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from __future__ import division
#from neuron import h
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.collections as mcoll
import matplotlib.path as mpath
import matplotlib.cm as cm
from matplotlib.collections import LineCollection
from matplotlib.colors import ListedColormap, Bou... | mohitganguly/IRBlock_Vanderbilt | 2/make_fig_2b.py | Python | gpl-3.0 | 679 | [
"NEURON"
] | b011b4a9423ef81c238eee7e8cf0f42bfe2b0b555c555fe9365adbe2658d5c76 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/scancode/api.py | Python | apache-2.0 | 8,844 | [
"VisIt"
] | 3a65429c23e5054d6dfffc2b1af776c800d8ffc47f8b9d7f97a81d9b09e2fe33 |
#!/usr/bin/env python
import os
from optparse import OptionParser
from subprocess import Popen,PIPE
import netCDF4 as nc
import numpy as np
def dim2vals(dims,ncf):
dim_vals = []
for i in range(len(dims)):
dim_vals.append(len(ncf.dimensions[dims[i]]))
return tuple(dim_vals)
def z_coords(N=20, theta_s=4.0, theta_... | dcherian/tools | ROMS/pmacc/tools/post_tools/rompy/convert_netcdf_for_bio_model.py | Python | mit | 7,269 | [
"NetCDF"
] | a3317feffa16f9676885fa210f42eaad5b7767ff078bcb9f5731c7ff483e4d64 |
#* 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 PyQt5.... | nuclear-wizard/moose | python/peacock/Input/ParamsByGroup.py | Python | lgpl-2.1 | 4,680 | [
"MOOSE"
] | 3e3fa7c4be9ff889b0743da39f087de5d3e82c7f551a5c552075a1a19109299d |
"""
*********
JSON data
*********
Generate and parse JSON serializable data for NetworkX graphs.
These formats are suitable for use with the d3.js examples http://d3js.org/
The three formats that you can generate with NetworkX are:
- node-link like in the d3.js example http://bl.ocks.org/mbostock/4062045
- tree li... | cogeorg/BlackRhino | networkx/readwrite/json_graph/__init__.py | Python | gpl-3.0 | 720 | [
"Cytoscape"
] | 82a6f1e318acde621ab2582db61fa7298ce34214407ce8c5d9a2b344507bd916 |
#!/usr/bin/env python
'''Generate models for affinity predictions'''
# variables:
# BALANCED(true)
# POSEPREDICT
# RECEPTOR(false)
# AFFMIN(0)
# AFFMAX(0)
# AFFSTEP(0)
basemodel = '''layer {
name: "data"
type: "MolGridData"
top: "data"
top: "label"
top: "affinity"
include {
phase: TEST
}
molgrid_... | gnina/scripts | affinity_search/makemodels1.py | Python | bsd-3-clause | 5,208 | [
"CRYSTAL"
] | e871bf43ef30f5a90acd947a58e8b7c1a8195b46c7df635d51388369249dfd7c |
#
# @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 ... | andysim/psi4 | psi4/driver/qcdb/molecule.py | Python | gpl-2.0 | 49,113 | [
"CFOUR",
"Jmol",
"Molpro",
"ORCA",
"Psi4",
"Q-Chem"
] | e574a393bc9dc02a8696278252ea3e5fd2b71a2767c0fa34902c19744daf20d8 |
#!/usr/bin/env python3
# sudo apt-get install python3-tk
# This file is part of PFunc. PFunc provides a set of simple tools for users
# to analyze preference functions and other function-valued traits.
#
# Copyright 2016-2022 Joseph Kilmer
#
# PFunc is free software: you can redistribute it and/or modify
# it under th... | Joccalor/PFunc | PFunc.py | Python | gpl-3.0 | 130,625 | [
"VisIt"
] | 7f9e3da7ab2ba47cf9abde9687fbf597a9481da1936a8dfdbdfdd05ac0417ad0 |
# $Id: MurckoScaffold.py 3672 2010-06-14 17:10:00Z landrgr1 $
#
# Created by Peter Gedeck, September 2008
#
"""
Generation of Murcko scaffolds from a molecule
"""
from rdkit import Chem
from rdkit.Chem import AllChem
murckoTransforms=[AllChem.ReactionFromSmarts('[*:1]-[!#1;D1]>>[*:1][H]'),
AllChem... | strets123/rdkit | rdkit/Chem/Scaffolds/MurckoScaffold.py | Python | bsd-3-clause | 4,308 | [
"RDKit"
] | 7a41e8e9fe3550d6b3b26bea108abdc47359d95a73f1769c3f4253cf157de420 |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-04-26 09:20:35
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-04-26 09:20:35 by Brian Cherinka
Last Modified On: 2016-04-26 09:20:35 by Brian
'''
import numpy
from decimal import Decimal
from psycopg... | bretthandrews/marvin | python/marvin/db/NumpyAdaptors.py | Python | bsd-3-clause | 4,343 | [
"Brian"
] | bb0d47dfeec7f34171adc679e5e01f9f0ffc4fedae46fd2679e1186d938137a1 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | ViralLeadership/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 223,502 | [
"Brian"
] | d4be60c8b219ac31ea244019a333cb3e66fdc96a1626305240952d70a40fef6a |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2012 OpenPlans
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | bhermansyah/DRR-datacenter | geonode/base/enumerations.py | Python | gpl-3.0 | 19,301 | [
"BWA",
"MOE"
] | 73755257f12643b79d40a2b632a668fcf6605a54ebb15d47182f80606b9e8990 |
# -*- coding: utf-8 -*-
from dominate.tags import *
from flask import Flask, request
from flask_nav import Nav, register_renderer
from flask_nav.elements import Navbar, View, Subgroup
from flask_nav.renderers import Renderer
from micawber import bootstrap_basic
from playhouse.sqlite_ext import SqliteExtDatabase
impo... | ilhamwk/accounting | app.py | Python | cc0-1.0 | 3,075 | [
"VisIt"
] | 377040ca6fa8927a00a42ea26980301430928cedf630aa6118dc69d470acd842 |
import os
import subprocess
import sys
import time
from pathlib import Path
from types import ModuleType
from typing import List
import _pytest.pytester as pytester_mod
import pytest
from _pytest.config import ExitCode
from _pytest.config import PytestPluginManager
from _pytest.monkeypatch import MonkeyPatch
