text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#
# Copyright (c) 2016 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... | yasharmaster/scancode-toolkit | tests/scancode/test_scan_cache.py | Python | apache-2.0 | 2,183 | [
"VisIt"
] | cac0feb540441d0d5842c8ecb0a25566265e49b9fbc2e89c612ea0bbac063c38 |
# The OARN Relief Nursery Database
# Copyright (C) 2015 Oregon Association of Relief Nurseries
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at... | wire-rabbit/oarn-database | oarndb/serializers/home_visit_serializers.py | Python | agpl-3.0 | 14,750 | [
"VisIt"
] | 78ce777ae2e52f5f6fa14a1c8a8c4faf2af50faa9c6a26a17942d068eeb6add0 |
from __future__ import print_function
import os
import sys
import pickle
from math import pi
import numpy as np
from ase.utils import prnt
from ase.units import Hartree, Bohr
class Heterostructure:
def __init__(self, q_points_abs, frequencies, interlayer_distances,
chi_monopole, v_monopole, ch... | robwarm/gpaw-symm | gpaw/response/heterostructure.py | Python | gpl-3.0 | 12,179 | [
"ASE"
] | b7d5a41ae82be307dc836405abb9e446f300fa67c67854dfbb90cd3822858010 |
__author__ = 'zhangxulong'
"""
==================
GMM classification
==================
Demonstration of Gaussian mixture models for classification.
See :ref:`gmm` for more information on the estimator.
Plots predicted labels on both training and held out test data using a
variety of GMM classifiers on the iris dataset... | daleloogn/realiseSID-from-Ratanpara | gmm_classification.py | Python | apache-2.0 | 3,785 | [
"Gaussian"
] | b752305d71412ed0434170d7f54375d7133082f6ca5594595b66c88f83aea6b3 |
#!/usr/bin/env python
"""
Launch the File Catalog shell
Example:
$ dirac-dms-filecatalog-cli
Starting DIRAC FileCatalog client
File Catalog Client $Revision: 1.17 $Date:
FC:/>help
Documented commands (type help <topic>):
========================================
add chmod find guid ls pwd ... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_filecatalog_cli.py | Python | gpl-3.0 | 2,168 | [
"DIRAC"
] | 38feeccfab63b1dae4454ee18b9aa07af291d270360291d4734fd7be12cd246e |
"""Find and deal with motifs in biological sequence data.
Representing DNA (or RNA or proteins) in a neural network can be difficult
since input sequences can have different lengths. One way to get around
this problem is to deal with sequences by finding common motifs, and counting
the number of times those motifs occ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/NeuralNetwork/Gene/Motif.py | Python | apache-2.0 | 8,212 | [
"Biopython"
] | cb24264281141029bf3c980754dde6f6026425c04020ead6a9539cc28b6610bb |
import argparse
import sys, os
import subprocess
#########################################
def parse_commandline():
if len(sys.argv)<=1:
print "Usage:"
print "%s -h" % sys.argv[0]
print "for the full list of command line options, or"
print "%s -p <pdb_root> [-l <ligand list>] [-w <workdir>] " % sys.argv[0]
e... | ivanamihalek/smallmol | gmx_lib/run_setup.py | Python | gpl-2.0 | 4,101 | [
"Gromacs"
] | d3f1207fb55fb33c14cea34cf1bf41069b4b868eea3a8463ed9501e55dd77482 |
from samcnet.mixturepoisson import *
import numpy as np
import samcnet.mh as mh
from samcnet.lori import *
import scipy.stats as st
import scipy.stats.distributions as di
import scipy
from sklearn.lda import LDA
from sklearn.svm import SVC
from sklearn.neighbors import KNeighborsClassifier as KNN
np.seterr(all='igno... | binarybana/samcnet | tests/all_poisson.py | Python | mit | 4,899 | [
"Gaussian"
] | bc5cd2eb81274c26cb5e56fd2c9a18cc4ceb3e6e149710893db38f992f814b30 |
from tcga_encoder.utils.helpers import *
from tcga_encoder.data.data import *
from tcga_encoder.definitions.tcga import *
#from tcga_encoder.definitions.nn import *
from tcga_encoder.definitions.locations import *
#from tcga_encoder.algorithms import *
import seaborn as sns
from sklearn.manifold import TSNE, locally_li... | tedmeeds/tcga_encoder | tcga_encoder/analyses/old/clustering_from_z_space.py | Python | mit | 8,825 | [
"Amber"
] | bfb0f0a3ea2e7263f66e31ddb11d1b74fc084cfdb89bc089d36b02df6d128c2d |
# This file is part of MyPaint.
# Copyright (C) 2018-2019 by the MyPaint Development Team.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option... | mypaint/mypaint | lib/floodfill.py | Python | gpl-2.0 | 32,353 | [
"Gaussian"
] | 6a8fc82f632fb8db690816f313012abe5080e7586983d73f7f888a48e164039b |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, unicode_literals
from django import template
from django.template.defaulttags import URLNode
from django.utils.http import urlencode
from django.utils.html import conditional_escape
from django.utils.safestring import mark_safe
from uturn.http import get... | roam/django-uturn | uturn/templatetags/uturn.py | Python | bsd-2-clause | 4,813 | [
"VisIt"
] | fe73120f74ea4ed1b4c8eefa5212323fa0d3c3af70134c94cd5ed40a994f5451 |
""" :mod: GFAL2_HTTPSStorage
=================
.. module: python
:synopsis: HTTPS module based on the GFAL2_StorageBase class.
"""
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger
class GFAL2_HTTPSStorage( GFAL2_StorageBase ):
""" .. class... | arrabito/DIRAC | Resources/Storage/GFAL2_HTTPSStorage.py | Python | gpl-3.0 | 884 | [
"DIRAC"
] | 316ae7257e8a316052423674ace739582a2c6f41e3f16c8a34c2ce551635c55d |
""" Module that contains client access to the Pilots handler.
