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from __future__ import division
import matplotlib
matplotlib.use('Agg')
import nibabel as nib
import os
from .utils import get_resource_path
"""
Builder
=======
Base function to build dynamic workflows using BIDS formatted data files.
"""
def builder(subject_id, subId, project_dir, data_dir, output_dir, output_fin... | cosanlab/cosanlab_preproc | cosanlab_preproc/_builder.py | Python | mit | 28,171 | [
"Brian",
"Gaussian"
] | a05deec3739a26552b06ebe9c432f737d8cfa3824e1a935b5450f125c2549471 |
# -*- coding: utf-8 -*-
"""
Tests the "preview" selector in the LMS that allows changing between Staff, Student, and Content Groups.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.tests.helpers import UniqueCourseTest, create_user_partition_json
from common.test.acceptance.pages.studio.auto_aut... | louyihua/edx-platform | common/test/acceptance/tests/lms/test_lms_user_preview.py | Python | agpl-3.0 | 16,868 | [
"VisIt"
] | 1c05dbe4b504230834080202f2b8a37bb7101b6fadf0038afbb6352201d1e6e7 |
# store.py - repository store handling for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
import errno
import hashlib
import os
i... | dscho/hg | mercurial/store.py | Python | gpl-2.0 | 17,398 | [
"VisIt"
] | 4f75a8c5f6da9a92df77328dab04b9f8ef216074f953b328c1ab4688e347c907 |
"""
Convenience functions for the construction of spatial weights based on
contiguity and distance criteria.
"""
__author__ = "Sergio J. Rey <srey@asu.edu> "
from Contiguity import buildContiguity, Queen, Rook
from Distance import knnW, Kernel, DistanceBand
from util import get_ids, get_points_array_from_shapefile, m... | sjsrey/pysal_core | pysal_core/weights/user.py | Python | bsd-3-clause | 34,093 | [
"COLUMBUS",
"Gaussian"
] | 2445712615016819dd40d7dc6c057ea556ab769dc7b7f226f5fa19358fe1c17f |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | rsouza/pypln.web | setup.py | Python | gpl-3.0 | 2,042 | [
"NAMD"
] | b88cb416eda08f7ab75b2b9a31a7dba028868bfb2baa39f6c762e2440cc2c382 |
# DeepCrystal Technologies 2017 - Patrick Hop
# MIT License - have fun!!
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import os
import numpy as np
np.random.seed(123)
from sklearn.ensemble import RandomForestRegressor
from sklearn import svm
import ten... | deepchem/deepchem | examples/adme/run_benchmarks.py | Python | mit | 4,236 | [
"CRYSTAL"
] | 92b7bef9c29e5278bbf23597499fad71740569fdb97d071e8372c1a42e1723b0 |
from DIRAC.Core.Base.Script import parseCommandLine
from DIRAC.FrameworkSystem.Client.LoggerClient import LoggerClient
parseCommandLine()
LClient = LoggerClient()
retval = LClient.getSites()
if not retval['OK']: print retval['Message']
else: print retval['Value'][0:2]
retval = LClient.getSystems()
if not retval['OK'... | Sbalbp/DIRAC | FrameworkSystem/test/testLoggerClient.py | Python | gpl-3.0 | 1,878 | [
"DIRAC"
] | 8ebc8f536482a5156b6fb757a3ed38cc534e0ff31dfaf332472262e2f88a83dd |
import os
import re
from collections import defaultdict
from operator import itemgetter
import logging
import sys
import pandas as pd
from scipy.interpolate import InterpolatedUnivariateSpline as spline
from scipy.integrate import quad
from scipy.optimize import minimize_scalar, fmin
from george import kernels
import ... | kgullikson88/General | CCF_Systematics.py | Python | gpl-3.0 | 37,468 | [
"Gaussian"
] | f7504f71e392f69467461454c9cf05f7747e784ee047cab874d9d8bc410571f8 |
import json
from django.template.loader import render_to_string
import six
default_app_config = 'bowtie_content.config.BowtieContentConfig'
class BowtieContent(six.text_type):
@property
def html(self):
html = []
if len(self):
content = json.loads(self)
for block in co... | django-bowtie/bowtie-content | bowtie_content/__init__.py | Python | mit | 679 | [
"Bowtie"
] | abd845266aec203059ed5c88f43231a000cd0c4c85828b09d34a34e416d9d13b |
#!/usr/bin/env python
"""
Uses pysam to bgzip a file
usage: %prog in_file out_file
"""
from galaxy import eggs
import pkg_resources; pkg_resources.require( "pysam" )
import ctabix, subprocess, tempfile, sys, optparse
def main():
# Read options, args.
parser = optparse.OptionParser()
parser.add_option( '... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/bgzip.py | Python | gpl-3.0 | 1,828 | [
"Galaxy",
"pysam"
] | 6b023173d10293233c31593ba17e6a024100fc4d282c69b60269216c40917a2e |
#!/usr/bin/python3
import datetime
from ui.xnova.xn_page_cache import XNovaPageCache
from ui.xnova.xn_parser_overview import OverviewParser
from ui.xnova.xn_parser_userinfo import UserInfoParser
from ui.xnova.xn_parser_imperium import ImperiumParser
from ui.xnova.xn_parser_curplanet import CurPlanetParser
from ui.xnova... | minlexx/xnovacmd | test_parser.py | Python | gpl-2.0 | 4,689 | [
"Galaxy"
] | 46b8d372232e24c2a11de9e262066e01a45e3aaf06c6978ca3be2bd49656583d |
r"""
Ordination methods (:mod:`skbio.stats.ordination`)
==================================================
.. currentmodule:: skbio.stats.ordination
This module contains several ordination methods, including Principal
Coordinate Analysis, Correspondence Analysis, Redundancy Analysis and
Canonical Correspondence Analy... | anderspitman/scikit-bio | skbio/stats/ordination/__init__.py | Python | bsd-3-clause | 3,853 | [
"scikit-bio"
] | 53a6f6d6572cad34aa34ddf750da0acc686db7ec7eb3217365addb88193390f4 |
# c: 14.04.2008, r: 14.04.2008
from __future__ import absolute_import
import numpy as nm
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/2d/square_unit_tri.mesh'
def get_pars(ts, coors, mode=None, extra_arg=None,
equations=None, term=None, problem=None, **kwargs):
if mode == 'special'... | lokik/sfepy | tests/test_functions.py | Python | bsd-3-clause | 5,962 | [
"VTK"
] | 93a54e540d0a838106b40703c8ba9e5473e894c612928d395716f5af313dbee9 |
from tvtk.api import tvtk
from mayavi import mlab
from enable.vtk_backend.vtk_window import EnableVTKWindow
def main():
from basic_move import Box
from enable.api import Container
container = Container()
box = Box(bounds=[30,30], position=[20,20], padding=5)
container.add(box)
# Create the mla... | tommy-u/enable | examples/enable/vtk_example.py | Python | bsd-3-clause | 1,051 | [
"Mayavi",
"VTK"
] | 99575ce8443a3cbb8704ccabdde80e89b25df980eff6b4454a07701da81eb60d |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAnnaffy(RPackage):
"""Annotation tools for Affymetrix biological metadata.
