text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# Copyright 2011-2013, Damian Johnson
# See LICENSE for licensing information
"""
Basic enumeration, providing ordered types for collections. These can be
constructed as simple type listings...
::
>>> from stem.util import enum
>>> insects = enum.Enum("ANT", "WASP", "LADYBUG", "FIREFLY")
>>> insects.ANT
'Ant... | arlolra/stem | stem/util/enum.py | Python | lgpl-3.0 | 4,333 | [
"Firefly"
] | 57f806c04acdd4ab5cebfef72e4ff4b401355652687c078d205f59ac02440684 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/encore/confdistmatrix.py | Python | gpl-2.0 | 14,795 | [
"MDAnalysis"
] | 2a2b67694945b73b207aed1a671a9772a020c71ed02fd74d48c8e65f00f583bc |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Protein.common_name'
db.add_column('neuroelectro_protein', 'common_name', self.... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0007_auto__add_field_protein_common_name__add_field_protein_is_channel.py | Python | gpl-2.0 | 8,187 | [
"NEURON"
] | 8eaa6aae36914583ddec8c20a7243170239fa24d45581bcaa914a453c908590b |
__all__ = ['TimestepperNAMD']
import logging
import os
import shutil
from typing import List, Optional, Union
import numpy as np
import miles.default as default
from miles import (BaseTimestepper, Chunk, ChunksNAMD, CollectiveVariables, Clock, Configuration, Mapping, PhaseSpacePoint, Transition, TrajectoryParser, ge... | clsb/miles | miles/timestepper_namd.py | Python | mit | 5,192 | [
"NAMD"
] | 4277805ece3017276df634b7762423b3294fa78aaaf32bc9ee8063b4a6ea2534 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import random
import unittest
import warnings
from pathlib import Path
import pytest # type: ignore
import numpy as np
from monty.os.path import which
from pymatgen.core.composition import Composition
from pymatge... | vorwerkc/pymatgen | pymatgen/core/tests/test_structure.py | Python | mit | 65,914 | [
"pymatgen"
] | ebb89b73e750b7873816288c449f93269be5131363b3c53b6db1fb3b47fb4344 |
from __future__ import absolute_import
import unittest
import math
import os
import numpy as np
from monty.serialization import loadfn
from pymatgen.analysis.elasticity.tensors import *
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.testing imp... | nisse3000/pymatgen | pymatgen/analysis/elasticity/tests/test_tensors.py | Python | mit | 26,543 | [
"pymatgen"
] | 96b65358aab237908f44182a834feae5a7b21b66af37ef714d84b343b6db4e72 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import warnings
import scipy.constants as const
from monty.json import MSONable
from pymatgen.analysis.structure_matcher import StructureMa... | johnson1228/pymatgen | pymatgen/analysis/diffusion_analyzer.py | Python | mit | 37,720 | [
"VASP",
"pymatgen"
] | d14f7dc4ad594d646274dcca0126d2bbf27dfa6b3fd699a8a331bc546533b48a |
# -*- coding: utf-8 -*-
#
# gPodder - A media aggregator and podcast client
# Copyright (c) 2005-2011 Thomas Perl and the gPodder Team
#
# gPodder 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... | elelay/gPodderAsRSSReader | src/gpodder/gtkui/frmntl/shownotes.py | Python | gpl-3.0 | 4,142 | [
"VisIt"
] | 1204247fd055073d948a269c448d4e5d4aaf42fe716939fc3618cbcf143fb73c |
import paraview
import paraview.simple
import paraview.servermanager as sm
import PVBase
import core.modules
import core.modules.module_registry
from pvconfig import QPVConfigWindow
from core.modules.vistrails_module import new_module, Module, ModuleError
from core.modules.module_registry import (registry, add_module,
