text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import numpy
from reikna.algorithms.pureparallel import PureParallel
from reikna.core.signature import Parameter, Annotation
import neuro.kernels as kernels
import logging
log = logging.getLogger("weightdecay")
def renormalize_kernel(ctx, array, norm, constraint):
kernel_cache, thread = ctx.kernel_cache, ctx.thre... | schreon/neuronaut | neuro/weightdecay.py | Python | mit | 2,871 | [
"NEURON"
] | 4f8855e065700ac8a0a47ad5970432d4cb38eb23f84079e4ffecea4374d229ca |
#
# @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 program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | doc/sphinxman/source/psi4doc/ext/psidomain.py | Python | gpl-2.0 | 1,221 | [
"Psi4"
] | 9936a9a0bbedb259b59cdf80156bd06ad3e3fa44b3aacbde22f581618848e030 |
import urlparse
def validanchor(current, href):
""" Returns true if the href on the current page is valid to visit.
current is the string URL of the current page and href is the string in the anchor.
We don't want to visit any other domains, mailto, emailto, javascript, and
fragments of the current ... | adamdoupe/enemy-of-the-state | validanchor.py | Python | gpl-2.0 | 722 | [
"VisIt"
] | 77d2abdda6a0ddcfd8fc5b9beae6cfc6576ffd1e3c4be04d59676fcd7a587d85 |
from __future__ import absolute_import
import unittest2 as unittest
import numpy as np
import warnings
from pymatgen.analysis.elasticity.stress import Stress
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.util.testing import PymatgenTest
class StressTest(PymatgenTest):
def setUp(self... | aykol/pymatgen | pymatgen/analysis/elasticity/tests/test_stress.py | Python | mit | 2,818 | [
"pymatgen"
] | 742a945457408ff6fcc77e309ec975d7da2a1e6e98b4310e520aecdff739209c |
from neuron import *;
import random;
import sys; # > For verbose
# TODO: Implement Momentum
class MLP:
# ! Protocol
# ! . . Neuron access is [column][row]
# ! . . Connection Wji (the weight of the output of a neuron i on a column before of j) is given by layer[column][j].W[i])
# > CONSTRUCTOR
##... | cabraile/RNA-Modules | mlp.py | Python | mit | 9,078 | [
"NEURON"
] | 7a72aa895302cab7ab9255ff326d48323529075dbf2ec7418d2688b50b0436f3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import warnings
from pymatgen import Composition
from pymatgen.analysis.reaction_calculator import Reaction, BalancedReaction, \
ReactionError, Compu... | gpetretto/pymatgen | pymatgen/analysis/tests/test_reaction_calculator.py | Python | mit | 15,713 | [
"pymatgen"
] | c4c2fbced103b0eb4f292c87bbf5dfbb4f60bbedcf47ee1e58b4a36b81707798 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import time
import unittest
import logging
import functools
from nose.tools import * # flake8: noqa (PEP8 asserts)
import mock
from modularodm import Q
from framework.auth.core import Auth
from website import... | acshi/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 37,201 | [
"Brian"
] | e98f8236317f7be159eb0ee04ebb16c6a41ddcdaf1523b0f9d5a40db6f3d4006 |
# xia2 information / input file reader
from __future__ import annotations
from collections import OrderedDict
class XInfo:
"""A class to represent all of the input to the xia2dpa system, with
enough information to allow structure solution, as parsed from a
.xinfo file, an example of which is in the sou... | xia2/xia2 | src/xia2/Handlers/XInfo.py | Python | bsd-3-clause | 17,890 | [
"CRYSTAL"
] | 60762e90e4288d0aa56ed4bf975b1789cf123ecee9e61ec4353d535d3a7a1001 |
# -*- coding: utf-8 -*-
import os
import rumps
class FireflyApp(rumps.App):
def __init__(self, coordinator):
self.coordinator = coordinator
rootdir = self.coordinator.get('rootdir')
confdata = self.coordinator.get('confdata')
icon = os.path.join(rootdir, confdata['icon_path... | itplanes/firefly-proxy | component/_ui_mac_app.py | Python | bsd-2-clause | 838 | [
"Firefly"
] | 43b5fcc3b162dc74672c4bf8f97aad603a6bcb187a71c8cf377aadafc4835f6d |
#! /usr/bin/env python
"""
This module contains a single class - Proxy - which implements proxying of
requests (and adding CORS headers). It is intended to run under a WSGI
webserver. See class documentation for additional details.
"""
from wsgiproxy.exactproxy import proxy_exact_request
from copy import deepcopy
... | spresse1/CORSProxy | CORSProxy/CORSProxy.py | Python | gpl-3.0 | 8,901 | [
"VisIt"
] | a1da579708b77b1ccb0fa896b24161ff1c04336e6b4108fa6257c75f33f3e087 |
from __future__ import division
from builtins import zip, range
import numpy as np
from numpy.random import random
na = np.newaxis
import scipy.stats as stats
import scipy.special as special
import scipy.linalg
from numpy.core.umath_tests import inner1d
from . import general
# TODO write cholesky versions
### data a... | mattjj/pyhsmm | pyhsmm/util/stats.py | Python | mit | 9,847 | [
"Gaussian"
