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msspec_python3
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Removed all f-strings. 

By replacing f-strings by the standard ".format" call,
the package can be now compatible with python3.5
This commit is contained in:
Sylvain Tricot 2021-09-27 17:49:48 +02:00
parent ec0fc248ce
commit 369e743197
17 changed files with 157 additions and 68 deletions
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5
src/msspec/__init__.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -16,8 +17,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/__init__.py
# Last modified: ven. 10 avril 2020 17:22:12
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
import ase

30
src/msspec/calcio.py
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@ -1,5 +1,25 @@
#!/usr/bin/env python
# coding: utf-8
# vim: set et ts=4 sw=4 fdm=indent mouse=a cc=+1 tw=80:
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
# This file is part of msspec.
#
# msspec is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# msspec is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/calcio.py
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
Module calcio
@ -910,7 +930,7 @@ class SpecIO(object):
if content != old_content:
with open(filename, 'w') as fd:
fd.write(content)
LOGGER.debug(f"Writing Spec input file written in {filename}")
LOGGER.debug("Writing Spec input file written in {}".format(filename))
modified = True
return modified
@ -1255,13 +1275,13 @@ class CompCurveIO(object):
data = []
for i in range(1, 13):
#data.append(np.loadtxt(prefix + f'{i:02d}' + '.txt')[-1])
results = np.loadtxt(prefix + f'{i:02d}' + '.txt')
results = np.loadtxt(prefix + '{:02d}'.format(i) + '.txt')
results = results.reshape((-1, 2))
data.append(results[index,1])
suffix = 'ren'
exp = {'int': None, 'ren': None, 'chi': None, 'cdf': None}
exp_ren = np.loadtxt(os.path.join('exp', 'div',
f'experiment_{suffix}.txt'))
'experiment_{}.txt'.format(suffix)))
calc_ren = np.loadtxt(os.path.join('calc', 'div',
f'calculation{index:d}_{suffix}.txt'))
'calculation{:d}_{}.txt'.format(index,suffix)))
return data, exp_ren, calc_ren

21
src/msspec/calculator.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -16,8 +17,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/calculator.py
# Last modified: ven. 10 avril 2020 17:19:24
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
@ -1122,7 +1123,7 @@ class RFACTOR(object):
for i in range(noif):
X, Y = args[2*i], args[2*i+1]
fname = os.path.join('calc',
f'calculation{self.stack_count:d}.txt')
'calculation{:d}.txt'.format(self.stack_count))
# And save to the working space
np.savetxt(fname, np.transpose([X, Y]))
self.stack_count += 1
@ -1130,7 +1131,7 @@ class RFACTOR(object):
# Update the list of input calculation files
self._params.calc_filename = []
for i in range(self.stack_count):
fname = os.path.join('calc', f'calculation{i:d}.txt')
fname = os.path.join('calc', 'calculation{:d}.txt'.format(i))
self._params.calc_filename.append(fname)
# Write the input file
@ -1225,23 +1226,23 @@ class RFACTOR(object):
dset_values.x, dset_values.yref = exp_data.T
# Append the calculated values
ycalc = calc_data[:,1]
dset_values.add_columns(**{f"calc{i:d}": ycalc})
dset_rfc.add_columns(**{f'variable_set{i:d}': rfc})
dset_values.add_columns(**{"calc{:d}".format(i): ycalc})
dset_rfc.add_columns(**{'variable_set{:d}'.format(i): rfc})
# Plot the curves
view_values.select('x', 'yref', legend='Reference values')
title = ''
for k,v in self.best_values.items():
title += f'{k}={v} '
view_values.select('x', f"calc{self.index:d}",
title += '{}={} '.format(k, v)
view_values.select('x', "calc{:d}".format(self.index),
legend="Best calculated values")
view_values.set_plot_options(title=title)
view_results.select('counts')
for i in range(self.stack_count):
view_rfc.select('rfactor_number', f'variable_set{i:d}',
legend=f"variables set #{i:d}")
view_rfc.select('rfactor_number', 'variable_set{:d}'.format(i),
legend="variables set #{:d}".format(i))
# Save the parameters
for p in self.get_parameters():
bundle = {'group': str(p.group),

5
src/msspec/cli.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -18,8 +19,8 @@
# along with msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/cli.py
# Last modified: jeu. 04 juin 2020 16:54:12
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
import sys

5
src/msspec/create_tests_results.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -18,8 +19,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/create_tests_results.py
# Last modified: ven. 10 avril 2020 17:29:16
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
from msspec.tests import create_tests_results