"""
from DIRAC.Core.Base.Client import Client, createClient
@createClient('WorkloadManagement/PilotManager')
class PilotManagerClient(Client):
""" PilotManagerClient sets url for the PilotManagerHandler.
"""
def __init__(self, url=None, **kwargs):
... | fstagni/DIRAC | WorkloadManagementSystem/Client/PilotManagerClient.py | Python | gpl-3.0 | 676 | [
"DIRAC"
] | 98a7176aaee887973f2e6cb4043b13fc9c6cbaf69b5810e8c11e80d8abe1979d |
# -*- coding: utf-8 -*-
"""
Add color cycling fun to your i3bar.
This is the most pointless yet most exciting module you can imagine.
It allows color cycling of modules. Imagine the joy of having the current time
change through the colors of the rainbow.
If you were completely insane you could also use it to impleme... | Andrwe/py3status | py3status/modules/rainbow.py | Python | bsd-3-clause | 6,459 | [
"exciting"
] | 4aa661681e710534baf1d435651e4ca288de2b87d51e0b0b8039aab795f9a5da |
# -*- coding: utf-8 -*-
"""
-------------------------------
**distributions**
-------------------------------
Description
-----------
Create shortest path distributions for path families and edges.
Copyright (C) 2017 Michael W. Ramsey <michael.ramsey@gmail.com>
License
--------
This program is free software: you ca... | Dennett/asp | asp/distributions.py | Python | gpl-3.0 | 46,633 | [
"Gaussian"
] | b5abd60ecdce6b066606f90bab2cdd73295e10664d68f18c62142d6170ae5b28 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, ... | sparkslabs/kamaelia | Sketches/MPS/BugReports/FixTests/Kamaelia/Kamaelia/Device/DVB/Parse/PrettifyTables.py | Python | apache-2.0 | 21,192 | [
"CRYSTAL"
] | 2ae210e157b193b005a6427d138f68d2b8a060b2bb627de9fae14265882780d7 |
from Sire.IO import *
from Sire.Mol import *
from Sire.System import *
from Sire.MM import *
from Sire.Base import *
from Sire.Units import *
print("Reading in the coordinates of the waterbox...")
amber = Amber()
(waters, space) = amber.readCrdTop("test/io/waterbox.crd", "test/io/waterbox.top")
print("...done!")
clj... | chryswoods/SireTests | unittests/SireMM/testsoftcljff.py | Python | gpl-2.0 | 2,414 | [
"Amber"
] | 1d7543d6ce84cb16a570ae0e11d9d19d5b1735563b70b2836458cba6e8ef0144 |
# test_inflate.py
#
# Test harness for inflate.S
#
# Written & released by Keir Fraser <keir.xen@gmail.com>
#
# This is free and unencumbered software released into the public domain.
# See the file COPYING for more details, or visit <http://unlicense.org>.
import crcmod.predefined
import struct, sys, os
# Command... | keirf/Amiga-Stuff | inflate/test_inflate.py | Python | unlicense | 3,983 | [
"VisIt"
] | f4a250a079f0fbcfa128e73081246f110ad29e446bb1bf84531aa5a3c70cf648 |
import ast
from copy import copy, deepcopy
from collections import defaultdict
from artiq.transforms.tools import is_ref_transparent, count_all_nodes
class _TargetLister(ast.NodeVisitor):
def __init__(self):
self.targets = set()
def visit_Name(self, node):
if isinstance(node.ctx, ast.Store):... | kgilmo/penning_artiq | artiq/transforms/remove_inter_assigns.py | Python | gpl-3.0 | 5,024 | [
"VisIt"
] | 3b71f238e4f78515f2563e2d614c39bbac076333e3953eba5c1af85f428e1846 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kobejean/tensorflow | tensorflow/contrib/bayesflow/python/kernel_tests/monte_carlo_test.py | Python | apache-2.0 | 10,222 | [
"Gaussian"
] | 2c283b130373bd8198e024501b3c94fbfa22384072fc4ca24402e774d593d568 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
"""
This module provides utilities for basic math operations.
"""
import collections
from six.moves import zip
import numpy as np
def abs_c... | gpetretto/pymatgen | pymatgen/util/num.py | Python | mit | 4,781 | [
"pymatgen"
] | c354b4a02da143eca4b5e05a4e0c88afb2951bc474e9f69439fa3201ff0b6086 |
#!/usr/bin/python2.4
#
# Copyright 2007 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 require... | google/transitfeed | transitfeed/shapelib.py | Python | apache-2.0 | 19,662 | [
"VisIt"
] | 11b97760c6e702684b9d23b45a06267c6d9c3018bbf77b308db5481a5b9a641e |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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... | googleapis/python-service-directory | tests/unit/gapic/servicedirectory_v1/test_registration_service.py | Python | apache-2.0 | 212,499 | [
"Octopus"
] | a5684537c378e891aacd1355b90d689be735c7d069f16c2b73a8338e6602bf5c |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2016 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... | nadeemsyed/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 443,979 | [
"MOOSE"
] | b5ddc7d9ee9107c5a468a46b64400e900a9d974ea35f252590dea218679a5f59 |
from __future__ import print_function
##############################################################################
#
# Author: Alejandro Molina-Sanchez
# Run real-time simulations with yambo
#
# Warning: Real-time simulations requires several data folders for running
# properly. Before using this scripts compulsivel... | henriquemiranda/yambo-py | tutorial/si/map-symm.py | Python | bsd-3-clause | 1,731 | [
"Yambo"
] | 19610d70771e8298f84610eaf4e37cb4d62901b1b0f5c2fefca27011eb4605b1 |
from __future__ import print_function
import psi4
from psi4.driver import qcdb
#! A test of the basis specification. Various basis sets are specified outright and in blocks, both
#! orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls
#! qcdb.BasisSet infrastructure. Checks th... | rmcgibbo/psi4public | tests/python/mints9/input.py | Python | lgpl-3.0 | 8,998 | [
"Psi4"
] | 7678e266ab88a0747d5106702c46365914750193656972739b6e55c1a8e75b2a |
# coding=utf-8
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | corona10/grumpy | grumpy-tools-src/grumpy_tools/compiler/expr_visitor.py | Python | apache-2.0 | 16,901 | [
"VisIt"
] | 35e92d1cb565d1336fbfb12404f975b2f97a9c18275099235e30f02e49c4e3ee |
#!/usr/bin/env python
# Copyright (c) 2006 John Gilman
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation file... | NarlikarLab/DIVERSITY | weblogoMod/test_corebio/test_transform.py | Python | gpl-3.0 | 5,194 | [
"Biopython"
] | 32a5f9e92323f05b9970ae14eeafb8e0bc2b42dc198133d87e156552e4a6fb2a |
"""ABCs."""
