text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_network_comparison_response.py | Python | apache-2.0 | 10,111 | [
"VisIt"
] | a6ea6fbf978cd79793ff4b8f7abbd5f186841e206192aa64a33a91b9c3ac100f |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
ren1.SetBackground(0,0,0)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.SetSize(300,300)
iren = vtk.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/EnSight/Testing/Python/EnSightIronProtBin.py | Python | gpl-3.0 | 1,556 | [
"VTK"
] | 6b4c158a0ab4c976ee5bad94b77056deebe6aab8d1938e3fb3f4a646c356dc4b |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | liesbethvanherpe/NeuroM | neurom/check/tests/test_runner.py | Python | bsd-3-clause | 8,706 | [
"NEURON"
] | 79d38ec55aa9c9d0a148c87e60a50553890a48678fb5072fd94d3dcd03b066ec |
### R_test.py
import sys
import os
from pyper import R
import unique
if 'Xdarwin' in sys.platform:
try:
path = unique.filepath("AltDatabase/tools/R/Mac/R")
r = R(RCMD=path,use_numpy=True)
#print '1'
except Exception:
#print '2'
r = R(use_numpy=True)
elif os.name == 'nt':... | wuxue/altanalyze | R_test.py | Python | apache-2.0 | 1,184 | [
"Bioconductor"
] | 967b2087910cbb98a8e74098e5b46a53c2c75c5a9e2f58905e004770d3e99fc0 |
import os
import types
import warnings
from os.path import join
from stat import ST_MTIME
from docutils import nodes
from docutils.parsers.rst.roles import set_classes
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
def mol_role(role, rawtext, text, lineno, inliner, options={}, content=[]):
... | askhl/ase | ase/utils/sphinx.py | Python | gpl-2.0 | 5,309 | [
"ASE"
] | a79994a0710f448164a3e4b8267caef4cb3e10ed2ee59d7e98b8df9769208628 |
#!/usr/bin/python
# -*-coding:utf8-*-
"""
Decompression all the zip and rar files in the specific directory.
"""
import os
import zipfile
import traceback
import argparse
from pprint import pprint
def find_path_file(specific_file, search_directory):
"""
result_path_filename
"""
result_path_filen... | openslack/openslack-crawler | scripts/decomperssion.py | Python | apache-2.0 | 2,025 | [
"VisIt"
] | 1200c7d11f715090a002c9fc18243ddf90dc35f8026bcb17cac542682909aa27 |
#
# Copyright (C) 2006-2017 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Import all RDKit chemist... | ptosco/rdkit | rdkit/Chem/AllChem.py | Python | bsd-3-clause | 15,859 | [
"RDKit"
] | 1c72c9500eb5797c7e2d6e52aa2c971a4ddac408806440afeebc55002f4c28c5 |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
#
# DicomPatcher
#
class DicomPatcher(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Pytho... | lassoan/SlicerDicomPatcher | DicomPatcher.py | Python | bsd-3-clause | 17,819 | [
"VTK"
] | 151551ce4e9dbdaf293cd16e385977f8bf384b4c4706cdca1c30a83724928e9c |
import moose
import pylab
import rdesigneur as rd
rdes = rd.rdesigneur(
chanProto = [
['./chans/hd.xml'],
['./chans/kap.xml'],
['./chans/kad.xml'],
['./chans/kdr.xml'],
['./chans/na3.xml'],
['./chans/nax.xml'],
['./chans/CaConc.xml'],
['./chans/Ca.xml'... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex9.2_spines_in_neuronal_morpho.py | Python | gpl-2.0 | 1,420 | [
"MOOSE"
] | 9226fb92a9d158cabfd3b60b4e7a1f972d358117b010d2f7f9e6e4d41d6fb6be |
from django.db import models
from django.core.cache import cache
from protein.models import Protein
from residue.models import Residue
from mutation.models import Mutation
from construct.schematics import generate_schematic
from common.diagrams_gpcr import DrawSnakePlot
import pickle
class Construct(models.Model):
... | fosfataza/protwis | construct/models.py | Python | apache-2.0 | 18,892 | [
"CRYSTAL"
] | 7ec3cc0f53a5505f2cab064c6048cb3ddc9f1247cc221f3fa1862591f6e716f2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '... | le9i0nx/ansible | lib/ansible/modules/system/runit.py | Python | gpl-3.0 | 8,269 | [
"Brian"
] | 81dd81cc98c55fd570361565c8457d62166edc2f0d8d68b8fc31bf0b8ddc5698 |
import ast
import codecs
import os
from setuptools import setup
here = os.path.abspath(os.path.dirname(__file__))
class VersionFinder(ast.NodeVisitor):
def __init__(self):
self.version = None
def visit_Assign(self, node):
if node.targets[0].id == '__version__':
self.version = n... | ticosax/envdir | setup.py | Python | mit | 1,718 | [
"VisIt"
] | 4b9a2127d0493a2355aff79eaaeedba7f8fac4aa2a70a0ccd5ec0dbfc489b0a2 |
#
# 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... | yasharmaster/scancode-toolkit | tests/extractcode/test_archive.py | Python | apache-2.0 | 121,536 | [
"VisIt"
] | 9829f7633fad077aad8a0f035e49f0fd894e140541da5a0d94a01c1c7a99f113 |
#!/usr/bin/python
"""Test of Orca output when tabbing on a page with imagemaps.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on a blank Firefox window.