23
src/msspec/data/__init__.py
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@ -1,5 +1,24 @@
# -*- encoding: utf-8 -*-
# vim: set fdm=indent ts=4 sw=4 sts=4 et ai tw=80 cc=+0 mouse=a nu : #
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
# This file is part of msspec.
#
# msspec is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# msspec is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/data/__init__.py
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
from .electron_be import electron_be

20
src/msspec/data/electron_be.py
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@ -1,4 +1,24 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
# This file is part of msspec.
#
# msspec is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# msspec is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/data/electron_be.py
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
Module electron_be

13
src/msspec/iodata.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -16,8 +17,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/iodata.py
# Last modified: ven. 10 avril 2020 17:23:11
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
@ -442,24 +443,24 @@ class DataSet(object):
for k, v in parameters.items():
if k == 'Cluster':
continue
s += f"# {k}:\n"
s += "# {}:\n".format(k)
if not(isinstance(v, list)):
v = [v,]
for p in v:
s += f"# {p['name']} = {p['value']} {p['unit']}\n"
s += "# {} = {} {}\n".format(p['name'], p['value'], p['unit'])
return s
colnames = self.columns()
with open(filename, mode) as fd:
# write the date and time of export
now = datetime.now()
fd.write(f"# Data exported on {now}\n")
fd.write("# Data exported on {}\n".format(now))
fd.write(rule)
# Append notes
fd.write("# NOTES:\n")
for line in self.notes.split('\n'):
fd.write(f"# {line}\n")
fd.write("# {}\n".format(line))
fd.write(rule)
# Append parameters

15
src/msspec/iodata_gi.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -15,9 +16,9 @@
# You should have received a copy of the GNU General Public License
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/iodata.py
# Last modified: ven. 10 avril 2020 17:23:11
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Source file : src/msspec/iodata_gi.py
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
@ -491,24 +492,24 @@ class DataSet(object):
for k, v in parameters.items():
if k == 'Cluster':
continue
s += f"# {k}:\n"
s += "# {}:\n".format(k)
if not(isinstance(v, list)):
v = [v,]
for p in v:
s += f"# {p['name']} = {p['value']} {p['unit']}\n"
s += "# {} = {} {}\n".format(p['name'], p['value'], p['unit'])
return s
colnames = self.columns()
with open(filename, mode) as fd:
# write the date and time of export
now = datetime.now()
fd.write(f"# Data exported on {now}\n")
fd.write("# Data exported on {}\n".format(now))
fd.write(rule)
# Append notes
fd.write("# NOTES:\n")
for line in self.notes.split('\n'):
fd.write(f"# {line}\n")
fd.write("# {}\n".format(line))
fd.write(rule)
# Append parameters

15
src/msspec/iodata_wx.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -15,9 +16,9 @@
# You should have received a copy of the GNU General Public License
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/iodata.py
# Last modified: ven. 10 avril 2020 17:23:11
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Source file : src/msspec/iodata_wx.py
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
@ -437,24 +438,24 @@ class DataSet(object):
for k, v in parameters.items():
if k == 'Cluster':
continue
s += f"# {k}:\n"
s += "# {}:\n".format(k)
if not(isinstance(v, list)):
v = [v,]
for p in v:
s += f"# {p['name']} = {p['value']} {p['unit']}\n"
s += "# {} = {} {}\n".format(p['name'], p['value'], p['unit'])
return s
colnames = self.columns()
with open(filename, mode) as fd:
# write the date and time of export
now = datetime.now()
fd.write(f"# Data exported on {now}\n")
fd.write("# Data exported on {}\n".format(now))
fd.write(rule)
# Append notes
fd.write("# NOTES:\n")
for line in self.notes.split('\n'):
fd.write(f"# {line}\n")
fd.write("# {}\n".format(line))
fd.write(rule)
# Append parameters

26
src/msspec/looper.py
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@ -1,6 +1,24 @@
# coding: utf8
# -*- encoding: future_fstrings -*-
# vim: set et sw=4 ts=4 nu tw=79 cc=+1:
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
# This file is part of msspec.
#
# msspec is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# msspec is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/looper.py
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
from collections import OrderedDict
from functools import partial
@ -21,7 +39,7 @@ class Variable:
self.doc = doc
def __repr__(self):
return f"<Variable(\'{self.name}\')>"
return "<Variable(\'{}\')>".format(self.name)
class Sweep:
def __init__(self, key, comments="", unit=None,

5
src/msspec/misc.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -18,8 +19,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/misc.py
# Last modified: ven. 10 avril 2020 17:30:42
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""

