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from __future__ import division
import abc
from warnings import warn
import numpy as np
from scipy.misc import imrotate
import scipy.linalg
import PIL.Image as PILImage
from menpo.base import Vectorizable
from menpo.landmark import LandmarkableViewable
from menpo.transform import (Translation, NonUniformScale,
... | jalabort/menpofast | menpofast/image/base.py | Python | bsd-2-clause | 56,008 | [
"Gaussian"
] | 53476b1b0beb2d7d0be0d786c43e0a1383c45f99e76997b6196d7f335d81ac7e |
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import rcParams
import corner
import pandas as pd
import os, sys, json
def Distrib(x):
'''Finds median and 68% interval of array x.'''
y = sorted(x)
up = y[int(0.8413*len(y))]
down = y[int(0.1587*len(y))]
med = y[int(0.5*len(y))]
... | paultheastronomer/N7 | posterior.py | Python | gpl-3.0 | 7,873 | [
"Dalton"
] | 30bbca06ad03b87723f833705c9d0540287846b0b5006418d2959c787944ef9a |
#!/usr/bin/env python
#
# 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 requir... | Aloomaio/googleads-python-lib | examples/adwords/v201809/advanced_operations/add_expanded_text_ad_with_upgraded_urls.py | Python | apache-2.0 | 3,840 | [
"VisIt"
] | b4dbf2c2e1fcff4be173f852198b9558179895f4a339ee8e11439a1f071542b0 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/basics/catalogcoverage.py | Python | agpl-3.0 | 6,157 | [
"Galaxy"
] | f2bf7daf469bdf1f884d24de58401327673bc0d0e29e142380fbcdbc460d7315 |
"""
PyGlow.py.
AdaFruit makes these fun little GPIO boards for the Raspberry Pi called
PiGlow. This Python module will let you watchen das blinkenlights.
Copyright (c) 2015 Matthew Hawkins <darthmdh@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associat... | darthmdh/pyglow | pyglow.py | Python | mit | 8,331 | [
"exciting"
] | 2bb23c1cff61f8b84fe31591c73e37a1ae2fa0d299d250e0fb7b8e813e3bb845 |
from bok_choy.web_app_test import WebAppTest
import ddt
from selenium.common.exceptions import NoSuchElementException, TimeoutException
from selenium.webdriver.common.by import By
from selenium.webdriver.support import expected_conditions as EC
from selenium.webdriver.support.select import Select
from selenium.webdrive... | janusnic/ecommerce | acceptance_tests/test_payment.py | Python | agpl-3.0 | 7,173 | [
"VisIt"
] | d7262728c16ed1b2cc85386cfcde13a697455d1a46d1bec7ba09c1305136105a |
# -*- coding: utf-8 -*-
"""Module for low-level parsing of nagios-style configuration files."""
from __future__ import absolute_import
import os
import re
import sys
import time
import pynag.Utils
from pynag.Utils import paths
from pynag.Utils import bytes2str
# TODO: Raise more specific errors in this module.
from ... | pynag/pynag | pynag/Parsers/config_parser.py | Python | gpl-2.0 | 69,829 | [
"MOE"
] | 77e4423d73c0a7afb4406d4b95088762d766a3de7b34a78ec632a126160b5d9b |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QAD Quantum Aided Design plugin
classe per gestire le variabili di ambiente
-------------------
begin : 2013-05-22
copyright : ii... | gam17/QAD | qad_variables.py | Python | gpl-3.0 | 102,744 | [
"ESPResSo"
] | 8c821457daee4fd894c89f43c968334c5cfa19d955e0ec7791c1d7dd98671f18 |
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide")
import MeshInfoFacto... | gleicher27/Tardigrade | moose/gui/plug_ins/PeacockApplication.py | Python | lgpl-2.1 | 8,501 | [
"MOOSE",
"VTK"
] | 2e447c0c6867dc0d81c6e900fd4b88eb17289ce6e6c2e17d4e05a293b83cc2a7 |
# $Id$
#
# Copyright (C) 2005-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import Chem
from rdkit.Chem ... | rdkit/rdkit-orig | rdkit/Chem/TemplateAlign.py | Python | bsd-3-clause | 3,130 | [
"RDKit"
] | ad9c2e3b5d11f209101b7486ad9e0394c77e763741527748a820fb3b141bcd4f |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
%prog rice_sorghum.blastp.filtered --qbed=rice.nolocaldups.bed --sbed=sorghum.nolocaldups.bed
Given a blast, we find the syntenic regions for every single gene. The algorithm
works by expanding the query gene to a window centered on the gene. A single
linkage algorith... | LyonsLab/coge | bin/quota-alignment/scripts/synteny_score.py | Python | bsd-2-clause | 15,015 | [
"BLAST"
] | 7c3247e84e7c2b53f55ae4e763d57448d432319ba612ef75f21fb10bf13ab401 |
import numpy as np
def expand_cell(atoms, cutoff=None, padding=None):
"""Return Cartesian coordinates atoms within a supercell
which contains repetitions of the unit cell which contains
at least one neighboring atom.
Parameters
----------
atoms : Atoms object
Atoms with the periodic b... | jboes/CatKit | catkit/gen/utils/coordinates.py | Python | gpl-3.0 | 8,716 | [
"ASE",
"pymatgen"
] | 9c7c8ffb0fde36e743fdb100e96cb21855d6c55cd3ee0f618dc7a35ae297a241 |
import sys
import os
import re
import time
import thread
import itertools
import functions.db as db
import functions.fileio_gui as f
import functions.printio_gui as p
import functions.message as m
from PyQt4 import QtCore, QtGui, uic
app = QtGui.QApplication(sys.argv)
ui_path = os.path.join('ui', 'DEEPN.ui')
if sys.p... | emptyewer/DEEPN | deepn.py | Python | mit | 20,500 | [
"BLAST"
] | fe13c22a2e2e9f6999f95f78939a14e9214b93472cc2e5ba6974ef0d512d648c |
# -*- coding: utf-8 -*-
"""
A Cell
A cell is a single input/output block. Worksheets are built out of
a list of cells.