Functi... | iulian787/spack | var/spack/repos/builtin/packages/r-annaffy/package.py | Python | lgpl-2.1 | 1,396 | [
"Bioconductor"
] | b8e01c0386f9500e17d791e1fb334235ca2256781f82aad005153534df61f17c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
from pymatgen.core.ion import Ion
from pymatgen.core.periodic_table import Element
from pymatgen.core.composition import Composition, CompositionError
i... | matk86/pymatgen | pymatgen/core/tests/test_ion.py | Python | mit | 5,066 | [
"pymatgen"
] | 1397605dee887ac46b95fdd844f883073f6221e619692dad1a78d3646084bf66 |
# Copyright 2014 The Oppia Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | prasanna08/oppia | core/controllers/reader_test.py | Python | apache-2.0 | 102,089 | [
"VisIt"
] | 03c59bb0d93273ba48e8810a8b4d913c533cc57f477dea06b8ecc1fa2be2183e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
import pychievements
def publish():
"""Publish to PyPi"""
os.system("python setup.py sdist upload")
if sys.argv[-1] == "publish":
publish()
... | PacketPerception/pychievements | setup.py | Python | mit | 1,268 | [
"Brian"
] | 71f6d9dff8e6ce0df7e5272e767d75267745a8c5f432c7d738913f777d4b8499 |
from vtk import *
vertexDegree = vtkProgrammableFilter()
def computeVertexDegree():
input = vertexDegree.GetInput()
output = vertexDegree.GetOutput()
output.ShallowCopy(input)
# Create output array
vertexArray = vtkIntArray()
vertexArray.SetName("VertexDegree")
vertexArray.SetNumberOfTuples(output.Get... | b3c/VTK-5.8 | Examples/Infovis/Python/vertex_degree_programmable.py | Python | bsd-3-clause | 1,348 | [
"VTK"
] | bb7bf573c39d75fb2f3530ac7bfaa11fc6945d8a904b091ff4811a5ca5833cff |
from netCDF4p import Dataset
import tempfile, unittest, os
import numpy as np
file_name = tempfile.mktemp(".nc")
xdim=None; ydim=121; zdim=169
datashape = (ydim,zdim)
data = np.ones(datashape,dtype=np.float)
class ShapeTestCase(unittest.TestCase):
def setUp(self):
self.file = file_name
f = Datase... | mathause/netCDF4p | test/tst_shape.py | Python | mit | 1,084 | [
"NetCDF"
] | 29cbf117ee012102139267ae61390eaba49b2e615a7da7db121d1267e4206e42 |
# the following line needed for unicode character in convert_anglestring
# -*- coding: latin-1 -*-
import ast
import constants as c
import copy
import datetime
import dateutil
import logging
import math
import meteorologicalfunctions as mf
import netCDF4
import numpy
import os
import platform
import pytz
import sys
imp... | OzFlux/OzFluxQC | scripts/qcutils.py | Python | gpl-3.0 | 82,118 | [
"NetCDF"
] | 44994994c3d1130bbde47374cf4e462d7d904d353b247b65a032c01f98e9d1e3 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | seankelly/buildbot | master/buildbot/changes/svnpoller.py | Python | gpl-2.0 | 17,861 | [
"Brian"
] | d47e7247b102c5179d69339ad25ca435fa8bcf05875939a23a389882e89d5959 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-service-ports
# Author : Stuart Paterson
########################################################################
"""
Print the service ports for the specified setup
"""
from __future__ ... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-service-ports.py | Python | gpl-3.0 | 1,118 | [
"DIRAC"
] | 7096d5bc9fc7ed1d736f54cdd5e38f9bd1d6b3690c7722086bbd8e42d1b684ea |
"""
This module contain solvers for all kinds of equations:
- algebraic or transcendental, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from __future__ import print_function, division
f... | kaichogami/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 122,379 | [
"Gaussian"
] | c432c72decc13e6ee72a2b4da1cf8e9fa9c99c84cfab836ecd5d10f844b59385 |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_bio(... | kshedstrom/pyroms | examples/cobalt-preproc/Clim_bio/remap_bio.py | Python | bsd-3-clause | 3,866 | [
"NetCDF"