#
sequence.append(WaitForWindo... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/imagemap.py | Python | lgpl-2.1 | 15,539 | [
"ORCA"
] | a8ac71d052685186e3c3b00993e5685073675d607dce99bf2681faf09efa21e6 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAneufinderdata(RPackage):
"""WGSCS Data for Demonstration Purposes
Whole-genome s... | LLNL/spack | var/spack/repos/builtin/packages/r-aneufinderdata/package.py | Python | lgpl-2.1 | 1,037 | [
"Bioconductor"
] | 441bbb9a1b2b9b168a11e84c72963977288cf59c6963c7fbf71bc9a89c2801f9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestGPURayCastIndependentComponentMIP.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyri... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Volume/Testing/Python/TestGPURayCastIndependentComponentMIP.py | Python | bsd-3-clause | 4,402 | [
"VTK"
] | c4d2438a5c4b7694ddcbb98fc2a8a18d4f6709d6a3b63f19e46b75f51aa3197e |
# Copyright 2017 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... | zasdfgbnm/tensorflow | tensorflow/contrib/py2tf/converters/for_loops.py | Python | apache-2.0 | 3,015 | [
"VisIt"
] | 1938ad8f8ed92427b21894eb1711f159d6c631465b8e2ac5cf697b98b2e824ca |
# monitor.py
#
# Copyright (C) 2011-2015 Red Hat, 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 2 of the License, or
# (at your option) any later version.
#
# This progr... | Be-ing/lorax | src/pylorax/monitor.py | Python | gpl-2.0 | 6,750 | [
"Brian"
] | 1fcb465a2536cfd7acf5ae327afd05619d3b474b0f797da1a8eeda4d429ff3ec |
from mdtraj.formats.arc import ArcTrajectoryFile
from mdtraj.formats.dcd import DCDTrajectoryFile
from mdtraj.formats.binpos import BINPOSTrajectoryFile
from mdtraj.formats.xtc import XTCTrajectoryFile
from mdtraj.formats.trr import TRRTrajectoryFile
from mdtraj.formats.hdf5 import HDF5TrajectoryFile
from mdtraj.format... | marscher/mdtraj | MDTraj/formats/__init__.py | Python | lgpl-2.1 | 508 | [
"MDTraj",
"NetCDF"
] | c38820cf4feb8aa57250a501273f4c1e613ae701904aa441f48e19d6c4bb553f |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from django.contrib.sites.models import Site
from django.http import HttpResponse
from django.test import TestCase
from django.utils.timezone import ... | vabs22/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 82,438 | [
"VisIt"
] | 4073fedc2e8b14f97d7e54974301de7f9b47fe09adea91a35cdd98f9fe9b7bef |
# Copyright (c) 2014, Max Zwiessele, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy; np = numpy
import itertools
from re import compile, _pattern_type
from param import ParamConcatenation
from parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing
impo... | TianpeiLuke/GPy | GPy/core/parameterization/parameterized.py | Python | bsd-3-clause | 19,199 | [
"VisIt"
] | c288e02b28124f0dbb948eb486c37c60e2788e159eac0c9714be84eefbda5db6 |
# coding=UTF8
## This file is part of VideoTester
## See http://video-tester.googlecode.com for more information
## Copyright 2011 Iñaki Úcar <i.ucar86@gmail.com>
## This program is published under a GPLv3 license
import logging
from platform import processor
from sys import exit
import os
def makeDir(dir):
"""
... | AlanZatarain/video-tester | VideoTester/config.py | Python | gpl-3.0 | 4,242 | [
"VisIt"
] | 9736743a3925d5fce5da5981200fe772a72879d9d6541790bffaedad60b4c271 |
ALLOWED = {"a",
"abandoned",
"able",
"aborted",
"abortion",
"about",
"above",
"absolute",
"absolutely",
"abuse",
"abused",
"accept",
"acceptable",
"according",
"accountants",
"accounting",
"across",
"act",
"action",
"actually",
"ad",
"add",
"address",
"administration",
"ads",
"advantage",
"advertise",
"afford",
"afraid... | samshadwell/TrumpScript | src/trumpscript/allowed_words.py | Python | mit | 22,006 | [
"VisIt"
] | 671c3e7856e3783bfc914ce8beb32fe6bb1189ae33527ab7f66e64fde992d0ce |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/media/__init__.py | Python | gpl-2.0 | 4,379 | [
"Brian"
] | 0659169a68bddb9092a8a8ba6c33e22eb35caf0dcda77a0e5c30d2ccb16782dd |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | costypetrisor/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 34,386 | [
"Brian"
] | bf2694247df331f0ee8644bd12c572bf0a8be18e8a68481decbe1d852619388c |
import os
import platform
def get_platform():
'''
:rtype: NativeString
:returns: Name of the platform the module is running on
'''
return platform.system()
def get_distribution():
'''
:rtype: NativeString or None
:returns: Name of the distribution the module is running on
'''
... | veger/ansible | lib/ansible/module_utils/common/sys_info.py | Python | gpl-3.0 | 3,294 | [
"VisIt"
] | 738996ed11e352e749baf97cdf8f5212c124e91e502c4567c7be133a98d0655c |
# Copyright 2018 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/distributions/normal_conjugate_posteriors_test.py | Python | apache-2.0 | 10,089 | [
"Gaussian"
] | e617c0ceaf97ad1d6ab9fbd1e22a1fcca9816aa4dca10552fa0fad2221c401d3 |
#!/usr/bin/env python
"""pyhdf: Python interface to the NCSA HDF4 library.