"""
###########################################################################
# Copyright (C) 2006 William Stein <wstein@gmail.com>
#
# Distributed under the terms of the GNU General Public ... | bollu/sagenb | sagenb/notebook/cell.py | Python | gpl-3.0 | 82,188 | [
"Jmol"
] | be16ede425887f763850f12bcc9fe36747b0887f3ccb12ea7c73785e79b17aa2 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""EMSL Api.
Usage:
EMSL_api.py list_basis [--basis=<basis_name>...]
[--atom=<atom_name>...]
[--db_path=<db_path> |--db_dump_path=<db_dump_path>]
[--average_mo_number]
EMSL_api.py list_atoms -... | LCPQ/EMSL_Basis_Set_Exchange_Local | EMSL_api.py | Python | mit | 6,549 | [
"GAMESS"
] | 0dbc3a3d36f2472996115eda538d7dc431a26e45033c9ce9ff98ba23766babd2 |
#!/usr/bin/env python
'''
Appendix D compliance support for CF 1.6
The definitions given here allow an application to compute dimensional
coordinate values from the dimensionless ones and associated variables. The
formulas are expressed for a gridpoint (n,k,j,i) where i and j are the
horizontal indices, k is the verti... | DanielJMaher/compliance-checker | compliance_checker/cf/appendix_d.py | Python | apache-2.0 | 3,189 | [
"NetCDF"
] | 5d05307d7ce3d176f58e16994794e9f132cc64962417be63970475611d6c584f |
# -*- coding: utf-8 -*-
"""Scheduler tasks for mirnaseq
Created Nov 2014
Copyright (C) Damien Farrell
"""
import os,sys,types,glob
import subprocess
import ConfigParser
from collections import OrderedDict
temppath = os.path.join(request.folder,'static/temp')
datapath = os.path.join(request.folder,'static/data')... | dmnfarrell/mirseqapp | models/tasks.py | Python | apache-2.0 | 9,614 | [
"Bowtie"
] | d5a47426194a8d8561b6f64708a5db4fb71361643f480045885093f27609a6d1 |
import numpy as np
from vtk import vtkContourFilter, vtkDepthSortPolyData
from ase.visualize.vtk.grid import vtkVolumeGrid
from ase.visualize.vtk.module import vtkPolyDataModule
from ase.visualize.vtk.pipeline import vtkSurfaceSmootherPipeline, \
vtkDepthSortPipeline
# --------... | grhawk/ASE | tools/ase/visualize/vtk/volume.py | Python | gpl-2.0 | 2,387 | [
"ASE",
"VTK"
] | 03b46f8fac5e1f70fe8b6e501288eeaeda6db44e5d2ca5021346885c12c37ca3 |
#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Bio.Wise contains modules for running and processing the output of
# some of the models in the Wise2 package by Ewan Birney av... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Wise/psw.py | Python | gpl-2.0 | 3,774 | [
"Biopython"
] | 2de54e438ef1a3af5ab741119ab31d1fdb98973556aaae8d198fc94ebbf2d1b4 |
# Natural Language Toolkit: Discourse Representation Theory (DRT)
#
# Author: Dan Garrette <dhgarrette@gmail.com>
#
# Copyright (C) 2001-2012 NLTK Project
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
import operator
from nltk.sem.logic import (APP, AbstractVariableExpression, AllExpression... | cortext/crawtextV2 | ~/venvs/crawler/lib/python2.7/site-packages/nltk/sem/drt.py | Python | mit | 49,147 | [
"VisIt"
] | 63332e9f2f3eba5dd9511a8f7a665563d91f7e7bd26a1cc193eb3d5003ecee8c |
# cTurtle.py is based on the following work:
# xturtle.py: a Tkinter based turtle graphics module for
#
# Copyright (C) 2006 Gregor Lingl, <glingl@aon.at>
#
# This software is provided 'as-is', without any express or implied
# warranty. In no event will the authors be held liable for any damages
# arising from the ... | ucsb-cs/cTurtle_screenshot | cTurtle/cTurtle.py | Python | bsd-2-clause | 105,064 | [
"TINKER"
] | 225a5e59aa83e11ce2882a67b3ea782864fc98ca7e5eef5b99d92f0fa9168267 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import itertools
import logging
from collections import defaultdict
import math
from math import cos
from math import sin
from fractions import... | tallakahath/pymatgen | pymatgen/symmetry/analyzer.py | Python | mit | 54,060 | [
"CRYSTAL",
"pymatgen"
] | 8a6508e7dedcf85d4cf470ff8d3b4dc0dcd7000e33c2ba474568334b7becd588 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes used to define a non-periodic molecule and a
periodic structure.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyrigh... | sonium0/pymatgen | pymatgen/core/structure.py | Python | mit | 113,707 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"pymatgen"
] | 09c1a6aac447453b47883147a21f17602ee9dadd72bee740911f9a2bd55e4613 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for reading Lobster output files. For more information
on LOBSTER see www.cohp.de.