] | 19cda5cab5e6a1176acb7e96cc2f04a4cf6f71cf7b12c2825bae9c77f01df0f9 |
##
# title: BreadInterface.App
# by: Brian Kim
# description: the top-level class that manages the
# Navigator and Settings.
# A developer could subclass this or just use it
# right out of the box.
#
from Lifecycle import Lifecycle
from Navigator import Navigator
from Settings import Settings
##
# app clas... | briansan/BreadInterface | py/BreadInterface/core/App.py | Python | bsd-2-clause | 869 | [
"Brian"
] | 81a4063641b2003d101f6ea2940db44d360a6309feea0fd565b9d99112543a33 |
# ScummVM - Graphic Adventure Engine
#
# ScummVM is the legal property of its developers, whose names
# are too numerous to list here. Please refer to the COPYRIGHT
# file distributed with this source distribution.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU ... | MaddTheSane/scummvm | devtools/tasmrecover/tasm/cpp.py | Python | gpl-2.0 | 20,440 | [
"VisIt"
] | 88918cb75fc0953a5772df37aa10acc902f027dc377beb204a9ac9e59d4de2d9 |
#!/usr/bin/python
import sys
num_of_test = 0 # number of test case (N)
debug = 0
num_N = 0
def open_read_file():
# file_name=raw_input()
#file_name="sample_input.txt"
#file_name="B-small-practice.in"
file_name="B-large-practice.in"
fin=open(file_name, 'r')
return fin
def prune_node(frm, to):
... | ashoksekar/python | CodeJam/2014/Round1A/FullBinaryTree/main.py | Python | gpl-2.0 | 1,951 | [
"VisIt"
] | f1adb3b119cecf914525032ca6e8c9e2c3a18b88e683f16fcd812a88cd347559 |
"""Postprocessing utils based on VTK library"""
import vtk
import os
import tempfile
vtk_version = vtk.vtkVersion().GetVTKMajorVersion()
def get_vtk_from_file(filename):
"""
Read VTK file.
Parameters
----------
filename : str
Name of the VTK file.
Returns
-------
vtkdata : V... | rc/sfepy | sfepy/postprocess/utils_vtk.py | Python | bsd-3-clause | 3,741 | [
"VTK"
] | d6d803ca459f815cf637a95de8d0e76ab0e597565da3166a156ff8f8c684b1de |
#!/usr/bin/python
from numpy import *
#from scipy import *
#import array
import os #next two lines helps me to run commandline agument in python
import sys
#import operator #use with the operator sorted
from operator import itemgetter
##########################################################################
#
#USAGE:... | altynbekm/Siesta | PlotDos.py | Python | gpl-3.0 | 2,363 | [
"SIESTA"
] | d3f52b6caf1d0a189f47bc98ff907db9bc89e414e17be3166d21b668cd607e11 |
# Copyright 2012 by Eric Talevich. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import collections
import warnings
from Bio import BiopythonWarning
from Bio.Alphabet import g... | zjuchenyuan/BioWeb | Lib/Bio/SeqIO/PdbIO.py | Python | mit | 10,486 | [
"Biopython"
] | 5ad0b9ba9d42d824c0322d2fb648cca2e65b82847118e0e6423558304268ebed |
#!/usr/bin/env python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# BornProfiler --- A package to calculate electrostatic free energies with APBS
# Written by Kaihsu Tai, Lennard van der Feltz, and Oliver Beckstein
# Released under th... | Becksteinlab/BornProfiler | scripts/apbs-bornprofile-BPauto.py | Python | gpl-3.0 | 7,084 | [
"CHARMM",
"MDAnalysis"
] | a581fc4cb1bcea23c1dd9e412e093e4d741094424625ec39743138cc12e61cb9 |
"""
We import our empty db and write our model changes to it.
NOTE: scheduler creates an additional table not captured in this model.
"""
__author__ = 'donal'
__project__ = 'dcleaner'
from . import db, login_manager
from werkzeug.security import generate_password_hash, check_password_hash
from sqlalchemy import Column... | carverdo/dcleaner | app/db_models.py | Python | mit | 6,765 | [
"VisIt"
] | 7ec1f99419ef609e178ccb51a54f17e4ef789d7c6f5e37361f1925b6491e495c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module implements various transmuter classes.
Transmuters are essentially classes that generate TransformedStructures from
various data sources. They enable the... | aykol/pymatgen | pymatgen/alchemy/transmuters.py | Python | mit | 16,733 | [
"VASP",
"pymatgen"
] | 6f9d22f264ae01e3d6ed3fc951ea0c7516d21015792e1e8d6dfc9dd2e6b742ce |
'''
Created on 2013-05-16
@author: brian
'''
import pygame
from entity import Entity
from src.ai import task
from src.abilities import *
class Headless(Entity):
living = "headless"
dead = "gore"
def __init__(self, world):
Entity.__init__(self, world)
self.health = self.maxHealth = 20
self.ai.addAI(... | Greymerk/python-rpg | src/entity/mobs/headless.py | Python | gpl-3.0 | 557 | [
"Brian"
] | 7b7c5f63300b517269eb05292ff1829152b29f3bbf47f0906e4edec12668294c |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt', 'os2' or 'ce'.
- os.curdir is a string representing the current directory ('.' or... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.2/Lib/os.py | Python | mit | 27,189 | [
"VisIt"
] | 47c6f0df43e24c7b4ca9aec5d3187adbff13243917b20e54528ea96422c74252 |
"""This module contains functional tests applicable to the Admin Backend."""
from fec.utils import SeleniumTestCase
class GeneralAdminPageTests(SeleniumTestCase):
"""Test General Expectations for Every Admin Page."""
def setUp(self):
"""Visit the admin page and login."""
