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pyerrors.py renamed to obs.py, h5py added as dependency
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14 changed files with 13 additions and 15 deletions
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@ -1,4 +1,4 @@
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from .pyerrors import *
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from .obs import *
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from .correlators import *
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from .fits import *
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from . import dirac
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@ -3,7 +3,7 @@ import numpy as np
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import autograd.numpy as anp
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import matplotlib.pyplot as plt
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import scipy.linalg
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from .pyerrors import Obs, dump_object, reweight, correlate
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from .obs import Obs, dump_object, reweight, correlate
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from .fits import least_squares
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from .linalg import eigh, inv, cholesky
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from .roots import find_root
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@ -11,7 +11,7 @@ from scipy.odr import ODR, Model, RealData
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import iminuit
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from autograd import jacobian
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from autograd import elementwise_grad as egrad
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from .pyerrors import Obs, derived_observable, covariance, pseudo_Obs
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from .obs import Obs, derived_observable, covariance, pseudo_Obs
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class Fit_result(Sequence):
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@ -4,7 +4,7 @@
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import ctypes
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import hashlib
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import autograd.numpy as np # Thinly-wrapped numpy
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from ..pyerrors import Obs
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from ..obs import Obs
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def read_ADerrors(file_path, bdio_path='./libbdio.so', **kwargs):
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@ -4,7 +4,7 @@
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import os
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import h5py
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import numpy as np
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from ..pyerrors import Obs, CObs
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from ..obs import Obs, CObs
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from ..correlators import Corr
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from ..npr import Npr_matrix
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@ -6,7 +6,7 @@ import fnmatch
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import re
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import struct
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import numpy as np # Thinly-wrapped numpy
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from ..pyerrors import Obs
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from ..obs import Obs
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def read_pbp(path, prefix, **kwargs):
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@ -6,7 +6,7 @@ import fnmatch
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import re
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import struct
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import numpy as np # Thinly-wrapped numpy
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from ..pyerrors import Obs
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from ..obs import Obs
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from ..fits import fit_lin
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@ -5,7 +5,7 @@ import os
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import fnmatch
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import re
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import numpy as np # Thinly-wrapped numpy
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from ..pyerrors import Obs
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from ..obs import Obs
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def read_sfcf(path, prefix, name, **kwargs):
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@ -4,7 +4,7 @@
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import numpy as np
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from autograd import jacobian
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import autograd.numpy as anp # Thinly-wrapped numpy
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from .pyerrors import derived_observable, CObs, Obs
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from .obs import derived_observable, CObs, Obs
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from functools import partial
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from autograd.extend import defvjp
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@ -2,7 +2,7 @@
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# coding: utf-8
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import numpy as np
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from .pyerrors import Obs
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from .obs import Obs
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def gen_correlated_data(means, cov, name, tau=0.5, samples=1000):
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@ -3,7 +3,7 @@
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import numpy as np
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import scipy.linalg
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from .pyerrors import Obs
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from .obs import Obs
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from .linalg import svd, eig, pinv
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@ -105,8 +105,6 @@ def matrix_pencil_method_old(data, p, noise_level=None, verbose=1, **kwargs):
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# Moore–Penrose pseudoinverse
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pinv_y1 = pinv(y1)
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# Note: Automatic differentiation of eig is implemented in the git of autograd
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# but not yet released to PyPi (1.3). The code is currently part of pyerrors
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e = eig((pinv_y1 @ y2), **kwargs)
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energy_levels = -np.log(np.abs(e))
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return sorted(energy_levels, key=lambda x: abs(x.value))
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@ -3,7 +3,7 @@
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import scipy.optimize
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from autograd import jacobian
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from .pyerrors import derived_observable, pseudo_Obs
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from .obs import derived_observable, pseudo_Obs
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def find_root(d, func, guess=1.0, **kwargs):
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2
setup.py
2
setup.py
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@ -9,5 +9,5 @@ setup(name='pyerrors',
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author_email='fabian.joswig@ed.ac.uk',
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packages=find_packages(),
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python_requires='>=3.6.0',
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install_requires=['numpy>=1.16', 'autograd>=1.2', 'numdifftools', 'matplotlib>=3.3', 'scipy', 'iminuit<2']
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install_requires=['numpy>=1.16', 'autograd>=1.2', 'numdifftools', 'matplotlib>=3.3', 'scipy', 'iminuit<2', 'h5py']
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)
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