"""
import collections
import fnmatch
import os
import re
import warnings
from collections import defaultdict
from typing import Any... | materialsproject/pymatgen | pymatgen/io/lobster/outputs.py | Python | mit | 65,137 | [
"VASP",
"pymatgen"
] | 19f35d7af4ef95771c111ca47868fcbe8bb72752c2ce57e619f50c2ea148aa33 |
"""This source manages a VTK dataset given to it. When this source is
pickled or persisted, it saves the data given to it in the form of a
gzipped string.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
import os
import tempfile
# Enthought l... | liulion/mayavi | mayavi/sources/vtk_data_source.py | Python | bsd-3-clause | 14,220 | [
"Mayavi",
"VTK"
] | c5ba4d6e2fffa3b270c7805c84f2bdb2e93df75d0b638b8137bfb214832e23e1 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
#
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Math... | sknepneklab/SAMoS | FormerAnalysis/cells_patches_stresses_defects_cells.py | Python | gpl-3.0 | 29,573 | [
"VTK"
] | 2a8759f654dbec7dcd42a1333570206353c9b0fe7a66da3a54008448265c8f9d |
# ======================================================================
# USER-GFMD - Elastic half-space methods for LAMMPS
# https://github.com/Atomistica/user-gfmd
#
# Copyright (2011-2016,2021)
# Lars Pastewka <lars.pastewka@imtek.uni-freiburg>,
# Tristan A. Sharp and others.
# See the AUTHORS file in the top... | Atomistica/user-gfmd | tests/lammps_log.py | Python | gpl-2.0 | 10,919 | [
"LAMMPS"
] | 89bfadab766a5e4d951091e4d5d6375ec5da66dc59a322ecca7b45820d351b5d |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
timestep = 2.0 * u.femtoseconds
equil_timestep = 1.0 * u.femtoseconds
padding = 0.9 * u.nanometers
cutoff = 0.95 * u.nanometers
friction = 0.25 / u.picoseconds
equil_friction = 2.0 / u.picoseconds
output_frequency = 1000
n_steps = 2... | kyleabeauchamp/fah-projects | code/fah_parameters.py | Python | gpl-2.0 | 436 | [
"OpenMM"
] | 19ca53132658ada7efc80663cb70c560de53b15f7c0a983092aaca9cf87ff491 |
import os
import glob
import unittest
import numpy as np
import numpy.testing
import cPickle as pickle
import run_steric_resolution
import subprocess
import mock
import sys
import MDAnalysis
import collections
class TestArgparse(unittest.TestCase):
'''Test argparse code.'''
def test_parser_simple_dppc_input(s... | tylerjereddy/steric-conflict-resolution | docker_build/tests.py | Python | mit | 23,732 | [
"MDAnalysis"
] | 96b7309c2d06fa7fe066815afeff3a91f52f13cfd7ca874773bbd03caef482d7 |
# Copyright 2014 by Kevin Wu.
# Revisions copyright 2014 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Provides code to access the REST-style KEGG online AP... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/KEGG/REST.py | Python | gpl-2.0 | 10,685 | [
"Biopython"
] | 137e5a220bfd9964c1db498fae9a0f26f75ddd91cf9938e33af5211cc65f3eaa |
"""
GMT accessor methods.
"""
import xarray as xr
from pygmt.exceptions import GMTInvalidInput
from pygmt.src.grdinfo import grdinfo
@xr.register_dataarray_accessor("gmt")
class GMTDataArrayAccessor:
"""
This is the GMT extension for :class:`xarray.DataArray`.
You can access various GMT specific metadata... | GenericMappingTools/gmt-python | pygmt/accessors.py | Python | bsd-3-clause | 2,372 | [
"NetCDF"
] | b9369a95c4986606f6d983f994998c58d2a2d9b6a5547b7531f3425bd90bf2d9 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Unit tests for grit.tool.android2grd'''
from __future__ import print_function
import os
import sys
if __name__ == '__main__':
... | endlessm/chromium-browser | tools/grit/grit/tool/android2grd_unittest.py | Python | bsd-3-clause | 7,387 | [
"xTB"
] | 235ebefb2a1e7ad71e3a6874eafa80df1a7e898666e967a8b17be3395b4930de |
import openvoronoi as ovd
import ovdvtk
import truetypetracer as ttt
import time
import vtk
import datetime
import math
# import random
import os
import sys
# import pickle
# import gzip
import ngc_writer
def drawCircle(myscreen, c, r, circlecolor):
ca = ovdvtk.Circle(center=(c.x, c.y, 0), radius=r, color=circle... | aewallin/openvoronoi | python_examples/ma-pocket/ma_pocket_11_components.py | Python | lgpl-2.1 | 24,661 | [
"VTK"
] | ad8fec0734309a8aaaa7edf4d85a042625f3f6a7d3a59e3a0eb3c9dc96e6a24b |
import logging
import numpy as np
from collections import OrderedDict
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
from theano.tensor.nnet.conv import conv2d, ConvOp
from theano.sandbox.cuda.blas import GpuCorrMM
from theano.sandbox.cuda.basic_ops impor... | CuriousAI/ladder | ladder.py | Python | mit | 26,219 | [
"Gaussian"
] | 1bb6e92e721ceb3801b314d0748de32de2fcc7b45cab99f2c8bccef241e60ea3 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides various representations of transformed structures. A
TransformedStructure is a structure that has been modified by undergoing a
series of transformations.