self.create_admin_and_... | FederationOfEgalitarianCommunities/FECWebsite | fec/functional_tests/admin_tests.py | Python | gpl-3.0 | 2,806 | [
"VisIt"
] | e3b8bd2426360258a8b3c1e7e1c40938151a691093235498dcc2d7061a766107 |
# -*- coding: utf-8 -*-
# Dioptas - GUI program for fast processing of 2D X-ray diffraction data
# Principal author: Clemens Prescher (clemens.prescher@gmail.com)
# Copyright (C) 2014-2019 GSECARS, University of Chicago, USA
# Copyright (C) 2015-2018 Institute for Geology and Mineralogy, University of Cologne, Germany
... | erangre/Dioptas | dioptas/tests/unit_tests/test_Pattern.py | Python | gpl-3.0 | 7,679 | [
"Gaussian"
] | 5c60440855964b32ee179898903ac6d712a3d6530fa5830efeb6ec455134b8c1 |
from __future__ import absolute_import, print_function, unicode_literals
import logging
import os
import random
import time
import threading
import stat
from builtins import str
import shutil
import functools
import uuid
from tempfile import NamedTemporaryFile
from pprint import pformat
from typing import (Any, Callab... | common-workflow-language/cwl-tes | cwl_tes/tes.py | Python | apache-2.0 | 20,077 | [
"VisIt"
] | 95f418bc6670ac90b1afe0afddc9e04e3885889ed710385733d305802defc2e0 |
########################################################################
# $HeadURL$
########################################################################
""" Handles KML generation
"""
__RCSID__ = "$Id$"
#############################################################################
class KMLData:
##############... | avedaee/DIRAC | Core/Utilities/KMLData.py | Python | gpl-3.0 | 5,105 | [
"DIRAC"
] | 54503e82aae62e0645b7204372b1f899b818ab6512588af9c27a77d0cfdc126a |
import os
import sys
import pkgutil
def LoadFolder(inputFolderPath):
infilePathList=[]
try:
for root, dirs, files in os.walk(inputFolderPath):
for file in files:
infilePathList.append(inputFolderPath+file)
except:
print('Error Code: 0015')
return infilePathLi... | liutairan/eMolFrag | eMolFrag_2017_06_19_01/loader.py | Python | gpl-3.0 | 3,639 | [
"RDKit"
] | 324e5573534118c00c8b2f8735926cc2fb634e6f2a916898945512384e4628d2 |
# $Id$
#
# Copyright (c) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" utility functionality for clusterin... | soerendip42/rdkit | rdkit/Chem/Fingerprints/ClusterMols.py | Python | bsd-3-clause | 6,049 | [
"RDKit"
] | 3f8b6a8ec065ed6f06a59c08b489811d31315000b6a8b9f8856c80b0f072f21b |
#!/usr/bin/env python
import os
import sys
try:
from setuptools import setup
from setuptools.extension import Extension
except ImportError:
raise RuntimeError('setuptools is required')
import versioneer
DESCRIPTION = ('A set of functions and classes for simulating the ' +
'performance o... | wholmgren/pvlib-python | setup.py | Python | bsd-3-clause | 4,214 | [
"pysam"
] | 275d738afafdd9f749659374ccfc3b8d7e816ff46c0df969a6586da6f377ae09 |
from __future__ import division
import pytest
import numpy as np
from scipy import sparse
from scipy.stats import kstest
import io
from sklearn.utils._testing import assert_allclose
from sklearn.utils._testing import assert_allclose_dense_sparse
from sklearn.utils._testing import assert_array_equal
from sklearn.uti... | bnaul/scikit-learn | sklearn/impute/tests/test_impute.py | Python | bsd-3-clause | 50,541 | [
"Gaussian"
] | ed3d9f24d795af27ceaf9a77bd986da707c7c9cae26f8d5a968c99281963b971 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kevin-coder/tensorflow-fork | tensorflow/python/ops/linalg/linalg_impl.py | Python | apache-2.0 | 21,603 | [
"Gaussian"
] | 480c70362781182d5b9a7299368f2c2ee00de280da4a0b47276107eeea266466 |
class Module:
def __init__(self, mainMenu, params=[]):
# metadata info about the module, not modified during runtime
self.info = {
# name for the module that will appear in module menus
'Name': 'PillageUser',
# list of one or more authors for the module
... | EmpireProject/Empire | lib/modules/python/collection/osx/pillage_user.py | Python | bsd-3-clause | 5,341 | [
"BLAST"
] | 366debd91fce9b33c49dcf3adc9511212df33e4f31ef7970ef365bb7ad195056 |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import nao, scf as scf_c
from pyscf.nao import prod_basis
class KnowValues(unittest.TestCase):
def test_gw(self):
""" This is GW """
mol = gto.M(verbose=0, atom='''Ag 0 0 -0.3707; Ag 0 0 0.... | gkc1000/pyscf | pyscf/nao/test/test_0092_ag2_ae.py | Python | apache-2.0 | 929 | [
"PySCF"
] | b6334e87b45c8a76bf397e98b447a010c630a864e8c252c0ebaa41c63a53b824 |
import re
import os
from markdown.util import etree
import logging
log = logging.getLogger(__name__)
import MooseDocs
from MooseTextPatternBase import MooseTextPatternBase
import utils
try:
import utils.MooseSourceParser
HAVE_MOOSE_CPP_PARSER = True
except:
HAVE_MOOSE_CPP_PARSER = False
class MooseCppMethod(M... | vityurkiv/Ox | python/MooseDocs/extensions/MooseCppMethod.py | Python | lgpl-2.1 | 2,351 | [
"MOOSE"
] | ee654bbdfa5bdb464865158dd67aae60c239980f467bdc3ede1ad44aa0f8a83b |
""" JobLoggingDB class is a front-end to the Job Logging Database.
The following methods are provided
addLoggingRecord()
getJobLoggingInfo()
getWMSTimeStamps()
"""
import time
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Base.DB impor... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/DB/JobLoggingDB.py | Python | gpl-3.0 | 5,875 | [
"DIRAC"
] | dc9b777dde79f6c244cd970153574dfa746028844943dff7d6c526eaec9fa129 |
# coding: utf-8
from sqlalchemy import Column, Integer, ForeignKey, Float, Boolean
from sqlalchemy.orm import mapper, relationship
from sqlalchemy.ext.declarative import declarative_base
import random
Base = declarative_base()
class Group(Base):
__tablename__ = 'groups'
id = Column(Integer, primary_key=True)... | rgarcia-herrera/party | model.py | Python | gpl-3.0 | 2,133 | [
"exciting"
] | 1d3f4104c29b4bee99cfa294f73b75d6c363b64436b187d1ca7126a54d96ec27 |
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 18 16:34:59 2015
@author: casimp
"""
import numpy as np
from numpy.polynomial.chebyshev import chebval
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from pyxe.fitting_tools import pawley_hkl, extract_parameters, array_fit_pawley
... | casimp/edi12 | pyxe/plotting_tools.py | Python | mit | 7,583 | [
"Gaussian"
] | a0ad8bfa61e469c1bf7ddf0f9f83f24e7892d1bb6328b4b94f053d114882a0e3 |
import itertools
from simphony.core.cuba import CUBA
from .atom_style import AtomStyle
class AtomStyleDescription(object):
""" Class describes atom style
Each atom style has a particular set of attributes that it supports
(or provides). This class contains a list of what attributes it
contains. N... | simphony/simphony-lammps-md | simlammps/common/atom_style_description.py | Python | bsd-2-clause | 4,091 | [
"LAMMPS"
] | 79f2a64e09dc11bd8ee2ca1c80fdd3e5840a7908213526019053e00a68efb03b |
"""
Primitive image processing functions for the hugs pipeline.