from _pyt... | RonnyPfannschmidt/pytest | testing/test_pytester.py | Python | mit | 27,907 | [
"Brian"
] | f281de960717f37ac57feba6584b5745f40d688f28083da1d60b98da12cbfe03 |
from sympy.core import S, C, sympify, Function
from sympy.ntheory import sieve
from math import sqrt
###############################################################################
######################## FACTORIAL and MULTI-FACTORIAL ########################
##########################################################... | pernici/sympy | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 12,993 | [
"VisIt"
] | 20ae74e4ca2905ddfd46bd46276fddc32adf576e2e6bc748d4eae70738152df5 |
from rest_framework import generics
import django_filters.rest_framework
from qmpy.web.serializers.entry import EntrySerializer
from qmpy.materials.entry import Entry, Composition
from qmpy.materials.formation_energy import FormationEnergy
from qmpy.analysis.vasp import Calculation
# from api_perm import *
from qmpy.u... | wolverton-research-group/qmpy | qmpy/web/views/api/entry_list_view.py | Python | mit | 7,913 | [
"VASP"
] | ba401f9a07db2c34dac20924b0fa1584900751f534d01a380548445c2a53958f |
"""
An abstract syntax tree walker that generates the minimal set of tokens
that results in the same tree and reports these tokens to a token
consumer.
"""
from bigrig import ast
from bigrig import token as t
from bigrig.visitor import NodeVisitor
from .precedence import precedence as get_precedence
NEEDS_SEMICOLON =... | jeffkistler/jscompiler | jscompiler/code_generator.py | Python | bsd-3-clause | 16,506 | [
"VisIt"
] | 9f80f4b312c514e3562603f7e6350248d44c85f980380bfe07cb0da8d0878b91 |
import html
import json
import uuid
import sys
import os
import datetime
from flask import Flask, request, redirect, render_template, send_file, session, send_from_directory
from werkzeug.exceptions import abort
import facebook
from accounts.users import UserJobs, JobDates
from communities import merge_similar
from ... | kanghj/dinner-tables-planner | app.py | Python | mit | 18,498 | [
"VisIt"
] | bc3ed1c6482c064b9fffdb8685c46e9abf237e357f35ce6dca4b6ec5ceb80f20 |
from .base import *
class group(object):
"""
cytoscape session interface as shown in CyREST's swagger documentation for 'group'.
:param url: an url of the type 'http://' + host + ':' + str(port) + '/' + version + '/'.
"""
def __init__(self, url):
self.__url = url + 'commands/group'
d... | idekerlab/py2cytoscape | py2cytoscape/cyrest/group.py | Python | mit | 10,777 | [
"Cytoscape"
] | 1cc80f5ebfa4658681a6210091909af89371e78a769ea1bdb13eb65ef226489f |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/epgservicenow.py | Python | gpl-2.0 | 7,570 | [
"VisIt"
] | 8d786605aade2e34c1139f6555f22fd2a525f768e052e568bde5d068d5b71d87 |
#!/usr/bin/python3
#
# Copyright (c) 2012 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/tools/bam_stats/common.py | Python | mit | 6,580 | [
"pysam"
] | d8cd07925883d0dde5ac82231f204906d4365fa7626e73a57b83161e2b9a8fd0 |
#!/usr/bin/env python
# $Id: cleanup.py 2459 2008-11-12 17:31:10Z oliver $
"""Remove files from a staged SGE python script: parses the SGE log
file to ssh into the node and remove the stage dir. Can also parse
some of my older Charmm/SGE log scripts that contain hostname and
scratch dir information.
"""
import sys,os... | CTCNano/GromacsWrapper | staging/extra/cleanup.py | Python | gpl-3.0 | 3,031 | [
"CHARMM"
] | 40d2e06172d2dc045e04d9349a2749e0808cfd395b205bc76da68770ed007dc2 |
# Copyright (c) 2012 OpenStack Foundation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | priya-pp/Tacker | tacker/tests/unit/test_policy.py | Python | apache-2.0 | 23,526 | [
"BLAST"
] | 3355531e0375252ad30ff6f8346fd503208e3685f231d585a19e9bbe70f07e33 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | hryamzik/ansible | lib/ansible/modules/network/avi/avi_actiongroupconfig.py | Python | gpl-3.0 | 5,477 | [
"VisIt"
] | c704a7ae8beff71483fb02e4fb8e71cd74baaa033ffe8c5eeee4b57f30b2bdec |
# Placeholder because parallel moved
# Remove this in version 1.0
from __future__ import absolute_import
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("parallel has moved to MDAnalysis.lib.parallel "
"and will be removed fr... | kain88-de/mdanalysis | package/MDAnalysis/core/parallel.py | Python | gpl-2.0 | 414 | [
"MDAnalysis"
] | 1fe95f545e0746548416c982366c76642619c9bdb9ff22c1110411766f9789df |
from django.conf.urls import url
from django.utils import timezone
from django.views.generic import RedirectView
from . import views
def get_current_date_str():
now = timezone.now()
return timezone.template_localtime(now).strftime("%Y-%m-%d")
urlpatterns = [
url(r'^$', views.index, name='index'),
# ex... | craighagan/rvumanager | rvusite/rvu/urls.py | Python | apache-2.0 | 1,596 | [
"VisIt"
] | 5c49b85c7d33d55949faae13610e59f377bbd6a2fdee4e86e5d9a6ad41b8ddb8 |
#! /usr/bin/python
import numpy as np
from astropy import units as u
from astropy import constants as c
'''
Calculates SNR and RV precision, given telescope and stellar parameters. Radial Velocity uncertainty based off of signal in a somewhat idealized spectrograph, and stellar type. Stellar spectra are BT-Settl, if i... | pdn4kd/reimagined-palm-tree | rvrms_demo.py | Python | mit | 9,730 | [
"Gaussian"
] | 8a0b304326734ec14358a2f8e311a98c6d0ed06679c2c9be8587e6bfa0a06d7c |
"""Generate HDL from stimulus models (when possible)."""
