initial commit

Author: mjlaine

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+# *.c
+
+# backup files
+*~
+*.bak
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/_build/
+doc/source/_generated
+
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# PyCharm files/directories
+.idea/
+
+

LICENSE.txt

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+Copyright (c) 2019, Marko Laine
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+The views and conclusions contained in the software and documentation are those
+of the author and should not be interpreted as representing official policies, 
+either expressed or implied, of his employer.

README.md

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+# EPPES

__init__.py

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+#
+
+from .eppes import eppes
+from .eppes import config
+from .eppes.eppes import *
+from .eppes.data import EppesData
+

eppes/__init__.py

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+#__all__ = ['eppes','config','plots']
+__all__ = ['eppes','config']
+
+from . import config
+from . import eppes
+from .data import EppesData
+from .eppes import *

eppes/config.py

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+# Options configuration for eppes
+# -*- coding: utf-8; -*-
+
+# order of options
+# 1. values given in the command line
+# 2. values read from config file 'eppes.cfg' or give as --config=myconfig.cfg
+# 3. defaults given in this file
+
+import argparse
+import configparser
+
+# default file options
+files = {
+    'mufile': 'mufile.dat',
+    'sigfile': 'sigfile.dat',
+    'wfile': 'wfile.dat',
+    'nfile': 'nfile.dat',
+    'scorefile': 'scores.dat',
+    'samplein': 'oldsample.dat',
+    'sampleout': 'sampleout.dat',
+    'boundsfile': '',
+    'w00file': '',
+    'winfofile': 'winfo.dat'
+}
+# other default values
+options_int = {
+           'sampleonly': 1,
+           'nsample': 10,
+           'verbosity': 1,
+           'maxn': -1,
+           'lognor': 0,
+           'useranks': 0
+           }
+options_float = {'maxsteprel': 0.0}
+options_str = {'combine_method': 'amean'}
+
+# combine options
+options = {**options_int, **options_float, **options_str}
+
+# create config parser and add defaults
+config = configparser.ConfigParser()
+config['files'] = files
+config['options'] = options
+
+# parser to read config file and command line args
+def parseargs(*cmdargs):
+    parser = argparse.ArgumentParser(description="Eppes options", add_help=False)
+    parser.add_argument("-c", "--config", dest='config_file', default='eppes.cfg', type=str)
+
+    args, remaining_argv = parser.parse_known_args(args = cmdargs)
+    # read options from config file
+    config.read(args.config_file)
+
+    # reload default options
+    files = dict(config['files'])
+    options = dict(config['options'])
+
+    for i in files.keys():
+        parser.add_argument('--'+i, type=str)
+    parser.set_defaults(**files)
+
+    for i in options_int.keys():
+        parser.add_argument('--'+i, type=int)
+    for i in options_float.keys():
+        parser.add_argument('--'+i, type=float)
+    for i in options_str.keys():
+        parser.add_argument('--'+i, type=str)
+    parser.set_defaults(**options)
+
+    # some extra arguments still
+    parser.add_argument("-q", "--quiet", dest='verbosity', default=0, nargs='?', type=int)
+    parser.add_argument("--showoptions", "-s", action='store_true')
+    parser.add_argument("-h", "--help", action='help')
+
+    opts = parser.parse_args(remaining_argv)
+
+    if opts.showoptions:
+        print('*Options values*')
+        for k, v in vars(opts).items():
+            print(k, ':', v)
+        parser.exit(0)
+
+    return opts