"""
from __future__ import division, print_function
import os
import numpy as np
import lsst.afw.detection as afwDet
from .utils import pixscale
from . import utils
from . import sextractor
from .morphology import Morphology
import sep
from scipy import ... | johnnygreco/hugs | hugs/primitives.py | Python | mit | 14,924 | [
"Gaussian"
] | 3f144fda4aa8ad46fb4f5aa8a921e5a6ff8b8c598e4be8e46deb87a9ded3140f |
"""Build assemblies using the aTRAM algorithm.."""
import os
import re
from multiprocessing import Pool
from os.path import basename, join, split, splitext
from subprocess import TimeoutExpired
from Bio import SeqIO
from . import assembler as assembly, bio, blast, db, db_atram, util
from .log import Logger
def ass... | juliema/aTRAM | lib/core_atram.py | Python | bsd-3-clause | 10,236 | [
"BLAST"
] | 4bfaf0e88f3d4d7c66a0b79dbaac5be57c85ae154584f5ec9fd6985ed067e6dd |
""" Author: Cole Howard
Title: Finnegan
An extinsible neural net designed to explore Convolutional Neural Networks and
Recurrent Neural Networks via extensive visualizations.
"""
import numpy as np
from sklearn.preprocessing import normalize
from layer import Layer
# from matplotlib import cm
# from matplotlib impo... | uglyboxer/finnegan | finnegan/network.py | Python | mit | 7,625 | [
"NEURON"
] | 5305d71187fd866af64a3f6a867c47b6423789b214ee2964fbd0f0d564e814ae |
# Copyright 2006-2010 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Bio.AlignIO support for the "clustal" output from CLUSTAL W and other tools.
You are e... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/AlignIO/ClustalIO.py | Python | gpl-2.0 | 21,480 | [
"Biopython"
] | 93752895bcda4bc227b84487698c6e7e9a3642444cc3028b7dc35af3fa9dadb3 |
""" This module contains functionality to aid in extracting workflows from
histories.
"""
from galaxy.util.odict import odict
from galaxy import exceptions
from galaxy import model
from galaxy.tools.parameters.basic import (
DataToolParameter,
DataCollectionToolParameter,
DrillDownSelectToolParameter,
S... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/workflow/extract.py | Python | gpl-3.0 | 14,480 | [
"Galaxy"
] | 7e626a014e997c2f49214da82a5e8fcffff76206f78de5c0f47df10e18fbf009 |
# -*- coding: utf-8 -*-
#
# This file is part of the bliss project
#
# Copyright (c) 2016 Beamline Control Unit, ESRF
# Distributed under the GNU LGPLv3. See LICENSE for more info.
"""X-Ray crystal diffraction physics (Bragg, Laue)
Disclaimer
----------
When an argument to any function represents a physical quantity... | tiagocoutinho/bliss | bliss/physics/diffraction.py | Python | lgpl-3.0 | 15,011 | [
"CRYSTAL"
] | 914240d921769ad1ca3301bb397565225a35cd40ddb4c6fc0bf146bac7c50505 |
import argparse
import asyncio
import importlib.util
import logging
from multiprocessing.process import BaseProcess
from multiprocessing import get_context
from packaging import version
import os
import signal
import sys
import traceback
from typing import Iterable, List, Optional, Text, Tuple
import aiohttp
from rasa... | RasaHQ/rasa_nlu | rasa/cli/x.py | Python | apache-2.0 | 17,660 | [
"VisIt"
] | 9648f8b96379e466bd4c93df03fa8b5647ddcf9a1784c400a102fde436816cda |
import io
import sys
import numpy as np
import json
import random
import hashlib
class Graph:
def __init__(self, size):
self.size = size
self.n_chars = int(np.ceil(np.log(size + 1)/np.log(16)))
self.node_name_pattern = ('%%0%dx' % self.n_chars) * 2
first_node = sel... | nikonyrh/graphcycles-python | graphGen.py | Python | apache-2.0 | 4,173 | [
"VisIt"
] | 21426684f245e69470820cd707ce694d6059013f0ea9c27bc0df5296fcf0455f |
__doc__="""
DaetTools model that describes the behavior of a water flowing in a pipe with the effect of biofim formation.
"""
from daetools.pyDAE import *
from daetools_extended.daemodel_extended import daeModelExtended
from daetools_extended.tools import get_node_tree, execute_recursive_method, get_initialdata_from... | Jaimenms/celldeposit-condenser | models/biofilm.py | Python | gpl-3.0 | 8,014 | [
"EPW"
] | 187bfbd48e99858e0fbd4bd3f4e2ae37b52b51ad7ee57c1ffdec669f4fdbb505 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import sys
import platform
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_build_ext):
def finalize_options(self):... | nisse3000/pymatgen | setup.py | Python | mit | 8,570 | [
"ABINIT",
"ASE",
"FEFF",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | 96f0ae552822efefa6aa95331d3ec67c6a6dfc2c84397e51c9e77e7cfe8a4bf6 |
# Copyright (c) 2003-2012 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program 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 2 of the License, o... | tkaitchuck/nupic | external/common/lib/python2.6/site-packages/pylint/checkers/variables.py | Python | gpl-3.0 | 24,792 | [
"VisIt"
] | 2e339018b6b2936619f720ffe29aa24c81eb5600f51eeb3561dc98e851271f64 |
from sympy import (meijerg, I, S, integrate, Integral, oo, gamma,
hyperexpand, exp, simplify, sqrt, pi, erf, sin, cos,
exp_polar, polar_lift, polygamma, hyper, log, expand_func)
from sympy.integrals.meijerint import (_rewrite_single, _rewrite1,
meijerint_indefinite, _infla... | lidavidm/mathics-heroku | venv/lib/python2.7/site-packages/sympy/integrals/tests/test_meijerint.py | Python | gpl-3.0 | 26,966 | [
"Gaussian"
] | 0eadf32685a34eba7713dee1f2aba1dbd7435ce456960734a80293bf110acf83 |
"""
Python script to create an AXI memory mapped CSR.