from . import HDLSimulationObject
from ..abshdl import HDLObject
from ..abshdl.signal import HDLSignal
from ..abshdl.highlvl import HDLBlock
from .util import concat
import ast
import inspect
import textwrap
import astunparse
class IllegalCodeError(Exception):... | brunosmmm/hdltools | hdltools/sim/hdl.py | Python | mit | 23,254 | [
"VisIt"
] | 6b5b41d54e64365841e6d70e2b4c48754ffe5d4b83b5ac2bde422f32693d7db6 |
import os
if os.geteuid() != 0:
exit("You need to have root privileges to run this script.\nPlease try again, this time using 'sudo'. Exiting.")
import urllib, json
response = urllib.urlopen("http://10.0.1.2/data/config.json")
data = json.loads(response.read())
if data["ip"] in open("/etc/hosts").read():
pr... | wyattjoh/atlantis.io | script/script.py | Python | mit | 611 | [
"VisIt"
] | d82cca2da5c2181f3582ea8262bb54d006d79f0416bf787b93628da26f26c4b7 |
import os
import pickle
import random
import numpy as np
from scipy.ndimage.filters import gaussian_filter
# PATHS
split_directory = '../data_shops/page_sets/splits/'
test_results_directory = '../test_results/'
snapshots_directory = '../models/snapshots/'
boxes_directory = '../data_shops/input_boxes/'
priors_directory... | gogartom/TextMaps | tools/utils.py | Python | mit | 3,195 | [
"Gaussian"
] | cadf362e9bbabd1de7684859fede454f9a5d324ae72a4efaf10550d4672a86f6 |
# 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... | hang-qi/models | inception/inception/cifar10.py | Python | apache-2.0 | 21,154 | [
"Gaussian"
] | 6970f1d64b09370c2511ba081065828641dbc6bde816bca5811fe89b3236e09f |
# Copyright 2008 by Jens Andersson and Wade Brainerd.
# This file is part of Colors! XO.
#
# Colors 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 ... | Daksh/Colors | colors.py | Python | gpl-3.0 | 89,780 | [
"FLEUR"
] | b992a49375775d5b4f6239f004251d8e1aae692e4269aa7012820659e112c76c |
#
# Copyright (C) 2013-2018 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 late... | hmenke/espresso | samples/minimal_random_number_generator.py | Python | gpl-3.0 | 1,620 | [
"ESPResSo"
] | bf705adf5fa23163bfcecaed36f007f57dd3dfc8cb20a5a02d53fbb0b02ca3c7 |
# Copyright 2018-present Facebook, 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
#
# Unless required by applicable law or agreed to i... | brettwooldridge/buck | scripts/top_down_stress_tester.py | Python | apache-2.0 | 7,114 | [
"VisIt"
] | bcd3c54b00122e840ebb04e526128f4bd20911842768b0792de45e63cda25b0d |
#!/usr/bin/python
from __future__ import division
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = [""]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
import subprocess, sys, re, inspect, time, shutil
from os import makedirs, sys... | Koonkie/MetaPathways_Python_Koonkie.3.0 | libs/python_modules/grid/BlastGrid.py | Python | mit | 23,442 | [
"BLAST"
] | 4b989723820a9d99ad3ee117649fba7fda2e906bc84294cf63848f01de201db0 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2011, MBARI"
__credits__ = ["Chander Ganesan, Open Technology Group"]
__license__ = "GPL"
__version__ = "$Revision: 1.1 $".split()[1]
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__status__ = "Development"
'''
The DAPloader... | duane-edgington/stoqs | stoqs/loaders/DAPloaders.py | Python | gpl-3.0 | 141,658 | [
"NetCDF"
] | 8f2d6609cf7942e8aa78b47ba83dea4cd4d8f7ffc6f8d996d0bb9a44eead0055 |
from __future__ import division
import abc
import warnings
import numpy as np
import six
np.seterr('warn')
from scipy.special import gamma as scipy_gamma
from scipy.special import gammaln as scipy_gammaln
from astropy.modeling.fitting import _fitter_to_model_params
from astropy.modeling import models
from stingray... | evandromr/stingray | stingray/modeling/posterior.py | Python | mit | 28,203 | [
"Gaussian"
] | 64cc024891bf62ae6b7aca038d1c887ea97f926094cc5d5306dc010e0e146d3b |
from __future__ import absolute_import, division, print_function, unicode_literals
from xarray import DataArray, Dataset
from mkgu import fetch
class DataPoint(object):
"""A DataPoint represents one value, usually a recording from one neuron or node,
in response to one presentation of a stimulus. """
d... | jjpr-mit/mkgu | mkgu/assemblies.py | Python | mit | 1,790 | [
"NEURON"
] | 31eab9b2ce6adc49cbace4c4eb93429289af4c3b52e3cde1f4851d56701beaa2 |
import numpy as np
import pandas as pd
from scipy.sparse import csc_matrix, lil_matrix, diags
from JacobianBased import IwamotoNR
np.set_printoptions(linewidth=10000, precision=3)
# pd.set_option('display.height', 1000)
pd.set_option('display.max_rows', 500)
pd.set_option('display.max_columns', 500)
pd.set_option('d... | SanPen/PracticalGridModeling | examples/topology_engine.py | Python | gpl-3.0 | 22,254 | [
"VisIt"
] | b9c8c692628777d47cc7c8023f92f084d12b144898da2d2fbfa8e10127ffdf8d |
#!/usr/bin/env python
'''manipulate SAM file.'''