... | VisTrails/VisTrails | contrib/ParaView/init.py | Python | bsd-3-clause | 7,747 | [
"ParaView",
"VTK"
] | ea0747c23ab4fede214c249a49a03f0281e386bfdbd8baf1e06d3c07d09267c3 |
from binary_tree_node import BinaryTreeNode
def build_balanced_tree():
root = BinaryTreeNode(5)
root.set_left(BinaryTreeNode(3))
root.set_right(BinaryTreeNode(9))
root.get_left().set_left(BinaryTreeNode(1))
root.get_left().set_right(BinaryTreeNode(4))
root.get_right().set_left(BinaryTreeNode(7)... | lzamparo/practice | exercises/traverse_trees.py | Python | mit | 1,412 | [
"VisIt"
] | 2017edc2c587baa3af7b3d260b0b6e7fe383eba42dfe174f423d8433b220abd7 |
# -*- coding: utf-8 -*-
#
# RDKit documentation build configuration file, created by
# sphinx-quickstart on Sun Aug 7 18:51:45 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | adalke/rdkit | Docs/Book/conf.py | Python | bsd-3-clause | 7,100 | [
"RDKit"
] | 33004aa30eaa98ba15f1c665c97f3f5553b6ef3c3cf970414be0e5730ba8d289 |
from __future__ import print_function, division
from sympy.core import Mul
from sympy.functions import DiracDelta, Heaviside
from sympy.core.compatibility import default_sort_key
from sympy.core.singleton import S
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bring... | kaushik94/sympy | sympy/integrals/deltafunctions.py | Python | bsd-3-clause | 7,414 | [
"DIRAC"
] | e94559017bc380b42e4d34a5fa80a11c513c6a96031a1ea3e48bff7a4cfc56e3 |
#!/usr/bin/env python3
# EDITABLE SECTIONS ARE MARKED WITH #@#
version = "2.6_3"
authors = ["Djurre H. de Jong", "Jaakko J. Uusitalo", "Tsjerk A. Wassenaar"]
# This program has grown to be pretty complex.
# The routines have been organized in different files.
# For working versions, all files can be incorporated b... | penuts7644/InsaneModel | src/main/webapp/insane/martinize.py | Python | gpl-3.0 | 251,038 | [
"ChemPy",
"GROMOS",
"Gromacs",
"PyMOL"
] | 20b6c505a3a3ad8ab14c3ef92c5b6a5c7215f965fd8ce9c95167ec820afbb610 |
#!/usr/bin/env python
"""Tests pycits wrapper for samtools_index.
sort, and IDXSTATS
NOTE TO DO:
consider changing this to PYSAM
https://github.com/pysam-developers/pysam
http://pysam.readthedocs.io/en/latest/"""
import os
import shutil
from pycits import samtools_index
from pycits import samtools_idxstats
from py... | widdowquinn/THAPBI-pycits | tests/test_wrapper_samtools.py | Python | mit | 5,023 | [
"pysam"
] | 28c89e6381564daa26ee560dd35f8a2fb533a10e2deb98be642d4a559cbaecdf |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/t/trinity.py | Python | gpl-2.0 | 14,516 | [
"BWA"
] | 663236e77e8fd0c096f02a31421dec2665838f41a93e102d136c5919d316efd2 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/util/tty/__init__.py | Python | lgpl-3.0 | 4,234 | [
"Psi4"
] | d7748b0c66956a3872abeaa1108a71178194dff6eedf1924ac70ec2e083c697c |
from time import sleep
from lettuce import step, world
from questionnaire.features.pages.questionnaires import QuestionnairePage
from questionnaire.models import Questionnaire, Section, SubSection, Question, QuestionGroup, QuestionGroupOrder, QuestionOption, Region
@step(u'I have a questionnaire with sections and sub... | eJRF/ejrf | questionnaire/features/questionnaire_steps.py | Python | bsd-3-clause | 9,787 | [
"VisIt"
] | 3ab829d8ef54eefdd5102bcd8b4b1a408e4e9920809f0b660e3fdb26a80c3a6a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
""" Copyright 2005 - 2008 Gunnar Wrobel
2011 - Brian Dolbec
Distributed under the terms of the GNU General Public License v2
"""
def encode(text, enc="UTF-8"):
