text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
This module implements an interface to the critic2 Bader analysis code.
For most Bader analysis purposes, users are referred to
pymatgen.command_line.bader_caller instead, this module is for advanced
usage requiring identification of critical points in the charge density.
This module depends on a compiled critic2... | davidwaroquiers/pymatgen | pymatgen/command_line/critic2_caller.py | Python | mit | 33,677 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | b72cb7be5b0a5567594e5c4da04111aa1e1437a70e437b7ce18c200a0f5bdaaa |
import os
import sys
from tqdm import tqdm
import numpy as np
from pymongo import MongoClient
from .seq2go_train import *
from .baselines import *
from .baselines import predict as bl
def init_encoder_decoder(input_vocab_size,
output_vocab_size,
input_embedding=No... | yotamfr/prot2vec | src/python/seq2go_predict.py | Python | mit | 9,169 | [
"BLAST"
] | c8d9c9a80a5da58dd623f4005abef7bd411bb2538a1cd9b32f025e44899f266c |
# Built-in
import os
import itertools as itt
# Common
import numpy as np
from scipy.interpolate import BSpline
import matplotlib.pyplot as plt
import matplotlib.lines as mlines
import matplotlib.patches as mpatches
import matplotlib.colors as mcolors
from matplotlib.colors import ListedColormap
import matplotlib.gri... | Didou09/tofu | tofu/spectro/_plot.py | Python | mit | 51,155 | [
"CRYSTAL"
] | 4d970b9ea1157e69623c0be679131e3ddb497833e253e61db28f774c4647f103 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/sequence/tests/test_protein.py | Python | bsd-3-clause | 4,458 | [
"scikit-bio"
] | c29a089b42c2cd7e4e2bd52765d047475150c98fea90c3b0f3285bf947b4d614 |
import numpy
import matplotlib.pyplot as plt
import math
import os
import scipy
import scipy.ndimage.filters
import scipy.ndimage.morphology
import skimage.io, skimage.util, skimage.filters, skimage.transform, skimage.feature, skimage.exposure
import sys
import networkx
def detect_local_minima(arr):
# http://stack... | bbbales2/neuron_tracker | extract_data.py | Python | gpl-3.0 | 14,122 | [
"NEURON"
] | d93b1e1447d3ca117e8cecba24fb66d12c56c42ff14f33d84b453f8df1c12a7c |
import datetime
import json
import logging
import md5
import random
import tba_config
import urllib
import uuid
import webapp2
from google.appengine.api import urlfetch
from google.appengine.ext import deferred
from google.appengine.ext import ndb
from consts.auth_type import AuthType
from controllers.base_controller... | verycumbersome/the-blue-alliance | controllers/api/api_base_controller.py | Python | mit | 10,458 | [
"VisIt"
] | bd79a7c7ca51031cac30735f00b34858418686e6f08e9e37a34c92e2e59105c3 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for LibraryContent block in LMS
"""
import ddt
import textwrap
from nose.plugins.attrib import attr
from common.test.acceptance.tests.helpers import UniqueCourseTest, TestWithSearchIndexMixin
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common... | TheMOOCAgency/edx-platform | common/test/acceptance/tests/lms/test_library.py | Python | agpl-3.0 | 13,662 | [
"VisIt"
] | 5fbda4d543735f7264b523a449ce731a6c7105cffe1a93041837bdd821c6cd76 |
import nas
import sys
import lib_nas
#import Lib_NAS_Rnas_IA_
# _bias_4_16 v3.0
# estructura Neuronal 4 bits --16 patrones de adaptacion
# @autor:Jose Luis Prado Seoane ---IT Security Researcher & Developer
# Research: Teoria de Sistemas Neuronales (I.A) --TSNB
# Redes Neuronales y su convergencia hacia modelos e ... | ciudadano72/TSNB_redes_neuronales | bias416.py | Python | gpl-3.0 | 4,784 | [
"NEURON"
] | 04b91f69fde9d3d139628ec2d59e2eeb84ee54474204d2d4a4036d1dfd9aa27d |
"""
Processes some of the entries in the configuration file: builds directory paths and lists
reads in the variables table
"""
import csv
import get_configuration as config
from collections import OrderedDict
def init(vartable):
'''
Set global variables and read the variables table vartable
'''
# b... | C2SM-RCM/CCLM2CMOR | src/CMORlight/settings.py | Python | gpl-3.0 | 3,969 | [
"NetCDF"
] | 8e26520469d19c04576975dd989137e0096b79f6fa6a95b7a82742a4c824ecd7 |
"""
This module is not a test file. It contains classes grouping some common
functionality, that is used in several test files.
"""
from __future__ import absolute_import
from sfepy.base.base import IndexedStruct
from sfepy.base.testing import TestCommon
import os.path as op
class NLSStatus(IndexedStruct):
"""
... | lokik/sfepy | tests/tests_basic.py | Python | bsd-3-clause | 4,467 | [
"VTK"
] | 30152ae89bef98d2514d72525f39fd4296f3a5080711c06af9e4a816cf7da956 |
##########################################################################
#
# Copyright (c) 2016, Image Engine Design Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistrib... | hradec/gaffer | python/IECoreArnoldTest/RendererTest.py | Python | bsd-3-clause | 125,928 | [
"Gaussian"
] | 530d6bde6abe35ac2523b244edbb6c9e8fb1452621077b2a96a4fb4cc993303c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
String functions
"""
from __future__ import unicode_literals
from __future__ import absolute_import
import sys
from sys import version_info
import re
import unicodedata
from binascii import hexlify, unhexlify
from heapq import heappush, heappop
import six
from six.m... | pqtoan/mathics | mathics/builtin/strings.py | Python | gpl-3.0 | 94,282 | [
"Galaxy"
] | a99a25d427ee64a3110ea1bc097b79007d34d43a17293dba0e0fb0a6422e1171 |
# Copyright 2014 Brian J. Downs
#
# 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 law or agreed to in writing, s... | briandowns/pyopenvswitch | __init__.py | Python | apache-2.0 | 1,079 | [
"Brian"
] | 4d8d5e929ed6ce8c50850041a47d0c35dc25ed93e7944b0233c8fdc4187ae3c0 |
# JoystickController.py
# Aaron Taylor
# Moose Abumeeiz
#
# Takes input from the joystick and simulates key presses for
# the corrisponding control
#
from pygame import *
class JoystickController:
"""Custom Joystick event class"""
def __init__(self, stick, thresh, leftStick=[115, 100, 119, 97], rightStick=[274, ... | ExPHAT/binding-of-isaac | JoystickController.py | Python | mit | 2,011 | [
"MOOSE"
] | 4ffe9d1e451f4555c7b728286493286b5f56b4499077f56ea427f5dba3e690c7 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-utils-file-adler
# Author :
########################################################################
"""
Calculate md5 of the supplied file
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core... | Sbalbp/DIRAC | Interfaces/scripts/dirac-utils-file-md5.py | Python | gpl-3.0 | 1,182 | [
"DIRAC"
] | d2c5dc823cf020ddefcd16f60cde9bd33e3671447af2cc788ef81f071e2b7fd3 |
#!/usr/bin/python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Test restraints module.