"""
import datetime
import json
import os
imp... | materialsproject/pymatgen | pymatgen/alchemy/materials.py | Python | mit | 13,884 | [
"VASP",
"pymatgen"
] | 726f66ea1bf987f257808adff2346ec4021fda22d4de117a44059e7eaea9929d |
#!/usr/bin/env python
# Standard packages
import os
import sys
import argparse
# Third-party packages
from toil.job import Job
# Package methods
from ddb import configuration
from ddb_ngsflow import gatk
from ddb_ngsflow import annotation
from ddb_ngsflow import pipeline
from ddb_ngsflow.align import bwa
from ddb_ng... | dgaston/ddb-ngsflow-scripts | workflow-testing_somatic_amplicon_annotation.py | Python | mit | 2,413 | [
"BWA"
] | dd4fc7fa20cf155efe53c9306890853f151f68d564338e8e17573c022af98ad8 |
#!/usr/bin/python3
#
# Copyright (c) 2013 Mikkel Schubert <MikkelSch@gmail.com>
#
# 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
... | MikkelSchubert/paleomix | paleomix/pipelines/bam/config.py | Python | mit | 4,128 | [
"BWA"
] | c554fecdf09768414e7ef462188c12a786616a188db8d7b1685b0f49af3d0b17 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-summarizedexperiment/package.py | Python | lgpl-2.1 | 2,284 | [
"Bioconductor"
] | 828be734ffc9fad625e43c7430d263115d89194213cb69549a5df04530129b61 |
from neuron import h, gui
## Define an axon
axon = h.Section(name='axon')
axon.diam = 1.
axon.L = 1000.
axon.nseg = 100 # We segment the axon into 100 pieces
## Passive membrane
axon.insert('pas')
## Parameters
axon.cm = 1. # 1 uF/cm^2
axon.Ra = 150. # 150 Ohm cm
axon.g_pas = 5e-5 # 5*10^-5 S/cm^2
# We a... | shhong/a310_cns_2017 | Assignment_1/axon_model.py | Python | gpl-3.0 | 912 | [
"NEURON"
] | 3de0ebfef906f6e945bae0a8d3b7b42ff8b9208e6d9f75c6d43da7f2dd274fb5 |
# experiment in scripting GAMESS-UK calculations
#
# notes
#
# - I had to hack the energy in from the outputreader to an attribute of calc
# need a better way to (request&) hold results.. for example matrices from punchfile
#
# - the codes habit of writing the resulting structure back over its input
# is rather un... | alexei-matveev/ccp1gui | scripts/water_surf.py | Python | gpl-2.0 | 5,018 | [
"GAMESS"
] | f97eff28404d8b758b956d154d17db2ba8519da4a94b7d6293317f6b30ce43b8 |
from urllib2 import urlopen
import lxml.html
import requests
import json
import csv
# dataReports = ["DataRequest","DataExemption","DataAppeal","DataProcessTime","DataFeewaiver","DataPerson","DataBacklog","DataConsultant","RequestDisposition","RequestDenial","RequestPending","Exemption3Statutes","appealDisposition","... | sunlightlabs/foia-data | data/foia.gov/scrape-foia-data-officialx.py | Python | gpl-3.0 | 3,189 | [
"ADF"
] | 7836acded27583bb07bfc451445cbaff0ac75e1c470cafe61afbdb235d228800 |
#!/usr/bin/env python
# Copyright (c) 2012-2013 ARM Limited
# All rights reserved
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implement... | haowu4682/gem5 | util/cpt_upgrader.py | Python | bsd-3-clause | 27,350 | [
"VisIt"
] | 5f6374c5db0294d30c37b48b1e47d5cad19d33c559273853d72f423b7466ab86 |
import cgi
import datetime
import random
import re
import sys
try:
import json
except ImportError:
import simplejson as json
try:
import unittest2 as unittest
except ImportError:
import unittest
from piwikapi.analytics import PiwikAnalytics
from piwikapi.exceptions import InvalidParameter
from piwikapi... | piwik/piwik-python-api | piwikapi/tests/tracking.py | Python | bsd-3-clause | 22,888 | [
"VisIt"
] | 637cf2dcf174b69602301e08c9450280d963d7e89c420a98cf3e6f15e149c80c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or ... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/reconstructSurface.py | Python | bsd-3-clause | 3,635 | [
"VTK"
] | 1157451cebfb80b11a147d21c3546358979bc1386985b87f239ff65df0b9549b |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para somosmovies
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse,urllib2,urllib,re
import os, sys
from core ... | CarlosCondor/pelisalacarta-xbmc-plus | pelisalacarta/channels/somosmovies.py | Python | gpl-3.0 | 8,052 | [
"ADF"
] | 521e97d6b943891849f06e9cb6042dd63bf881fa295752cb58f9705b036eae49 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 11 14:36:29 2017
@author: derek
"""
import os
import tensorflow as tf
import numpy as np
def _parse_function(example_proto):
"""Reads tfrecords with features {shape: (height,width,depth) of cube data,
label: (malignancy, lobulation, spicul... | dereknewman/cancer_detection | train_label_cat_cubes.py | Python | mit | 13,818 | [
"Gaussian"
] | 519c7cda8157a3c50a78a89cf8e9f1ba4825dd6f1587eff469fd5489078892b3 |
#
# @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 | psi4/driver/driver.py | Python | gpl-2.0 | 109,988 | [
"Gaussian",
"Psi4"
] | 23f5fadaab37b9ce3251735a53703519c0465462eabefdd3bd862069051432f3 |
# python version 1.0 DO NOT EDIT
#
# Generated by smidump version 0.4.8:
#
# smidump -f python VRRP-MIB
FILENAME = "VRRP-MIB"
MIB = {
"moduleName" : "VRRP-MIB",
"VRRP-MIB" : {
"nodetype" : "module",
"language" : "SMIv2",
"organization" :
"""IETF VRRP Working Gro... | alexanderfefelov/nav | python/nav/smidumps/vrrp_mib.py | Python | gpl-2.0 | 42,949 | [
"Brian"
] | 53ecc3d9d04e4871430a71719f41b1a54fc6e7c5ed617910b9f9bcb178ca317c |
#!/usr/bin/python
# script for histogramming size of forward and reverse reads sizes in a bowtie output
# version 1
# Usage histogrammer.py <bowtie input> <output> <Normalization Factor>
import sys, re, os
def field_controle (input):
bOUT = open (input)
sampleline = bOUT.readline() # for test of first file l... | JuPeg/tools-artbio | unstable/local_tools/histogrammer.py | Python | mit | 1,268 | [
"Bowtie"
] | 9f303d598a988c974cb7e8f4c7f9f80240104aa70c67be0227b0b77e9c27b78a |
###=============General Regex strings===============###
FLOAT_REGEX = r'\-?(?:\d+\.?\d*|\d*\.?\d+)'
###=============Phonon Regex strings===============###
# Header regex. Looks for lines in the following format:
# q-pt= 1 0.000000 0.000000 0.000000 1.0000000000 0.000000 0.000000 1.000000
PHONON... | ScreamingUdder/mantid | scripts/Inelastic/dos/load_helper.py | Python | gpl-3.0 | 1,855 | [
"CASTEP"
] | e5a905b76e6fe6eee244429e941e96410b235c897caa56a6ba561285e9be2208 |
from ase.structure import bulk
from sys import argv
from ase.dft.kpoints import ibz_points, get_bandpath
from gpaw import *
from ase import *
from gpaw.test import gen
from gpaw import setup_paths
import os
"""This calculation has the following structure.