] | f8dd92080740b7c491dd877fd4c43674b61761cd8df0f406b8bfdf71e791b94f |
# http://www.scipy.org/Cookbook/RANSAC
import numpy
import scipy # use numpy if scipy unavailable
import scipy.linalg # use numpy if scipy unavailable
## Copyright (c) 2004-2007, Andrew D. Straw. All rights reserved.
## Redistribution and use in source and binary forms, with or without
## modification, are permitted... | ghisvail/irtk-legacy | wrapping/cython/scripts/lib/ransac.py | Python | bsd-3-clause | 9,025 | [
"Gaussian"
] | 92f2a31ae4414a645f0e7f08b91d1b3662df3d0b7a79cb6736f513ed90c95706 |
from setuptools import setup
setup(name='spectrassembler',
version='0.0.1',
description='Tool (experimental) to compute layout from overlaps with spectral algorithm',
url='https://github.com/antrec/spectrassembler',
author='Antoine Recanati',
author_email = '',
license='MIT',
... | ThomasWollmann/bioconda-recipes | recipes/spectrassembler/setup.py | Python | mit | 545 | [
"Biopython"
] | b74783a75999cafc007b2dfd8c9fd057d9fc7e0b387518b1afa0e1dc8aec7b1e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
import numpy as np
import scipy
from scipy import stats
from pymatgen.analysis.defects.core import DefectCorrection
from pymatgen.analysis.defects.utils import ang_to_bohr, hart_to_ev, eV_to_k, \... | montoyjh/pymatgen | pymatgen/analysis/defects/corrections.py | Python | mit | 20,624 | [
"pymatgen"
] | 37415332a4628b53ad372fae0439bedef8145ecc6806b4e3c76fde6e5ca7d0b5 |
import lb_loader
import simtk.openmm.app as app
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 3000
temperature = 300. * u.kelvin
hydrogenMass = 3.0 * u.amu
#system, posit... | kyleabeauchamp/HMCNotes | code/old/test_xhmc_respa.py | Python | gpl-2.0 | 2,263 | [
"OpenMM"
] | 6c6fea9f8a8290752e1de8a2ed73ebca2a13bfb508e193cedbf878209b32e29c |
import logging
from pydap_extras.handlers.pcic import RawPcicSqlHandler, ClimoPcicSqlHandler
from pdp_util.pcds_index import PcdsNetworkIndex, PcdsStationIndex, PcdsIsClimoIndex
from paste.httpexceptions import HTTPNotFound, HTTPSeeOther
logger = logging.getLogger(__name__)
class PcdsDispatcher(object):
"""This... | pacificclimate/pdp_util | pdp_util/pcds_dispatch.py | Python | gpl-3.0 | 5,372 | [
"MOE"
] | 30b79b7da1ada245aa6657fede072fb29c6d5da781d7d2ae2bf47179b285666c |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
from __future__ import print_function
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import... | goddoe/CADL | session-5/libs/utils.py | Python | apache-2.0 | 21,427 | [
"Gaussian"
] | fd53bfd66a0e5fe47d44461f98907c11f4a55a43d9e112cd097acc4d0309d05b |
import os
import sys
import vtk
import collada
def writePolyData(polyDataList, outFile):
mb = vtk.vtkMultiBlockDataSet()
mb.SetNumberOfBlocks(len(polyDataList))
for i, polyData in enumerate(polyDataList):
print i, type(polyData)
mb.SetBlock(i, polyData)
writer = vtk. vtkXMLMultiBloc... | openhumanoids/oh-distro | software/models/atlas_v3/meshes/convertCollada.py | Python | bsd-3-clause | 5,733 | [
"VTK"
] | 7f9916ac71b5dfabe2033a26cb638001179390434c72a47051d03a50e5126c6a |
# -*- coding: utf-8 -*-
{
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for the area.": '一个位置指定对此区域的地理区域。 这可以是一个位置的位置层次结构,或者一组位置",或位置的一个界限的区域。',
"Acronym of the organization's name, eg. IFRC... | devinbalkind/eden | languages/zh-cn.py | Python | mit | 221,981 | [
"VisIt"
] | d9ca07f9cc4cfae43f361f9b6cdf3edee70fdd2d8748faca45c529ebbe705737 |
from __future__ import print_function
import sys
import requests
from datetime import date
from bokeh.widgetobjects import HBox, VBox, TableColumn, HandsonTable, ObjectExplorer
from bokeh.objects import Plot, ColumnDataSource, DataRange1d, Glyph, LinearAxis, DatetimeAxis, Grid, HoverTool
from bokeh.glyphs import Line... | sahat/bokeh | examples/glyphs/widgets_server.py | Python | bsd-3-clause | 2,259 | [
"VisIt"
] | b48996f5f8639c96242b0236e4a5ea740fc669ce2d2f7f054fa8448175301fc7 |
from __future__ import with_statement
import os
import re
import platform
import time
import fnmatch
import sys
import tempfile
from os import environ
from sos.utilities import ImporterHelper, \
import_module, \
get_hash_name, \
shell_out
from so... | portante/sosreport | sos/policies/__init__.py | Python | gpl-2.0 | 12,849 | [
"VisIt"
] | 60f6132eebb6b73e0c6a47c5a4fc19a71636bee27fe594ad61b6958de42c42c0 |
from __future__ import (absolute_import, division, print_function)
import numpy as np
import stresstesting
from mantid.simpleapi import Abins, mtd, DeleteWorkspace
from AbinsModules import AbinsConstants, AbinsTestHelpers
def skip_tests():
return not hasattr(np, "einsum")
class HelperTestingClass(object):
d... | wdzhou/mantid | Testing/SystemTests/tests/analysis/AbinsTest.py | Python | gpl-3.0 | 13,792 | [
"CASTEP",
"CRYSTAL"
] | 3122bc59383510b28c3cc0a2c24c80022f429740bb60e87de7aa4e0984309627 |
# pylint: disable=too-many-ancestors
""" View Set for Gym Item Serializer """
from rest_framework import viewsets
from app.models.gym_item import GymItem