#import built-in modules
import os,sys
import re
import string
from optparse import OptionParser
import warnings
import string
import collections
import math
import sets
import random
#import third-party modules
from bx.bitset import *
from bx.bitset_builders import *
... | parlar/calls2xls | external/CrossMap/usr/lib64/python2.7/site-packages/cmmodule/SAM.py | Python | mit | 154,432 | [
"pysam"
] | d3a0bb9b22d2b628fbf099b9a4b235db9cdb52c934c4f1fe5f81e776a6ea3d71 |
'''
http://pymolwiki.org/index.php/cgo_arrow
(c) 2013 Thomas Holder, Schrodinger Inc.
License: BSD-2-Clause
'''
from pymol import cmd, cgo, CmdException
def cgo_arrow(atom1='pk1', atom2='pk2', radius=0.5, gap=0.0, hlength=-1, hradius=-1,
color='blue red', name='', state=0):
'''
DESCRIPTION
C... | gnina/scripts | cgo_arrow.py | Python | bsd-3-clause | 2,135 | [
"ChemPy",
"PyMOL"
] | e1f4cf286661be7730f9505db3b2912108e989364d4fe082cae586f4f1f914bb |
# -*- 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
urlpat... | ssharpjr/twoscoops | config/urls.py | Python | bsd-3-clause | 1,279 | [
"VisIt"
] | a11fb01292c52c795a773bacd2c35ce221853c2b5462f96942e8632aebf143f0 |
#!/usr/bin/python
#
# Copyright 2004 by Centaur Software Engineering, Inc.
#
#
# This file is part of The CSE Python Library.
#
# The CSE Python Library 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 Foundati... | boudewijnrempt/HyvesDesktop | 3rdparty/socorro/socorro/lib/ConfigurationManager.py | Python | gpl-2.0 | 22,481 | [
"exciting"
] | 4dca0b2c1598a4cc8e14ef927647b83e4c0b628a78e833ff14c48b145f71286c |
# coding=utf-8
import json
import os
import responses
import watson_developer_cloud
@responses.activate
def test_success():
dilemmas_url = 'https://gateway.watsonplatform.net/tradeoff-analytics/api/v1/dilemmas'
dilemmas_response = '{"problem": {"options": [{"values": {"price": 239, "RAM": 2048, "weight": 130}... | semplea/characters-meta | python/alchemy/test/test_tradeoff_analytics_v1.py | Python | mit | 2,074 | [
"Galaxy"
] | 16fa8f1495bdbb90ac9afec9b10adf51f2a08dc2056c2867b3aa8c527dea0b9b |
"""
==================
Visualize surfaces
==================
Here is a simple tutorial that shows how to visualize surfaces using DIPY. It
also shows how to load/save, get/set and update vtkPolyData and show
surfaces.
vtkPolyData is a structure used by VTK to represent surfaces and other data
structures. Here we show... | matthieudumont/dipy | doc/examples/viz_surfaces.py | Python | bsd-3-clause | 2,840 | [
"VTK"
] | b61e0b7e36bbab3f69df6ee8ecba69fc3b91419dbd60beb3871dc4372748e705 |
from splinter import Browser
import time
import os
import six
import json
import re
from bitpay.client import Client
from bitpay import key_utils
ROOT_ADDRESS = os.environ['RCROOTADDRESS']
USER_NAME = os.environ['RCTESTUSER']
PASSWORD = os.environ['RCTESTPASSWORD']
PEM = '-----BEGIN EC PRIVATE KEY-----\nMHQCAQEEICg7E4... | bitpay/bitpay-python | features/steps/pair_steps.py | Python | mit | 5,800 | [
"VisIt"
] | 8200493797a1ce0e801f0940d51b049099b535a2032318e16af1b8e25c134e65 |
'''
Uses numerical integration to calculate accurate values for gfd, and then
determines the beta's at which to transition between polynomial orders of
approximation.
This only really needed to be run once, but it's here in case changes are
made that require rerunning it.