"""
from math import ceil, log2
from jinja2 import Template
class Register(object):
"""A single register in a CSR"""
def __init__(self, addr, label, mode, initial_value=0):
super(Register, self).__init__()
self.addr = addr
self.label = label
self.mode = ... | BBN-Q/VHDL-Components | src/axi_csr.py | Python | mpl-2.0 | 7,722 | [
"Brian"
] | eb4f64d06a108575a849d934036e029d5a62819287fc6351ae7226a14ea13e44 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import tempfile
from monty.json import MontyDecoder
from pymatgen.io.vasp.sets import *
from pymatgen.io.vasp.inputs import Poscar, Kpoints
from pymatgen.core import Specie, Lattice, ... | tschaume/pymatgen | pymatgen/io/vasp/tests/test_sets.py | Python | mit | 48,881 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | a2a146db8fb1b98282de2cfce59087eb17291db8a9e4a70e07a7ac533f9968b4 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/periodic_1960/regrid_Me2CO_emissions_n96e_360d_1960.py | Python | gpl-3.0 | 7,135 | [
"NetCDF"
] | 534316a0e10e1c3e469d5019905c61dcf0e0412a025f8252a0a684b3aa125964 |
"""
Analyse individual snapshot spectra from APOGEE.
"""
import numpy as np
import os
from six.moves import cPickle as pickle
from astropy.table import Table
import AnniesLasso as tc
model_filename = "apogee-rg-custom-17label-REGULARIZED-theta_linalg_init-bfgs_factr0.1_pgtol1e-6-fmin_xtol-1e-6-ftol-1e-6.pickle.bac... | peraktong/AnniesLasso | sandbox-scripts/gravelbox_individual_visit_snr.py | Python | mit | 8,811 | [
"VisIt"
] | 81f3bafb3a2668fdc5235af80cc70a1e34e8821149e44197c6dc500f58ffa4a7 |
"""
Module to parse NAMD log files.
"""
from __future__ import absolute_import
try:
from future_builtins import zip
except ImportError:
pass
from .basefile import ReadOnlyTextFile
__all__ = ['NamdLogFile']
class NamdLogFile(ReadOnlyTextFile):
"""Parse a NAMD log file."""
filetype = "NAMD log"
... | HuiLiuCode/pymdlog | pymdlog/namdlogfile.py | Python | gpl-3.0 | 1,364 | [
"NAMD"
] | be74cc1593872a67d8f906ffd9b53e769faea9b3714ac77ba0bb3b2532a169af |
from itertools import chain
from contextlib import contextmanager
from collections import Counter
from ..graph import GraphVisitor, Root
from ..graph import AbstractNode, AbstractField, AbstractLink, AbstractOption
from .errors import Errors
class GraphValidationError(TypeError):
def __init__(self, errors):
... | vmagamedov/hiku | hiku/validate/graph.py | Python | bsd-3-clause | 5,124 | [
"VisIt"
] | 0c77df61a05d6dd2be0a9a3df969d39e49c7946af3cedd098142e0926636eac0 |
#\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\#
import os
import inspect
import GangaCore.Utility.Virtualization
from GangaCore import _gangaVersion
from GangaCore.Core.Sandbox.WNSandbox import PYTHON_DIR
from GangaDirac.Lib.RTHandlers.DiracRTHUtils import dirac_inputdata, dirac_ouputdat... | ganga-devs/ganga | ganga/GangaDirac/Lib/RTHandlers/ExeDiracRTHandler.py | Python | gpl-3.0 | 9,951 | [
"DIRAC"
] | f9756dc8024c587013bee4c51cbd315d57a252d8e4ef039be48d33e2c629d6f5 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/AbinsModules/CalculateSingleCrystal.py | Python | gpl-3.0 | 2,776 | [
"CRYSTAL"
] | ae6c8aada4ac1eab0a2e795ccd11e2230480401727965a87b54e6c3083786d7f |
"""Tests for PhononMoment."""
from io import StringIO
import numpy as np
from phonopy import Phonopy
from phonopy.phonon.moment import PhononMoment
result_full_range = """
1.000000 1.000000 1.000000
4.063222 4.236805 3.889623
17.935854 19.412820 16.458756
1.000000 1.000000 1.000000
3.530039 3.621065 3.451... | atztogo/phonopy | test/phonon/test_moment.py | Python | bsd-3-clause | 1,830 | [
"phonopy"
] | 4cfef385d9f721c1dfb78541969e24d9e6b07c651c978d14ec9dcc951e73a2a7 |
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
# pyeq2 is a collection of equations expressed as Python classes
#
# Copyright (C) 2013 James R. Phillips
# 2548 Vera Cruz Drive
# Birmingham, AL 35235 USA
#
# email: zunzun@zunzun.com
#
... | burkesquires/pyeq2 | Models_2D/Peak.py | Python | bsd-2-clause | 104,834 | [
"Gaussian"
] | d4c160448db7d71816585feb2ee289b9b3c5a4ab2c000ab626ce58ca40de3e58 |
#!/usr/bin/env python3
import os
import json
import uuid
import subprocess
import unittest
from xml.etree import ElementTree as ET
from io import BytesIO
import urllib3 # type: ignore
import logging
logging.disable(logging.CRITICAL)
logger = logging.getLogger('pymisp')
from pymisp import PyMISP, MISPOrganisation, M... | MISP/MISP | tests/testlive_comprehensive_local.py | Python | agpl-3.0 | 32,271 | [
"Amber"
] | 21deebb27b5590898d7a591da11b51e5821dba44c284e926e3f986ef230c48d2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# convolution - http://www.songho.ca/dsp/convolution/convolution.html