11
src/msspec/parameters.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -18,8 +19,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/parameters.py
# Last modified: ven. 10 avril 2020 17:31:50
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
@ -2012,20 +2013,20 @@ class CompCurveGeneralParameters(BaseParameters):
value = p.allowed_values.index(p.value)
self.compcurve_parameters.general_norm = value
LOGGER.info("Curve Comparison: Normalization mode set to "
f"\"{p.value}\"")
"\"{}\"".format(p.value))
def bind_rescale(self, p):
self.compcurve_parameters.general_iscale = int(p.value)
state = "deactivated"
if p.value:
state = "activated"
LOGGER.info(f"Curve Comparison: Rescaling of data {state}")
LOGGER.info("Curve Comparison: Rescaling of data {}".format(state))
def bind_function(self, p):
value = p.allowed_values.index(p.value)
self.compcurve_parameters.general_icur = value
LOGGER.info("Curve Comparison: Type of data used for comparison "
f"set to \"{p.value}\"")
"set to \"{}\"".format(p.value))

5
src/msspec/tests.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -16,8 +17,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/tests.py
# Last modified: ven. 10 avril 2020 17:33:28
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
import os

19
src/msspec/utils.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -18,8 +19,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/utils.py
# Last modified: ven. 10 avril 2020 15:49:35
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
"""
@ -66,7 +67,7 @@ class ForeignPotential(object):
self.phagen_data = {'types': []}
def write(self, filename, prototypical_atoms):
LOGGER.debug(f"Writing Phagen input potential file: {filename}")
LOGGER.debug("Writing Phagen input potential file: {}".format(filename))
def DEPRECATEDappend_atom_potential(atom):
Z = atom.number
@ -77,8 +78,8 @@ class ForeignPotential(object):
itypes.append(i)
# Check now that we have only one type in the list
# otherwise we do not know yet how to deal with this.
assert len(itypes) > 0, f"Cannot find the data for atom with Z={Z}"
assert len(itypes) == 1, f"Too many datasets for atom with Z={Z}"
assert len(itypes) > 0, "Cannot find the data for atom with Z={}".format(Z)
assert len(itypes) == 1, "Too many datasets for atom with Z={}".format(Z)
# So far so good, let's write the block
t = self.phagen_data['types'][itypes[0]]
s = "{:<7d}{:<10d}{:1.4f}\n".format(
@ -91,7 +92,7 @@ class ForeignPotential(object):
def append_atom_potential(atom):
line_fmt = "{:+1.8e} " * 4 + "\n"
atom_type = atom.get('atom_type')
assert atom_type != None, f"Unable get the atom type!"
assert atom_type != None, "Unable get the atom type!"
for t in self.phagen_data['types']:
if t['atom_type'] == atom_type:
s = "{:<7d}{:<10d}{:1.4f}\n".format(
@ -134,7 +135,7 @@ class SPRKKRPotential(ForeignPotential):
self.potfile = potfile
self.load_sprkkr_atom_types()
for f in exported_files:
LOGGER.info(f"Loading file {f}...")
LOGGER.info("Loading file {}...".format(f))
# get the IT from the filename
m=re.match('SPRKKR-IT_(?P<IT>\d+)-PHAGEN.*', os.path.basename(f))
it = int(m.group('IT'))
@ -188,7 +189,7 @@ class SPRKKRPotential(ForeignPotential):
return data
# load info in *.pot file
LOGGER.info(f"Loading SPRKKR *.pot file {self.potfile}...")
LOGGER.info("Loading SPRKKR *.pot file {}...".format(self.potfile))
with open(self.potfile, 'r') as fd:
content = fd.read()
@ -229,7 +230,7 @@ class SPRKKRPotential(ForeignPotential):
IT = occupation['ITOQ']
atom = self.atoms[i]
atom.set('atom_type', IT)
LOGGER.debug(f"Site #{IQ} is type #{IT}, atom {atom}")
LOGGER.debug("Site #{} is type #{}, atom {}".format(IQ, IT, atom))

5
src/msspec/version.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# coding: utf-8
#
# Copyright © 2016-2020 - Rennes Physics Institute
#
@ -16,8 +17,8 @@
# along with this msspec. If not, see <http://www.gnu.org/licenses/>.
#
# Source file : src/msspec/version.py
# Last modified: ven. 10 avril 2020 17:34:38
# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
# Last modified: Mon, 27 Sep 2021 17:49:48 +0200
# Committed by : sylvain tricot <sylvain.tricot@univ-rennes1.fr>
import os

2
src/options.mk
View File

@ -1,6 +1,6 @@
PYTHON = python
PYMAJ = 3
PYMIN = 6
PYMIN = 5
FC = gfortran
F2PY = f2py3 --f77exec=$(FC) --f90exec=$(FC)