In order to run this, the branchless generali... | scott-maddox/fdint | scripts/templates/gen_gfd_BSs.py | Python | bsd-3-clause | 2,724 | [
"DIRAC"
] | 38b8ddd6b8a25927b895521274ee17275e567349ec84ced473aabb078585436e |
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | espressopp/espressopp | src/tools/prepareComplexMolecules.py | Python | gpl-3.0 | 11,685 | [
"ESPResSo",
"Gromacs"
] | 4eb996b999c4e7dc95649c155eaf7abe76075a416d93bf16f11fdb3bf5bb53ef |
#!usr/bin/env python
"""
test to see how to write a custom ugrid file reader
"""
import numpy as np
import netCDF4
import pyugrid
def load_gnome_tri(filename):
"""
load an fvcom/gnome netcdf file
:param filename: the path to the file to load
:returns: an UGRID object with the data from the file
... | rsignell-usgs/notebook | pyugrid/test_bed/load_gnome_tri.py | Python | mit | 5,610 | [
"NetCDF"
] | e775a3a54a2ece5d931d8f4abdcda1a76005376aec53605a44f4af29318cc65e |
from pycalphad.fitting import build_pymc_model, plot_results, setup_dataset, Dataset
from pycalphad import Database
from sumatra.projects import load_project
from sumatra.parameters import build_parameters
from sumatra.datastore.filesystem import DataFile
from corner import corner
import tables
import matplotlib
matplo... | richardotis/pycalphad-fitting | run.py | Python | mit | 6,885 | [
"pycalphad"
] | c293f13c3ff941081e9e1ada7c9a7cb54577aa7e479c071aba958ecbdf829d6c |
import constant
from model import *
from synapse import *
from potential import *
__all__ = 'Neuron',
class Neuron:
name_ = 0
def __init__(self, model, name=None):
if name is None:
name = "Neuron #" + str(Neuron.name_)
Neuron.name_ += 1
self.name = str(name)
se... | lennart96/neurons | neuron.py | Python | isc | 2,306 | [
"NEURON"
] | cd2ac8a583836909c0d9b3af842155e21b9843c3af560169ba8854970809539a |
#!/usr/bin/pvpython
from paraview.simple import *
#position camera
view = GetActiveView()
if not view:
view = CreateRenderView()
#draw the object
Show()
dp = GetDisplayProperties()
#set point color
dp.AmbientColor = [1, 1, 1] #red
#set surface color
dp.DiffuseColor = [0, 1, 0] #blue
#set point size
dp.Point... | wegatron/SSCCE | python/paraview_pc_white.py | Python | gpl-3.0 | 388 | [
"ParaView"
] | 989dc3c8d2af8eb5c7f10c9b6b6bb146c4a3a85d9fb59119db8c71c9f67ef8dc |
from __future__ import division, print_function
import numpy as np
from scipy.stats import gamma, exponnorm
class synthetic_light_curve_generator:
def __init__(self, T, N, rseed=None):
"""
Class for simple synthetic light curve generation
Light curves are time series of stellar mag... | phuijse/P4J | P4J/generator.py | Python | mit | 11,977 | [
"Gaussian"
] | 52d1f981dd3b7efce936dc779b7b861b08946b0346346f788aae5ae01c07e3db |
# 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/chkfile.py | Python | apache-2.0 | 5,788 | [
"PySCF"
] | 180a0fcd71f577aacc8dc7bbe61b6461e11b57c5b3f0ee5ebf59064fdbaeb51b |
import unittest
import numpy
from pyscf.pbc import gto
from pyscf.pbc import scf,cc
from pyscf import cc as mol_cc
from pyscf.pbc.tools.pbc import super_cell
#from pyscf import lib
#from pyscf.pbc import gto
#from pyscf.pbc import scf,cc
#from pyscf.pbc.cc import kccsd_uhf
#from pyscf.pbc.cc import kccsd
#from pys... | gkc1000/pyscf | pyscf/pbc/cc/test/test_kuccsd_supercell_vs_kpts.py | Python | apache-2.0 | 1,546 | [
"PySCF"
] | d8185db65a1c2805c492692a3a9d13ba8d4a238e9fb6ebc658ee52e13311a3f7 |
#
# Copyright (c) 2011, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyrigh... | greglandrum/rdkit | rdkit/Chem/UnitTestInchi.py | Python | bsd-3-clause | 12,581 | [
"RDKit"
] | 0a134fb0f2f299c3a7cb15dbd6144d5c248bbbb905e38272aca11decc8d1a1fa |
"""GuitarSet Loader
.. admonition:: Dataset Info
:class: dropdown
GuitarSet provides audio recordings of a variety of musical excerpts
played on an acoustic guitar, along with time-aligned annotations
including pitch contours, string and fret positions, chords, beats,
downbeats, and keys.
Gui... | mir-dataset-loaders/mirdata | mirdata/datasets/guitarset.py | Python | bsd-3-clause | 18,966 | [
"VisIt"
] | 73148b127d5e2f949c09430e36fe5f8deb3b86fbd65d9919f0a1fef5bb002647 |
from __future__ import print_function
import re, sys, datetime, csv, pkgutil
from . import net, shared
try:
from io import StringIO
except ImportError:
from cStringIO import StringIO
def pkgdata(name):
data = pkgutil.get_data("pythonwhois", name)
if sys.version_info < (3, 0):
return data
else:
return data.de... | shilad/geo-provenance | py/pythonwhois/parse.py | Python | apache-2.0 | 74,488 | [
"MOE"
] | 2c1398180c9377faf4266e5792ebfd61cb71d9fcdea854def5a079a0eea557a9 |
#!/usr/bin/env python3
import configparser
import backend
import json
from flask import Flask
from flask_restful import Resource, Api, reqparse
from flask.ext import restful
from flask.ext.restful.utils import cors
config = configparser.ConfigParser()
config.read('config.ini')
print(config.sections())
recommender =... | giocatori86/AdamGoodPlanner | frontend_prototypeversion/Working BackEnd/__main__.py | Python | mit | 2,563 | [
"VisIt"
] | a8eba0cbc833596441fbfa8f707e9ff192f77660e0a846df1eefe0da011afaa0 |
# -*- coding: utf-8 -*-
#
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.... | kallimachos/rst | doc/conf.py | Python | gpl-3.0 | 7,211 | [
"Brian"
] | b7158afb3dfbce83a71857d06a1bc116cb5ea9ecafb35b6808fc8d59b52850fb |
#! /usr/bin/python2
import subprocess
import sys
import os
import time
from subprocess import PIPE
import socket
default_params = ''
output_file_prefix = 'output'
if len(sys.argv) > 1:
output_file_prefix = sys.argv[1]
#
# SCENARIO
#
# 0: radial dam break
# 1: gaussian
# 2: balanced steady state u
# 3: balanced ste... | schreiberx/sweet | archive/benchmarks_plane/rexi_tests_lrz/2015_12_27_scalability_rexi_spec/params.py | Python | mit | 5,458 | [
"Gaussian"
] | 3c9663951d3e363b540bafababa27ac4923dbc4382bf6f68cdb53c0df8665e16 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.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 publish... | jaddison/ansible | lib/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 5,506 | [
"Brian"
] | 7dc92d1ce5c31aab67a6d47445a8f429afc27c332cebe91b3a6919bf24461570 |
#!/usr/bin/env python
'''
starting code on MKW 11 first
goal is to calculate the extent of the image, C30, for example
Before running:
* copy final *.tab to /home/rfinn/research/LocalClusters/EllipseTables/MKW11/.