# Authors: Guillaume Favelier <guillaume.favelier@gmail.com
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from abc import ABC, abstractmethod, abstractclassmethod
from contextlib import nullcontext
import warnings
from ..utils import tight_layout
class _AbstractRenderer(A... | pravsripad/mne-python | mne/viz/backends/_abstract.py | Python | bsd-3-clause | 25,141 | [
"Mayavi"
] | 1f051ca12bc67657b5e01abf32d3b4a3cb356c47e5e5d1583ca3ecfdc1c6cdd4 |
# proxy module
from __future__ import absolute_import
from mayavi.core.engine import *
| enthought/etsproxy | enthought/mayavi/core/engine.py | Python | bsd-3-clause | 87 | [
"Mayavi"
] | fd31d64bed0f7f29cc9b2a528aace2da5bc09c891a19499a22362b8f5b1d541f |
import lmfit
import numpy as np
from matplotlib import pyplot as plt
# construct data
x = np.linspace(-4, 4)
y = np.exp(-x**2)
noise = np.random.randn(x.size) * 0.1
y += noise
# define model and fit
model = lmfit.models.GaussianModel()
model.guess(y, x=x)
fit = model.fit(y, x=x, weights=1/noise**2)
fig = fit.plot()... | DiamondLightSource/auto_tomo_calibration-experimental | old_code_scripts/simulate_data/lmfit-py/examples/plot_fit.py | Python | apache-2.0 | 577 | [
"Gaussian"
] | 20ebe92fc0ef0a1323fad456cac3b24ea26238dfaa4b6fa43ea614d27c4fc7fb |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/io/test/test_molpro.py | Python | gpl-3.0 | 7,209 | [
"Molpro",
"Psi4"
] | 9904223be57f275a54364bb08a0dd0c726454a24a5f6a5c205f3a257234cf143 |
#The purpose of this script is to chop big molecules to small fragments by some kind of rules, so that some other molecules can be generated with these fragments.
#Main process:
#1. Use RDKit to make fragments by breaking some bonds and save these fragments to sdf files. Besides dummy atoms and hydrogens, if there ar... | liutairan/eMolFrag | Old versions/eMolFrag_2016_12_28_01/chopRDKit02.py | Python | gpl-3.0 | 20,348 | [
"RDKit"
] | e31c3b8ff7492ea797f006a743a2dcf54c9c40118717a1dcf811e53eeb6fb776 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_networkprofile.py | Python | bsd-3-clause | 3,710 | [
"VisIt"
] | 92a9adbc1088ebf3a4448394c8d7ea34cbc6a96a1c94e04c4eb0338258f573fe |
import datetime
import pytest
from pytvdb.models import SeriesData, SeriesSearchData, SeriesActorsData, BasicEpisode, SeriesEpisodes, BaseModel, \
SeriesEpisodesSummary, Episode
class TestModels:
@pytest.mark.unit
def test_jsonify(self):
data = {
"aliases": [
"Doctor ... | jwbaker/pytvdb | tests/test_models.py | Python | unlicense | 23,279 | [
"Firefly"
] | 521443bd3614a0685cc8d07e56c924fd6837cc614fb5ff8b97e55f849956ad6d |
"""GOG functions"""
import json
import logging
import os
import re
import time
from datetime import datetime, timedelta
import requests
from django.conf import settings
from django.utils import timezone
from django.db.models import Q
from django.db import IntegrityError
from common.util import get_auto_increment_slug... | lutris/website | providers/gog.py | Python | agpl-3.0 | 15,001 | [
"Galaxy"
] | 00afb947317de4a9fd0fcc40046cc66c47033316bd07aeb27e8f68a9a20e9f1b |
#!/usr/bin/python
# -------------------------------------------------------------------------
# ( Web front-end for CS' jamtemplate )
# ( Copyright (C) 2009 by Vincent Knecht <vknecht@users.sourceforge.net> )
# ( ... | garinh/cs | bin/progen.py | Python | lgpl-2.1 | 9,166 | [
"CRYSTAL"
] | b6859d79d51113318dcb1c3f7ddf5e34fce0a0d38f13bc904aa2091bef4c7abe |
# Copyright (c) 2006-2011, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 BioGeek <jeroen.vangoey@gmail.com>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Eevee (Alex Munroe) <amunroe@yelp.com>
# Copyright (c) 2015... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/astroid/astroid/manager.py | Python | mit | 14,204 | [
"VisIt"
] | cd5ebabb5287c8ad718d91b8dff3e2d5f697d559581a8972f2c581dfeac513bd |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-allow-site
# Author : Stuart Paterson
########################################################################
"""
Add Site to Active mask for current Setup
"""
from __future__ import pr... | petricm/DIRAC | Interfaces/scripts/dirac-admin-allow-site.py | Python | gpl-3.0 | 3,095 | [
"DIRAC"
] | 5bd2ef11c82492dadae68bfa6e61909cf010f92261d513f3f8608801fc4bd193 |
from setuptools import setup
setup(
name = 'pypremis',
version = '1.0.0b',
url = 'https://github.com/uchicago-library/uchicagoldr-premiswork',
author = "Brian Balsamo <balsamo@uchicago.edu>",
author_email = "balsamo@uchicago.edu",
packages = ['pypremis'],
description = "A set of python clas... | uchicago-library/uchicagoldr-premiswork | setup.py | Python | gpl-3.0 | 782 | [
"Brian"
] | 86eebe22873e2bed15677b49c2813f044cdc3f9976a0e7d67f96ba39ded6cd05 |
#!/usr/bin/python
"""
Copyright 2012 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | waypointMaps.py | Python | agpl-3.0 | 2,719 | [
"Galaxy"
] | 0714436fb0ea2400fa0740dc1be30159041c8f5a35f792817f111a1dc77f6c41 |
#!/usr/bin/env python3.5
#
# (C) 2017, Markus Wildi, wildi.markus@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
... | RTS2/rts2 | scripts/u_point/transform/u_sofa.py | Python | lgpl-3.0 | 11,842 | [
"VisIt"