from app.serializers.gym_item import GymItemSerializer
from app.views.view_sets.common import create_gym_visit
class GymItemViewSet(viewsets.ModelViewSet):
"""
... | Gimpneek/exclusive-raid-gym-tracker | app/views/view_sets/gym_item_view_set.py | Python | gpl-3.0 | 937 | [
"VisIt"
] | c2d68301d8b3f4f5b3f3042450af90aec866f98fc1bb22a8dd4e2e181eb62061 |
# -*- coding: utf-8 -*-
"""Resonant Raman intensities"""
from __future__ import print_function
import pickle
import os
import sys
import numpy as np
import ase.units as units
from ase.parallel import rank, parprint, paropen
from ase.vibrations import Vibrations
from ase.utils.timing import Timer
# XXX remove gpaw ... | suttond/MODOI | ase/vibrations/raman.py | Python | lgpl-3.0 | 9,894 | [
"ASE",
"GPAW",
"Gaussian"
] | e1fd1e5a6ddb03259cfc2800663e2f7ee4aefe47177cf2f3fc80d457b439eb3d |
from deepmonster.machinery import Architecture
from deepmonster.nnet.simple import FullyConnectedLayer
from deepmonster.nnet.activations import LeakyRectifier, Identity
from deepmonster.nnet.initializations import Initialization, Gaussian
class WrongArch(Architecture):
pass
class DummyArch(Architecture):
def ... | olimastro/DeepMonster | deepmonster/testing/dummy-experiment/architecture.py | Python | mit | 865 | [
"Gaussian"
] | 3568c88676c5b7af7bd75d30dc883b6cbed73696b23e3c082a078fb9cbc52e9f |
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Candy, adam.candy@imperia... | adamcandy/QGIS-Meshing | plugins/mesh_surface/scripts/MeshOperations.py | Python | lgpl-2.1 | 8,416 | [
"NetCDF"
] | c35c5679928326fc9b52ca5917b988651edb6f7dcd4e201cc1bc8a13ffd6df47 |
#!/usr/bin/env python
from Bio import SeqIO, Seq
from .make_paths import get_cns_file_path
from .make_paths import get_fastq_pair_name
from .make_paths import get_phylip_file_path
from .make_paths import get_codeml_phylip_file_path
from .make_paths import get_nexus_file_path
def get_cns_files_for_fasta(fasta, fw_fq... | TheCulliganMan/cgap | cgap/convert_to_phylip.py | Python | gpl-3.0 | 3,066 | [
"Biopython"
] | 9265d85b9050f33e8017d7b367e7dd676c95cb6fecc08b5e391460fa09fdea0a |
"""
Chooses a set of components to make a running program.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import locale
from logging import debug, warn, info
from zeroinstall.injector.reader import MissingLocalFeed
from zeroinstall.... | timdiels/zeroinstall | zeroinstall/injector/solver.py | Python | lgpl-2.1 | 24,179 | [
"VisIt"
] | 6439e1231a531c248051a026fe709835cd06f42cd3bbe6e3d8fe5f5264711061 |
from __future__ import print_function
import sys
import os
from pyimpute import load_training_rasters, load_targets, impute
from pyimpute import stratified_sample_raster
from sklearn.ensemble import ExtraTreesClassifier
from sklearn import cross_validation
from collections import OrderedDict
import logging
logger = lo... | perrygeo/pyimpute | examples/example_raster_sampling.py | Python | bsd-3-clause | 2,790 | [
"ADF"
] | 4a2239c5e0bf89e7514802a798ae7404e2ed804b2b75d775b302e4a0a0e8160d |
# -*- coding: utf-8 -*-
############################ Copyrights and license ############################
# #
# Copyright 2012 Christopher Gilbert <christopher.john.gilbert@gmail.com> #
# Copyright 2012 Steve English <steve.english@naveta... | mgorny/PyGithub | github/Repository.py | Python | lgpl-3.0 | 139,566 | [
"Brian"
] | 81dec626733c518385963cb7b956beccb6e7006b2d1ea74446ae25c166847f7d |
'''
Uses intrinsic (dust removed) AB fluxes/mags to select ELGs,LRGs,QSOs,STARs
Makes color-color plots that reproduce the FDR
Single band, mag distributions, plotted using "as observed" AB fluxes/mags,
since these are what one adds into a CP image
'''
if __name__ == '__main__':
import matplotlib
matplotli... | legacysurvey/pipeline | py/obiwan/decals_sim_priors.py | Python | gpl-2.0 | 94,661 | [
"Galaxy",
"Gaussian"
] | 7d431d23e3d94b3093700b0ed8045b05f1dfd93c66444cd09ab6942f59f9961a |
import cgen as c
from sympy import Mod
import pytest
from devito import Grid, Eq, Function, Operator
from devito.ir.equations import DummyEq
from devito.ir.iet import (Block, Expression, Callable, FindSections,
FindSymbols, IsPerfectIteration, Transformer,
Conditio... | opesci/devito | tests/test_visitors.py | Python | mit | 10,114 | [
"VisIt"
] | 8ddd4608b863be8c4060254a32d0128758be99d4ef0e42bba17a03c9076b0e4d |
#* 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/lgpl-2.1.html
from .moose... | nuclear-wizard/moose | python/mooseutils/__init__.py | Python | lgpl-2.1 | 1,748 | [
"MOOSE"
] | 4c405676b7031a1c6a8508deaefa72b769d548beb8b04e96f5125635027ecc45 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/delegates/languagedelegate.py | Python | gpl-2.0 | 1,251 | [
"VisIt"
] | 6112b8cff2bd72c659bbb38104338fc674e4304149850fd6112445161f3f7ff7 |
#!/usr/bin/env python
from vtk import *
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
reader = vtkXGMLReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/Infovis/fsm.gml")
reader.Update()