* run
galTablesV4.py '*.tab'
to convert *.tab to *.dat files
Steps:
* cull the sample so only ... | rfinn/LCS | paper1code/LCScalcC30.py | Python | gpl-3.0 | 737 | [
"Galaxy"
] | c8318e38ee920b797d1636cee0844d5fc727ae7d5e00954a49f872cc479b3ada |
import numpy as np
from nose.tools import (
assert_true,)
from hyperspy import signals
from hyperspy import components
class TestRemoveBackground1DGaussian:
def setUp(self):
gaussian = components.Gaussian()
gaussian.A.value = 10
gaussian.centre.value = 10
gaussian.sigma.value... | sillvan/hyperspy | hyperspy/tests/signal/test_remove_background.py | Python | gpl-3.0 | 1,897 | [
"Gaussian"
] | c2db8a13f2a86b87a0cd2f1e032be24d409b8fe44784094f3fcb17e87ac625c8 |
"""
Created on Oct 29, 2014
Common functions that can be useful in any Python module development
"""
import vtk
import sys
import traceback
import numpy as np
import SimpleITK as sitk
import subprocess
from . import file_conventions
from .geometry_topology_data import *
class Util:
# Constants
OK = 0
ER... | acil-bwh/SlicerCIP | Scripted/CIP_/CIP/logic/Util.py | Python | bsd-3-clause | 15,676 | [
"VTK"
] | 524b952ffbcfe32564d68cb4529939e1ca5baf5aa429447b1c4577bc90340345 |
# -*- coding: utf-8 -*-
""" ChemconnectUtil.py Some of the command function are written """
__author__ = "Harsha Rani"
__copyright__ = "Copyright 2017, Harsha Rani and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer... | BhallaLab/moose | moose-core/python/moose/chemUtil/chemConnectUtil.py | Python | gpl-3.0 | 12,543 | [
"MOOSE"
] | 370355dd20a2b13d4937b94fbb9c32335257456f4bf98844b894e401a9dc3e44 |
# 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... | BackupTheBerlios/espressopp | src/analysis/IntraChainDistSq.py | Python | gpl-3.0 | 1,766 | [
"ESPResSo"
] | 8622d47d51a0ab6d4e11aec0142341d3f97558db1e80bd9a7eeac7264be2b0a8 |
""" an XML-RPC server to allow remote control of PyMol
Author: Greg Landrum (glandrum@users.sourceforge.net)
Created: January 2002
$LastChangedDate$
License: 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, f... | jandom/rdkit | External/pymol/modules/pymol/rpc.py | Python | bsd-3-clause | 17,656 | [
"PyMOL",
"RDKit"
] | b8c604a5df85392f98ab11decb61c26f3570cd2653d31aebe6dbff0cb2d71a71 |
from couchforms.models import XFormInstance
import fluff
from corehq.fluff.calculators import xform as xcalculators
from fluff.filters import ANDFilter, NOTFilter
from casexml.apps.case.models import CommCareCase
from corehq.apps.fixtures.models import FixtureDataType, FixtureDataItem
from corehq.apps.groups.models imp... | gmimano/commcaretest | custom/reports/care_sa/models.py | Python | bsd-3-clause | 13,371 | [
"VisIt"
] | 507e8377ea8a91b17a366a34194b36cb066ce55fcd6ce1737e5a31f9f5f61d67 |
# 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.
#
"""Deal with Motifs or Signatures allowing ambiguity in the sequences.
This class contains Schema which deal with Motifs and Signatures at
a higher ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/NeuralNetwork/Gene/Schema.py | Python | apache-2.0 | 26,273 | [
"Biopython"
] | 3590b3e045c9a66c7dedbee4e55fe444ca9e482b2cb2f439ddd26eabbb7ae891 |
# ***** 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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/test/unit/test_util_loop.py | Python | gpl-2.0 | 8,519 | [
"Brian"
] | 87e55f806890dc1280f5f15f93fce046c627642f8ce2f47cde8998a74d8ac2dd |
import logging, os, sys, time, sets, tempfile
from galaxy import util
from cgi import escape
log = logging.getLogger(__name__)
# Constants for data states
DATA_NEW, DATA_OK, DATA_FAKE = 'new', 'ok', 'fake'
class Data( object ):
def set_peek( self, dataset ):
dataset.peek = ''
dataset.blurb = 'da... | jmchilton/galaxy-central | galaxy/datatypes/data.py | Python | mit | 4,218 | [
"Galaxy"
] | 10b977c8a5cae662471ab883b59c57cf22853c553447e42a8c5bc0d0ed09d724 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division
from collections import namedtuple
"""
Copyright (C) 2016 Wesley Fraser
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, eithe... | fraserw/PyMOP | trippy/bgFinder.py | Python | gpl-2.0 | 9,471 | [
"Gaussian"
] | 21bed0f36018f6f40916126ced3fa6e7e3b4e08f21fa8cb05ea107f2de80eb5a |
# Copyright (c) 2011-2012 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Module that handles interactions with a Validation Pool.
The validation pool is the set of commits that are ready to be validated i.e.
ready ... | coreos/chromite | buildbot/validation_pool.py | Python | bsd-3-clause | 59,104 | [
"VisIt"
] | dba0a602b6a34ed47d99ec5bdb77237a1001f31dac6c3db56ac849dcd7159026 |
#!/usr/bin/python
"""
A simple routine to load in a LIGGGHTS hybrid dump file containing
contact and contact force data and convert into a .vtk unstructured
grid which can be used to visualise the force network.