] | 7ad889397f2dec90138a8b6c5b505ca9145cef24ed58b5d12988489d04c7fc9f |
#!/usr/bin/env python3
# Copyright (c) 2008-10 Qtrac Ltd. All rights reserved.
# This program or module 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
# version 3 of the Li... | x1o/QuickExpenses | mkpyqt.py | Python | gpl-2.0 | 9,262 | [
"Brian"
] | 5d786811272b874d3c2513288e421223258aea313e822dba30e2b7b4feac22bf |
#!/usr/bin/env python
# PythonJS to CoffeeScript Translator
# by Brett Hartshorn - copyright 2014
# License: "New BSD"
import sys
import ast
import pythonjs
class TransformSuperCalls( ast.NodeVisitor ):
def __init__(self, node, class_names):
self._class_names = class_names
self.visit(node)
def visit_Call(self, ... | pombredanne/PythonJS | pythonjs/pythonjs_to_coffee.py | Python | bsd-3-clause | 12,118 | [
"VisIt"
] | 06bbc9780657d078d0e954041fd3f1ee3bedc06a8161d6921319021bd0b74b0d |
# -*- coding: utf-8 -*-
""" *==LICENSE==*
CyanWorlds.com Engine - MMOG client, server and tools
Copyright (C) 2011 Cyan Worlds, Inc.
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... | zrax/moul-scripts | Python/xDialogStartUp.py | Python | gpl-3.0 | 34,291 | [
"VisIt"
] | 70ec3eb4db8aa27d238e13062f59a48f2466131ef01fccfeb20e40e78634308b |
import numpy as np
import numpy.ma as ma
import scipy.linalg
import scipy.optimize
import scipy.stats
import typing
import warnings
from numpy import diag, exp, sqrt
from numpy.matlib import repmat
from sklearn.metrics import euclidean_distances
from typing import Union, List
def columnwise_normalizes(*Xs) -> typing.... | sanghack81/SDCIT | sdcit/utils.py | Python | mit | 8,035 | [
"Gaussian"
] | 74c19349aada245f504d363c43a9e21dd359fe4e3679500ea2c8844afa60d5be |
# -*- coding: utf-8 -*-
"""
--------------------------------------------------------------------------
cvglmnet.m: cross-validation for glmnet
--------------------------------------------------------------------------
DESCRIPTION:
Does k-fold cross-validation for glmnet, produces a plot, and returns
a value ... | bbalasub1/glmnet_python | glmnet_python/cvglmnet.py | Python | gpl-3.0 | 14,576 | [
"Gaussian"
] | e057501b588b55df4710717f804351c88206a45de31546fada46d10914a86804 |
#!/usr/bin/env python
'''
compare
-------
Contains code necessary to evaluate the objective function,
.. math:: \chi^2 = w^2 (x_r - x_c)^2
where :math:`w` is a weight, :math:`x_r` is the reference data point's value,
and :math:`x_c` is the calculated or force field's value for the data point.
'''
from __future__ imp... | ericchansen/q2mm | q2mm/compare.py | Python | mit | 16,246 | [
"MacroModel"
] | 699ca8c359a073ecd06fdc819f57fddaf08d44aed504a5f00e33351643a7588e |
import director
import math
import textwrap
import drc as lcmdrc
import bot_core as lcmbotcore
import vtkAll as vtk
from director import transformUtils
from director import visualization as vis
from director import objectmodel as om
from director import lcmUtils
from director import ikconstraints
from director import c... | RobotLocomotion/director | src/python/director/drivingplanner.py | Python | bsd-3-clause | 69,106 | [
"VTK"
] | 033db24ede4306cee6bc9f842b31c4956f35c8cb03965335768e6bb5ca09a0a8 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | kyl191/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 20,263 | [
"Galaxy"
] | 1f4f3aa96ec309f824764c3d267320551a6774c06e6b89e8f8956e0c8023abe1 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 07 13:37:47 2016
"""
__version__ = "1.0"
__license__ = "MIT"
__author__ ="GP Greeff"
import numpy as np
import cv2
import matplotlib.pyplot as plt
#from math import sqrt as math_sqrt
from QtLoadSaveObjects import make_config_dict
np.seterr(invalid='raise')
#========... | gpgreeff/filament_vision_sensing | ROIA.py | Python | mit | 48,160 | [
"Gaussian"
] | 956507ec58047af46764439969694ef9ba8ac86a3fa01e88f478bc8bf41492bc |
"""
Author: Vic Jackson
I'm saving several tools that seem to get a lot of use into one convenient place to save time on
lookup and for ease of import.