strategy = vtkSpanTreeLayoutStrategy()
strategy.DepthFirstSpanningTreeOn()
view = vtkGraphLayoutView... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Infovis/Python/graph3d.py | Python | gpl-3.0 | 2,311 | [
"VTK"
] | 374c24ed46e7fc4830f2fce9c07266b5b6a000c67696161dd38f03bedf6ba61f |
#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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
... | Multiscale-Genomics/mg-process-fastq | process_align_bowtie.py | Python | apache-2.0 | 6,242 | [
"BWA"
] | 7a1b7c4b1bec9a9713e30d02871f439b7e6ca2a7745a4d60bf3fe71750c4401a |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/models.py | Python | gpl-3.0 | 933 | [
"Brian"
] | d83991c367ff26e23d7bf55be6f9e94527e3f8b9870454716fc3b40b96a0609c |
#!/usr/bin/env python
import os
from optparse import OptionParser, OptionGroup
from bs_index.wg_build import *
from bs_index.rrbs_build import *
from bs_utils.utils import *
if __name__ == '__main__':
parser = OptionParser()
parser.add_option("-f", "--file", dest="filename", help="Input your reference geno... | BioInfoTools/BSVF | bin/BSseeker2/bs_seeker2-build.py | Python | lgpl-3.0 | 4,853 | [
"Bowtie"
] | 764b8dd74cb7611fe4eeb98aeba47a2510487cf25ef693f46bf679659e06cf49 |
# Copyright 2014-2018 The PySCF Developers. 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 appl... | gkc1000/pyscf | pyscf/df/test/test_df.py | Python | apache-2.0 | 4,131 | [
"PySCF"
] | 69fcb753f0328437d964452ead66b7fb851ea8118af5d8c2ba4e95b919388e58 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Image pipeline
reader = vtk.vtkImageReader()
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetFilePrefix("" + str(V... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestRange3D.py | Python | gpl-3.0 | 702 | [
"VTK"
] | 3c5ef6ea1db9b767f17095107189cce0421d8b9a9642d91fa3dbacaae71f6b7b |
import FFPopSim as h
import numpy as np
from matplotlib import pyplot as plt
import random as rd
L=100
pop=h.haploid_highd(L)
pop.outcrossing_rate=0.1
pop.crossover_rate=1.0/pop.L
pop.mutation_rate=5.0/pop.L
pop.carrying_capacity=30
#track the loci 10, 50 and 90
pop.track_locus_genealogy([10,50,90])
#initialize the... | wrshoemaker/ffpopsim | examples/neutral_coalescent.py | Python | gpl-3.0 | 1,560 | [
"Biopython"
] | 34291ef836219131c7e0078d976182e45f668388247360d9a721029e9eec66ba |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import division, print_function, unicode_literals
from encoder import character_count
import os
import h5py
import brainstorm as bs
from brainstorm.data_iterators import OneHot, Minibatches
#from brainstorm.handlers import PyCudaHandler
bs.global_rnd.set_s... | pinae/WikipediaLoader | train.py | Python | gpl-3.0 | 2,486 | [
"Gaussian"
] | 3b8c1479aafaa3f451aad89159aad4d234dc454ec44a566765e095ac9765078f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpa... | acercado/jd-ph-cms | config/urls.py | Python | bsd-3-clause | 1,518 | [
"VisIt"
] | 3cc834268d32574654e4dcd4c3b5b50b62e4b59fc50c7e59ada9c51344c4d1fb |
# Author: Brian Westerman
# Date: 4/28/2016
# CS251 Final Project
import numpy as np
import pandas as pd
import sklearn.linear_model as sklearnLinearModel
import sklearn.svm as sklearnSVM
import matplotlib.pyplot as plt
# Read in data
fundedCompanies = pd.read_excel("/Users/Brian/Downloads/cb_data_xlsx_sample.xlsx", ... | bhwester/computer-science-projects | data_analysis_and_visualization_system/finalproject.py | Python | mit | 2,965 | [
"Brian"
] | 997cd22581d04f09d7ecdcbe98c8373853d6e41cfd54caf5ada33a901b15ede4 |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright(c) 2010, Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
#
"""Provides a rebuild file of USE flags or keywords used and by
what packages according to the Installed package database"""
from __f... | djanderson/equery | pym/gentoolkit/analyse/rebuild.py | Python | gpl-2.0 | 7,056 | [
"Brian"
] | 3674fd96efd8817db74fedad2639a8d97f72581b10b5a0a691a973a468fcd19d |
# !/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free softwar... | jimsize/PySolFC | pysollib/game.py | Python | gpl-3.0 | 122,465 | [
"CASINO"
] | f19bb57cb3dd1d744c3bc10d8bb6c33aebf4a3b9bf9e6625ec495512d3ab8088 |
## Absolute location where all raw files are
RAWDATA_DIR = '/home/cmb-06/as/skchoudh/dna/Oct_10_2016_HuR_Human_Mouse_Liver/Ribo-Seq-Mouse/Penalva_L_03222017'
## Output directory
OUT_DIR = '/staging/as/skchoudh/Oct_10_2016_HuR_Human_Mouse_Liver/Ribo-Seq_mouse'
## Absolute location to 're-ribo/scripts' directory
SR... | saketkc/ribo-seq-snakemake | configs/Oct_10_2016_HuR_Mouse.py | Python | bsd-3-clause | 2,336 | [
"HTSeq",
"pysam"
] | 171da89dcbbddd825fd6d54319072f0753781394e8e5a5e7747d6a761c86bf63 |
import os
import numpy as np
from ase.units import Bohr, Hartree
elk_parameters = {
'swidth': Hartree,
}
class ELK:
def __init__(self, dir='.', xc=None, kpts=None, tasks=[0], **kwargs):
for key, value in kwargs.items():
if key in elk_parameters:
kwargs[key] /= elk_par... | conwayje/ase-python | ase/calculators/elk.py | Python | gpl-2.0 | 15,308 | [
