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[Fix] Fix further mutable default arguments and smaller issues.

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This commit is contained in:
Fabian Joswig 2024-12-24 17:34:06 +01:00
parent 668fa62793
commit 4089238ddd
9 changed files with 44 additions and 28 deletions
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4
pyerrors/__init__.py
View file

@ -1,4 +1,4 @@
r'''
r"""
# What is pyerrors?
`pyerrors` is a python package for error computation and propagation of Markov chain Monte Carlo data.
It is based on the gamma method [arXiv:hep-lat/0306017](https://arxiv.org/abs/hep-lat/0306017). Some of its features are:
@ -476,7 +476,7 @@ The array `cdata` contains information about the contribution of auxiliary obser
A JSON schema that may be used to verify the correctness of a file with respect to the format definition is stored in ./examples/json_schema.json. The schema is a self-descriptive format definition and contains an exemplary file.
Julia I/O routines for the json.gz format, compatible with [ADerrors.jl](https://gitlab.ift.uam-csic.es/alberto/aderrors.jl), can be found [here](https://github.com/fjosw/ADjson.jl).
'''
"""
from .obs import *
from .correlators import *
from .fits import *

8
pyerrors/fits.py
View file

@ -71,7 +71,7 @@ class Fit_result(Sequence):
def least_squares(x, y, func, priors=None, silent=False, **kwargs):
r'''Performs a non-linear fit to y = func(x).
r"""Performs a non-linear fit to y = func(x).
```
Parameters
@ -224,7 +224,7 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
chisquare/d.o.f.: 0.5388013574561786 # random
fit parameters [1.11897846 0.96361162 0.92325319] # random
'''
"""
output = Fit_result()
if (isinstance(x, dict) and isinstance(y, dict) and isinstance(func, dict)):
@ -504,7 +504,7 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
def total_least_squares(x, y, func, silent=False, **kwargs):
r'''Performs a non-linear fit to y = func(x) and returns a list of Obs corresponding to the fit parameters.
r"""Performs a non-linear fit to y = func(x) and returns a list of Obs corresponding to the fit parameters.
Parameters
----------
@ -553,7 +553,7 @@ def total_least_squares(x, y, func, silent=False, **kwargs):
-------
output : Fit_result
Parameters and information on the fitted result.
'''
"""
output = Fit_result()

4
pyerrors/input/__init__.py
View file

@ -1,10 +1,10 @@
r'''
r"""
`pyerrors` includes an `input` submodule in which input routines and parsers for the output of various numerical programs are contained.
# Jackknife samples
For comparison with other analysis workflows `pyerrors` can also generate jackknife samples from an `Obs` object or import jackknife samples into an `Obs` object.
See `pyerrors.obs.Obs.export_jackknife` and `pyerrors.obs.import_jackknife` for details.
'''
"""
from . import bdio as bdio
from . import dobs as dobs
from . import hadrons as hadrons

20
pyerrors/input/dobs.py
View file

@ -85,7 +85,7 @@ def _dict_to_xmlstring_spaces(d, space=' '):
return o
def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
def create_pobs_string(obsl, name, spec='', origin='', symbol=None, enstag=None):
"""Export a list of Obs or structures containing Obs to an xml string
according to the Zeuthen pobs format.
@ -113,6 +113,8 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
XML formatted string of the input data
"""
if symbol is None:
symbol = []
od = {}
ename = obsl[0].e_names[0]
names = list(obsl[0].deltas.keys())
@ -176,7 +178,7 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
return rs
def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], enstag=None, gz=True):
def write_pobs(obsl, fname, name, spec='', origin='', symbol=None, enstag=None, gz=True):
"""Export a list of Obs or structures containing Obs to a .xml.gz file
according to the Zeuthen pobs format.
@ -206,6 +208,8 @@ def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], enstag=None, gz
-------
None
"""
if symbol is None:
symbol = []
pobsstring = create_pobs_string(obsl, name, spec, origin, symbol, enstag)
if not fname.endswith('.xml') and not fname.endswith('.gz'):
@ -309,7 +313,7 @@ def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
full_output : bool
If True, a dict containing auxiliary information and the data is returned.
If False, only the data is returned as list.
separatior_insertion: str or int
separator_insertion: str or int
str: replace all occurences of "separator_insertion" within the replica names
by "|%s" % (separator_insertion) when constructing the names of the replica.
int: Insert the separator "|" at the position given by separator_insertion.
@ -409,7 +413,7 @@ def import_dobs_string(content, full_output=False, separator_insertion=True):
full_output : bool
If True, a dict containing auxiliary information and the data is returned.
If False, only the data is returned as list.
separatior_insertion: str, int or bool
separator_insertion: str, int or bool
str: replace all occurences of "separator_insertion" within the replica names
by "|%s" % (separator_insertion) when constructing the names of the replica.
int: Insert the separator "|" at the position given by separator_insertion.
@ -677,7 +681,7 @@ def _dobsdict_to_xmlstring_spaces(d, space=' '):
return o
def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=None, enstags=None):
def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=None, who=None, enstags=None):
"""Generate the string for the export of a list of Obs or structures containing Obs