These are really just a complete python noob's attempt to gather all the useful tools that I've
come across so far in my perpetually futile attempts to pass myself off... | etherwar/vtools | vtools/vtools.py | Python | mit | 16,165 | [
"Brian"
] | b1a5d073bfc0784545f0454f98010d60390d077a0b6c70613bfd77939d533458 |
# (C) 2012, Michael DeHaan, <michael.dehaan@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 published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any la... | wincent/ansible | plugins/callbacks/osx_say.py | Python | gpl-3.0 | 2,896 | [
"exciting"
] | 6ddf71af70f5895af348b9e02236a695137f72b868c77c00dcf3886b3371591a |
# -*- coding: utf-8 -*-
# Copyright 2020 Google LLC
#
# 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... | googleapis/python-analytics-data | tests/unit/gapic/data_v1alpha/test_alpha_analytics_data.py | Python | apache-2.0 | 68,446 | [
"Octopus"
] | 077a8605365f76da8626f62838aad0db7a5f24512b4e2075fa6f3df058384f5e |
# Etienne St-Onge
from __future__ import division
import h5py
import importlib
import logging
import numpy as np
from scipy.ndimage import map_coordinates
from nibabel.affines import apply_affine
# Import vtk functions
def import_vtk():
try:
vtk_lib = importlib.import_module('vtk')
except ImportErr... | StongeEtienne/trimeshpy | trimeshpy/vtk_util.py | Python | mit | 10,963 | [
"VTK"
] | c08cb339e6800204c9ef31da110b9246d5891a83e428f62bc1971edb9d45d509 |
data = (
'ha', # 0x00
'hu', # 0x01
'hi', # 0x02
'haa', # 0x03
'hee', # 0x04
'he', # 0x05
'ho', # 0x06
'[?]', # 0x07
'la', # 0x08
'lu', # 0x09
'li', # 0x0a
'laa', # 0x0b
'lee', # 0x0c
'le', # 0x0d
'lo', # 0x0e
'lwa', # 0x0f
'hha', # 0x10
'hhu', # 0x... | gquirozbogner/contentbox-master | third_party/unidecode/x012.py | Python | apache-2.0 | 4,576 | [
"BWA"
] | a7ce0ad91a4a65aae186d2526ce4dce941288644449ec0138f24dbc46256d693 |
#!/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... | gkc1000/pyscf | pyscf/prop/ssc/uhf.py | Python | apache-2.0 | 20,588 | [
"Gaussian",
"PySCF"
] | ab2e120bb01681caf47fc849f3bde772d130583e101baae5a023bd5a3225bef6 |
# This file is part of seq_crumbs.
# seq_crumbs 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.
# seq_crumbs is distributed in the hop... | JoseBlanca/seq_crumbs | test/seq/test_seq_filters.py | Python | gpl-3.0 | 28,208 | [
"BLAST"
] | 0ea81cf3158a2e8ab2e6780429bb5e26c06415762ba1e7efebf7ad4f1cc0e141 |
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 7 10:20:05 2014
@author: Jukka Saarelma
"""
import numpy as np
import matplotlib.pyplot as plt
import json
# The FDTD library is loaded as module
import libPyFDTD as pf
###############################################################################
# Assign simulati... | juuli/ParallelFDTD | python/testBench.py | Python | mit | 5,057 | [
"Gaussian"
] | 2bb2656ce0cbf66394cbf13db084e63e091238ad9390529448b813444d4a39d4 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import pytest
import ... | ansible/ansible | test/units/galaxy/test_collection.py | Python | gpl-3.0 | 41,259 | [
"Galaxy"
] | f74d0ce7cc9f54a1a7417d28d291f5d5ca32f3cf4f7f7c018882cace9f217ff9 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_BC_biomass_emissions_n96e_360d.py | Python | gpl-3.0 | 17,408 | [
"NetCDF"
] | 778074dce31c8191c5c33266e28814d098f58f8a4b89209522a99d954d75df3c |
#!/usr/bin/env python
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COP... | Kleptobismol/scikit-bio | skbio/diversity/alpha/_gini.py | Python | bsd-3-clause | 3,640 | [
"scikit-bio"
] | 74694b1ecd3cde3c3a2ad339acc8ec630faf03d4805d3a87389632090df15f71 |
# -*- coding: utf-8 -*-
# Generated by Django 1.9 on 2016-02-20 04:31
from __future__ import unicode_literals
import datetime
import django.core.validators
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
initial = True
dependencies = [
... | fenglb/mysite | accounts/migrations/0001_initial.py | Python | cc0-1.0 | 5,608 | [
"VisIt"
] | 568050bfb194c5c7e339a197f61630cae959092e1e22343f5a4403c0780da34d |
import vtk
from VtkRenderer import *
import numpy as np
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
WIDTH=640
HEIGHT=480
renWin.SetSize(WIDTH,HEIGHT)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindo... | sameeptandon/sail-car-log | process/tests/testVtkEllipsoid.py | Python | bsd-2-clause | 710 | [
"VTK"
] | 5c395a889e1d2d9d8078fe682768cd3f927c026376fe9a368f9e4dee9b92c0c2 |
# coding: utf-8
# Copyright (c) 2013 Jorge Javier Araya Navarro <jorgean@lavabit.org>
#
# This file is free software: you may copy, redistribute 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... | shackra/thomas-aquinas | summa/director.py | Python | bsd-3-clause | 26,992 | [
"VisIt"
] | ef2d8447e62a7e5880c3c2e6c6ccbe86f6639b8178f1177184f9e7289dd247eb |
# ======================================================================
# Atomistica - Interatomic potential library and molecular dynamics code
# https://github.com/Atomistica/atomistica
#
# Copyright (2005-2020) Lars Pastewka <lars.pastewka@imtek.uni-freiburg.de>
# and others. See the AUTHORS file in the top-level A... | Atomistica/atomistica | src/python/atomistica/deformation.py | Python | gpl-2.0 | 4,481 | [
"LAMMPS"
] | 6a1bd3c2d8a96609b959d7d3a9476c728c703fa7e25c7450d801c930196fc17c |
#!/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... | gkc1000/pyscf | pyscf/doci/doci_slow.py | Python | apache-2.0 | 10,896 | [
"PySCF"
] | 41f781fb6a1a908a385362686a94e74899228cd3438e319c08d2e06261bc5ddf |
# -*- coding: utf-8 -*-
import datetime as dt
from flask.ext.login import UserMixin
from octopus.extensions import bcrypt
from sqlalchemy.ext.associationproxy import association_proxy
from sqlalchemy.orm import backref
from octopus.database import (
Column,
db,
Model,
ReferenceCol,
relationship,
SurrogateP... | quaintm/octopus | octopus/models.py | Python | bsd-3-clause | 11,403 | [
"Octopus"
] | 640b1ded7784e5796d1cab611fd8815db82db0bfe7113e5dade88245822ae828 |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/ao2mo/test/test_outcore.py | Python | apache-2.0 | 4,958 | [
"PySCF"