"ASE",
"Elk"
] | 43785bfcde3a7deba26295a393fd262bd569facd9ed193910014ae8e1a59f465 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | iemejia/incubator-beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner.py | Python | apache-2.0 | 70,672 | [
"VisIt"
] | 81d26316bfcc2a4b9773fea02b3a48f20a15ca15fe216b06b95c34e80142b6e0 |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC.Core.DISET.private.InnerRPCClient import InnerRPCClient
class _MagicMethod:
def __init__( self, doRPCFunc, remoteFuncName ):
self.__doRPCFunc = doRPCFunc
self.__remoteFuncName = remoteFuncName
def __getattr__( self, remoteFuncName ):
return _MagicMethod( sel... | Sbalbp/DIRAC | Core/DISET/RPCClient.py | Python | gpl-3.0 | 1,462 | [
"DIRAC"
] | eb62f26d94574f678c472657782be208bc9f2289b3f7a0b9a7e8e04c6df1eadc |
# Copyright 2015 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... | wangyum/tensorflow | tensorflow/tools/common/public_api.py | Python | apache-2.0 | 3,938 | [
"VisIt"
] | f111b589225375eaf1e7e5548697a34ded25ee36167f585198c0e8fd054758bc |
""" Test class for FileCatalogComponents
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access
# imports
from mock import MagicMock
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.DirectoryManager.DirectoryTreeBase... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/test/Test_DataManagement_FileCatalogComponents.py | Python | gpl-3.0 | 3,310 | [
"DIRAC"
] | 9d6249875a49fe543c81c62dcee8fa667bbcdc82e3ce3f2536a274a63816f159 |
r"""
Thermo-elasticity with a computed temperature demonstrating equation sequence
solver.
Uses `dw_biot` term with an isotropic coefficient for thermo-elastic coupling.
The equation sequence solver (``'ess'`` in ``solvers``) automatically solves
first the temperature distribution and then the elasticity problem with... | RexFuzzle/sfepy | examples/multi_physics/thermo_elasticity_ess.py | Python | bsd-3-clause | 2,836 | [
"VTK"
] | 3d3dae27df153d3fe2c3f817a9c6641b2b23961636cf1272444b9acede8ceb9d |
# 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... | capoe/espressopp.soap | src/analysis/__init__.py | Python | gpl-3.0 | 2,894 | [
"ESPResSo"
] | 043c173868ad12ef2d008a8ec364b9ea86de68090a577e8f00510212894c9cff |
'''Create and analyse gravity forward models from geogrids using Noddy
Created on Feb 8, 2015
@author: flow
'''
import os, sys
import pickle
import numpy as np
import matplotlib.pyplot as plt
sys.path.append("/Users/flow/git/pygeomod/pygeomod")
sys.path.append("/Users/flow/git/pynoddy/pynoddy")
import geogrid
impo... | Leguark/pygeomod | pygeomod/legacy/grav_from_geogrids.py | Python | mit | 13,124 | [
"VTK"
] | b72e53bc55c5659a13e3a84b9c53efb24023cbda1b899fb77d3c8505346f7162 |
#!/usr/bin/env python
'''
To run this script:
PYTHONPATH=../../ python example.py
'''
from egfrd import *
from vtklogger import VTKLogger
'''
The reaction network:
A <-> B
A + B <-> C
C -> 0
'''
def run( ):
''' Dimensions.
'''
L = 1e-6 # Size of simulation box.
D = 1e-12 ... | gfrd/gfrd | samples/example/example.py | Python | gpl-2.0 | 8,996 | [
"ParaView",
"VTK"
] | 8ded7a77143fb20c3c33ebca76204e1f4544467f626aa557c8d350023c6d7d92 |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License
# Version 1.1 (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.mozil... | anisku11/sublimeku | Packages/CodeComplice/libs/textinfo.py | Python | mit | 88,937 | [
"VisIt"
] | 9c6db60159def2a353fb09d76ef5139aaeb24ad62b423d75f6dcc2b6c21aff1d |
#!/usr/bin/python
"""A statistics object for a label/region image."""
# build-in modules
import math
# third-party modules
import scipy
# path changes
# own modules
from medpy.core import Logger
# information
__author__ = "Oskar Maier"
__version__ = "e0.3, 2011-12-21"
__email__ = "oskar.maier@googlemail.com"
__st... | kleinfeld/medpy | medpy/filter/LabelImageStatistics.py | Python | gpl-3.0 | 12,617 | [
"Gaussian"
] | a2ed66306770d9254ffd760974dad195e68271ade3e8cee708490284a1991d18 |
"""Perform GATK based filtering: soft filters, CNNs and VQSR.
"""
import os
import gzip
from distutils.version import LooseVersion
from bcbio import broad, utils
from bcbio.distributed.transaction import file_transaction
from bcbio.log import logger
from bcbio.pipeline import config_utils
from bcbio.pipeline import da... | vladsaveliev/bcbio-nextgen | bcbio/variation/gatkfilter.py | Python | mit | 14,698 | [
"BWA"
] | 1e0d447d3905600c75c90355f7843c8e6ff7815d3a71b75d362b7c200207e4d9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2019 Satpy developers
#
# satpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ... | pytroll/satpy | satpy/tests/reader_tests/test_fci_l2_nc.py | Python | gpl-3.0 | 24,768 | [
"NetCDF"
] | f87e8f8c32b1df773a856d615d96d8d2ccc84686d4d540770a9eea1f618fca3a |
# -*- coding: utf-8 -*-
""" Database library to store update progress and results.
This module provides the database library for Software Management.
(c) 2015, 2016 - Jaguar Land Rover.
