pyerrors.py renamed to obs.py, h5py added as dependency

This commit is contained in:
Fabian Joswig 2021-11-07 11:24:56 +00:00
parent 012bf8ad17
commit 9805ee2b4b
14 changed files with 13 additions and 15 deletions

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@ -1,4 +1,4 @@
from .pyerrors import *
from .obs import *
from .correlators import *
from .fits import *
from . import dirac

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@ -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

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@ -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):

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@ -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):

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@ -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

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@ -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):

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@ -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

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@ -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):

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@ -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

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@ -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):

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@ -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):
# MoorePenrose 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))

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@ -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):

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@ -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']
)