1) Calculate the ground state of Diamond.
2) Calculate the ban... | qsnake/gpaw | gpaw/test/diamond_gllb.py | Python | gpl-3.0 | 2,145 | [
"ASE",
"GPAW"
] | 62ca983b63464e81afc885a958b002bb99e49a53f32a5997ec23c2d5a31c1084 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | lib/spack/spack/test/url_parse.py | Python | lgpl-2.1 | 20,083 | [
"BLAST",
"Gromacs",
"HOOMD-blue",
"Jmol",
"Octopus",
"VisIt"
] | 4e17472ef33d2914eb89563d31fde86ff49e8f20ea2870da86d29f1fe502f411 |
import numpy as np
import nengo
from nengo.networks.product import Product
from nengo.utils.decorators import memoize
def circconv(a, b, invert_a=False, invert_b=False, axis=-1):
"""A reference Numpy implementation of circular convolution"""
A = np.fft.fft(a, axis=axis)
B = np.fft.fft(b, axis=axis)
i... | ZeitgeberH/nengo | nengo/networks/circularconvolution.py | Python | gpl-3.0 | 6,254 | [
"NEURON"
] | c293940e6d89fdac86e3aca45676b6a6b7863b270e109148397c911833e76deb |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-aldex2/package.py | Python | lgpl-2.1 | 2,580 | [
"Bioconductor"
] | 94da34f194d12fa157b42e9952fb35fbb1db35e9c395b89f77085b455f0ccd35 |
"""
Find subhalo galaxy distances from the main halo as a function of redshift, halo mass, etc.
:Warning: All functions are rather poorly written as I was in a hurry.
One should improve them before using. One could remove several
loops and do many things with table joins which are now separate loop... | sniemi/SamPy | bolshoi/subhaloDistances.py | Python | bsd-2-clause | 16,670 | [
"Galaxy"
] | 74b294d46a3f6f29ab330881d2846ed7b005c57ffecdb08310ec38fe4c3e879d |
# 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/nao/m_density_cart.py | Python | apache-2.0 | 1,025 | [
"PySCF"
] | ca1210d391d90691eecc472fce9b138c0568415761ac3b6140fe69a6cd9d6f46 |
#!/usr/bin/env python
## Copyright 2015 Novartis Institutes for BioMedical Research
## Inc.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
##
#... | Novartis/EQP-cluster | exon-pipeline-scripts/bin/util-lib/extractPipelineMetaData.py | Python | apache-2.0 | 31,828 | [
"HTSeq"
] | 82f3dfff2110a7872d5cf7073f582ca5ae536b131311f3ef8552b6cb06f457f5 |
########################################################################
# $HeadURL $
# File: PutAndRegister.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 07:43:24
########################################################################
""" :mod: PutAndRegister
====================
.. module... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/PutAndRegister.py | Python | gpl-3.0 | 9,599 | [
"DIRAC"
] | 24b4f8b081502a8811676ed3f79ac5b2787cd7d3b99c2b0c8c39e572864761bb |
from __future__ import print_function
import unittest
import doctest
from rdkit import Chem
from rdkit.Chem import MCS, FragmentMatcher, MACCSkeys, Descriptors, TemplateAlign
from rdkit.Chem import Recap, BRICS, AllChem, PropertyMol, SaltRemover
def load_tests(loader, tests, ignore): # pylint: disable=unused-argumen... | rvianello/rdkit | rdkit/Chem/UnitTestDocTestsChem.py | Python | bsd-3-clause | 1,320 | [
"RDKit"
] | 331e2b4b35db36a172138e7eca3fcc431a61c37e4cc30009685e414e95ad936d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import logging
import math
import itertools
import warnings
from collections import OrderedDict
import six
import numpy as np
from monty.json ... | johnson1228/pymatgen | pymatgen/electronic_structure/plotter.py | Python | mit | 182,636 | [
"BoltzTrap",
"CRYSTAL",
"Gaussian",
"Mayavi",
"VASP",
"pymatgen"
] | d4246aa339030033835e7bf3beb70716ea075601a2a5c3a503e7604c289b06e7 |
"""
validation of ast trees
"""
from .visitors import NodeVisitor
from .nodes import CtreeNode
from .nodes import ast
from .c.nodes import SymbolRef
from .util import flatten
class DeclFinder(NodeVisitor):
"""
Returns the first use of a particular symbol.