The pyhdf package wraps the functionality of the NCSA HDF version
4 library inside a Python OOP framework. The SD (scientific dataset),
VS (Vdata) and V (Vgroup) APIs are currently implemented. SD datasets
are read/written through numpy arrays... | fhs/pyhdf | setup.py | Python | mit | 5,088 | [
"NetCDF"
] | 758fa4615eaa58e7f9dbed4f7a205c8d2701969eff7d92d6f7562deb791a6235 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
import warnings
from monty.dev import requires
from monty.json import MSONable
try:
import f90nml
except Exception:
f90nml = None
"""
This module defines IO ShengBTE for reading, updating, and writing ... | fraricci/pymatgen | pymatgen/io/shengbte.py | Python | mit | 5,708 | [
"CRYSTAL",
"ESPResSo",
"Gaussian",
"pymatgen"
] | 410cb0da44ad7750bac3b791d35890c416cfab5e2a564792fc7b41c88bed664a |
# -*- coding: utf-8 -*-
# pylint: disable=bad-continuation
"""
Certificate HTML webview.
"""
import logging
import urllib
import json
import MySQLdb as mdb
import pytz
from pytz import timezone, utc
import urllib2
import commands
from datetime import datetime
from dateutil import tz
from uuid import uuid4
from django.c... | kmoocdev2/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 51,894 | [
"VisIt"
] | e70f3eabc5c8cba2957af8b8a2678feaa85d6f011874f3be18f16c2a309ceccd |
###############################################################################
# Re-implementation of the ProcessPoolExecutor more robust to faults
#
# author: Thomas Moreau and Olivier Grisel
#
# adapted from concurrent/futures/process_pool_executor.py (17/02/2017)
# * Backport for python2.7/3.3,
# * Add an extra m... | vortex-ape/scikit-learn | sklearn/externals/joblib/externals/loky/process_executor.py | Python | bsd-3-clause | 44,856 | [
"Brian"
] | 897156cbda510e7302c2a6e54caf165f65038b736687e9782b7fcc74f584cdc7 |
import re
from enkiblog.core.testing.navigator import Navigatable
def convert(name):
klass_name = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', klass_name).lower()
class SiteNode(Navigatable):
# pylint: disable=abstract-method
name = None
nodes = None
... | enkidulan/enkiblog | src/enkiblog/core/testing/site.py | Python | apache-2.0 | 6,027 | [
"VisIt"
] | 671b01e88bd225038c62fa44fb6f68a6d2059a01c9d993718bd1786440d60ecd |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_comp_coulomb_pack.py | Python | apache-2.0 | 2,018 | [
"PySCF"
] | 83663f457a1442cd6feb3b3d3fbc8db776201d87c73b257716bb9b1820fbbeec |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | cmouse/buildbot | pkg/buildbot_pkg.py | Python | gpl-2.0 | 8,371 | [
"GULP"
] | 9328642527c5c9c9537c52c870e5878340b5d59bb126770b3c783681b185b540 |
# -*- coding: utf-8 -*-
"""
Demo for Gaussian process functionality in probls.gaussian_process.
Created on Thu Nov 17 16:58:40 2016
@author: lballes
"""
import os
import sys
sys.path.insert(0, os.path.abspath('..'))
import numpy as np
import matplotlib.pyplot as plt
import time
from probls import gaussian_process
... | ProbabilisticNumerics/probabilistic_line_search | test/demo_gaussian_process.py | Python | apache-2.0 | 1,029 | [
"Gaussian"
] | 519c4367d183e3b33230f7fe5fd1d3b365d76b6386bb43f1607d399dcaa6d5c5 |
# ==================================================================================================
#
# Copyright (c) 2016, Chen Kian Wee (chenkianwee@gmail.com)
#
# This file is part of py4design
#
# py4design is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | chenkianwee/envuo | py4design/py2radiance/__init__.py | Python | gpl-3.0 | 54,079 | [
"EPW",
"VisIt"
] | 87f63b8d5cbfafb34c056e890add006a11334f374b78df0ea1fa20dae340131a |
#################
#
# This file is part of
# ToBaCCo - Topologically-Based Crystal Constructor
#
# Copyright 2017 Yamil J. Colon <yamilcolon2015@u.northwestern.edu>
# Diego Gomez-Gualdron <dgomezgualdron@mines.edu>
# Ben Bucior <ben.bucior@gmail.com>
#
# ToBaCCo is free software: ... | tobacco-mofs/tobacco | connect_nodetonode.py | Python | lgpl-3.0 | 13,252 | [
"CRYSTAL"
] | 90028464a67f0cc603769bae56b4e4a962d77929cc593f86489aeb7696ad5023 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/nccmp/package.py | Python | lgpl-2.1 | 1,949 | [
"NetCDF"
] | 40233b6fd4ffc3c2bc2273bd6ba867ff0ea37ddb3e587e31fa8b332ce4c52113 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, absolute_import
from os.path import abspath, dirname, join, normpath
from setuptools import find_packages, setup
import sys
INSTALL_PYTHON_REQUIRES = []