"""py2, py3 compatibility function"""
if hasattr(text, 'decode'):
try:
r... | jmesmon/layman | layman/compatibility.py | Python | gpl-2.0 | 1,314 | [
"Brian"
] | 2520423f8a80341ad17ea3edd6912b5b049359c34576ea224af3ef380fafd35f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes to create phase diagrams.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version... | xhqu1981/pymatgen | pymatgen/phasediagram/maker.py | Python | mit | 18,066 | [
"pymatgen"
] | 20f5479ffe3b5208314aea159b6a5913bd04e3fd27b51d3a1ab9a394494806fc |
# Load required libraries
from SimpleCV.base import *
from SimpleCV.Color import *
from SimpleCV.LineScan import *
from numpy import int32
from numpy import uint8
from EXIF import *
if not init_options_handler.headless:
import pygame as pg
import scipy.ndimage as ndimage
import scipy.stats.stats as sss #for aut... | jayrambhia/SimpleCV2 | SimpleCV/ImageClass.py | Python | bsd-3-clause | 496,357 | [
"Gaussian",
"VisIt"
] | 32ffca4bf619077aafa994f0e2e8097a565e995fef5cd389bfb1c1723aab5953 |
from __future__ import annotations
import fnmatch
import itertools
import logging
import os
import re
import tempfile
from datetime import datetime
from functools import partial
from io import StringIO
from typing import IO, Any, Iterator
from urllib.parse import quote
from zipfile import ZipFile, is_zipfile
import s... | abilian/abilian-sbe | src/abilian/sbe/apps/documents/views/folders.py | Python | lgpl-2.1 | 33,725 | [
"VisIt"
] | 1887f19cfc523e5ae0cd94b0629b2c517440becf2eacb4090b56653b3056edee |
# Copyright (c) 2014-2018 Matteo Degiacomi and Valentina Erastova
#
# Assemble 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.
# Assemb... | degiacom/assemble | Assemble_GUI.py | Python | gpl-3.0 | 47,235 | [
"Gromacs"
] | 8b943b1bf3f7b247fbed50adca4b464db58c3aa62086518d4a055ff8d134e331 |
import numpy as np
import tqdm
import deepx.config
backend = deepx.config.get_backend()
import tensorflow as tf
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
tf.enable_eager_execution(config=config)
if backend == 'pytorch':
import torch
from deepx.backend import T
from deepx import nn, stats
fro... | sharadmv/deepx | examples/vae.py | Python | mit | 2,339 | [
"Gaussian"
] | a43c7c7858636efba87ecc8a41889200c414e8e06917230e059fd09c20cf7d2e |
"""
This module defines export functions for decision trees.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Dawe <noel@dawe.me>
# Satrajit Gosh <satrajit.ghosh@gmail.com>
# Trevor... | glemaitre/scikit-learn | sklearn/tree/_export.py | Python | bsd-3-clause | 37,333 | [
"Brian"
] | 51917616698ed0ce58605dd6975d04984ce3a1f83bfc70fc3f0057b56d722175 |
# test_deepbasket.py ---
#
# Filename: test_deepbasket.py
# Description:
# Author:
# Maintainer:
# Created: Mon Jul 16 16:12:55 2012 (+0530)
# Version:
# Last-Updated: Thu Nov 8 17:55:59 2012 (+0530)
# By: subha
# Update #: 497
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#... | BhallaLab/moose-examples | traub_2005/py/test_deepbasket.py | Python | gpl-2.0 | 1,531 | [
"MOOSE"
] | bb5710c42e1113b59d54ae53bd5458335d9e7739d2d6a85d7f3feff4138860b7 |
import os as _os
on_rtd = _os.environ.get('READTHEDOCS', None) == 'True'
if not on_rtd:
import numpy as _np
import matplotlib.pyplot as _plt
from .curve_fit_unscaled import curve_fit_unscaled as _curve_fit_unscaled
from ..matplotlib.figure import figure as _figure
import logging
logger = logging.getLogger(__na... | joelfrederico/SciSalt | scisalt/scipy/gaussfit.py | Python | mit | 5,102 | [
"Gaussian"