# Copyright (C) 2011-2012 The CPHHPC Project lead by Brian Vinter
#
# This file is part of CPHHPC Toolbox.
#
# CPHHPC Toolbox is free software: you can redistribute it and/or modif... | Ektorus/bohrium | test/cil/Unittest/Benchmarks/IronPython/cphhpc/signal/convolution.py | Python | lgpl-3.0 | 3,399 | [
"Brian"
] | 188472f64d569fec8287b11a898a6e653f7ecb7a1eee345804f49ae9ed03dd74 |
# This program is explicitly written for PYTHON3.X and will not work under Python2.X
import numpy as np
import shutil
from scipy.special import binom
from scipy.sparse import coo_matrix, csr_matrix, issparse
from scipy.sparse import identity as spidentity
from scipy.special import erf
import scipy.linalg as la
from nu... | marvinlenk/subsystem_entropy_epsplots | pyplot_eps/mpEntropy.py | Python | bsd-2-clause | 69,287 | [
"Gaussian"
] | 67345b1b4cf6bec3b18c5f00f2cb856ec871d5e43fada9574e244e5d6aeb3658 |
import numpy as np
from skimage import feature
from scipy import ndimage
import time
def register_rigid(stack, field, z_estimate, z_range, yaw=0, pitch=0, roll=0):
""" Registers using skimage.feature match_template.
Rotates the stack, cross-correlates the field at each position and returns the score,
coo... | fabiansinz/pipeline | python/pipeline/utils/registration.py | Python | lgpl-3.0 | 10,165 | [
"Gaussian"
] | 4e54211b8487090fb3e8864f92bd9fc974ecf4d8483bd227a1c0d38b28898aac |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""This package implements basic input and output capabilities for Abinit."""
from .netcdf import (
NO_DEFAULT,
ETSF_Reader,
NetcdfReader,
NetcdfReaderError,
as_etsfreader,
as_ncreader,
structure_fr... | materialsproject/pymatgen | pymatgen/io/abinit/__init__.py | Python | mit | 660 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | a7635c11e2493ffe05523eddb04eb41518f16c687568c1952c6eca51f86c29b5 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/repeatmasker/package.py | Python | lgpl-2.1 | 3,252 | [
"BLAST"
] | f2ab314d1d9800c23e8ab1fc12dfec788b8312da0d216c2b1e68027951f70ff0 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | marscher/PyEMMA | pyemma/coordinates/tests/test_featurereader_and_tica_projection.py | Python | lgpl-3.0 | 5,622 | [
"MDTraj"
] | 74b106ad55f4659a8bf01e07258749d9e2c0c4d252d1f8585a567a7de13c6236 |
"""
A Python interface for Discount, the C Markdown parser
This module contains ``libmarkdown``, a ctypes binding for Discount,
as well as ``Markdown``, a helper class built on top of this library.
Visit the Discount homepage:
http://www.pell.portland.or.us/~orc/Code/discount/
Basic usage examples:
>>> md = Mar... | hepochen/py-discount | discount/__init__.py | Python | bsd-3-clause | 11,708 | [
"VisIt"
] | 439e20b3327bd8982427b39c94f22928812b4f1943de601a84145e980564dc95 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# Configuration, please edit
# Data about this site
BLOG_AUTHOR = "Mumbai Ultimate"
BLOG_TITLE = "Mumbai Ultimate"
# This is the main URL for your site. It will be used
# in a prominent link
SITE_URL = "http://mumbaiultimate.in/"
# This is t... | punchagan/mumbaiultimate.in | conf.py | Python | bsd-3-clause | 27,593 | [
"VisIt"
] | 1913f9dd0f9c3a56de6d513bd94fb6a70977a33c94c8c1b71615638efed90b77 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Make randomly displaced POSCAR files from the non-displaced POSCAR file.
Usage:
make-displaced-POSCARs.py [options] POSCAR
Options:
-h, --help Show this help message and exit.
--random-type=RTYPE
Specify random number type. [default: uniform]
-d... | ryokbys/nap | nappy/vasp/make_displaced_POSCARs.py | Python | mit | 6,814 | [
"ASE",
"VASP"
] | 828820a8129f879127068de53be514ce31d93cf870c24b22acc724d2cc07e8f7 |
"""
Line-based and matrix-based plotting commands using MatPlotLib.
Before importing this file, you will probably want to do something
like:
from matplotlib import rcParams
rcParams['backend']='TkAgg'
to select a backend, or else select an appropriate one in your
matplotlib.rc file (if any). There are many back... | jesuscript/topo-mpi | topo/command/pylabplot.py | Python | bsd-3-clause | 49,227 | [
"Gaussian",
"NEURON"
] | 29f883bc52f2eb5e545d2d29b4452580651a1f3ae5f928b29ca89c251bdaada1 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kobejean/tensorflow | tensorflow/python/autograph/converters/asserts.py | Python | apache-2.0 | 1,734 | [
"VisIt"
] | 7e8042180bea0093cec3f9c9560023bffadac6c90b350c28da8335a4ff3fdf8f |
"""Frequency correction class for MRSI modality."""