# We are intending to keep up to date with the supported Django versions.
# For the official suppor... | rdegges/django-twilio | setup.py | Python | unlicense | 3,578 | [
"VisIt"
] | 1d6976ee42d74798163ecdd8a180eaf83ff173ca5615c92ad1fe58c6b1db2fa6 |
import yaml
from numpy import zeros, array
# Own modules
from lmp_types import *
import lmp_force_field as force_field
import container
import PolyLibScan.helpers.idGenerator as idGenerator
class Environment(object):
'''Acts as a Container for then entire
simulation. It stores all particles, interactions
... | luminescence/PolyLibScan | Tools/environment.py | Python | mit | 4,853 | [
"LAMMPS"
] | 37cc7e00b57875db6c7c3e08b8bad1728211704487a7cc450914b07b7bb1d91a |
from erukar.system.engine import MaterialGood
class AtheriteCrystal(MaterialGood):
BaseName = "Atherite Crystal"
BriefDescription = "a chunk of crystalline atherite"
BasePricePerSingle = 52
WeightPerSingle = 0.5
| etkirsch/legends-of-erukar | erukar/content/inventory/materials/raw/AtheriteCrystal.py | Python | agpl-3.0 | 229 | [
"CRYSTAL"
] | 3208aaf0f320525ede4e754c45af8d911863b88560cf1c48371e6ac358c717c8 |
#!/usr/bin/env python
'''
Module for rendering simple optical outputs using raytracing.
'''
# System imports
import os
import sys
import pdb
# Scipy and related imports
import numpy as np
import scipy.linalg as lin
import scipy.ndimage as ndim
import matplotlib.pyplot as plt
import Image
# ---... | vishwa91/OptSys | modules/lf_2d.py | Python | mit | 11,672 | [
"Gaussian"
] | 3a5f8ff8ee9b25f64f76aaa5e6b1c718096b5837e19083a993bb1eb6398b3898 |
# -*- coding: utf-8 -*-
#
# brette_gerstner_fig_3d.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 2 of the ... | hakonsbm/nest-simulator | pynest/examples/brette_gerstner_fig_3d.py | Python | gpl-2.0 | 3,266 | [
"NEURON"
] | 9e809c584a5a20be96fc0604668df7c9457b384a0caca24a5f21f2d141cfb5eb |
from typing import Dict, List, Optional
import numpy as np
from openfermion.utils import wedge
from openfermion.ops import InteractionRDM
import openfermioncirq.experiments.hfvqe.util as ccu
from openfermioncirq.experiments.hfvqe.objective import generate_hamiltonian
# pylint: disable=C
def kdelta(i: int, j: int):
... | quantumlib/OpenFermion-Cirq | openfermioncirq/experiments/hfvqe/analysis.py | Python | apache-2.0 | 13,014 | [
"Gaussian"
] | 9e87a0c3a1a2868e9ce06663a4e686803df68cc91ef27c663a783a6ae7fd3ab2 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
from builtins import * # pylint: disable=unused-import, redefined-builtin
from past.builtins import basestring
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.parser ... | oxc/Flexget | flexget/plugins/internal/api_trakt.py | Python | mit | 50,822 | [
"VisIt"
] | 6511a222fcade3e12e028974b5ed8d9732246b95d2ebd587d48c8108fc691b98 |
# 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.
import warnings
warnings.warn("Bio.SeqIO.FASTA is deprecated." \
+ " We hope the new code in Bio.SeqIO will be suitable for" \
... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SeqIO/FASTA.py | Python | apache-2.0 | 3,031 | [
"BioPerl",
"Biopython"
] | 14a5ffaf191e79ddd7afa495caa5511c4161255af910b8e4a16a7dbd1b471b75 |
from nose.tools import assert_true, assert_equal, raises
import numpy as np
from hyperspy.signals import Signal
from hyperspy.components import Gaussian
class Test1D():
def setUp(self):
gaussian = Gaussian()
gaussian.A.value = 20
gaussian.sigma.value = 10
gaussian.centre.value = ... | pburdet/hyperspy | hyperspy/tests/signal/test_integrate_in_range.py | Python | gpl-3.0 | 679 | [
"Gaussian"
] | 7f4d78200cfbc7c6fee4fa0b9714c81603c3659c2710d5e9ecc8cf904a4632a5 |
#!/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/mcscf/newton_casscf.py | Python | apache-2.0 | 35,576 | [
"PySCF"
] | 481a137cbbb7e6393d5d9e2c8f49eaa29892a0adaeb40bb1339a90dd8c5ebbd2 |
""" A collection of mutations that can be used. """
import numpy as np
from random import random, randrange
from math import ceil, cos, sin, pi
from ase.ga.utilities import atoms_too_close
from ase.ga.utilities import atoms_too_close_two_sets
from ase.ga.offspring_creator import OffspringCreator
from ase import Atoms
... | askhl/ase | ase/ga/standardmutations.py | Python | gpl-2.0 | 8,514 | [
"ASE",
"Dalton"
] | a13ec54cf40789de72b7de18e8ef64f63174f93a3bdcaf19e3ed2581372c19e7 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/scf/hf_symm.py | Python | apache-2.0 | 37,250 | [
"PySCF"
] | 8e35a0cb8a8bd5d058760475ae6289a2bb749d8d81ed3d90c2150df2b6670318 |
#! /usr/bin/env python
#
# Copyright (C) 2016 Jing Lu <ajingnk@gmail.com>
# License: Apache
# -*- coding: utf-8 -*-
# pylint: disable=too-few-public-methods
import datetime
import os
import subprocess
import shutil
from rdkit import Chem
from rdkit.Chem.Draw import MolToFile
from .types import FingerPrintType
from ... | ajing/ChemTreeMap | backend/treebuild/tree_build.py | Python | apache-2.0 | 7,895 | [
"RDKit"
] | e9da1c058c12b56352acccc7bbe4b5ae081a5694bf9398f062f9970255e4c5bf |
#!/usr/bin/env python
import sys
from optparse import OptionParser
import math
import vtk
# parse command line
p = OptionParser(usage="""usage: %prog [options] <gridfile> <vtrfile_base>
Converts the griddata file (suitable for PiecewiseMultilinear functions) into vtr format.