] | b10d9abd9f2c08e578642b231028d3b0b3d562043b4fbb1e4c3c7d1cc597caf3 |
# -*- coding: utf-8 -*-
from django.test import TestCase
#from mock import patch
import mock
from .models import User
# Create your tests here.
class UserTests(TestCase):
@mock.patch('webfaction.tasks.create_user.delay')
def test_creation(self, create_user_task):
preferred_name = u'Brian'
... | gfavre/beyondthehost | beyondthehost/webfaction/test_models.py | Python | mit | 3,779 | [
"Brian"
] | 32daef03794cbb3813791eb2cbe2dfc1c517c94575912ade9e58e78660642bd4 |
"""
The model class definition
==========================
A *model* here is a complete model that is able to be simulated. It is the top
most class in this project and is the one that mostly interacts with the users.
.. autoclass:: Model
:members:
:special-members:
"""
from .readosm import read_osm
from .ne... | tschijnmo/osmABTS | osmABTS/model.py | Python | mit | 7,331 | [
"VisIt"
] | 220414b7f17b11596e07475e29c823e12691b5e84c21a2ee3072226e1fc33c62 |
import logging
import os
import textwrap
from jinja2 import Template
from six.moves.configparser import ConfigParser, NoSectionError
from conans.errors import ConanException
from conans.model.env_info import unquote
from conans.paths import DEFAULT_PROFILE_NAME, conan_expand_user, CACERT_FILE
from conans.util.dates i... | conan-io/conan | conans/client/conf/__init__.py | Python | mit | 34,070 | [
"VTK"
] | 589918d189a49ded4927166fd67edcf9dc70aa0514bfc0aa903cf64db098ce82 |
"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into bui... | ponadto/openbabel | test/testsym.py | Python | gpl-2.0 | 15,200 | [
"RDKit"
] | b2d3c55ef7070a646bed31bfcc21df165541273cbb2f03f1175ee53f2a09a694 |
# Copyright 2019 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... | xzturn/tensorflow | tensorflow/python/keras/layers/preprocessing/image_preprocessing.py | Python | apache-2.0 | 45,784 | [
"Gaussian"
] | 166c45ce9a0be4418aac4523ce206ca5964a62764f218dce26ba8121e4d64e19 |
#!/bin/env python
""" Showing last hour history of FTS transfers. """
import sys
import DIRAC
from DIRAC import gLogger, gConfig, S_OK
from DIRAC.Core.Base import Script
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.ConfigurationSystem.Client import PathFinder
__RCSID__ = "$Id$"
colors = { "yellow" : ... | sposs/DIRAC | DataManagementSystem/scripts/dirac-dms-show-fts-status.py | Python | gpl-3.0 | 5,027 | [
"DIRAC"
] | 4f272aaa42f0d38959488b2114266ffd7fdde415d9ff61cdc826dd49dd1bdb2a |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from matplotlib.externals import six
import os
import sys
from hashlib import md5
from docutils import nodes
from docutils.parsers.rst import directives
import warnings
from matplotlib import rcParams
from m... | rbalda/neural_ocr | env/lib/python2.7/site-packages/matplotlib/sphinxext/mathmpl.py | Python | mit | 3,883 | [
"VisIt"
] | 36f5a0349aa7ed77fc908e052defcca7476720a08de356b24d478d0305c01364 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/cluecode/test_copyrights_lines.py | Python | apache-2.0 | 11,779 | [
"VisIt"
] | 9082da02b259a901ac36222bcdf82b84f9e2191ae9a4301171fe96ff9a9bc93a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import hashlib
import tempfile
import unittest
import pytest # type: ignore
from _pytest.monkeypatch import MonkeyPatch # type: ignore
from monty.json import MontyDecoder