"""
# =====================================================... | andrrizzi/yank | Yank/tests/test_restraints.py | Python | mit | 8,683 | [
"NetCDF"
] | 0ce2a41e9ea4f2d4379adcfc8463a45cd96e7e839666eb6137983ae3b36fd689 |
'''
sobel_filter.py - given a color RGB image, try different
Sobel filters for edge detection
Author: Esha Uboweja (euboweja)
'''
# Import Libraries
import cv2
import numpy as np
import sys
# Callback function for trackbar
def nothing(x):
pass
# Read image in color format
if len(sys.argv) > 1:
im_name = sys.a... | eknight7/cv_build18 | filtering/sobel_filter.py | Python | mit | 1,088 | [
"Gaussian"
] | 1a4502469d4ffc15c4a28616dbcb51c14f332f20d651911b31a3fbf2cf42d05f |
# mako/ast.py
# Copyright 2006-2021 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""utilities for analyzing expressions and blocks of Python
code, as well as generating Python from AST no... | sqlalchemy/mako | mako/ast.py | Python | mit | 6,642 | [
"VisIt"
] | dbe30889223d0d994f05912ae3e5863658a67bd533924172037aa3d358da0d1f |
"""
rm_tools.py
Written by Michael Bell
Base classes for doing RM synthesis and RM CLEANing. These classes operate
on single lines of sight.
Copyright 2012 Michael Bell, Henrik Junklewitz
This file is part of the pyrmsynth package.
pyrmsynth is free software: you can redistribute it and/or modify
it under the term... | mrbell/pyrmsynth | rm_tools/rm_tools.py | Python | gpl-3.0 | 20,015 | [
"Gaussian"
] | b15be437f53fb0537c594f25113476fef50b8bbedc0e047b3966900a2cd8cd7e |
# -*- coding: utf-8 -*-
'''
:author: Patrick Lauer
This class holds the Artificial Bee Colony(ABC) algorithm, based on Karaboga (2007):
D. Karaboga, AN IDEA BASED ON HONEY BEE SWARM FOR NUMERICAL OPTIMIZATION,TECHNICAL REPORT-TR06, Erciyes University, Engineering Faculty, Computer Engineering Department 2005.
D. Ka... | gitporst/spotpy | spotpy/algorithms/abc.py | Python | mit | 9,796 | [
"Gaussian"
] | e073a770e8c7f9b9351add85a7efcb85de5674cff05d0c0b5f8685bd07ef82ce |
# pytype: skip-file
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# Modified by Google LLC
# License: BSD 3 clause
"""Scikit-learn Gaussian Mixture Model rewritten in TF."""
import abc
import math
import time
from typing import Optional
import warnings
from... | google-research/federated | generalization/utils/tf_gaussian_mixture.py | Python | apache-2.0 | 24,886 | [
"Gaussian"
] | 402d02ade01093db4bd435145dc6bb8367906a1625a58a729bdbf8a00b642f4f |
import astropy.cosmology as co
aa=co.Planck15
import astropy.io.fits as fits
import matplotlib.pyplot as p
import numpy as n
import os
import sys
# global cosmo quantities
z_min = float(sys.argv[1])
z_max = float(sys.argv[2])
#imf = 'kroupa'
#lO2_min = float(sys.argv[3]) # 'salpeter'
SNlimit = 5
smf_ilbert13 = lamb... | JohanComparat/pySU | spm/bin_SMF/smf_sdss_eboss.py | Python | cc0-1.0 | 15,868 | [
"Firefly",
"Galaxy"
] | dc012a919ab1d55501cb71baa37da5bc2847a24aac92b71ed41510796b349209 |
#
# @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
#... | rmcgibbo/psi4public | psi4/driver/constants/__init__.py | Python | lgpl-3.0 | 963 | [
"Psi4"
] | 98449f8a50dc1a62b729f6565ba3d46a23fe63fd877b94af9534d5425cf77328 |
# 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.
"""Codon tables based on those from the NCBI.