Eg
%prog mygrid.txt mygrid
This program... | yipenggao/moose | python/GridVTKData/griddeddata_to_vtk.py | Python | lgpl-2.1 | 4,325 | [
"VTK"
] | 90abb80f461be108720678f1c35e8a7d454a6f1a10ef4dda97ac7444626bdd6b |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/qiime2 | qiime2/core/testing/type.py | Python | bsd-3-clause | 2,037 | [
"Octopus"
] | 0b2b4aaa51969e0865346cd5b3313b700afa2d37bbcdb2cd60d332545eac0906 |
#!/usr/bin/pytho
"""
Created on Fri Jun 24 16:49:07 2016
@author: noel
For a description of the program, type:
python mmcif_to_pdb.py
Future functionality: The following functions only make sense when
working with the whole Protein Databank.
1. In the future this file could be used to read FASTA files and compare to... | noelcjr/EntropyMaxima | em/scripts/gen_csv.py | Python | gpl-3.0 | 6,012 | [
"CHARMM"
] | c3328a2a9891ca2798a787bb18ad49cfe760afc06c6b39a900bb006992fea137 |
"""Example using the operator of fixed-displacement linearized deformation.
The linearized deformation operator with fixed displacement ``v`` maps
a given template ``I`` to the function ``x --> I(x + v(x))``.
This operator is linear (in ``I``).
This example considers a 2D case, where the displacement field ``v``
is a... | kohr-h/odl | examples/deform/linearized_fixed_displacement.py | Python | mpl-2.0 | 2,245 | [
"Gaussian"
] | 481122c9ad3ce99ec4d0f8673f9d85d5259551a4b2f33bb06b2bb0ac35d8c802 |
from frappe import _
def get_data():
return [
{
"label": _("Documents"),
"icon": "icon-star",
"items": [
{
"type": "doctype",
"name": "Lead",
"description": _("Database of potential customers."),
},
{
"type": "doctype",
"name": "Customer",
"description": _("Custome... | indictranstech/trufil-erpnext | erpnext/config/crm.py | Python | agpl-3.0 | 3,863 | [
"VisIt"
] | 72e6c606f816d2bd859de00f16d97fb56d3e6559017b0ce14573196d8a12ecf5 |
import os
import re
from datetime import datetime
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from django.db import connection, models, transaction
from django.db.models import Q, permalink
from django.utils.html import escape
from django.utils.safestring import mark_safe
f... | asutherland/opc-reviewboard | reviewboard/reviews/models.py | Python | mit | 40,512 | [
"VisIt"
] | 07bf637c3c7cc1cba095818e4f0df97596f86c22a905baecd5d04dd6a0b5c18f |
#---------------------------------------#
# This file is part of EbmLib.
#
# EbmLib 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.
#
#... | thomlake/EbmLib | ebmlib/rbm/disccdktrainer.py | Python | gpl-3.0 | 8,698 | [
"CDK"
] | c30ad2449e015d3c44b7b46ff266de56c5a627e769909d548edb95f36db803d7 |
# -*- coding: iso-8859-1 -*-
############################################################
#Example 5: Adding a custom takestep routine. This example
#takes 100 monte carlo steps as one basin hopping step
############################################################
import numpy as np
import pygmin.potentials.lj as lj
i... | js850/PyGMIN | examples/basinhopping_no_system_class/6_reseeding.py | Python | gpl-3.0 | 1,590 | [
"PyMOL"
] | 6d01baf906af2f6dbfc752eaa786311a30cb3c2131a72cbd5bcf57acdf04617a |
from __future__ import print_function
import numpy
from molml.features import CoulombMatrix
from molml.crystal import GenerallizedCrystal, EwaldSumMatrix, SineMatrix
# Define some base data
H2_ELES = ['H', 'H']
H2_NUMS = [1, 1]
H2_COORDS = numpy.array([
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
])
H2_CONNS = {
... | crcollins/molml | examples/crystal.py | Python | mit | 1,117 | [
"CRYSTAL"
] | bc7a948d85a1c5379e76d18e49788fda9ccdd9bfedf1a474f2aa057c634b27e0 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Geometry optimization with solvent model
'''
from pyscf import gto, scf, dft
from pyscf import solvent
from pyscf.geomopt import geometric_solver
mol = gto.M(atom='''
C 0.000000 0.000000 -0.542500
O 0.000000 0.0... | gkc1000/pyscf | examples/geomopt/14-with_solvent.py | Python | apache-2.0 | 570 | [
"PySCF"
] | 67060db4d7d47db429083ae7fa0d582e922374cd661122558107b0446aea0b3e |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_traj = sys.argv[1]
my_struc = sys.argv[2]
u = Universe(my_struc,my_traj)
end = my_traj.find('.pdb')
fout_name = my_traj[0:end] + '_glob_bg_dist2.dat'
a1 = u.selectAtoms("segid A and resid 29")
b1 = u.selectAtoms("segid B and res... | demharters/git_scripts | dist_mhcii_glob_bg.py | Python | apache-2.0 | 599 | [
"MDAnalysis"
] | 8aeecdc3c8d14530114d4e91fd287eb6d69e6ecd8b40211cc5e660487545f06c |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.... | h2so5/Twemoji4Android | nototools/extra_locale_data.py | Python | mit | 14,693 | [
"MOE",
"MOOSE"
] | eaa45ae173d464905874ba511db9112db4bd98ee6c0156cba018256f8a1246a5 |
"""
Student Views
"""
import datetime
import logging
import re
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logo... | nttks/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 130,213 | [
"VisIt"
] | 7610d612fa3d73dc4d09124d2e91f7324f7c2a72d0199ef1485a8fea0c12a4b3 |
#!/usr/bin/env python
"""
Read a chromosome of wiggle data, and write it as a npy array, as
well as averages over regions of progressively larger size in powers of 10
"""
from __future__ import division
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.wiggle
fr... | volpino/Yeps-EURAC | lib/galaxy/datatypes/indexers/wiggle.py | Python | mit | 2,247 | [
"Galaxy"
] | 0da489256b6996a67fc0f6935be602fa9504e23f4bbadda590efb7d600351183 |
# /usr/bin/python3
# coding=utf-8
# Point Of No Return (Training)
"""
Copy of the game file, includes only nessessary content and no graphical code.