"""
def __init__(self):
self.decl = N... | alphaFred/Sejits4Fpgas | sejits4fpgas/src/vhdl_ctree/analyses.py | Python | gpl-3.0 | 1,176 | [
"VisIt"
] | 9f272d514714459b683ea2cb6280a207e48b967ead22895eedf1c981400da76d |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from io import StringIO
import os
import pytest
from unittest.mock import patch, Mock
from astropy import units as u
from astropy import coordinates as coord
from astropy.table import Table
from astropy.coordinates import SkyCoord
from astropy.time impor... | ceb8/astroquery | astroquery/alma/tests/test_alma.py | Python | bsd-3-clause | 19,329 | [
"Galaxy"
] | 8c3dfb3b62e796fd6494374c50180ee238f6e7f1a0ed9057d0b5bfa16b144945 |
import datetime
import gzip
from itertools import count
import os
curdir = os.path.join(os.getcwd(), os.path.dirname(__file__))
import sys
import threading
import time
import urllib
import cherrypy
from cherrypy._cpcompat import next, ntob, quote, xrange
from cherrypy.lib import httputil
gif_bytes = ntob('GIF89a\x01\... | evilhero/mylar | lib/cherrypy/test/test_caching.py | Python | gpl-3.0 | 13,057 | [
"VisIt"
] | b45f2472ef0b42e41aae9bb26a1f3c4b3b257196f502312b71a975600678051f |
import sys
import numpy
from netCDF4._netCDF4 import num2date
from datetime import datetime as datetime
from Log import Log
class GlobalAttributes():
def __init__(self, data):
self.data = data
self.attributesList = {}
self.create_attribute_list()
def create_attribute_list(self):
... | plocan/netCDF-Generator | src/GlobalAttributes.py | Python | gpl-3.0 | 3,616 | [
"NetCDF"
] | 2316f094498c78c66e60d0454f888a60b36664504261276b69ef37058e93d37f |
"""
Samplers for perses automated molecular design.
TODO
----
* Determine where `System` object should be stored: In `SamplerState` or in `Thermodynamic State`, or both, or neither?
* Can we create a generalized, extensible `SamplerState` that also stores chemical/thermodynamic state information?
* Can we create a gen... | choderalab/perses | perses/samplers/samplers.py | Python | mit | 45,378 | [
"MDTraj",
"OpenMM"
] | d33bcd5dcab8eaefa1d37987e6106726c9178eab0f02b039bbb42c0b8dbe6336 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor | remindor/preferences_dialog.py | Python | gpl-3.0 | 14,975 | [
"Brian",
"VisIt"
] | 1b8eff9c0bd61025a3f78876129592bfd2e6e292e2152c13f42e9fdbd39bcca3 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/mesh/mesh.py | Python | lgpl-2.1 | 1,525 | [
"MOOSE",
"VTK"
] | 22a1e1b300d7a9cd965513e82d3a8f305f4a5a5e571cc85b529447730f4eb736 |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: nn/base.py
# Basic definitions for layers of neurons
################################################################################
# Doc string, reSt... | anki1909/peach | peach/nn/base.py | Python | lgpl-2.1 | 8,686 | [
"NEURON"
] | 8071296afb293ba7953d223cd8bd1b7c92416c50414401ca78a2d053c7553595 |
import os
import time
import warnings
import numpy as np
from collections import OrderedDict
try:
from tqdm import tqdm
HAS_TQDM = True
except:
HAS_TQDM = False
try:
from grizli.utils import GTable as Table
except:
from astropy.table import Table
import astropy.io.fits as pyfits
import astro... | gbrammer/eazy-py | eazy/photoz.py | Python | mit | 226,550 | [
"Galaxy",
"Gaussian"
] | ef12524b307149fe06e149f008b2ab1f4ea27bc120439be211c3b3f30850ff8a |
# -*- coding: utf-8 -*-
# ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.11.1
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# + nbsphinx="hidden"
# %run n... | adrn/gala | docs/tutorials/pyia-gala-orbit.py | Python | mit | 9,030 | [
"Galaxy"
] | 25f0ec99fa9c196bb8e1d98d9d9f370f4512f4a15b2515513210dd70d5dfd5e5 |
#!/usr/bin/python
# Modify the solute geometry and charges in Gromacs .gro and .top files
# Use with 5 arguments:
# 1 (read): generic system file
# 2 (read): .top file
# 3 (read): .gro file
# 4 (write): modified .top file
# 5 (write): modified .gro file
import sys
import re
import math
import copy
#===========... | Jellby/ASEP-MD | Tests/scripts/gen2gromacs.py | Python | gpl-3.0 | 9,989 | [
"Gromacs"
] | c5f366808fe37b87e2f86f641552e9af00bffb2ae872c61cc7ed08880f0d4edd |
"""
Helper functions for the course complete event that was originally included with the Badging MVP.
"""
import hashlib
import logging
from django.urls import reverse
from django.utils.text import slugify
from django.utils.translation import ugettext_lazy as _
from lms.djangoapps.badges.models import BadgeAssertio... | eduNEXT/edunext-platform | lms/djangoapps/badges/events/course_complete.py | Python | agpl-3.0 | 4,517 | [
"VisIt"