These tables are based on parsing the NCBI file:
ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt
Last upd... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Data/CodonTable.py | Python | gpl-2.0 | 42,181 | [
"Biopython"
] | 78b2587cf0fe522bf50d6ea85fb30c81dade689dbb0fe29fd5d9d78298815c91 |
#!/usr/bin/env python
#
# Copyright (C) 2013-2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ 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, eithe... | espressopp/espressopp | testsuite/AdResS/HAdResS/test_HAdResS.py | Python | gpl-3.0 | 12,807 | [
"ESPResSo"
] | 72e2205542acfa2116cd793ff9a0985e6ae668d3b0a9200b82edb3a1b504a1e1 |
import os
import unittest
import numpy as np
from pymatgen.analysis.graphs import StructureGraph
from pymatgen.core.structure import Structure
from pymatgen.electronic_structure.cohp import Cohp
from pymatgen.electronic_structure.core import Spin
from pymatgen.io.lobster.lobsterenv import LobsterNeighbors
from pymatge... | gmatteo/pymatgen | pymatgen/io/lobster/tests/test_lobsterenv.py | Python | mit | 21,890 | [
"pymatgen"
] | 5ad503005c6c6f0090f363689f6bc9e1d82d343cf19ff5c38a355d739f23d116 |
from django.conf.urls import url
from crystal_dashboard.dashboards.crystal.policies.bw_slos import views
urlpatterns = [
url(r'^create/$', views.CreateView.as_view(), name='create'),
url(r'^update/(?P<slo_id>[^/]+)/$', views.UpdateView.as_view(), name='update')
]
| Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/policies/bw_slos/urls.py | Python | gpl-3.0 | 273 | [
"CRYSTAL"
] | 0d9b02d78e2bfd4d510248572521589481d7194f60cc20721f46a4c343ca739c |
# -*- coding: utf-8 -*-
from __future__ import division
import itertools
import multiprocessing
import pickle
import numpy as np
from scipy import optimize
import emcee
from george import GP
from .pca import PCA
from .util import atleast_2d_column
__all__ = 'MultiGP',
class _GPProcess(multiprocessing.Process):
... | jbernhard/mtd | mtd/multigp.py | Python | mit | 13,459 | [
"Gaussian"
] | b7206c9b182e2cf8f8ef9e25d0085187a80e61063c097a95e19e4a30c3b6b4e3 |
import numpy as np
import cv2
import pdb
import _warnings as warnings
import scipy.ndimage as ndi
from scipy.ndimage.interpolation import map_coordinates
from scipy.ndimage.filters import gaussian_filter
EPSILON = 1e-8
SWITCHES = {
0: 'elastic_transform',
1: 'gamma_augmentation',
}
def get_augmenting_funci... | kacper1095/asl-translator | api/src/keras_extensions/data_tools/augmenting_tools.py | Python | gpl-3.0 | 8,021 | [
"Gaussian"
] | e822b3a794cb5c37cb9732d141a9bc20a29841c52916e846911982237c2d3a02 |
# mload.py ---
#
# Filename: mload.py
# Description:
# Author:
# Maintainer:
# Created: Fri Feb 8 09:38:40 2013 (+0530)
# Version:
# Last-Updated: Wed May 22 12:16:35 2013 (+0530)
# By: subha
# Update #: 213
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Utility to load models and detect file... | dilawar/moose-full | moose-gui/mload.py | Python | gpl-2.0 | 7,466 | [
"MOOSE"
] | 79c05d21b2af7cde580caaac35ac69519d7a2ebd29a2f17209c270c687b1d8ed |
import numpy as np
from openpathsampling.netcdfplus import StorableObject
# The decorator @restores_ allows us to restore the object from a JSON
# string completely and can thus be stored automatically
class PES(StorableObject):
"""Abstract base class for toy potential energy surfaces.
"""
# For now, we... | jhprinz/openpathsampling | openpathsampling/engines/toy/pes.py | Python | lgpl-2.1 | 8,778 | [
"Gaussian"
] | 7b2f6bc8b77c7a3eaddfb1dcbee495ef781dc35345b4ea8cb4bb09ab37c5eb0a |
#! /usr/bin/env python
# MMapArea.py
# This file is part of CharTr
#
# Copyright (C) 2006 - Don Scorgie <Don@Scorgie.org> (labyrinth part)
# Copyright (C) 2008 - Nicolas Bigeard <ga6ri3l@gmail.com>
# CharTr is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | google-code/chartr | debian/chartr/usr/local/lib/python2.6/dist-packages/chartr/MMapArea.py | Python | gpl-3.0 | 89,008 | [
"FLEUR"
] | 5f3f76dd5ed51381a566d253c411dcb0f745819d010fdfb1448c350b041a3294 |
# ./sumocfg.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:e92452c8d3e28a9e27abfc9994d2007779e7f4c9
# Generated 2018-02-11 20:56:40.825355 by PyXB version 1.2.6 using Python 3.6.3.final.0
# Namespace AbsentNamespace0
from __future__ import unicode_literals
import pyxb
import pyxb.binding
import pyxb.binding.saxer
i... | TrafficSenseMSD/core | ts_core/config/bindings/sumocfg.py | Python | epl-1.0 | 486,708 | [
"VTK"
] | f866ebc28a089ab088452ea19b723e9cc73a772b382d323c32c103c6cec1c57d |
import re
from dark.taxonomy import LineageFetcher
from dark.filter import TitleFilter
from dark.score import HigherIsBetterScore
def bestAlignment(readAlignments):
"""
Find the best alignment for a read. This is the one whose first HSP
has the best score.
Note that the comparison of HSP score value... | terrycojones/dark-matter | dark/alignments.py | Python | mit | 19,331 | [
"BLAST"
] | 45e1f3d0ba4a40b8d2c190424a1f79d332c666217798e372ca0ddeec15e4ec47 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
NWChem Editor
##################
"""
from exatomic import Editor as _Editor
class Editor(_Editor):
def __init__(self, *args, **kwargs):
super(Editor, self).__init__... | exa-analytics/exatomic | exatomic/nwchem/editor.py | Python | apache-2.0 | 567 | [
"Gaussian",
"NWChem"
] | e22ed2ad422b7c43692d942eb0d791ab0bcb295d39533d59d1b2396bc897cb1d |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | modules/combined/examples/geochem-porous_flow/forge/porous_flow.py | Python | lgpl-2.1 | 2,380 | [
"MOOSE"
] | 6c1929acd0b0a155e5ef3fab34227f86212365fd5134d8ba86020b8b749fea4c |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
import json
import frappe
import frappe.utils
from frappe import _
from frappe.contacts.doctype.address.address import get_company_address
from frappe.desk.notifications import clear_doctype... | frappe/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | gpl-3.0 | 38,302 | [
"VisIt"
] | b25cd6f4abe5bdaa9370443ac425a88c2b1f7f5c8649cc86df385c8a6bfe8aa3 |
# Copyright 2013-2021 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 RTopgo(RPackage):
"""Enrichment Analysis for Gene Ontology
topGO package provides ... | LLNL/spack | var/spack/repos/builtin/packages/r-topgo/package.py | Python | lgpl-2.1 | 1,695 | [
"Bioconductor"
] | 06765f2cea727437cba2aec91cb9707d5e7195202157e36aea27b5f24c10b9d0 |
from django.conf import settings
class PageHelper:
def __init__(self):
self.base_url = settings.FUNCTIONAL_TEST_BASE_URL
def load_creativecolibri_homepage(self, b):
b.visit(self._get_absolute_url(""))
def load_course_browse_page(self, b):
b.visit(self._get_absolute_url("/cou... | CariZa/django-spectacles | spectacles/pagehelper.py | Python | mit | 433 | [
"VisIt"
] | ba3f073790102cac72ef0a296bf296154d51f8d1fd908ecc0426d85750cfc95e |
import hashlib
from django.conf import settings
from django.contrib import messages
from django.contrib.auth.models import User
from cl.users.models import UserProfile
def create_stub_account(user_data, profile_data):
email = user_data['email']
new_user = User.objects.create_user(
# Username can onl... | voutilad/courtlistener | cl/users/utils.py | Python | agpl-3.0 | 6,834 | [
"VisIt"
] | 9f95fd4e42be5021a0b0fb9e2286b4f328e2f52dd5f1a29ff895322c7adf5e50 |
from setuptools import setup
setup(
name='spatialtree',
version='0.1',
description='Module for building spatial spill trees (KD, PCA, RP, 2-means)',
author='Brian McFee',
author_email='bmcfee@cs.ucsd.edu',
url='http://www-cse.ucsd.edu/~bmcfee/code/spatialtree/',
packages=['spatialtree'],
... | bmcfee/spatialtree | setup.py | Python | gpl-3.0 | 993 | [
"Brian"
] | 989e68fa70de7cb4331ee7b0fad20d9700713dfc37d2c700ecc4c5d7a7463f66 |
# -*- coding: utf-8 -*-
"""
jinja2.compiler
~~~~~~~~~~~~~~~
Compiles nodes into python code.