Contributing author: Mark Bentley, Space Research Institute,
Austrian Academy of Sciences, mark.bentley@oe... | sn-amber/mylpp | src/dump2force.py | Python | gpl-2.0 | 8,918 | [
"ParaView",
"VTK"
] | 90660123a8087e31217a499071522394ee3f6b895042fb3c040ec15df05e505e |
"""Mimetype lookup helpers
@todo: Use the following to set up an internal header matcher:
- http://www.fileformat.info/format/arc/corion.htm
- http://www.fileformat.info/format/zoo/corion.htm
@todo: Fix this so it handles "one ext to multiple mimetypes" mappings properly
@todo: The extension checker needs to b... | ssokolow/unball | unball/mimetypes.py | Python | gpl-2.0 | 7,153 | [
"ADF"
] | 051ead9c8605b25fb64286acce679cdef086a006dd7f156aa5ed5ec9c9531614 |
#!/usr/bin/env python
from __future__ import division
import argparse
import sys
import pysam
from pycluster import cluster as cl, parse_clusters
# import pdb
def rpc_classify(cfile, prefix, insert_handles, gcov_dict,
cluster_bedpe, event_bedpe):
"""
Classify a set of rpcluster output.
... | talkowski-lab/Holmes | classifier/rpc_classify.py | Python | mit | 5,090 | [
"pysam"
] | 2e11149d0930a556dfb1858af6674deadee57ae57b317843b923ec9f7596fd51 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from __future__ import print_function
import string
import random
from termcolor import colored
from studio.launch.base import manager
from .contrib import build_structure
pypi_manager = manager.subcommand('pypi')
def _init_microsite(appname, socket_po... | qisanstudio/qstudio-launch | src/studio/launch/commands/pypi_commands.py | Python | mit | 3,578 | [
"GULP"
] | 8b6d622d5715a76ff2c9039b08af5ed2e8fcd1cf959647ac1746708162a4835a |
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, \
Union, Optional, Sequence, AbstractSet, Callable, Iterable
from typing.re import Match
from django.db import models
from django.db.models.query import QuerySet
from django.db.models import Manager, Sum, CASCADE
from django.conf import settings... | rishig/zulip | zerver/models.py | Python | apache-2.0 | 119,305 | [
"VisIt"
] | eed1740c7f1e60f8f013bc65f0b21a477f3269d71fadb8bc8c349850b60d950f |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | hehongliang/tensorflow | tensorflow/python/autograph/converters/control_flow.py | Python | apache-2.0 | 14,155 | [
"VisIt"
] | 9876d4245f0e94fe13105c8b6692eeba7a219512dbf25bf542989ae878f6aa68 |
#!/usr/bin/python
#
# CCLib_proxy Utilities
# Copyright (c) 2014 Ioannis Charalampidis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | wavesoft/CCLib | Python/cc_write_flash.py | Python | gpl-3.0 | 2,943 | [
"cclib"
] | 74db24ed9006f5b51be016a4fa440868c5ec1b8108901d448ad7113de4a86831 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/stats/ordination/_correspondence_analysis.py | Python | bsd-3-clause | 7,512 | [
"scikit-bio"
] | 24bed3c4f733d7cf7ce46bd669b1d01a04362eda2e071b64c6016dd10c8a2abd |
# This file is part of xrayutilities.
#
# xrayutilities is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed... | dkriegner/xrayutilities | examples/xrayutilities_define_material.py | Python | gpl-2.0 | 1,920 | [
"CRYSTAL"
] | 3d13cfc3c9bbf885ea3878e749e47f8f915a7306cd6d1d56c811f5e67d5533ab |
#!/usr/bin/env python
"""
Parse SAM/BAM file to find proper read pairs
"""
import os
import sys
import pysam
import pdb
import argparse
import datetime
import bisect
from string import lower
from MethylAnalyzer.MethError import MethError
from MethylAnalyzer.UtilityFuncs import check_file
def main(FLAG, min_ins, max... | epigenomics/methylmaps | scripts/parse_sam.py | Python | gpl-3.0 | 6,808 | [
"pysam"
] | dbe9984f3b093fcdb35b39d5464174b2d96d5994ad7b0babc891de830605243b |
from admin.osf_groups.views import (
OSFGroupsView,
OSFGroupsListView,
OSFGroupsFormView
)
from admin_tests.utilities import setup_log_view
from nose import tools as nt
from django.test import RequestFactory
from tests.base import AdminTestCase
from osf_tests.factories import UserFactory, ProjectFactory, O... | mfraezz/osf.io | admin_tests/osf_groups/test_views.py | Python | apache-2.0 | 3,863 | [
"Brian"
] | 3780ce567951a642864d0bc1a8ee1075cc458578cc74c4f109b650032563726a |
#!/usr/bin/env python
# Retrieves data from external data source applications and stores in a dataset file.
# Data source application parameters are temporarily stored in the dataset file.
import socket, urllib, sys, os
from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg...
from... | lappsgrid-incubator/docker-galaxy-lappsgrid | tools/data_source/data_source.py | Python | apache-2.0 | 5,654 | [
"Galaxy"
] | b5af1b6eda6ed79dfaa1876300e96ed9bc0ee6cc748b3926226f18a636849921 |
"""
Unit tests for enrollment methods in views.py
"""
import ddt
from mock import patch
from django.test.utils import override_settings
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from courseware.tests.helpers import LoginEnrollmentTestCase
from courseware.tests.modulesto... | geekaia/edx-platform | lms/djangoapps/instructor/tests/test_legacy_enrollment.py | Python | agpl-3.0 | 14,981 | [
"VisIt"
] | 2c772f5f11d0eafe738263be6137eaa6fb54fcf1eddafff3320149ce33243d12 |
#!/usr/bin/python
import numpy as np
from numpy.random import randn,dirichlet
from scipy.linalg import det, inv
from scipy.cluster import vq
from scipy.special import psi,gammaln
from core import *
try:
from _vbgmm1d import _evaluateHiddenState_C, _lnPD_C
ext_imported = True
except:
ext_imported = False
#print... | lucidfrontier45/PyVB | pyvb/old_ver/vbgmm1d2.py | Python | bsd-3-clause | 8,212 | [
"Gaussian"
] | e185493e34c052c2784a39725f7327886d0e4cede83918974184509aa647e4c9 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
import collections
import logging
import threading
import itertools
import time
import types
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
... | clinton-hall/nzbToMedia | libs/py2/concurrent/futures/_base.py | Python | gpl-3.0 | 23,798 | [
"Brian"
] | ed26b17e68f079e2a0c396d832a084d3d57fc3843403b37932d70577257cca92 |
# -*- coding: utf-8 -*-
# Copyright 2008-2014 Jaap Karssenberg <jaap.karssenberg@gmail.com>
'''This module defines the ExportTemplateContext, which is a dictionary
used to set the template parameters when exporting.