] | 44439ac93ddc115015bcedea71d48d08664cdafe099d2a06a01e97529b9390d9 |
# -*- coding: utf-8 -*-
#
# This file is part of EventGhost.
# Copyright © 2005-2020 EventGhost Project <http://www.eventghost.net/>
#
# EventGhost 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... | EventGhost/EventGhost | eg/Classes/CheckUpdate.py | Python | gpl-2.0 | 5,663 | [
"VisIt"
] | 467880f6a99aecc3b327f73133de5876fcf97889ed97f78cee919150f5354034 |
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# 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 your option) any later version.
#
# This library ... | FedoraScientific/salome-hexablock | doc/pyplots/test_prism_quads.py | Python | lgpl-2.1 | 1,628 | [
"VTK"
] | f2e453e7fcc653933e880e458c2fe3dcf17be74e4bfcd58f8524a27b3cb3d9ff |
# Copyright 2019 Microsoft Corporation
# Copyright The Cloud Custodian Authors.
# SPDX-License-Identifier: Apache-2.0
"""
Azure Functions
"""
# Docker version from https://hub.docker.com/r/microsoft/azure-functions/
FUNCTION_DOCKER_VERSION = 'DOCKER|mcr.microsoft.com/azure-functions/python:3.0-python3.8'
FUNCTION_EXT_... | capitalone/cloud-custodian | tools/c7n_azure/c7n_azure/constants.py | Python | apache-2.0 | 4,152 | [
"ASE"
] | 67d71de1b8c12a79c5f1c282375b8b7a321f4d891ede84fa10c0303110a9dc11 |
#!/usr/bin/env python
#
# Copyright 2008 Jose Fonseca
#
# This program 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 3 of the License, or
# (at your option) any later version.
#
# This ... | lethalman/valag | xdot.py | Python | gpl-3.0 | 87,648 | [
"FLEUR"
] | b07664afac0809a5b27cb60a51662a96058bea6cc80abc4de9e8bd02a94e3d86 |
import numpy as np
import matplotlib.pyplot as plt
from generate_data import generate_timeseries_set as gtss
from plotter import *
from parameters import *
# ------------------------------------------------- CREATE TOY DATA!
if __name__ == '__main__':
print 'Creating some toy data...\n'
nStates = 4
numTS = ... | mathDR/BP-AR-HMM | EasyDemo.py | Python | mit | 3,065 | [
"Gaussian"
] | 5d4f63acb18699c3c9d060213a716d6f5d8b24f0e1248db343d6563ac7423674 |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Module: netcdf_to_shape.py
Created on Sun Jul 28 15:51:04 2013
@author: gcoombes
Dexcription: Create a shapefile of contours or probability regions from teh netcdf data
"""
### IMPORTS ###
from __future__ import print_function
import sys, os
import time
from itertoo... | gjcoombes/banks | banks/netcdf_to_shape.py | Python | mit | 5,527 | [
"NetCDF"
] | f53772b8acf349a87410a8bf711378e13a49484d100a9d33fef38bc45dcd52b5 |
""" A mock of the DataManager, used for testing purposes
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
from mock import MagicMock
from DIRAC import S_OK
dm_mock = Mag... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Client/test/mock_DM.py | Python | gpl-3.0 | 1,268 | [
"DIRAC"
] | 8b750b497fc788222093f4b8b0d50583cd19ba1b4c7a5487001dd22fa455c6d2 |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/conversion/test/test_cp2k.py | Python | gpl-3.0 | 2,320 | [
"CP2K"
] | 845b4ab482f38523d722f33a85e9d874c5e87139a6873f8ded9674c1a1f695af |
""" Python test discovery, setup and run of test functions. """
import py
import inspect
import sys
import pytest
from _pytest.mark import MarkDecorator
from py._code.code import TerminalRepr
import _pytest
cutdir = py.path.local(_pytest.__file__).dirpath()
NoneType = type(None)
NOTSET = object()
isfunction = inspect... | mitodl/xanalytics | pytest/python.py | Python | mit | 78,409 | [
"VisIt"
] | b262817eab4177920c5e71f15c78a74a6b9c0bd27ef047bd1e7b07c391a44179 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2006-2010 Edgewall Software
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://genshi.edgewall.org/wiki/License.