@author: anon-42
@version: beta
"""
import numpy as np
import ann#artifical_neural_net as ann
import act_func as af
import trainer as tr
import replay_memory as rm
impo... | anon-42/ANN-PONR-Python3 | PointOfNoReturn_Training.py | Python | mit | 12,933 | [
"VisIt"
] | 62282a1d427e5f788544b8f65d49976ef03aef11ed57302a565ceed201d01cfd |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | TheMOOCAgency/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 115,441 | [
"VisIt"
] | 1b5fe0953fbd57c9c2921b895b22143d04797737e2af1264828402630649a21e |
#!/usr/bin/env python
"""
Many thanks to Brian Rosner <oebfare.com> for letting me include
this code in Test Utils.
"""
import os
import sys
from optparse import OptionParser
from django.conf import settings
from django.core.management import call_command
def main():
"""
The entry point for the script. This scr... | frac/django-test-utils | test_utils/bin/django_test_runner.py | Python | mit | 2,670 | [
"Brian"
] | 4b93721d53c1f247daa3bec50abfbc9d75485a159ad1cec5ff7db8d9d25abe02 |
#!/usr/bin/env python
import pygimli as g
from pygimli.mplviewer import drawMesh, drawModel,drawSelectedMeshBoundaries
import pylab as P
import numpy as np
def getaxes():
fig = P.figure()
left, width = 0.1, 0.6
rect1 = [left, 0.75, width, 0.15]
rect2 = [left, 0.05, width, 0.69]
ax1 = fig.add_ax... | florian-wagner/gimli | tests/fop/gravimetric/testGravimetry.py | Python | gpl-3.0 | 12,595 | [
"VTK"
] | e219a17f019bcbf8b8238f71a79b943cb27e3c6a15df8fcadcb86ef0e7bf37de |
# ########################################################################
# # $HeadURL $
# # File: TransferAgent.py
# # Author: Krzysztof.Ciba@NOSPAMgmail.com
# # Date: 2011/05/30 09:40:33
# ########################################################################
# """ :mod: TransferAgent
# ===================
#
#... | calancha/DIRAC | DataManagementSystem/Agent/TransferAgent.py | Python | gpl-3.0 | 52,611 | [
"DIRAC"
] | dfacb794213eadc5c58f9a81a748372e748bd2fe33d06ce9ec009e8b57b7d899 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------... | nateprewitt/pipenv | pipenv/vendor/concurrent27/futures/process.py | Python | mit | 14,988 | [
"Brian"
] | b5c0151c4e6ea14b474a87539da0f03587f0de82279182594dc302926e2ab885 |
#!/usr/bin/env python
"""Example code of DDPG on OpenAI Gym environments.