Mozilla Public License 2.0
"""
from storm.locals import *
from datetime import datetime
import settings
import logging
import trace... | rstreif/genivi_software_management | common/database.py | Python | mpl-2.0 | 18,453 | [
"Jaguar"
] | 8533d31e3462a474b16bbf5813e994abaa4e702a83400257c46eeeee43ee9879 |
from django.conf import settings
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.PDB import *
from Bio.PDB.PDBIO import Select
from common.definitions import *
from protein.models import Protein, ProteinSegment
from residue.models import Residue
from structure.functions import BlastSearch... | protwis/protwis | structure/assign_generic_numbers_gpcr.py | Python | apache-2.0 | 14,006 | [
"BLAST"
] | 1f60ed156584c148f3d497718c4a4d81e5d83aa948e377d10ebd610ade3e2c5b |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import ast
import linecache
import logging
import o... | suutari/shoop | _misc/doccov.py | Python | agpl-3.0 | 13,327 | [
"VisIt"
] | 0127236c1c44aab7803716ac1856611821ee8fad6407051c004a5ba99fa3194f |
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
import logging
import secrets
import smtplib
import peewee
import db
def send_email():
msg = MIMEMultipart()
msg['to'] = secrets.admin_address # pylint: disable=no-member
msg['from'] = secrets.from_address # pylint: dis... | NBISweden/swefreq | scripts/checkRequests.py | Python | gpl-3.0 | 1,110 | [
"VisIt"
] | 0c4f33d6d02a4ba4f422d79c14fbf291ddea027affff952f064784dcec53ea13 |
## Aditya Gilra, NCBS, Bangalore, 2012
"""
Inside the .../Demos/GranuleCell/ directory supplied with MOOSE, run
python testNeuroML_Gran98.py
(other channels and morph xml files are already present in this same directory).
The soma name below is hard coded for gran98, else any other file can be used by modifying this s... | dilawar/moose-full | moose-examples/neuroml/allChannelsCell/allChannelsCell.py | Python | gpl-2.0 | 2,106 | [
"MOOSE"
] | e5966aebee737d4be7fa2c05cacae2353d478d5f6cbf9d8eb99ab5f82641d3c6 |
"""
Test handling of alerts.
"""
from bok_choy.web_app_test import WebAppTest
from .pages import AlertPage
class AlertTest(WebAppTest):
"""
Test handling of alerts.
"""
def setUp(self):
super(AlertTest, self).setUp()
self.alert = AlertPage(self.browser)
self.alert.visit()
... | drptbl/bok-choy | tests/test_alert.py | Python | apache-2.0 | 665 | [
"VisIt"
] | f193935c3927f51f598c5af44bcf79010edbd5e1c2afb9bb21cddaeb9dba673a |
""" DIRAC FileCatalog plugin class to manage file metadata
"""
import six
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.Time import queryTime
from DIRAC.Core.Utilities.List import intListToString
from DIRAC.DataManagementSystem.Client.MetaQuery import (
FILE_STANDARD_METAKEYS,
FILES_TABLE_METAKEYS,
... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/FileMetadata/FileMetadata.py | Python | gpl-3.0 | 27,387 | [
"DIRAC"
] | 028ef411ec4f5072ceb326f025bae1d6987d397a7a1f4ec892e8791e337249e4 |
# proxy module
from __future__ import absolute_import
from mayavi.action.filters import *
| enthought/etsproxy | enthought/mayavi/action/filters.py | Python | bsd-3-clause | 90 | [
"Mayavi"
] | c061e7ca79a66a8640005e8950621ef4cc99294d3b0f35f0b76f9c06bc36e6fc |
# machine_mode.py (contains classes for various playfield devices)
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from mpf.system.tasks import ... | jabdoa2/mpf | mpf/system/machine_mode.py | Python | mit | 3,834 | [
"Brian"
] | 4db6924cb601bc0a1fe8acae7dc55b9bc604563d0f249ac8240dadf2c60b5a87 |
#!/usr/bin/env python3
from netcdfTools import *
from utilities import selectFromList, removeEntriesFromList
from plotTools import addToPlot, userLabels
import sys
import argparse
import numpy as np
import matplotlib.pyplot as plt
'''
Description:
Author: Mikko Auvinen
mikko.auvinen@fmi.fi
Finnish Me... | mjsauvinen/P4UL | pyNetCDF/plotNetCdf1D.py | Python | mit | 5,570 | [
"NetCDF"
] | 01ff8df64fbe30aab95a19e7813495586353c1790f5326952d89e25fb4975553 |
from pycparser import parse_file
from minic.c_ast_to_minic import *
from minic.minic_ast import *
from minic.mutils import *
from check_in1 import *
from check_in2 import *
import sys
import copy
class ReadVariable(NodeVisitor):
def __init__(self):
#record the loop in function
#self.loop = {}
... | martylee/Python | CSC410-Project-1-master/check_ins/check_in3.py | Python | gpl-2.0 | 5,820 | [
"VisIt"
] | 3fc013f27a6cd3dd58e740c8a2bcfaed688916bbc812395e6d31997a99fc9e04 |
# (c) 2014, Brian Coca <bcoca@ansible.com>
#
# 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
# (at your option) any later version.... | camradal/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 4,040 | [
"Brian"
] | 648b016904d338a37bfcb907663ce1ac0f7ec6301603ae24a0f6d2c749e110f1 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | smu/geometry/utilities.py | Python | apache-2.0 | 9,740 | [
"RDKit",
"VisIt"
] | 12c27e2f862820f39f62868b458632f838d0d23c0a567abacf28e681adf0c869 |
import dataclasses
from random import Random
from typing import Tuple, List
import pytest