] | fe95c07397f95d57394fe3c24ffb9bc236564e661efdaf2666e6002d0bf696bb |
#!/usr/bin/env python3
#
# Copyright (c) Bo Peng and the University of Texas MD Anderson Cancer Center
# Distributed under the terms of the 3-clause BSD License.
import ast
import copy
import os
import subprocess
import sys
import time
from collections import defaultdict
from collections.abc import Mapping, Sequence
f... | bpeng2000/SOS | src/sos/step_executor.py | Python | gpl-3.0 | 96,815 | [
"VisIt"
] | 1d8c738c34020a5a376de60b0adfdc5b9c1e7490f2ba6499836a2af95b76f676 |
import ast
import astunparse
from cStringIO import StringIO
class Transformer(ast.NodeTransformer):
def __init__(self):
super(Transformer, self).__init__()
def visit_Call(self, node):
child = self.visit(node.func)
if isinstance(child.value, ast.Call):
keyword = nameAndArgsT... | rymurr/q | rubbish/translate.py | Python | mit | 4,208 | [
"VisIt"
] | ef238ab6cda4c85aebb3b1fbb2b963d25841aa2464ad095cb4735a93ac5cb416 |
# Orca
#
# Copyright (C) 2013 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at yo... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/Qt/script.py | Python | gpl-3.0 | 1,607 | [
"ORCA"
] | b0ed120efbafcc88eafe2b006afa72755a987863bca32a4e3274106c42971160 |
# This file is part of Sequana software
#
# Copyright (c) 2016-2021 - Sequana Development Team
#
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.r... | sequana/sequana | sequana/gff3.py | Python | bsd-3-clause | 21,973 | [
"pysam"
] | a9299aca791c92e7fd790a3febf801cfe95b4a27ca2906425e434f3d905f5df5 |
# IDJCmixprefs.py: Preferences window code for IDJC
# Copyright (C) 2005-2011 Stephen Fairchild (s-fairchild@users.sourceforge.net)
#
# 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, ei... | leofiore/idjc | python/preferences.py | Python | gpl-2.0 | 70,397 | [
"Brian"
] | edccabc1c622ed599d35d2d6616ab833e75268ac1a108429f8edb596e59c95e8 |
import os, re
from subprocess import *
from time import strftime, gmtime, ctime, localtime, asctime
TERM_COLS = 110
LIBMESH_OPTIONS = {
'mesh_mode' : { 're_option' : r'#define\s+LIBMESH_ENABLE_PARMESH\s+(\d+)',
'default' : 'SERIAL',
'options' :
... | cpritam/moose | python/TestHarness/util.py | Python | lgpl-2.1 | 12,077 | [
"MOOSE",
"VTK"
] | 12ffaed52d5e574c9c6c3c5a296957306419c67191bc0e911c5917a6f88d1cae |
#!/usr/bin/env python
# Copyright 2014-2019 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/hessian/uks.py | Python | apache-2.0 | 25,816 | [
"PySCF"
] | f19a89d92e1e1ede792542d16e7e94d5cc66826235c2ef451fc50a270388a3c6 |
import itertools as it
import numpy as np
import scipy.io.netcdf as cdf
import pandas as pd
class GcmsFile(object):
'''Base class for all GCMS files.
This object is meant to be subclassed and can't be instantiated directly.
Subclasses must define a _ref_file method that extracts the information
... | rnelsonchem/gcmstools | gcmstools/filetypes.py | Python | bsd-3-clause | 3,526 | [
"NetCDF"
] | 0c1a62d4132b50e62ae05beb21e492cb688315c7548a8f1f5e6226dd75e7fded |
#!/usr/bin/env python
"""
Get VM instances available in the configured cloud sites
"""
from DIRAC import gLogger, exit as DIRACExit
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
site = None
ce = None
image = None
voName = None
def setCE(args):
global ce
ce = args
def setSite(args):
... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_vm_endpoint_status.py | Python | gpl-3.0 | 2,032 | [
"DIRAC"
] | f076e7693ade1ef698ab3c9637ef628ef14bf1e311f2ba76a43e8a1833dbf60b |
'''
#=============================================================================
# FileName: calc_mw_logp.py
# Desc:
# Author: jlpeng
# Email: jlpeng1201@gmail.com
# HomePage:
# Created: 2014-10-11 17:53:08
# LastChange: 2015-03-10 16:23:18
# History:
#======================... | Jianlong-Peng/rp | python/calc_mw_logp.py | Python | gpl-2.0 | 1,845 | [
"Pybel"
] | 13df74cf9ff9eee773791a9aae24da7044a456a4010cd14b6b5d7becea79f25e |
########################################################################
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/02/13 07:55:31
########################################################################
""" :mod: ProcessPoolTests
=======================
.. module: ProcessPoolTests
:synopsis:... | fstagni/DIRAC | Core/Utilities/test/Test_ProcessPool.py | Python | gpl-3.0 | 12,696 | [
"DIRAC"
] | d83da4026fe587375defda120d9d42447b45c06cc6182ddbf9722d44f7902173 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 3 12:07:10 2017
@author: svimal
"""
from osgeo import gdal, osr
import xarray as xr
import numpy as np
def create_geotiff(netcdf_filename, var_name, out_TIFF_filename): # , soil=False # where there are multiple layers of soil
"""
creates ... | solomonvimal/UCLA-Hydro | MRPI/Python/NetCDF_to_GeoTiff.py | Python | gpl-3.0 | 3,219 | [
"NetCDF"
] | 923c87d8099d2a23523a28bf7ea982879f7fd82849afc9800de0064e4e4bbd21 |
global astrom
global tmpdir
tmpdir = '/usr/work/pkelly/'
astrom = 'solve-field'
import traceback, tempfile
def mk_tab(list):
import astropy, astropy.io.fits as pyfits
from pyfits import Column
import numarray
cols = []
for ele in list:
array = ele[0]
name = ele[1]
v... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_test.save.py | Python | mit | 215,745 | [
"Galaxy"
] | b35b4751073911418d17c3c0023ded1a513b30f311911f85675e1d4c4c128e28 |
from mpi4py import MPI
from neuron import h
import pylab
def load_model(filename):
cell = h.CellSwc(filename, 0, 0, 0)
for sec in h.allsec():
sec.insert('hh')
return cell
def set_iclamp(stim_sec_name, pc=0):
stim = 0
for sec in h.allsec():
if(sec.name() == stim_sec_name):
... | DaisukeMiyamoto/multisplit | hoc/init.py | Python | gpl-2.0 | 3,112 | [
"NEURON"
] | a906802b96d375c607a1669905a69562baaa6d662ff9fc2b752254e150c1872e |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2015, 2016 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This program is distributed in... | tsdgeos/snapcraft | snapcraft/tests/test_commands_list_plugins.py | Python | gpl-3.0 | 2,646 | [
"GULP"
] | b6dabce75faff926c5d2d49c2db8311800c5041e9ed3413f9a97cb516f23c700 |
#!/usr/bin/env python
# pragma: no testimport
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.or... | hjanime/VisTrails | vistrails/tests/runtestsuite.py | Python | bsd-3-clause | 20,500 | [
"VTK"
] | b9597f575f9400b9ba98987a9844d617cd43155d5c61408e9f6b5a9bee636897 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
import sys
import re
from collections import defaultdict
try:
... | ramisetti/lammps | tools/moltemplate/moltemplate/charge_by_bond.py | Python | gpl-2.0 | 17,866 | [
"LAMMPS"
] | d48127fdb5176efbcfcd14546304551db07c5685f47ae1379000d4b0101190ea |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides utility classes for string operations.