#
# This software consist... | davidfraser/genshi | genshi/template/eval.py | Python | bsd-3-clause | 21,073 | [
"VisIt"
] | aeb31fe94a53581a29216236290e1f4309523482af8bb0c015c3f4a17fab8830 |
import numpy as np
import unittest
import os
import discretize
try:
import vtk
except ImportError:
has_vtk = False
else:
has_vtk = True
class TestTensorMeshIO(unittest.TestCase):
def setUp(self):
h = np.ones(16)
mesh = discretize.TensorMesh([h, 2 * h, 3 * h])
self.mesh = mesh
... | simpeg/discretize | tests/base/test_tensor_io.py | Python | mit | 5,436 | [
"VTK"
] | 1a31d7d8915ba5b03c671a84cc05a9237da85be068d3a561fe925270938e9778 |
#!/usr/bin/env python
#import argparse
#from glob import glob
#-s test_samples.txt
#-b /mnt/lfs2/hend6746/wolves/reference/canfam31/canfam31.fa
#-i /mnt/lfs2/hend6746/
from os.path import join as jp
from os.path import abspath
import os
import sys
import argparse
parser = argparse.ArgumentParser()
parser.add_argumen... | shendri4/wolves_capture_130 | bam2vcf_GATK_wolves_chromosome.py | Python | apache-2.0 | 3,036 | [
"BWA"
] | f71c8768108ce99e693356e8500da08163baa8b8b48af214a5e5d06f65620119 |
# -*- coding: utf-8 -*-
#
# gap_junctions_inhibitory_network.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | terhorstd/nest-simulator | pynest/examples/gap_junctions_inhibitory_network.py | Python | gpl-2.0 | 6,036 | [
"NEURON"
] | 260befe41940f67ea5e7ce26e18e30998a14c467253a7e2167ccd38539c7a1b8 |
# Local Polynomial Approximation Smoother
#
# Smooths the data by fitting a 2nd order polynomial to a small window around
# each data sample using gaussian weighted least squares. This implementation uses
# the SciPy.ndimage convolve function.
#
import sys,os
import numpy as np
from scipy.ndimage import convolve
#
# ... | waynegm/OpendTect-Plugins | bin/python/wmpy/Experimental/LocalPolynomialApproximation/ex_lpa_smooth_scipy.py | Python | gpl-3.0 | 2,093 | [
"Gaussian"
] | ea79cad5bfffe828f6816a9b574c236cb1e5cee34d96d016063ba5eb1de24f5a |
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# Laurent El Shafey <Laurent.El-Shafey@idiap.ch>
# Sat Jul 21 19:31:41 2012 +0200
#
# Copyright (C) 2011-2014 Idiap Research Institute, Martigny, Switzerland
"""Tests the Weighted Gaussian
"""
import numpy
import math
import nose.tools
import bob.ip.base
import b... | tiagofrepereira2012/bob.ip.base | bob/ip/base/test/test_weightedGaussian.py | Python | bsd-3-clause | 3,174 | [
"Gaussian"
] | 7c9b01ac90d752f177d44863a1bb31d243a9f89b3b2b4a302be38f76792b05c3 |
############################################################################
# GE class representing SGE batch system
# 10.11.2014
# Author: A.T.
############################################################################
""" Torque.py is a DIRAC independent class representing Torque batch system.
Torque objec... | arrabito/DIRAC | Resources/Computing/BatchSystems/GE.py | Python | gpl-3.0 | 6,819 | [
"DIRAC"
] | bff3a822225d9a3a0c9c90328a48a7db7c758c2b7fb625e0af5a86fc8b245d53 |
# coding: utf8
#
# python-ipfix (c) 2013 Brian Trammell.
#
# Many thanks to the mPlane consortium (http://www.ict-mplane.eu) for
# its material support of this effort.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by t... | britram/python-ipfix | ipfix/message.py | Python | lgpl-3.0 | 28,142 | [
"Brian"
] | 72bd4b1b20561a7d6e3099808ff3dbda24116ef7268de3a1bdeeccf4ee984ee1 |
#
# Copyright (C) University College London, 2007-2012, all rights reserved.
#
# This file is part of HemeLB and is provided to you under the terms of
# the GNU LGPL. Please see LICENSE in the top level directory for full
# details.
#
from __future__ import absolute_import
import wx
from .Layout import H, V, Stret... | jenshnielsen/hemelb | Tools/setuptool/HemeLbSetupTool/View/ToolPanel.py | Python | lgpl-3.0 | 17,998 | [
"VTK"
] | 1d5bfa14c0ab755cb03f27d52d882944da396a8484549e72113eb742bfb55b7d |
# Copyright (c) 2016, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from yambopy.netcdf import *
from itertools import product
class YamboExcitonWeight(YamboSaveDB):
def __init__(self,filename,save='SAVE',path='.'):
#read save database
... | alexmoratalla/yambo-py | yambopy/excitonweight.py | Python | bsd-3-clause | 3,917 | [
"NetCDF",
"Yambo"
] | 8911dd63b683d8fa05e4e58d52c01e2314dbef1176655805f0fac2bbc7cb5f9e |
import mdtraj as md
import numpy as np
import simtk.unit as u
from .snapshot import Snapshot
from .topology import Topology, MDTrajTopology
from openpathsampling.engines import Trajectory, NoEngine, SnapshotDescriptor
__author__ = 'Jan-Hendrik Prinz'
class TopologyEngine(NoEngine):
_default_options = {}
de... | jhprinz/openpathsampling | openpathsampling/engines/openmm/tools.py | Python | lgpl-2.1 | 9,216 | [
"MDTraj",
"OpenMM"
] | 550ca3e5f6eee027c9bfa72eb2d05530ed0d8432895bd190feb61c8695707f33 |
#coding=utf-8
import tornado.web, time, json, xxtea, hashlib
from controller.base import BaseHandler
from util.function import not_need_login, hash
from tornado import gen
from tornado.escape import url_escape, utf8
from util.sendemail import Sendemail
class AjaxHandler(BaseHandler):
@not_need_login
def prepar... | resec/superhero | controller/auth.py | Python | mit | 9,168 | [
"VisIt"
] | 47c81d08a7839a8fc53d535483ebd28690a9ece3a9d260d057835e9cbbf26d95 |
"""
Views for the verification flow
"""
import json
import logging
import decimal
import datetime
from collections import namedtuple
from pytz import UTC
from django.utils import timezone
from ipware.ip import get_ip
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http impor... | antonve/s4-project-mooc | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 57,375 | [
"VisIt"