:copyright: (c) 2017 by the Jinja Team.
:license: BSD, see LICENSE for more details.
"""
from itertools import chain
from copy import deepcopy
from keyword import iskeyword as is_python_keyword
from functo... | astaninger/speakout | venv/lib/python3.6/site-packages/jinja2/compiler.py | Python | mit | 65,386 | [
"VisIt"
] | 06a0b953a27139b49185b9724ff6ba4e9e46b44539cf7512d5ae232d06b1c60a |
"""
@name: Modules/House/Security/_test/test_motion_detectors.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2019-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Nov 29, 2019
@summary: Test
Passed all 13 tests - DBK - 2018-02-13
"""
__updated__ = '201... | DBrianKimmel/PyHouse | Project/src/Modules/House/Security/Motiondetectors/_test/test_motion_detectors.py | Python | mit | 2,687 | [
"Brian"
] | a9165477fcd1f6cf81c4156d63b842876d262fadcdbb044010e74bc70c7ba517 |
########################################################################
# $HeadURL$
# File : DownloadInputData.py
# Author : Stuart Paterson
########################################################################
""" The Download Input Data module wraps around the Replica Management
components to provide acc... | avedaee/DIRAC | WorkloadManagementSystem/Client/DownloadInputData.py | Python | gpl-3.0 | 13,954 | [
"DIRAC"
] | 8ee6eeeba845e2e83100fbfba7d5489de2b12ce9997af92f6fa07fc9d43875fc |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/ParticleAccess.py | Python | gpl-3.0 | 1,517 | [
"ESPResSo"
] | 5ac2de9e0053c46a75c8cfe44f8deb49ddf0ef41fcef627b3e08c90b24114eb1 |
###############################################################################
# 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/interfaces/cams.py | Python | lgpl-3.0 | 4,982 | [
"NetCDF"
] | c10630aae8e6ad9426c615c0b9dc41bdde75f8729e6e8ad7e5f74fe681bc4fd7 |
# example.py
#
# Sort a list of a dicts on a common key
rows = [
{'fname': 'Brian', 'lname': 'Jones', 'uid': 1003},
{'fname': 'David', 'lname': 'Beazley', 'uid': 1002},
{'fname': 'John', 'lname': 'Cleese', 'uid': 1001},
{'fname': 'Big', 'lname': 'Jones', 'uid': 1004}
]
from operator import itemgetter
... | tuanavu/python-cookbook-3rd | src/1/sort_a_list_of_dictionaries_by_a_common_key/example.py | Python | mit | 665 | [
"Brian"
] | 24aa74c8ca8d2f617e88620e82b0faa87e708f0dad31cd5a9cbf847b12bd5a51 |
# Author: Travis Oliphant 2001
# Author: Nathan Woods 2013 (nquad &c)
from __future__ import division, print_function, absolute_import
import sys
import warnings
from functools import partial
from . import _quadpack
import numpy
from numpy import Inf
__all__ = ['quad', 'dblquad', 'tplquad', 'nquad', 'quad_explain',
... | jamestwebber/scipy | scipy/integrate/quadpack.py | Python | bsd-3-clause | 36,505 | [
"Gaussian"
] | 6cbbe668a2e6ae15fec9b32f60cf40e2944a6a6ae023408886631aac68ed4f5a |
import sys
import os
import argparse
import tempfile
from appdirs import AppDirs
from .parser import ParserImproved
from .ast_transformer import ASTTransformer
from .codegen import CodeGenerator
def main():
argparser = argparse.ArgumentParser(description='Translator from extended C to normal C')
argparser.a... | KivApple/c_ext | c_ext/main.py | Python | mit | 3,605 | [
"VisIt"
] | 3fadd9c4beb3ec66135f6b0ca0ada5315a3a50b2130a4b3d8f83190cdfef8981 |
import os.path
from pulsar.client import PathMapper
from pulsar.client.action_mapper import path_type
from .test_utils import TempDirectoryTestCase
from galaxy.util.bunch import Bunch
class PathMapperTestCase(TempDirectoryTestCase):
def test_input(self):
local_path = os.path.join(os.path.dirname(self.t... | ssorgatem/pulsar | test/path_mapper_test.py | Python | apache-2.0 | 3,537 | [
"Galaxy"
] | 6080f802282ecbb16232704c835331ede0328b125ab1efe4fefc755be69615d6 |
#!/usr/bin/env python3
"""The influence of windowing of log. sweep signals when using a
Kaiser Window by fixing beta (=7) and fade_in (=0).
fstart = 1 Hz
fstop = 22050 Hz
"""
import sys
sys.path.append('..')