Export template parameters supported::
generator
.name -- "Zim x.xx"
.user
title
naviga... | Osndok/zim-desktop-wiki | zim/export/template.py | Python | gpl-2.0 | 15,765 | [
"VisIt"
] | 7b0ec7f42dee7e2b712609227150804f55916d924198f164f015b3dd27f112cb |
#######################################################################
#
# Copyright (C) 2001-2015, Michele Cappellari
# E-mail: michele.cappellari_at_physics.ox.ac.uk
#
# This software is provided as is without any warranty whatsoever.
# Permission to use, for non-commercial purposes is granted.
# Permission to modif... | cebarbosa/fossilgroups | ppxf/ppxf_util.py | Python | gpl-3.0 | 13,759 | [
"Galaxy",
"Gaussian"
] | e159664e94a79186bcae5755b6c6240c8099cb57ee83558573caca0019ef0a6c |
####################Drug Mean Residence Time Prediction ############################
#Author:Mengyuan Zhu, Binghe Wang
#Email: mzhu7@gsu.edu
#Department of Chemistry
#Georgia State University
#Usage: python mrt.py filename
##########################################################################
import numpy
from skl... | MengyuanZhu/PK_predict | mrt.py | Python | gpl-2.0 | 1,397 | [
"Pybel"
] | 80a6938cb701b60e94ade9ea18fe8917fa1a4d74962113a87cc16708e87a45cc |
def itemTemplate():
return ['object/tangible/loot/creature_loot/collections/shared_purple_rnd_cut_gem_style1.iff']
def customItemName():
return 'Rare Nova Crystal'
def biolink():
return 1
def requiredCL():
return 80
| agry/NGECore2 | scripts/loot/lootItems/veryrareloot/rare_nova_crystal.py | Python | lgpl-3.0 | 234 | [
"CRYSTAL"
] | 830576204f3bf82e9dc56fc7959cefae9af32415da772e933aa9bf09fa3a77d1 |
#!/usr/bin/env python
"""
This script regenerates the enum values in pymatgen.core.libxc_func.py.
It requires in input the path of the `libxc_docs.txt` file contained in libxc/src
The script parses this file, creates a new json file inside pymatgen.core
and update the enum values declared in LibxcFunc.
The script must ... | vorwerkc/pymatgen | dev_scripts/regen_libxcfunc.py | Python | mit | 3,520 | [
"pymatgen"
] | f4d6e1c3eec24eea7718a006d44883f6c32e18b315c8614809d5385c05805e83 |
#
# Copyright (C) 2013-2019 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... | KaiSzuttor/espresso | testsuite/python/writevtf.py | Python | gpl-3.0 | 5,882 | [
"ESPResSo"
] | cc3889c224861718f4441cb0cc4c893a8d15ff5f17b7dd5815a81cd59c6aaca6 |
# Copyright (c) 2014-2016 Genome Research Ltd.
#
# This file is part of IVA.
#
# IVA 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.
# ... | sanger-pathogens/iva | iva/tests/qc_test.py | Python | gpl-3.0 | 31,483 | [
"pysam"
] | 25805dcc4cb21a2f95ffc61ac615478275d3a932983f9fe05ed32ba2d5095b11 |
import fiona
import numpy as np
from numpy.linalg import norm
def compute_normals_2d(datadict):
"""compute vertex normals by averaging incident edge normals"""
def orthogonal(vec):
v = np.array([-vec[1], vec[0]])
return v/norm(v)
def normal(p,q):
"""returns unit vector orthogo... | Ylannl/masb2d | shp_reader.py | Python | gpl-3.0 | 2,999 | [
"Gaussian"
] | 072215fbc86fcc8181e3dbd8acc1bca07443d01fdf8ea62261a47e45bf71a89e |
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(... | mick-d/nipype_source | nipype/interfaces/ants/segmentation.py | Python | bsd-3-clause | 11,513 | [
"Gaussian"
] | 4305f14822cc4e2884c4da48d4b94b32fc2059f4cf74cdecad23e1d1414f48be |
# From: Bayesian Models for Astrophysical Data, Cambridge Univ. Press
# (c) 2017, Joseph M. Hilbe, Rafael S. de Souza and Emille E. O. Ishida
#
# you are kindly asked to include the complete citation if you used this
# material in a publication
#
# Code 10.2 Normal linear model, in Python using Stan, for assessing ... | astrobayes/BMAD | chapter_10/code_10.2.py | Python | gpl-3.0 | 2,536 | [
"Galaxy",
"Gaussian"
] | c22cd508b448bc50f0cbbcf4b7dac682b9e142bc7853ed82b7889f0b771358b2 |
# Copyright 1999 by Jeffrey Chang. 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.
# Patched by Brad Chapman.
# Chris Wroe added modifications for work in myGrid
"""Code to inv... | zjuchenyuan/BioWeb | Lib/Bio/Blast/NCBIWWW.py | Python | mit | 10,801 | [
"BLAST",
"Biopython"
] | f074004e8d9a944cd2dce3bfea74120c1b1ee26806a54d955c00668e5978e41d |
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