from randovania.game_description import default_database
from randovania.game_description.game_description import GameDescription
from randovania.game_description.requirements import Requirement, ResourceRequirement
from randova... | henriquegemignani/randovania | test/generator/test_generator_reach.py | Python | gpl-3.0 | 12,643 | [
"Amber"
] | 98d8df51a3467a024a73dd95e1d115b07f3c39474c7b8698240ab40b3d4f82ad |
#!/usr/bin/python
# Write the initial topology file for position-restrained simulations in swarm free energy calculations
# Bjorn Wesen, July 2014
# Position restraints in Gromacs work by supplying the restrained atoms coordinates to grompp
# by the extra -r option from a .gro file, and also supplying the force consta... | soellman/copernicus | cpc/lib/swarms/position_restraints.py | Python | gpl-2.0 | 5,547 | [
"Gromacs"
] | e58378f103ef77eebe2fe5fec3999d559101c3cc1efb54fd6b77add0c3c091b7 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/line_sample/line_sample_elem.py | Python | lgpl-2.1 | 1,714 | [
"MOOSE"
] | f8dc1ff6c3ab02fe1501348ad74a3a8d8aa1317d84c6ea854161e3462c744aab |
#!/usr/bin/env python
from __future__ import print_function
import vtk
tse = vtk.vtkTimeSourceExample()
ex = tse.GetExecutive()
tse.UpdateInformation()
# inspect available time range and time steps
print(ex.GetOutputInformation())
# make it grow because bounds are easy to inspect
# tse.SetGrowing(1)
ex.SetUpdateTim... | lorensen/VTKExamples | src/Python/Untested/HasBugs/Visualization/UnstructuredTransientVolumeRendering.py | Python | apache-2.0 | 3,843 | [
"VTK"
] | 34ba6a1590588ece5397d0085d61c062858ff54069a2974663ee5bf41e5fba99 |
# coding=utf-8
# Copyright 2016 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 app... | aisk/grumpy | compiler/expr_visitor.py | Python | apache-2.0 | 20,073 | [
"VisIt"
] | d4c7bca387e0c18976997cecd0fdb3a86ad63e0b417ae8c4909741af874bba45 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# 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, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/analyze_gyration_tensor.py | Python | gpl-3.0 | 3,811 | [
"ESPResSo"
] | ad4be37ddd0695d758b4565d9860eaca83b699b975b252ab078ce3751c817f97 |
#!/usr/bin/env python
"""
Created on April 20 2014
@author: Alan L. Hutchison, alanlhutchison@uchicago.edu, Aaron R. Dinner Group, University of Chicago
This script is one in a series of scripts for running empirical JTK_CYCLE analysis as described in
Hutchison, Maienschein-Cline, and Chiang et al. Improved statisti... | alanlhutchison/empirical-JTK_CYCLE-with-asymmetry | previous_files/jtk7.py | Python | mit | 19,118 | [
"Gaussian"
] | 35a8faeae9563129a14992c3c3f33c604a7d91ea39915f18d98a7d37d004295b |
# -*- coding: utf-8 -*-
# @Author: yancz1989
# @Date: 2017-02-19 08:22:23
# @Last Modified by: yancz1989
# @Last Modified time: 2017-02-19 08:22:51
# 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 ... | yancz1989/cancer | tf_upgrade.py | Python | mit | 25,527 | [
"VisIt"
] | fcdd4e42c719fc172fb7c759d087b468bfd6e377aa4d3ece0542f72c3df657c7 |
# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8
# Copyright (c) 2003, 2008, 2010, 2011, 2012 Janne Blomqvist
# This source code file is subject to the terms of the MIT (Expat)
# License. See the file LICENSE for details.
"""This module defines a utility functions for dealing with vasp
supercells. Instead of th... | oren88/vasputil | vasputil/supercell.py | Python | mit | 7,372 | [
"ASE",
"VASP"
] | d26714681de805a5367a987341768931f0059df1c0e52382fb7db68697d4ab7d |
""" Hosts BaseTransport class, which is a base for PlainTransport and SSLTransport
BaseTransport is used by the client and the service, it describes an opened connection.
Here a diagram of basic Client/Service exchange
Client -> ServiceReactor : Connect
Client<-->Service : Handshake (only in SSLTransport)
Cl... | andresailer/DIRAC | Core/DISET/private/Transports/BaseTransport.py | Python | gpl-3.0 | 12,029 | [
"DIRAC"
] | 46d8eb9f1d41a370985dceb7bb65aa22097751b07904527440d0d0c2be483761 |
# Copyright (c) 2013, 2014 Alan Saul
# Licensed under the BSD 3-clause license (see LICENSE.txt)
#
#Parts of this file were influenced by the Matlab GPML framework written by
#Carl Edward Rasmussen & Hannes Nickisch, however all bugs are our own.
#
#The GPML code is released under the FreeBSD License.
#Copyright (c) 20... | jameshensman/GPy | GPy/inference/latent_function_inference/laplace.py | Python | bsd-3-clause | 20,520 | [
"Gaussian"
] | 612a2bb465e2fae06c64c726dafd9a375f49cbb96703e411dffdf68886942511 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. 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
#
# U... | sunqm/pyscf | pyscf/adc/dfadc.py | Python | apache-2.0 | 4,120 | [
"PySCF"
] | 2f5feba4ee78361b7f8bb5aaf77c09ac62b87ab2b392c1bff3f822b0a6200dc6 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_seproperties.py | Python | gpl-3.0 | 4,171 | [
"VisIt"
] | 1713bd35597adcaf207f97aed5ab113d682ede7e099a39251a3baf1309f9ecdb |
"""
bace dataset loader.