import measurement_chain
import plotting
import calculation
import generation
import matplotlib.py... | spatialaudio/sweep | log_sweep_kaiser_window_script2/log_sweep_kaiser_window_script2.py | Python | mit | 2,113 | [
"DIRAC"
] | 7935a24f2c677fc766413f2ac2be1dc3ed9882fd7266e7be0c5ac3a6f1595b3a |
##########################################################################
#
# Copyright (c) 2012, John Haddon. All rights reserved.
# Copyright (c) 2013, Image Engine Design Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that ... | appleseedhq/gaffer | python/Gaffer/PythonExpressionEngine.py | Python | bsd-3-clause | 13,020 | [
"VisIt"
] | f12114e30e52137b6ba685b535c53b63ceb3d877a81a51271c418d92bc3db687 |
from neuron import h
from math import sqrt, pi
import os
from Cell3D import *
####################################################################
# Setting up params
####################################################################
Vrest = -94.5896010066
h.v_init = -94.5896010066
h.celsius = 34.0 # same as e... | Neurosim-lab/netpyne | examples/M1detailed/cells/ITcell.py | Python | mit | 12,425 | [
"NEURON"
] | 17b6531f95c0343d34f633400ec39ef784015b8239d811286d4ca6a744bd4447 |
from vtk import *
database = vtkSQLDatabase.CreateFromURL("mysql://enron@vizdb.srn.sandia.gov:3306/enron")
database.Open("enron")
edge_query = database.GetQueryInstance()
edge_query.SetQuery("select sendID, recvID, weight from email_arcs")
vertex_query = database.GetQueryInstance()
vertex_query.SetQuery("select firs... | b3c/VTK-5.8 | Examples/Infovis/Python/mysql_database.py | Python | bsd-3-clause | 1,181 | [
"VTK"
] | 744bc9ef08930f81ab62f0d360cc19f9eef52fe8e6fc4244a929d59382b15e40 |
# Copyright (C) 2016 by Clearcode <http://clearcode.cc>
# and associates (see AUTHORS).
# This file is part of pytest-dbfixtures.
# pytest-dbfixtures 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, ei... | mmaslowskicc/pytest-dbfixtures | src/pytest_dbfixtures/factories/dynamodb.py | Python | lgpl-3.0 | 4,542 | [
"VisIt"
] | accb8e5c61ad87ea876e75166a9bc1fd0af7f28d9a9c0cecec70fd4f38b23bf0 |
"""
Statistics (:mod:`skbio.stats`)
===============================
.. currentmodule:: skbio.stats
This package contains various statistical methods, including ordination
techniques and distance matrix-based statistics.
Subpackages
-----------
.. autosummary::
:toctree: generated/
distance
ordination
s... | JWDebelius/scikit-bio | skbio/stats/__init__.py | Python | bsd-3-clause | 960 | [
"scikit-bio"
] | fbe83a4710c3b894531397dd29be97ba68ec6802e6c4027129b0765f8dd2f5a0 |
import os
from tornado.web import StaticFileHandler, HTTPError
from DIRAC import rootPath
class StaticHandler( StaticFileHandler ):
def initialize( self, pathList, default_filename = None ):
self.pathList = [ os.path.abspath( path ) + os.path.sep for path in pathList ]
self.default_filename = default_file... | atsareg/WebAppDIRAC | Core/StaticHandler.py | Python | gpl-3.0 | 813 | [
"DIRAC"
] | 1bbb9987cd26272c566570dbef592175436d6ad00275845743035f4a2050d4d4 |
# Copyright 2014 Google Inc. 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 law or agree... | itielshwartz/BackendApi | lib/oauth2client/tools.py | Python | apache-2.0 | 9,198 | [
"VisIt"
] | 8743cea0237a4fd31a7c781f9d3fea8bf7b6151d46f9ca46914e64815f8c7b4c |
"""
The energy test module verifies that the Model class produces the
correct abstract syntax tree for the energy.
"""
import pytest
from sympy import S
from pycalphad import Database, Model, ReferenceState
from pycalphad.core.utils import make_callable
from pycalphad.tests.datasets import ALCRNI_TDB, FEMN_TDB, FE_MN_... | tkphd/pycalphad | pycalphad/tests/test_energy.py | Python | mit | 28,633 | [
"pycalphad"
] | b0bf779c618be4141ed6f07f64a4976ac08d5f474768fd5d7bbabad9fde21d6d |
"""
[10/23/2012] Challenge #106 [Difficult] (Mongolian Grill)
https://www.reddit.com/r/dailyprogrammer/comments/11xyiz/10232012_challenge_106_difficult_mongolian_grill/
One of my favorite places to eat is HuHot, a Mongolian Grill style restaurant. At HuHot, you take a bowl and visit any
number of vegetable, meat, no... | DayGitH/Python-Challenges | DailyProgrammer/DP20121023C.py | Python | mit | 1,635 | [
"VisIt"
] | 7672e27b9898c470421a29f4064c9c7c7e1a664127a42cb4d85c28cce4de8b74 |
"""
Tests for Coulomb matrix calculation.
"""
import numpy as np
import unittest
from deepchem.feat import coulomb_matrices as cm
from deepchem.utils import conformers
class TestCoulombMatrix(unittest.TestCase):
"""
Tests for CoulombMatrix.
"""
def setUp(self):
"""
Set up tests.
"""
... | ktaneishi/deepchem | deepchem/feat/tests/test_coulomb_matrices.py | Python | mit | 3,678 | [
"RDKit"
] | 3f2cf0ac55a82a6172027816dc116e1733c9e8ad9d0a954f680c17f447a9cdda |
from datetime import datetime, timedelta
from netCDF4 import Dataset
from netCDF4 import num2date
import numpy as np
import time
import os
__author__ = 'Trond Kristiansen'
__email__ = 'trond.kristiansen@imr.no'
__created__ = datetime(2014, 1, 23)
__modified__ = datetime(2014, 1, 23)
__version__ = "0.1"
__status... | trondkr/OceanLight | IOwrite.py | Python | mit | 2,407 | [
"NetCDF"
] | 63b096de238d9b408fd394dfa81c664105297ffba04e06e8e934284b85cbc652 |
#!/usr/bin/env python
# File: plot_uvj_vs_icd.py
# Created on: Wed 07 Nov 2012 09:20:44 AM CST
# Last Change: Thu Feb 28 20:35:04 2013
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import pylab as pyl
from mpl_toolkits.axes_grid1 import AxesGrid
from mk_galaxy_struc import mk_galaxy_struc
from colsort import ... | boada/ICD | sandbox/legacy_plot_code/plot_uvj_p1ar.py | Python | mit | 3,454 | [
"Galaxy"