to a .xml.gz file according to the Zeuthen dobs format.
@ -708,6 +712,8 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
xml_str : str
XML string generated from the data
"""
if symbol is None:
symbol = []
if enstags is None:
enstags = {}
od = {}
@ -866,7 +872,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
return rs
def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=None, enstags=None, gz=True):
def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=None, who=None, enstags=None, gz=True):
"""Export a list of Obs or structures containing Obs to a .xml.gz file
according to the Zeuthen dobs format.
@ -900,6 +906,8 @@ def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=No
-------
None
"""
if symbol is None:
symbol = []
if enstags is None:
enstags = {}

12
pyerrors/input/hadrons.py
View file

@ -245,7 +245,7 @@ def extract_t0_hd5(path, filestem, ens_id, obs='Clover energy density', fit_rang
return fit_t0(t2E_dict, fit_range, plot_fit=kwargs.get('plot_fit'))
def read_DistillationContraction_hd5(path, ens_id, diagrams=["direct"], idl=None):
def read_DistillationContraction_hd5(path, ens_id, diagrams=None, idl=None):
"""Read hadrons DistillationContraction hdf5 files in given directory structure
Parameters
@ -265,6 +265,8 @@ def read_DistillationContraction_hd5(path, ens_id, diagrams=["direct"], idl=None
extracted DistillationContration data
"""
if diagrams is None:
diagrams = ["direct"]
res_dict = {}
directories, idx = _get_files(path, "data", idl)
@ -486,7 +488,7 @@ def read_Bilinear_hd5(path, filestem, ens_id, idl=None):
return result_dict
def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=["VA", "AV"]):
def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=None):
"""Read hadrons FourquarkFullyConnected hdf5 file and output an array of CObs
Parameters
@ -508,6 +510,8 @@ def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=["VA", "AV"]):
extracted fourquark matrizes
"""
if vertices is None:
vertices = ["VA", "AV"]
files, idx = _get_files(path, filestem, idl)
mom_in = None
@ -596,7 +600,7 @@ def _get_lorentz_names(name):
assert len(name) == 2
if 'S' in name or 'P' in name:
if not set(name) <= set(['S', 'P']):
if not set(name) <= {'S', 'P'}:
raise Exception("'" + name + "' is not a Lorentz scalar")
g_names = {'S': 'Identity',
@ -605,7 +609,7 @@ def _get_lorentz_names(name):
res.append((g_names[name[0]], g_names[name[1]]))
else:
if not set(name) <= set(['V', 'A']):
if not set(name) <= {'V', 'A'}:
raise Exception("'" + name + "' is not a Lorentz scalar")
for ind in lorentz_index:

6
pyerrors/input/openQCD.py
View file

@ -596,7 +596,9 @@ def _parse_array_openQCD2(d, n, size, wa, quadrupel=False):
return arr
def _find_files(path, prefix, postfix, ext, known_files=[]):
def _find_files(path, prefix, postfix, ext, known_files=None):
if known_files is None:
known_files = []
found = []
files = []
@ -1268,7 +1270,7 @@ def read_ms5_xsf(path, prefix, qc, corr, sep="r", **kwargs):
idl_wanted = True
if 'idl' in kwargs:
idl_wanted = (cnfg in expected_idl[repnum])
left_idl = left_idl - set([cnfg])
left_idl = left_idl - {cnfg}
if idl_wanted:
cnfgs[repnum].append(cnfg)

14
pyerrors/input/sfcf.py
View file

@ -176,7 +176,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
# Exclude folders with different names
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*'):
ls = list(set(ls) - set([exc]))
ls = list(set(ls) - {exc})
if not appended:
ls = sort_names(ls)
@ -343,7 +343,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
name_ls = ls
for exc in name_ls:
if not fnmatch.fnmatch(exc, prefix + '*.' + name):
name_ls = list(set(name_ls) - set([exc]))
name_ls = list(set(name_ls) - {exc})
name_ls = sort_names(name_ls)
pattern = intern[name]['spec'][quarks][off][w][w2]['pattern']
deltas = []
@ -460,7 +460,9 @@ def _extract_corr_type(corr_type):
return b2b, single
def _find_files(rep_path, prefix, compact, files=[]):
def _find_files(rep_path, prefix, compact, files=None):
if files is None:
files = []
sub_ls = []
if not files == []:
files.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
@ -474,12 +476,12 @@ def _find_files(rep_path, prefix, compact, files=[]):
if compact:
for exc in sub_ls:
if not fnmatch.fnmatch(exc, prefix + '*'):
sub_ls = list(set(sub_ls) - set([exc]))
sub_ls = list(set(sub_ls) - {exc})
sub_ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
else:
for exc in sub_ls:
if not fnmatch.fnmatch(exc, 'cfg*'):
sub_ls = list(set(sub_ls) - set([exc]))
sub_ls = list(set(sub_ls) - {exc})
sub_ls.sort(key=lambda x: int(x[3:]))
files = sub_ls
if len(files) == 0:
@ -665,7 +667,7 @@ def _get_appended_rep_names(ls, prefix, name, ens_name=None):
new_names = []
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*.' + name):
ls = list(set(ls) - set([exc]))
ls = list(set(ls) - {exc})
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
for entry in ls:
myentry = entry[:-len(name) - 1]

2
pyerrors/input/utils.py
View file

@ -112,7 +112,7 @@ def check_params(path, param_hash, prefix, param_prefix="parameters_"):
# Exclude folders with different names
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*'):
ls = list(set(ls) - set([exc]))
ls = list(set(ls) - {exc})
ls = sort_names(ls)
nums = {}

2
pyerrors/misc.py
View file

@ -174,7 +174,7 @@ def gen_correlated_data(means, cov, name, tau=0.5, samples=1000):
return [Obs([dat], [name]) for dat in corr_data.T]
def _assert_equal_properties(ol, otype=Obs):
def _assert_equal_properties(ol):
otype = type(ol[0])
for o in ol[1:]:
if not isinstance(o, otype):