import os
import cPickle as pickle
import numpy as np
from joblib import Parallel, delayed
from scipy.special import wofz
from scipy.optimize import curve_fit
from ..data_management import MRSIModality
from ..data_management import GTModality
from ..utils.valida... | glemaitre/protoclass | protoclass/preprocessing/mrsi_frequency_correction.py | Python | gpl-2.0 | 10,325 | [
"Gaussian"
] | 7b27b80a6be5d8abb6f2960e774fe1ae5ca4a68dbe5519b78c56d1d5dda79d4e |
from __future__ import division
"""
PyProcess
@author: Cameron Davidson-Pilon
"""
import numpy as np
import scipy as sp
import scipy.stats as stats
from scipy.special import gammainc
import warnings
import matplotlib.pyplot as plt
import pdb
np.seterr( divide="raise")
#TODO change all generate_ to sample_
class ... | CamDavidsonPilon/PyProcess | pyprocess/pyprocess.py | Python | mit | 73,110 | [
"Gaussian"
] | 492eabaaad6660385aac57f5c9640c3161b2919ae633d34246421928e7612a2f |
#!/usr/bin/env python
from distutils.core import setup
setup(name='MethylAnalyzer',
version='0.1.0',
description='Analyze Methyl-MAPS data',
author='Yurong Xin',
author_email='xinyuro@pi.cpmc.columbia.edu',
url='http://github.com/epigenomics/methylmaps',
packages=['MethylAnalyzer']... | epigenomics/methylmaps | setup.py | Python | gpl-3.0 | 773 | [
"pysam"
] | 129994128681a455c21aa445318479d595ff1704605532060775a54db3dd9aac |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**IS Utilities implementation.**
Contact : ole.moller.nielsen@gmail.com
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fre... | dynaryu/inasafe | safe/utilities/utilities.py | Python | gpl-3.0 | 12,694 | [
"VisIt"
] | 8646563513482ae686d654695df620b67d187de96dcddbe6e0845b8518ad070f |
from pyspark import SparkContext
from pyspark import SparkConf
from least_squares import RandLeastSquares
from rowmatrix import RowMatrix
from utils import pickle_write
import time
import sys
import os
import argparse
import ConfigParser
import scipy.stats
import numpy as np
import logging.config
def print_params(args... | chocjy/randomized-LS-solvers | src/run_ls.py | Python | apache-2.0 | 10,099 | [
"Gaussian"
] | d41b1e2ec23162e80f0062d7a3e1a87558846f1d45a2eb5cf99061eb3e8de389 |
# encoding: utf-8
"""
Tests for IPConfigurable.configurable
Authors:
* Brian Granger
* Fernando Perez (design help)
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The ful... | Carreau/IPConfigurable | IPConfigurable/test/test_configurable.py | Python | bsd-3-clause | 11,215 | [
"Brian"
] | e0ea4c633d7bbe2aed51804c5f4f8bfb102e0dfdc70f266c81440ab3f023f7c0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jH0ward/psi4 | psi4/share/psi4/databases/BAKERJCC93.py | Python | lgpl-3.0 | 42,456 | [
"Psi4"
] | b0ce2744f325c487ffcce9da07aedf06d7d8f808f9656f4b08094c4dcca44aa5 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/total_chr08.py | Python | mit | 32,997 | [
"MCell"
] | 82fb9b406fceccebbf444b82b0114940a78ffc91edb09d2ef330fda1b43b600c |
# -*- coding: utf-8 -*-
"""
Preliminary code for ray tracing with Python and VTK
Thanks to
https://pyscience.wordpress.com/2014/10/05/from-ray-casting-to-ray-tracing-with-python-and-vtk/
In order to proceed, you will have to exit the renderwindow, it is waiting for your input.
@author: Adamos Kyriokou, Jaap Verhegge... | Gjacquenot/PyRayTracer | raytracer/raytracer.py | Python | mit | 36,942 | [
"VTK"
] | 26d23ec202752f4206562a6d2709688daae90e04f4d62813a0a9592aad249e07 |
"""User-friendly public interface to polynomial functions. """
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple, Rational
)
from sympy.core.mul import _keep_coeff
from sympy.core.basic import preorder_traversal
from sympy.core.sympify import (
sympify, SympifyError,
)
from sympy.... | lidavidm/mathics-heroku | venv/lib/python2.7/site-packages/sympy/polys/polytools.py | Python | gpl-3.0 | 163,118 | [
"Gaussian"
] | e206e823fb921a07b4ac85dda4300a7ab312168ce8634747d1e7e1dabd11269d |
""" ComponentMonitoring class is a front-end to the Component monitoring Database
"""
__RCSID__ = "$Id$"
import random
import types
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Utilities import Time, List, Network
class ComponentMonitoringDB( DB ):
def __init__( self... | sposs/DIRAC | FrameworkSystem/DB/ComponentMonitoringDB.py | Python | gpl-3.0 | 21,234 | [
"DIRAC"
] | b5ea34df91a856674787fe67e7c4f4664b04558becf3253a57cc881e22ecb9e9 |
# -*- coding: utf-8 -*-
"""This module contains various utility functions."""
import inspect
import itertools
import math
import ast
import os
import tokenize
import copy
from types import LambdaType
# pylint: disable=unused-import
from typing import (Callable, Dict, Iterator, List, NamedTuple, Optional, Sequence, Tup... | HPAC/matchpy | matchpy/utils.py | Python | mit | 23,029 | [
"VisIt"
] | 2d04901fd8cbfd43550e53dcf6b15dfa71bf23579420e827ce0139d51a805cd2 |
###############################################################################
# Copyright 2016 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "EC-CAS diags" package.
#
# "EC-CAS diags" is free software: you can redistribute it and/or modify
# it under... | neishm/EC-CAS-diags | eccas_diags/diagnostics/where_holes.py | Python | lgpl-3.0 | 1,364 | [
"NetCDF"
] | 91767e89225153521dd982e6d1ddc3144705c33a47986d20ca88707b9abd94bc |
###############################################################################
#
# coverageWindows.py - calculate coverage of windows within sequences
#
###############################################################################
# #
# T... | Ecogenomics/CheckM | checkm/coverageWindows.py | Python | gpl-3.0 | 10,610 | [
"pysam"
] | b33dfaeb55643cc20f5e9c98e60241d695a56c2bad68ecc241831abb29a8b603 |
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