diff --git a/pyerrors/__init__.py b/pyerrors/__init__.py index 855606da..db7b6859 100644 --- a/pyerrors/__init__.py +++ b/pyerrors/__init__.py @@ -1,4 +1,4 @@ -from .pyerrors import * +from .obs import * from .correlators import * from .fits import * from . import dirac diff --git a/pyerrors/correlators.py b/pyerrors/correlators.py index 1d11bedb..8459f1f5 100644 --- a/pyerrors/correlators.py +++ b/pyerrors/correlators.py @@ -3,7 +3,7 @@ import numpy as np import autograd.numpy as anp import matplotlib.pyplot as plt import scipy.linalg -from .pyerrors import Obs, dump_object, reweight, correlate +from .obs import Obs, dump_object, reweight, correlate from .fits import least_squares from .linalg import eigh, inv, cholesky from .roots import find_root diff --git a/pyerrors/fits.py b/pyerrors/fits.py index 06d8abf4..82a83f3a 100644 --- a/pyerrors/fits.py +++ b/pyerrors/fits.py @@ -11,7 +11,7 @@ from scipy.odr import ODR, Model, RealData import iminuit from autograd import jacobian from autograd import elementwise_grad as egrad -from .pyerrors import Obs, derived_observable, covariance, pseudo_Obs +from .obs import Obs, derived_observable, covariance, pseudo_Obs class Fit_result(Sequence): diff --git a/pyerrors/input/bdio.py b/pyerrors/input/bdio.py index 4c4eec03..3e29924b 100644 --- a/pyerrors/input/bdio.py +++ b/pyerrors/input/bdio.py @@ -4,7 +4,7 @@ import ctypes import hashlib import autograd.numpy as np # Thinly-wrapped numpy -from ..pyerrors import Obs +from ..obs import Obs def read_ADerrors(file_path, bdio_path='./libbdio.so', **kwargs): diff --git a/pyerrors/input/hadrons.py b/pyerrors/input/hadrons.py index ac1bb78a..c184ad8f 100644 --- a/pyerrors/input/hadrons.py +++ b/pyerrors/input/hadrons.py @@ -4,7 +4,7 @@ import os import h5py import numpy as np -from ..pyerrors import Obs, CObs +from ..obs import Obs, CObs from ..correlators import Corr from ..npr import Npr_matrix diff --git a/pyerrors/input/misc.py b/pyerrors/input/misc.py index 0cb10f74..b1328241 100644 --- a/pyerrors/input/misc.py +++ b/pyerrors/input/misc.py @@ -6,7 +6,7 @@ import fnmatch import re import struct import numpy as np # Thinly-wrapped numpy -from ..pyerrors import Obs +from ..obs import Obs def read_pbp(path, prefix, **kwargs): diff --git a/pyerrors/input/openQCD.py b/pyerrors/input/openQCD.py index 9aaf30be..1710a25e 100644 --- a/pyerrors/input/openQCD.py +++ b/pyerrors/input/openQCD.py @@ -6,7 +6,7 @@ import fnmatch import re import struct import numpy as np # Thinly-wrapped numpy -from ..pyerrors import Obs +from ..obs import Obs from ..fits import fit_lin diff --git a/pyerrors/input/sfcf.py b/pyerrors/input/sfcf.py index c6309cfe..3f079b79 100644 --- a/pyerrors/input/sfcf.py +++ b/pyerrors/input/sfcf.py @@ -5,7 +5,7 @@ import os import fnmatch import re import numpy as np # Thinly-wrapped numpy -from ..pyerrors import Obs +from ..obs import Obs def read_sfcf(path, prefix, name, **kwargs): diff --git a/pyerrors/linalg.py b/pyerrors/linalg.py index 0f08d72b..6f6d757a 100644 --- a/pyerrors/linalg.py +++ b/pyerrors/linalg.py @@ -4,7 +4,7 @@ import numpy as np from autograd import jacobian import autograd.numpy as anp # Thinly-wrapped numpy -from .pyerrors import derived_observable, CObs, Obs +from .obs import derived_observable, CObs, Obs from functools import partial from autograd.extend import defvjp diff --git a/pyerrors/misc.py b/pyerrors/misc.py index 920518e5..04f29dc2 100644 --- a/pyerrors/misc.py +++ b/pyerrors/misc.py @@ -2,7 +2,7 @@ # coding: utf-8 import numpy as np -from .pyerrors import Obs +from .obs import Obs def gen_correlated_data(means, cov, name, tau=0.5, samples=1000): diff --git a/pyerrors/mpm.py b/pyerrors/mpm.py index c835b1e2..00ace703 100644 --- a/pyerrors/mpm.py +++ b/pyerrors/mpm.py @@ -3,7 +3,7 @@ import numpy as np import scipy.linalg -from .pyerrors import Obs +from .obs import Obs from .linalg import svd, eig, pinv @@ -105,8 +105,6 @@ def matrix_pencil_method_old(data, p, noise_level=None, verbose=1, **kwargs): # Moore–Penrose pseudoinverse pinv_y1 = pinv(y1) - # Note: Automatic differentiation of eig is implemented in the git of autograd - # but not yet released to PyPi (1.3). The code is currently part of pyerrors e = eig((pinv_y1 @ y2), **kwargs) energy_levels = -np.log(np.abs(e)) return sorted(energy_levels, key=lambda x: abs(x.value)) diff --git a/pyerrors/pyerrors.py b/pyerrors/obs.py similarity index 100% rename from pyerrors/pyerrors.py rename to pyerrors/obs.py diff --git a/pyerrors/roots.py b/pyerrors/roots.py index 0c7c1566..792b2e63 100644 --- a/pyerrors/roots.py +++ b/pyerrors/roots.py @@ -3,7 +3,7 @@ import scipy.optimize from autograd import jacobian -from .pyerrors import derived_observable, pseudo_Obs +from .obs import derived_observable, pseudo_Obs def find_root(d, func, guess=1.0, **kwargs): diff --git a/setup.py b/setup.py index 20e4803b..d632fdcb 100644 --- a/setup.py +++ b/setup.py @@ -9,5 +9,5 @@ setup(name='pyerrors', author_email='fabian.joswig@ed.ac.uk', packages=find_packages(), python_requires='>=3.6.0', - install_requires=['numpy>=1.16', 'autograd>=1.2', 'numdifftools', 'matplotlib>=3.3', 'scipy', 'iminuit<2'] + install_requires=['numpy>=1.16', 'autograd>=1.2', 'numdifftools', 'matplotlib>=3.3', 'scipy', 'iminuit<2', 'h5py'] )