] | 67a5cddc17b9bce1f12eec0b2612ccb05029e45b36d37b1dfa8bda50a3db4ec0 |
#!/usr/bin/python
# This was written for educational purpose only. Use it at your own risk.
# Author will be not responsible for any damage!
# Intended for authorized Web Application Pen Testing!
# You need to download the MySQLdb API from http://sourceforge.net/projects/mysql-python
# save all users list at user... | knightmare2600/d4rkc0de | others/doorknocker.py | Python | gpl-2.0 | 8,537 | [
"VisIt"
] | 9c3a31cc23f68abf06a0b6e13ff23c6a6b114f6e8806dc0e032e1a66122ca9b0 |
# Packages locations
SIMBODYHOME="/home/lspirido/Installers/simbody/SimTK-3.0"
SIMBODYSRC="/home/lspirido/Installers/simbody/simbody-Simbody-3.0"
MOLMODELHOME="/home/lspirido/Installers/molmodel/molmodel-3.0.0"
PYTHONHOME="/share/apps/miniconda/2"
PYTHON2_6_INCLUDE="/usr/include/python2.6"
BOOSTHOME="/home/lspirido/In... | nashmit/GMolModel | paths.py | Python | gpl-3.0 | 480 | [
"Amber"
] | 60697328d2c7e54a218271503cd009fef048fd4ed733295867cb7d3d49eed9e3 |
'''
Created on 26.10.2012
@author: mhoefli
'''
from ConfigParser import ConfigParser
class SecureConfigParser(object, ConfigParser):
def __init__(self):
ConfigParser.__init__(self)
self.allowed = {}
self.errormsg = {}
# self.optionxform = str
def setdefault(self, section, opti... | martinhoefling/fretutils | lib/FRETUtils/Config.py | Python | bsd-3-clause | 9,093 | [
"Gaussian"
] | 55698dd001249b31177fdf4a62528162b4162ca767089151a099d54c0856d5fe |
from helpers import compute_volume
import pygmsh
def test():
with pygmsh.geo.Geometry() as geom:
geom.add_circle(
[0.0, 0.0, 0.0],
1.0,
mesh_size=0.1,
num_sections=4,
# If compound==False, the section borders have to be points of the
... | nschloe/pygmsh | tests/built_in/test_circle.py | Python | gpl-3.0 | 749 | [
"VTK"
] | da55d7806216e278753e7ecb26e735290bd63d12bbfdf473267f39a6f3f2259f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2009-2010 Brian G. Matherly
#
# 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; ... | arunkgupta/gramps | gramps/gen/ggettext.py | Python | gpl-2.0 | 3,003 | [
"Brian"
] | 6112c0e9692fccfb19f50ecc4d395a3937378a8d0d0e0b474f6b3546cc9c639c |
from constants import *
from operator import itemgetter
import web
import os
import codecs
import urllib
from models import *
# Form Handlers
LoginForm = web.form.Form(
web.form.Textbox('ra', web.form.notnull, Class="form-control"),
web.form.Password('senha', web.form.notnull, Class="form-control"),
web.fo... | faraj7/gda | forms.py | Python | gpl-3.0 | 4,544 | [
"MOE"
] | 7dd9bc00c06788491ff668cc28bdd785f5a78815ead9a50924eaaa7dc81b6db0 |
#!/usr/bin/env python
# coding=utf-8
import unittest
import gflags
import time
import sys
from ct.crypto import cert
from ct.crypto import error
from ct.crypto.asn1 import oid
from ct.crypto.asn1 import x509_extension as x509_ext
from ct.crypto.asn1 import x509_name
FLAGS = gflags.FLAGS
gflags.DEFINE_string("testdat... | wreese/megacfs | vendor/github.com/google/certificate-transparency/python/ct/crypto/cert_test.py | Python | apache-2.0 | 31,229 | [
"VisIt"
] | ccc12f2eccb9dccc9b627664c212f0c2503f437c1c42d22202020c124cc0a847 |
import sys
import nibabel as nib
import numpy as np
import json
from nilearn.image import resample_to_img, reorder_img, new_img_like
from scipy.ndimage import binary_erosion
def load_json(filename):
with open(filename, 'r') as opened_file:
return json.load(opened_file)
def dump_json(dataobj, filename):... | ellisdg/3DUnetCNN | unet3d/utils/utils.py | Python | mit | 13,527 | [
"VTK"
] | 6f5f4d6f71a1d65c14de4ad81ebb386b0966ed19421f53ecdf114f00ba920bda |
from scdl import download
from scdl import colors
from bs4 import BeautifulSoup
import urllib
import os
DOWNLOAD_PATH = os.path.expanduser('~/Music/Soundcloud/Crawler/') # choose where to download tracks
future_urls = [] # a queue for URLs to visit in the future
visited_urls = [] # a list of URLs already visited
... | joengelm/scdl | scdl/scrawl.py | Python | mit | 1,831 | [
"VisIt"
] | fccc3350cbdabfb65e48a139e3b76702bae578fc7eecf46e7d8d10e27462afbc |
import numpy as np
import cv2
import sys
import scipy
from scipy import io
import skimage
from skimage import transform
import json
import pprint
import os
import subprocess
import re
import math
import argparse
# extract people and content from the video
# expects command-line argument "--filename FILENAME"
pp = ppr... | uid/ed-vid-parse | vid_from_file.py | Python | mit | 12,078 | [
"NEURON"
] | bb8dc5365f33ecc6032a4399b58125395e707b4a5786dd606afe9fc6494df4a4 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as np
import arrayfire as af
af.set_backend('cpu')
af.set_device(0)