"""
import os
import deepchem as dc
from deepchem.molnet.load_function.molnet_loader import TransformerGenerator, _MolnetLoader
from deepchem.data import Dataset
from typing import List, Optional, Tuple, Union
BACE_URL = "https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/bace.c... | deepchem/deepchem | deepchem/molnet/load_function/bace_datasets.py | Python | mit | 5,152 | [
"CRYSTAL"
] | 6f70bb7fc0579b2e0492e7d6c282806c9dda47a90fa005eeafa78d6518d0db9d |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import re
imp... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py | Python | mit | 118,793 | [
"Gaussian"
] | d8921e3e081dee7cda284e1a58aad3b98040e0140dc04b6791093b1cb4da0e23 |
"""
A first test for the ELBO on the catalysis problem.
The target is consisted of an uninformative prior and a Gaussian likelihood.
The approximating mixture has two components.
Author:
Panagiotis Tsilifis
Date:
6/6/2014
"""
import numpy as np
import matplotlib.pyplot as plt
import os
import cPickle as p... | ebilionis/variational-reformulation-of-inverse-problems | unittests/test_up_1.py | Python | gpl-2.0 | 4,660 | [
"Gaussian"
] | 16f3f12d9421c67f877125481f510913b4c57e3f7de6d4e9e2a9350d29841b23 |
# Copyright (c) 2015-2016 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | j0lly/molecule | molecule/config.py | Python | mit | 9,617 | [
"Galaxy"
] | 34355499c4cbff09e50e21781bb9401cbad24a386bb1b6028fc628c963533663 |
"""Python module for running PTM on an Asap list of atoms.
This module runs Polyhedral Template Matching on an Atoms object from ASE/Asap.
It requires that both ASE and Asap are installed.
This module can also be used as inspiration for how to use Polyhedral Template
Matching in other codes.
"""
import asap3
import... | schiotz/polyhedral-template-matching | ptm.py | Python | mit | 4,755 | [
"ASE",
"CRYSTAL"
] | 63500452f6a120dfbb37a17da95d02341553fcaf048b429d8bf1709b06871c52 |
#!/usr/bin/python
# Run this script to merge all (.gif or .png) icons from icons/ into one .png.
# This is to avoid making many request when loading all the small icons.
#
# Files icons.png and icons_png.css will be created.
# Include the css in your html and instead of background and width/height use
# <span class='i... | marcinwrochna/www-app | images/mapIcons.py | Python | mit | 2,479 | [
"VisIt"
] | ca01f9485877cf227e11f2ea85281a58154be1709d2f43a6cc7727fdfcdf6637 |
import sys
import os
import logging
sys.path.append(os.environ["PWD"])
from pyga import *
population_size = 10
elite_count = 2
crossover_points = 2
crossover_mutate_probability = 0.2
max_weight = 15
city_names = ['a', 'b', 'c', 'd']
distances = [
# a b c d
[ 0, 130, 180, 300], # a
[130, 0, 32... | Eyjafjallajokull/pyga | examples/salesman.py | Python | mit | 2,047 | [
"VisIt"
] | 623c874fe291d3f6f2f878bc1da0f01009341ead67f79fbe97b779b4f33c2333 |
from collections import Counter
def iso_convert(iso2c):
"""
Takes a two character ISO country code and returns the corresponding 3
character ISO country code.
Parameters
----------
iso2c: A two character ISO country code.
Returns
-------
iso3c: A three character ISO country code.
... | chilland/hermes | resources/geolocation.py | Python | mit | 7,349 | [
"BWA"
] | 75d1eea5d6c58302a216ff6a6d4f1d8a66080da6c4da91d0412c1d64d2aa02ca |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/gnm.py | Python | gpl-2.0 | 15,844 | [
"Gaussian",
"MDAnalysis"
] | 8c7decf83fbb724cb1af25b144e2bf61765049022dd94394d690a4f821738fe7 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# 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, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/minimize_energy.py | Python | gpl-3.0 | 3,574 | [
"ESPResSo"
] | c34ad828d70cbf615f700babb0cf28eb1a3a5550f5f87f22e2d1bb2e76b98295 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatterns = [
url(r'^$', TemplateView.as_view(template_name='page... | CoutinhoElias/danibraz | config/urls.py | Python | mit | 1,953 | [
"VisIt"
] | 440a65230b223d58735aeeaf695338ff790862323ca91b4ddf60454cf3ef96a8 |
from __future__ import print_function
from argparse import RawTextHelpFormatter
import datetime
import os
import zipfile
from lxml import html
import requests
from tqdm import tqdm
from django.conf import settings
from django.core.management import BaseCommand, CommandError
from openprescribing.utils import mkdir_p... | annapowellsmith/openpresc | openprescribing/pipeline/management/commands/fetch_prescribing_data.py | Python | mit | 5,227 | [
"VisIt"
] | cd34da006aa3b862f06040365db4e288bde4ada59aeb77a24d6b5a119c8ec7fe |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
# skeleton of an AUI-based viewer module
# copy and modify for your own purposes.
# set to False for 3D viewer, True for 2D image viewer
IMAGE_VIEWER = True
# import the frame, i.e. the wx window containing everything
impor... | nagyistoce/devide | modules/viewers/SkeletonAUIViewer.py | Python | bsd-3-clause | 8,071 | [
"VTK"
] | b010e2791065e73409c09b833f5a0db500444fdb1d312cbe8f599e9e681b6b22 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2020, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later.... | cclib/cclib | test/regression.py | Python | bsd-3-clause | 150,734 | [
"ADF",
"Dalton",
"Firefly",
"GAMESS",
"Gaussian",
"Jaguar",
"MOLCAS",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"Q-Chem",
"TURBOMOLE",
"cclib"
] | 885fc95c0c06cc70875b243327ae48babfe71f98fd540343287fa674da84d18e |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.