] | cef35eb1c324b757d10c0c9719d959a64caa911d6f0010246b9280103e177579 |
###
# Copyright 2008-2011 Diamond Light Source Ltd.
# This file is part of Diffcalc.
#
# Diffcalc 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... | DiamondLightSource/diffcalc | test/diffcalc/ub/test_calculation.py | Python | gpl-3.0 | 8,005 | [
"CRYSTAL"
] | ce389ea281005e960a35e409c7729aebf1dcf07ce34b4eb0df3c763e326f5109 |
import logging
import os
from datetime import datetime, timedelta
from galaxy import util, web
from galaxy.model.orm import and_, func, or_
from galaxy.util import inflector
from galaxy.web.form_builder import CheckboxField
from string import punctuation as PUNCTUATION
import galaxy.queue_worker
from tool_shed.util im... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/base/controllers/admin.py | Python | gpl-3.0 | 64,800 | [
"Galaxy"
] | 7f8fa6203f8ca037a73ebc2642656708ed0b7887c0f8e70af712a32310ee431e |
import os,sys
parentdir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.insert(0,parentdir)
from pyN import *
single_neuron = AdExPopulation(name='neuron', N=1)
brain = Network(populations=[single_neuron])
stim = [{'start':10,'stop':100,'mV':14,'neurons':[0]}]
results = brain.simulate(experimen... | ericjang/pyN | pyn_examples/6_AxEx_neuron.py | Python | bsd-2-clause | 496 | [
"NEURON"
] | 809a025ca27c0b1c9edeca9eea2ba04d3f13ac0245d8823cd56d75ed0bd529cd |
# -*- coding: utf-8 -*-
# md_format_converter.GromacsTrajOutput.py
#
# Copyright (C) 2012-2016 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
Manages addition of Gromacs output information to se... | KarlTDebiec/MDFormatConverter | GromacsTrajOutput.py | Python | bsd-3-clause | 2,962 | [
"Gromacs"
] | c0d30cd95c75e8939f979ba2a266b7d7295045d5c663d3a08dd4c90592182d68 |
import os
import sys
from paraview.simple import *
if len(sys.argv) != 3:
print "usage: dir = sys.argv[1], filename = sys.argv[2]\n"
exit()
dir = sys.argv[1]
filename = sys.argv[2]
#dir = r"c:\Users\Dmitry\Downloads\R20H20Post"
#filename = "input"
#os.chdir(r"c:\Users\Dmitry\Downloads\R20H20Post")
vtk_ext = 'vtu'
... | dmitryikh/nla3d | snippets/paraview_snippets.py | Python | mit | 1,293 | [
"ParaView",
"VTK"
] | d56bba5fc1cf9e623cf9e90d9beda66e2a1a3089a29ae74751a142bc950c980b |
# -*- coding: utf-8 -*-
#
# Copyright 2014 David Emms
#
# This program (OrthoFinder) is distributed under the terms of the GNU General Public License v3
#
# 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 Sof... | davidemms/OrthoFinder | scripts_of/blast_file_processor.py | Python | gpl-3.0 | 4,962 | [
"BLAST"
] | 400b59c28e6fbb12ab832950b1d89f99efc826ea7dcd31404781b3d2c8158edb |
import numpy as np
import pandas as pd
import mdtraj as md
filename = "./test.h5"
filename2 = "./test2.h5"
t = md.load(filename)[0:3]
top, bonds = t.top.to_dataframe()
print(top[0:10])
top.resSeq += (310 - 43)
t._topology = md.Topology.from_dataframe(top, bonds)
top, bonds = t.top.to_dataframe()
print(top[0:10])
... | hainm/MSMs | attic/src/code/hmsm/test_mdtraj_bug.py | Python | gpl-2.0 | 415 | [
"MDTraj"
] | 7f5f8ce58c1e2f5d5b71fadc69df21bcd45d1ab61a8b9346b7ce3ce47a895cdb |
"""Helpers to work with COPASI files."""
from pathlib import Path
import libsbml
def write_ids_to_names(input_path: Path, output_path: Path) -> None:
"""Write SBML ids as names."""
doc: libsbml.SBMLDocument = libsbml.readSBMLFromFile(str(input_path))
elements = doc.getListOfAllElements()
for element ... | matthiaskoenig/sbmlutils | src/sbmlutils/converters/copasi.py | Python | lgpl-3.0 | 455 | [
"COPASI"
] | b37db95cd692a1f8c6cd7df278d0838319b104795ff57f96c1cfe50372df8528 |
import os
import sys
import time
import subprocess as sub
from setuptools import setup
from setuptools.command.bdist_egg import bdist_egg
def cmd_exists(cmd):
return sub.call(["which", cmd], stdout=sub.PIPE, stderr=sub.PIPE) == 0
class MGEScanInstall(bdist_egg):
def run(self):
if cmd_exists("make") an... | MGEScan/mgescan | setup.py | Python | gpl-3.0 | 3,402 | [
"Galaxy"
] | 8a45235b7b9071e8c9262c574e184586a8d5ca44b5191b24d1f25a10fe27842f |
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