from cola.ops.operators import Diagonal, Kronecker, BlockDiag, Product
-from cola.utils import export
 from cola.linalg.algorithm_base import Algorithm, Auto
-from cola.linalg.decompositions.decompositions import Cholesky, LU, Arnoldi, Lanczos
-from cola.linalg.decompositions.decompositions import plu, cholesky
+from cola.linalg.decompositions.decompositions import LU, Arnoldi, Cholesky, Lanczos, cholesky, plu
 from cola.linalg.trace.diag_trace import trace
 from cola.linalg.unary.unary import log
+from cola.ops.operators import (
+    BlockDiag,
+    Diagonal,
+    Identity,
+    Kronecker,
+    LinearOperator,
+    Permutation,
+    Product,
+    ScalarMul,
+    Triangular,
+)
+from cola.utils import export
 
 
 def product(xs):

cola/linalg/preconditioning/preconditioners.py

@@ -1,7 +1,9 @@
 from typing import Union
-from cola.ops import LinearOperator
-from cola.linalg.eig.power_iteration import power_iteration
+
 from plum import dispatch
+
+from cola.linalg.eig.power_iteration import power_iteration
+from cola.ops import LinearOperator
 from cola.utils import export
 
 

cola/linalg/tbd/nullspace.py

@@ -1,10 +1,12 @@
-from cola.ops import LinearOperator, Array
-from cola.backends import get_library_fns
-from cola.utils import export
 import logging
+
 import numpy as np
 from plum import dispatch
 
+from cola.backends import get_library_fns
+from cola.ops import Array, LinearOperator
+from cola.utils import export
+
 eigmax = None  # TODO: fix
 
 

cola/linalg/tbd/slq.py

@@ -1,7 +1,8 @@
 from typing import Callable
-from cola.ops import LinearOperator
+
 from cola.linalg.decompositions.lanczos import lanczos
 from cola.linalg.inverse.cg import cg
+from cola.ops import LinearOperator
 from cola.utils import export
 from cola.utils.custom_autodiff import iterative_autograd
 

cola/linalg/tbd/svrg.py

@@ -1,9 +1,11 @@
 import numpy as np
+
 import cola
+
 # from cola.linalg.eigs import eigmax
-from cola.ops import Sum, Product, Dense
-from cola.ops import I_like
+from cola.ops import Dense, I_like, Product, Sum
 from cola.utils import export
+
 # import standard Union type
 
 

cola/linalg/trace/__init__.py

@@ -1,4 +1,5 @@
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/trace/diag_trace.py

@@ -1,12 +1,23 @@
 from functools import reduce
-from cola.utils import export, dispatch
-from cola.ops.operators import LinearOperator, I_like, Diagonal, Identity
-from cola.ops.operators import BlockDiag, ScalarMul, Sum, Dense
-from cola.ops.operators import Kronecker, KronSum
-from cola.linalg.algorithm_base import Algorithm, Auto
-from cola.linalg.trace.diagonal_estimation import Hutch, HutchPP, Exact
+
 import numpy as np
 
+from cola.linalg.algorithm_base import Algorithm, Auto
+from cola.linalg.trace.diagonal_estimation import Exact, Hutch, HutchPP
+from cola.ops.operators import (
+    BlockDiag,
+    Dense,
+    Diagonal,
+    I_like,
+    Identity,
+    Kronecker,
+    KronSum,
+    LinearOperator,
+    ScalarMul,
+    Sum,
+)
+from cola.utils import dispatch, export
+
 
 @export
 @dispatch.abstract

cola/linalg/trace/diagonal_estimation.py

@@ -1,9 +1,11 @@
+from dataclasses import dataclass
+from typing import Any, Optional
+
 import numpy as np
-from cola.utils import export
-from cola.ops import I_like, LinearOperator
+
 from cola.linalg.algorithm_base import Algorithm
-from dataclasses import dataclass
-from typing import Optional, Any
+from cola.ops import I_like, LinearOperator
+from cola.utils import export
 
 PRNGKey = Any
 

cola/linalg/unary/__init__.py

@@ -1,4 +1,5 @@
 import pkgutil
+
 from cola.utils import import_from_all
 
 __all__ = []

cola/linalg/unary/unary.py

@@ -1,22 +1,32 @@
-from plum import dispatch
 from dataclasses import dataclass
+from functools import reduce
 from numbers import Number
 from typing import Callable
-from functools import reduce
+
 import numpy as np
-from plum import parametric
+from plum import dispatch, parametric
+
+from cola.annotations import PSD, SelfAdjoint
 from cola.fns import lazify
-from cola.ops import LinearOperator
-from cola.ops import Diagonal, Identity, ScalarMul
-from cola.ops import BlockDiag, Kronecker, KronSum, I_like, Transpose, Adjoint
-from cola.annotations import SelfAdjoint, PSD
 from cola.linalg.algorithm_base import Algorithm, Auto
-from cola.linalg.inverse.inv import inv
+from cola.linalg.decompositions.arnoldi import arnoldi
+from cola.linalg.decompositions.decompositions import LU, Arnoldi, Cholesky, Lanczos
+from cola.linalg.decompositions.lanczos import lanczos
 from cola.linalg.inverse.cg import CG
 from cola.linalg.inverse.gmres import GMRES
-from cola.linalg.decompositions.lanczos import lanczos
-from cola.linalg.decompositions.arnoldi import arnoldi
-from cola.linalg.decompositions.decompositions import Arnoldi, Lanczos, LU, Cholesky
+from cola.linalg.inverse.inv import inv
+from cola.ops import (
+    Adjoint,
+    BlockDiag,
+    Diagonal,
+    I_like,
+    Identity,
+    Kronecker,
+    KronSum,
+    LinearOperator,
+    ScalarMul,
+    Transpose,
+)
 from cola.utils import export