from dg_maxwell import lagrange
from dg_maxwell import utils
from dg_maxwell import isoparam
from dg_maxwell import wave_equation
# The domain of the function.
x_nodes = af.np_to_af_a... | amanabt/DG_Maxwell | dg_maxwell/params.py | Python | gpl-3.0 | 4,117 | [
"Gaussian"
] | 0ba4ee25244448e9aa43c28700cdce9ed016d8a75b8009d62d4b6f6e873fbe62 |
# Do all the relevant imports
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import cv2
# Read in the image and convert to grayscale
# Note: in the previous example we were reading a .jpg
# Here we read a .png and convert to 0,255 bytescale
image = mpimg.imread('..\images\exit-ram... | jabeerahmed/testrepo | term1/Lessons/LaneDetection/canny_edges.py | Python | gpl-2.0 | 762 | [
"Gaussian"
] | e97db8aa069adb3239b5672e12e4c1f6a6a6e1b34c758b130669f7c6b9fd25a2 |
from gpaw import GPAW
from gpaw.lrtddft import LrTDDFT
c = GPAW('Be_gs_8bands.gpw')
istart=0 # band index of the first occ. band to consider
jend=8 # band index of the last unocc. band to consider
lr = LrTDDFT(c, xc='LDA', istart=istart, jend=jend,
nspins=2) # force the calculation of triplet excitation... | robwarm/gpaw-symm | doc/documentation/tddft/Be_8bands_lrtddft.py | Python | gpl-3.0 | 349 | [
"GPAW"
] | 54da10011263b6fc14ddb34873263ad21182d0d699fa5cbca5f781fe2753f5c0 |
from __future__ import print_function
import os
from shutil import copyfile
from .utils import get_builds, get_ggd_channels, get_species
SPECIES_LIST = sorted(get_species())
GENOME_BUILDS = sorted(get_builds("*"))
CHANNEL_LIST = [x.encode("ascii") for x in get_ggd_channels()]
GENOMIC_COORDINATE_LIST = [
"0-based... | gogetdata/ggd-cli | ggd/make_meta_recipe.py | Python | mit | 14,308 | [
"Bioconda"
] | 1cd23296f4fa2c7816f329c6466dc8bbec97b562fd61ab4fb279faeb6afca77e |
from osgeo import gdal
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
wrf_out_file = "wrfout_v2_Lambert.nc"
ds_lon = gdal.Open('NETCDF:"'+wrf_out_file+'":XLONG')
ds_lat = gdal.Open('NETCDF:"'+wrf_out_file+'":XLAT')
ds_t2 = gdal.Open('NETCDF:"'+wrf_out_file+'":T2')
map = Basemap(llcrnrlon=-9... | krischer/BasemapTutorial | code_examples/wrf/read_wrf.py | Python | cc0-1.0 | 490 | [
"NetCDF"
] | 0032baba8e8ae24110d7bf9148b1f4dd2f8f70b558ad53ef357b280d4646bd41 |
import os, jinja2
from flask import Flask
from urllib import unquote
from datetime import datetime
#from flask.ext.login import LoginManager, current_user
#login_manager = LoginManager()
# obtain the base path of the application
BASE_PATH = os.path.dirname( # service base directory
os.path.dirname( ... | JiscPER/magnificent-octopus | octopus/core.py | Python | apache-2.0 | 4,270 | [
"Octopus"
] | 36c2b46d2b344c07f3805c2d1598a871de8db84fc85eec619dc0c2e53d0e3145 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/util/_misc.py | Python | bsd-3-clause | 12,577 | [
"scikit-bio"
] | 54b458f92083efe31df0bd5e9fec652cefcdca9ede658842acf6700e8ef4b45d |
#!/usr/bin/env python
"""
Helper functions for the turbogo program. Can be called outside of turbogo.py
with proper args provided.
"""
import logging
import re
import unicodedata
import os
import sys
import time
from subprocess import Popen, PIPE
"""
-------------------------------------------------------------------... | pbulsink/turbocontrol | turbocontrol/turbogo_helpers.py | Python | mit | 25,894 | [
"TURBOMOLE"
] | f42f039c7b6e801f11f57734765fb76cdca7d7d301376e84947faef152a9af6f |
from logging import getLogger
from boto.exception import EC2ResponseError
import boto.ec2
import boto.vpc
from cachetools import ttl_cache
from dalton.config.models import Rule
from dalton.service import SecurityGroupService
log = getLogger(__name__)
class Ec2SecurityGroupService(SecurityGroupService):
"""
... | signal/dalton | dalton/ec2.py | Python | apache-2.0 | 4,783 | [
"Dalton"
] | 0fa40003baeb06549200399c16fdae3e59f7f68f42f991e624ed8993657cc91a |
#
# imputil.py
#
# Written by Greg Stein. Public Domain.
# No Copyright, no Rights Reserved, and no Warranties.
#
# Utilities to help out with custom import mechanisms.
#
# Additional modifications were contribed by Marc-Andre Lemburg and
# Gordon McMillan.
#
__version__ = '0.3'
# note: avoid importing non-builtin mo... | toontownfunserver/Panda3D-1.9.0 | direct/pyinst/imputil.py | Python | bsd-3-clause | 16,401 | [
"BLAST"
] | d07d4011e46a50481becd4ef8a92ab5f5bb247220fb30dc1649e834e7c61e288 |
"""
Predicting potential dopants
"""
import warnings
import numpy as np
from pymatgen.analysis.structure_prediction.substitution_probability import (
SubstitutionPredictor,
)
from pymatgen.core.periodic_table import Element, Species
def get_dopants_from_substitution_probabilities(structure, num_dopants=5, thre... | materialsproject/pymatgen | pymatgen/analysis/structure_prediction/dopant_predictor.py | Python | mit | 7,419 | [
"pymatgen"
] | 78529941b0529dd7fa30abfd9ca0c1696a31e876bac776dad12945a85df8501a |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example to run heat-bath selected CI
'''
from pyscf import gto, scf, ao2mo, hci
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = '6-31g',
)
myhf = scf.RHF(mol).run()
cisolver = hci.SCI(mol)
nmo = myhf.mo_coeff.shape[1]
nelec... | gkc1000/pyscf | examples/hci/00-simple_hci.py | Python | apache-2.0 | 490 | [
"PySCF"
] | 0fbf2b40722ed6c4ade99254675b16c683ed568f026f6a68ffde4c20d6fb895c |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting model 'EphysPropSyn'
db.delete_table('neuroelectro_ephyspropsyn')
# Delet... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0013_auto__del_ephyspropsyn__del_neuronephyslink__del_ephysprop__del_datata.py | Python | gpl-2.0 | 10,695 | [
"NEURON"
] | ac4412f030fe11eec60670bcc910f332549426c0dfc675294f2465e0d8d5aa06 |
# force floating point division. Can still use integer with //
from __future__ import division
# This file is used for importing the common utilities classes.
import numpy as np
import matplotlib.pyplot as plt
import sys
from scipy import constants
def run():
"""
<Description>
Args:
param1: This ... | prheenan/Research | Perkins/Projects/Protein/myosin-nug2-4x-construct/2017-1-30-mass/main_mass_calc.py | Python | gpl-3.0 | 1,525 | [
"Avogadro"
] | 1d9727714ca9827dc6dfdc661a7420996ed1177e47f8f901ae3cee6280153cc1 |
'''
Created on Dec 22, 2010
@author: kbrisbin
'''
from authorization.oauth import OAuth
from sql.sqlbuilder import SQL
import ftclient
from fileimport.fileimporter import CSVImporter
if __name__ == "__main__":
import sys, getpass
consumer_key = sys.argv[1]
consumer_secret = getpass.getpass("Enter your secret:... | MapofLife/MOL | earthengine/gft-mod/src/samples/oauth_example.py | Python | bsd-3-clause | 1,580 | [
"VisIt"