For DDPG, see: https://arxiv.org/abs/1509.02971
"""
from __future__ import division
import argparse
import collections
import copy
import random
import gym
import numpy as np
import chainer
from chainer import functions as F
from chainer impor... | jnishi/chainer | examples/reinforcement_learning/ddpg_pendulum.py | Python | mit | 9,192 | [
"Gaussian"
] | 876c9544190c43957ba6543cd52e8a79be4b7615ab97aee3417402d2cb346be0 |
'''
Created on Mar 14, 2014
@author: alinar
'''
from . import chain
import numpy as np
import random
class Molecule:
def __init__(self,name_=""):
self.chains = []
self.name = name_ #if needed!#
self.bonds_established = False
def AddChain(self,chain_id_str=" "):
new_... | alinar/Molar | molar/molecule.py | Python | gpl-2.0 | 8,910 | [
"VTK"
] | b56fffd061ed8bc260eaf4c42776e2f2171ef71cbc2827ca790de0f765d1360f |
"""
Courseware views functions
"""
import logging
import urllib
import json
from collections import defaultdict
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlr... | abdoosh00/edraak | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 36,829 | [
"VisIt"
] | 675a7b51894b2cea1148ce36a57b93a24ed6ec4317f85f2deac9549fa4da977e |
#!/usr/bin/env python
#
# $File: MlPenetrance.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribu... | BoPeng/simuPOP | docs/MlPenetrance.py | Python | gpl-2.0 | 1,453 | [
"VisIt"
] | 0b4f9a8e7c3e3a5912db63efed1caa7cfefae2a17ba02a20cf5707321fa59ab7 |
from datetime import datetime
import hashlib
import random
from sqlalchemy import (
and_,
func
)
from galaxy import model
from galaxy import util
import logging
log = logging.getLogger( __name__ )
VALID_JOB_HASH_STRATEGIES = ["job", "user", "history", "workflow_invocation"]
class RuleHelper( object ):
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/rule_helper.py | Python | gpl-3.0 | 7,764 | [
"Galaxy"
] | 36a0539abe566f770715c1d418f44192cfb8870d3dd9c3258ff3e603651a72d4 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Simple program for ITK image read/write in Python
# import itk
import numpy as np
from loguru import logger
import os.path
import re
import pydicom as dicom
dicom.config.debug(False)
import os.path as op
from typing import Union
from pathlib import Path
from . imp... | mjirik/io3d | io3d/datawriter.py | Python | mit | 24,059 | [
"VTK"
] | 6a704ffd6ac1f32ecc07dc1a203f01f78f669ee4e68ccc6bae75d82f2ee3c743 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of crazyhash.
#
# crazyhash 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) an... | buguroo/crazyhash | src/crazyhash/constants.py | Python | gpl-3.0 | 15,508 | [
"Amber",
"Elk",
"Jaguar",
"MOOSE",
"Octopus"
] | 2126c67326620526ef44244982ea3dd5d49060ed199c5e3113ed3418d8cbe68d |
"""
Set up the plot figures, axes, and items to be done for each frame.
This module is imported by the plotting routines and then the
function setplot is called to set the plot parameters.
This plotting function is for plotting when the surface-flagging method
is used.
The main difference is that the inner product ... | clawpack/adjoint | paper1_examples/tsunami_Alaska/compare/setplot_sflag.py | Python | bsd-2-clause | 8,539 | [
"NetCDF"
] | 6c98aa274d7d3eb5ae71e1b66d109fa534414614b9945d9e9e09de20088ed40f |
############################################################################
# multi2fasta.py
# written by Thomas Nelson, October 2, 2014
# thomas dot c dot nelson at gmail dot com
# This script requires the Biopython module and nothing else
# Get the Biopython module here here: http://biopython.org/wiki/Download
# Th... | nelsont03038/multi2fasta | multi2fasta.py | Python | gpl-3.0 | 920 | [
"Biopython"
] | 575dd8397bd0f889bc4e18c513499a4c501fc28aa64e60aeabf6e4def344a2ce |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | arunkgupta/gramps | gramps/plugins/tool/rebuild.py | Python | gpl-2.0 | 3,561 | [
"Brian"
] | 4c1cba0c55f0ee458d8d19aa837c31cfe3b4fd339a85e1a830ec0f958c817f5a |
# Copyright (c) 2001, Stanford University
# All rights reserved.
#
# See the file LICENSE.txt for information on redistributing this software.
#
# Authors:
# Brian Paul
"""Chromium SPU, Node and Mothership classes used by the config tool.
This may eventually get rolled into the similar classes defined
in the mothers... | alown/chromium | mothership/tools/crtypes.py | Python | bsd-3-clause | 31,951 | [
"Brian"
] | 4669f65bb4ef8306dd03e6a8fc63d518e1f8d120bcad77dd179539d2007b424b |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2015 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 F... | tiagocardosos/stoq | stoqlib/gui/test/test_gridsearch.py | Python | gpl-2.0 | 2,128 | [
"VisIt"
] | 5f7f572b65477a3d9de2e4cc7370eeb0f6f4a64300c598077a1e36d78424c316 |
import sublime
import threading
import json
import sys
import time
import urllib.request
from .threads import ThreadTracker
from .threads import ThreadProgress
from .threads import PanelThreadProgress
from .printer import PanelPrinter
import MavensMate.lib.command_helper as command_helper
from MavensMate.lib.response_h... | ralphcallaway/MavensMate-SublimeText | lib/adapter.py | Python | gpl-3.0 | 9,203 | [
"VisIt"
] | 21dceaba83829eb7ba1c23a27a815eba515a56c23c10276818c39410a39fc069 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | fredrikw/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 96,356 | [
"Gaussian"
] | 8f123fbb7bcd3e29a736c44c3b52251f305f548f95bea035030afaef32c126e8 |
'''
ps = psi4.Solver
with psi4.quite_run():
ps.prepare_chkpt(mo_coeff, fock_on_mo, nelec, e_scf, nuclear_repulsion)
ecc = ps.energy('CCSD', c.shape[1], hcore_on_mo, eri_on_mo)
rdm1, rdm2 = ps.density(mo_coeff.shape[1])
eccsdt = ps.energy('CCSD(T)', c.shape[1], hcore_on_mo, eri_on_mo)
rdm1, rdm2 = p... | sunqm/psi4-cc | psi4/__init__.py | Python | gpl-2.0 | 434 | [
"Psi4"