"""
import re
from fractions import Fraction
def str_delimited(results, header=None, delimiter="\t"):
"""
Given a tuple of tuples, genera... | davidwaroquiers/pymatgen | pymatgen/util/string.py | Python | mit | 11,727 | [
"pymatgen"
] | 5e5cdcb7a94a708b8a8a26d60d9e5e3ae212352d0748e9e74bfe8eefdce9edea |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@diku.dk>, Rune M. Friborg <runef@diku.dk>
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 restrict... | runefriborg/pycsp | test/unix/multiprocesstest.py | Python | mit | 7,496 | [
"Brian"
] | f95aa4e12f19324501dbee4fcfb39f6e4ba13eb18c4c1a6ac366eae314c72639 |
# Copyright (c) 2012, Daniel Zerbino
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# (1) Redistributions of source code must retain the above copyright
# notice, this list of conditions an... | dzerbino/cn-avg | cnavg/avg/balanced.py | Python | bsd-3-clause | 11,551 | [
"Gaussian"
] | e8d9dad83300295187b96abf450bdcd8bad66fa8d7123c789dcdcc66236aeeab |
import os
import vtkAll as vtk
from ddapp import botpy
import math
import time
import numpy as np
from ddapp import transformUtils
from ddapp import lcmUtils
from ddapp.timercallback import TimerCallback
from ddapp import objectmodel as om
from ddapp import visualization as vis
from ddapp import applogic as app
from d... | RussTedrake/director | src/python/ddapp/handdriver.py | Python | bsd-3-clause | 5,831 | [
"VTK"
] | 73411621e362255e1a933f54e878d93985ae3c9e8181b525f2b5e30d52ddb347 |
#!/usr/bin/python
# Copyright (c) 2012, United States Government, as represented by the
# Administrator of the National Aeronautics and Space Administration.
# All rights reserved.
#
# The NASA Tensegrity Robotics Toolkit (NTRT) v1 platform is licensed
# under the Apache License, Version 2.0 (the "License");
# you may... | UnionEvoRobo/NTRTsim | scripts/PostProcess.py | Python | apache-2.0 | 2,157 | [
"Brian"
] | 8548917e3919d90d6a00981ddeb5071e9a1b44aac648099c211ebc79b161786f |
#-------------
# Some sections of the code below have been copied from
# MongoEngine.
#
# https://github.com/MongoEngine/mongoengine
#
# Copyright (c) 2009 See AUTHORS
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"... | Magicked/crits | crits/core/user.py | Python | mit | 55,765 | [
"Amber"
] | 6cadbfa438b6bec28f504f8541ab3d59db007f0477a8bb5b7363c8ffb60b6b2b |
import json
import sys
import networkx as nx
from networkx.algorithms import weakly_connected_component_subgraphs
from collections import defaultdict
from itertools import chain, ifilter
from functools import partial
from synapseclustering import tree_max_density
from numpy import subtract
from numpy.linalg import no... | htem/CATMAID | django/applications/catmaid/control/graph.py | Python | agpl-3.0 | 19,693 | [
"NEURON"
] | 783454da0a0ad0414e79af3f102c679ca57076f9d4710a4ac21f713c475c04cf |
#
# Copyright 2022 Lucas Frérot (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Founda... | libAtoms/matscipy | matscipy/molecules.py | Python | lgpl-2.1 | 6,143 | [
"ASE",
"Matscipy"
] | bafb0fd5ff1d4804391e2f96de9eada7e6c7fa352dc2565a4aedd2233dfda112 |
# -*- coding: utf-8 -*-
"""
Script to generate phoSim input catalog that has sprinkled lens systems inside.
It is also setup to run visits from a selected set in kraken_1042.
To use:
- need Om10 setup
- sims stack setup, currently sims_catUtils must be a branch https://github.com/lsst/sims_catUtils/tree/newTwin... | rbiswas4/Twinkles | twinkles/generatePhosimInput.py | Python | mit | 5,960 | [
"VisIt"
] | 5fb8f87368d0092cb40e13f105293a21dfb3c243dc9befb380a966a874415422 |
"""
functions to access the data dictionary in a clearer way
"""
import os
import toolz as tz
from bcbio.utils import file_exists, to_single_data, deepish_copy, flatten
from bcbio.log import logger
from collections import namedtuple
import sys
LOOKUPS = {
"config": {"keys": ['config']},
"tmp_dir": {"keys": ['... | chapmanb/bcbio-nextgen | bcbio/pipeline/datadict.py | Python | mit | 20,182 | [
"Galaxy"
] | 8e9c1a211169b2ef1908cfcc6e576916f31db657397a0ed19e8fafcb94cbd25e |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | evenmarbles/rlglued | tests/test_1_agent.py | Python | bsd-3-clause | 2,003 | [
"Brian"
] | 3a79e2a075ea7c8e65e14167072818da457da9d703a2d8aaded538b2757614ef |
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