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

pyerrors/__init__.py

@@ -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 *

pyerrors/fits.py

@@ -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()
 

pyerrors/input/__init__.py

@@ -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

pyerrors/input/dobs.py

@@ -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 = {}
 

pyerrors/input/hadrons.py

@@ -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:

pyerrors/input/openQCD.py

@@ -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)
 

pyerrors/input/sfcf.py

@@ -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]

pyerrors/input/utils.py

@@ -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 = {}

pyerrors/misc.py

@@ -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):