] | 3208cda8572558e626eae4315e99345acd4c7640232f685a3dcdaf05e6fc3436 |
# Copyright (C) 2018 Alex Nitz
# 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) any later version.
#
# This program is distributed in the ho... | ligo-cbc/pycbc | pycbc/inference/models/single_template.py | Python | gpl-3.0 | 5,837 | [
"Gaussian"
] | 06633236f8fb2afde44b998d8f310da562ed2dcdd24e2cdac04b4d493ce5ef88 |
#!/usr/bin/env python
# -*- 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 Licens... | eustislab/horton | tools/harmonics.py | Python | gpl-3.0 | 8,747 | [
"Gaussian"
] | e82dace7611f7ea702165c2108bf471d205f994a7e8b7797620f5c1a8df05ef0 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import glob
class Chombo(MakefilePackage):
"""The Chombo package provides a set of tools for imp... | rspavel/spack | var/spack/repos/builtin/packages/chombo/package.py | Python | lgpl-2.1 | 4,676 | [
"Brian"
] | 6e14345ffc5e96f7b6ed841b1f420959d953bbd9a347ce242d8886dfe6f8ee89 |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from copy import deepcopy
from cStringIO import StringIO
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse,
... | synergeticsedx/deployment-wipro | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 22,563 | [
"VisIt"
] | d6fed1bbf4b735b3a44068e510b586ea404ca0feb90c9ac0a0511b00d61966eb |
#!/usr/bin/env python
"""
Suffix tree implementation using Ukkonen's algorithm.
"""
import sys
import os
class SuffixTree(object):
class Node(object):
""" Suffix tree node. Contains offset, length of substring from T
labeling the incoming edge. Also contains outgoing edges, and some
... | BenLangmead/comp-genomics-class | notebooks/suf_tree.py | Python | gpl-2.0 | 24,222 | [
"VisIt"
] | 988a9e7eec20ad6e3e98f3afc90d689d4fd5e00730acbad5439a7086f1144c93 |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | KEHANG/RMG-Py | rmgpy/molecule/molecule.py | Python | mit | 77,501 | [
"RDKit",
"cclib"
] | ae00d0e50df71f2430bca1f2f76a334d9f288c3f7fcbfc10d5456b5cc7d07b82 |
# Copyright 2015 datawire. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | datawire/quark | quarkc/grammar.py | Python | apache-2.0 | 2,039 | [
"VisIt"
] | 1ffb40b2efd32d8de1d2a52a9d04459cafcbe5b453e696853f0e5d8e3f9be67e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes for parsing the FEFF output files.
Currently supports the xmu.dat, ldos.dat output files are for non-spin case.
"""
from collections import defaultdict, OrderedDict
import re... | gVallverdu/pymatgen | pymatgen/io/feff/outputs.py | Python | mit | 15,159 | [
"FEFF",
"pymatgen"
] | 569a1472924d355a2235872cc9ce350d0faf6de0671656d93a090173523668f0 |
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
#
# paf.py
# formats
#
# Created by Haibao Tang on 09/03/20
# Copyright © 2020 Haibao Tang. All rights reserved.
#
import sys
import logging
from jcvi.formats.base import must_open
from jcvi.apps.base import OptionParser, ActionDispatcher
class PAFLine:
"""
PAF ... | tanghaibao/jcvi | jcvi/formats/paf.py | Python | bsd-2-clause | 2,900 | [
"BLAST"
] | 10501ff9c5e3598105bf274776ff2d5b6abefc4a872fe6af4065024583f4637b |
import sys
from limix.core.mean import MeanKronSum
from limix.core.covar import Cov3KronSumLR
from limix.hcache import Cached, cached
from limix.utils.util_functions import vec
import pdb
import numpy as NP
import scipy as sp
import scipy.linalg as la
import time as TIME
from .gp_base import GP
from limix.core.gp impo... | PMBio/limix | limix/core/gp/gp3kronSumLR.py | Python | apache-2.0 | 6,205 | [
"Gaussian"
] | 6d8a1517ce0df2bd9e2f2702b1569659e357ee06a4ff90a5fe41d22f9ff43c26 |
#!/usr/bin/env python
# ----------------------------------------------------------------------
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you ca... | scottpurdy/NAB | run.py | Python | agpl-3.0 | 7,709 | [
"Gaussian"
] | 686aa75baaf8ec326e78207df32a53b14109a8db613bbc8e0edd4883d7182a94 |
#! /usr/bin/env python3
"""Script to create the Windows installer for BLAST command line applications"""
# $Id: make_win.py 495893 2016-03-22 15:02:30Z camacho $
#
# Author: Christiam camacho
from __future__ import print_function
import os, sys, os.path
import shutil
from optparse import OptionParser
SCRIPT_DIR = os.p... | kyungtaekLIM/PSI-BLASTexB | src/ncbi-blast-2.5.0+/c++/scripts/projects/igblast/post_build/win/make_win.py | Python | lgpl-3.0 | 3,438 | [
"BLAST"
] | 11f8b0ae15a97d23a0317411ca97fb25fb925b05e4446c940a674a952ec0319f |
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | hjanime/VisTrails | vistrails/packages/vtk/vtkhandler.py | Python | bsd-3-clause | 8,298 | [
"VTK"
] | 9e845dcdd97197230c909f5e523d274044378cf922292121693c46a9ebcfce41 |
# Copyright 2013 Velodyne Acoustics, 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... | frizaro/Veloview | VelodyneHDL/python/veloview/kiwiviewerExporter.py | Python | apache-2.0 | 3,296 | [
"ParaView"
] | a241fdf4e285bf9c8e89a1c2ac6ae74e2ae8717087f320888061dea9e55cc260 |
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