] | 548cac7cce02f05226c656c04f6848e2cbdde37a1982fac7a9f67bd62accfd8f |
#
# Copyright 2016 The BigDL Authors.
#
# 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 law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/detector/anomaly/th_detector.py | Python | apache-2.0 | 9,094 | [
"Gaussian"
] | 64bb8ae537f1b7ee31a3ad6746f44bcab734240f9549ed56c5847b2edeacb746 |
'''
(c) GeneGenie Bioinformatics Ltd. 2018
Licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=wrong-import-order
from gg_learn.keras import k_folds_nn
from gg_learn.utils.biochem_ut... | synbiochem/synbiochem-learn | gg_learn/study/solubility.py | Python | mit | 955 | [
"RDKit",
"VisIt"
] | 8a56a2a6fd34ac24a24b8f83b891bf8850989f27f6571eb452496add671f511e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible 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
# ... | t0mk/ansible | lib/ansible/modules/network/lenovo/cnos_facts.py | Python | gpl-3.0 | 4,774 | [
"VisIt"
] | f44ee0d4e4b01f35bb9874ecd1250a1140f8ab405e6144bc0f82427c91bb2c03 |
# -*- coding: utf-8 -*-
"""
Statistical measures of spike trains (e.g., Fano factor) and functions to estimate firing rates.
:copyright: Copyright 2014-2015 by the Elephant team, see AUTHORS.txt.
:license: Modified BSD, see LICENSE.txt for details.
"""
from __future__ import division, print_function
import numpy as ... | sonjagruen/elephant | elephant/statistics.py | Python | bsd-3-clause | 30,740 | [
"Gaussian",
"NEURON"
] | d42f27ac29d1f16e2a302721d5450f97825e7126d972f9fe5159db264dd3d2cb |
#!/usr/bin/env ipython
from pylab import *
from numpy import *
from scipy.io.netcdf import netcdf_file
from datetime import datetime, time, timedelta
#------------ shared libraries:
"""
--- antes de modificar cosas, tener en cuenta los bugs en:
'../../shared_lib/COMENTARIOS.txt'
"""
import sys
sys.path.append('../../... | jimsrc/seatos | sheaths.icmes/src/extract.py | Python | mit | 5,572 | [
"NetCDF"
] | f108375897861134bd6d7ae7dd308d9b2b20c7536fd78569fd156a9cf68e5b2a |
"""
@name: PyHouse/src/Modules/_test/test_Security.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2018 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 31, 2015
@Summary:
Passed all tests - DBK - 2018-02-13
"""
__updated__ = '2018-02-13'
from twiste... | DBrianKimmel/PyHouse | Project/src/Modules/House/_test/test_Security.py | Python | mit | 798 | [
"Brian"
] | 32dc0844832fb1a3c4a1852c9871b9a65aa28479177420107d176dc99a18abf9 |
#!/usr/bin/env python
import itertools
import sys
import numpy as np
import HTSeq as hts
class MergePeaksAcrossDigestions:
def __init__(self, l_fp):#, min_peak_score=None, min_core_score=None, iv=None):
# Read peaks
l_peak_fp = []
for (i, fp) in enumerate(l_fp):
fh = hts.BED_Reader(fp)
l_peak = [gf for g... | jurgnjn/biokludge | scripts/peakheaps/peakheaps.py | Python | gpl-2.0 | 4,209 | [
"HTSeq"
] | 95c7c057b5116fabafda6c49045de3a7c6265c039b0f7657d0572324794f357c |
import vtk
from Volume import Volume
from Cut import Cut
from CutIndicator import CutIndicator
from Notification import Notifier
class ElementCollector:
def __init__(self, model):
self.notifier = Notifier()
self.model = model
self.lut = vtk.vtkLookupTable()
lut_num = model.n_level... | FedericoV/FractalMammaryLobule | modeler/view/elements/ElementCollector.py | Python | gpl-3.0 | 1,388 | [
"VTK"
] | 25408e061e8a1b134e340f5fc32ad704c0a27981467f204bbcb1b4da2d598422 |
# -*- coding: utf-8 -*-
"""
E2E tests for the LMS.
"""
import time
from .helpers import UniqueCourseTest
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.lms.courseware import CoursewarePage
from ..pages.lms.annotation_component import AnnotationComponentPage
from ..fixtures.course import CourseFixture, ... | c0710204/edx-platform | common/test/acceptance/tests/test_annotatable.py | Python | agpl-3.0 | 5,369 | [
"VisIt"
] | c50d928b2f2d76f05a468322c303220749527f4e5ba43d0a6bb72d976d4e88f8 |
"""
Preferences dialog.
@author: Chris Scott
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
import os
import logging
import datetime
import multiprocessing as mp
import functools
from PySide2 import QtGui, QtCore, QtWidgets
import numpy as n... | chrisdjscott/Atoman | atoman/gui/preferences.py | Python | mit | 35,864 | [
"VTK"
] | cae58680abe5e1f75eb4bfa645f8b28622422e0bc1a4078fe1357ee738cd858d |
"""
Extensions to SQLAlchemy for altering existing tables.
At the moment, this isn't so much based off of ANSI as much as
things that just happen to work with multiple databases.
"""
import sqlalchemy as sa
from sqlalchemy.schema import SchemaVisitor
from sqlalchemy.engine.default import DefaultDialect
from ... | odubno/microblog | venv/lib/python2.7/site-packages/migrate/changeset/ansisql.py | Python | bsd-3-clause | 11,422 | [
"VisIt"
] | 8c0797647357ecd53618fc21b5dcb36f3458fb99e3deb27ed11768dafe975961 |
#!/usr/bin/env python
import numpy
import numpy
from pyscf import gto
from pyscf import scf
from pyscf import mcscf
from pyscf import lo
from pyscf import mrpt
ehf = []
emc = []
ept = []
def run(b, dm, mo, ci=None):
mol = gto.M(
verbose = 5,
output = 'cr2-%2.1f.out' % b,
atom = 'Cr 0 0 0; ... | gkc1000/pyscf | examples/mrpt/02-cr2_nevpt2/cr2-scan.py | Python | apache-2.0 | 1,228 | [
"PySCF"
] | 8631999caf0987d17f4498615ba241e56e3bb8763455cd6e7872f858a1329da0 |
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