from pymatgen.core import SETTINGS... | richardtran415/pymatgen | pymatgen/io/vasp/tests/test_sets.py | Python | mit | 66,049 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | cdc164f8edbe0a6844c03e1f3da755a100c9564952997a16b1a7303d4ba19743 |
#!/usr/bin/env python
from __future__ import print_function
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import seaborn as sbn
import sys
from tqdm import tqdm
import mdtraj as md
### parameters ###
reference_file = '/path/to/reference/pdb_or_gro'
structure_file = refe... | TaizoAyase/mdtools | rmsd/calc_RMSD.py | Python | gpl-2.0 | 1,468 | [
"MDTraj"
] | 3325db2735ba0ed3cf792e8f8167df569e035d0d88b05b2c32d677ccee7e55a8 |
# -*- coding: utf8 -*-
from ..typing import Modifier
class Default(Modifier):
def __init__(self, value):
self.value = value
self.old_value = None
def visit(self, handler):
self.old_value = handler.__dict__.get('default', None)
handler.__dict__['default'] = self.value
def r... | apieum/eventize | eventize/modifiers/descriptors.py | Python | lgpl-3.0 | 396 | [
"VisIt"
] | ce8ae8eef123b0a833fdf5cc18d4e63abe67ab61ef470101cbe5e9e057e3bb2f |
from django.conf import settings
from residue.models import Residue
from protein.models import Protein, ProteinSegment
from structure.models import Structure
from structure.functions import BlastSearch, BlastSearchOnline
from Bio import SeqIO, pairwise2
from Bio.PDB import PDBParser, PPBuilder
import Bio.PDB... | cmunk/protwis | structure/sequence_parser.py | Python | apache-2.0 | 23,435 | [
"BLAST"
] | 94379947c2c22c31c86cd8f5e33be772a99b35efb4d5f67f104aa14bc50c54e6 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | experimental/single_model_uncertainty/models/wide_resnet.py | Python | apache-2.0 | 9,170 | [
"Gaussian"
] | d869719fbd06f80023221b281e093793a1bbc4eac815897d0fa4c799b16349f2 |
'''
Funciones propias de pyENL
'''
from fluids import atmosphere as atm
from fluids import compressible as comp
from fluids import control_valve as cv
from CoolProp.CoolProp import PropsSI as proppyENL
from CoolProp.CoolProp import HAPropsSI as haproppyENP
from pint import _DEFAULT_REGISTRY as pyENLu
try:
pyENLu.l... | jon85p/pyENL | pyENL_fcns/functions.py | Python | mit | 24,259 | [
"Avogadro"
] | e061792cdd1fc1621cc524e9cccb054846c80b02c0839688952e66a0342c5571 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | tests/func_tests/test_pop3.py | Python | lgpl-3.0 | 2,544 | [
"VisIt"
] | 57cb1b27ac4ab153a9b163971a74aa1bf37fe1f1a4805d2b3184a608a914aa57 |
import time
from datetime import date
from unittest import mock, skip
from django.test import override_settings
from selenium.webdriver.common.keys import Keys
from mainapp.models import Person
from mainapp.tests.live.chromedriver_test_case import ChromeDriverTestCase
from mainapp.tests.live.helper import (
MockM... | meine-stadt-transparent/meine-stadt-transparent | mainapp/tests/live/test_facetted_search.py | Python | mit | 7,373 | [
"VisIt"
] | deba3a19f00380af464364f6d28da5c7c32bfb746fb9142026de00ad63019025 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/Delaunay2DAlpha.py | Python | gpl-3.0 | 1,253 | [
"VTK"
] | 609287bd8f14c93002440ad8dbeda362856951a7f8bc5b7b259cfbfa4ac9e889 |
#!/usr/bin/python
'''
Use this in the same way as Python's SimpleHTTPServer:
./ssi_server.py [port]
The only difference is that, for files ending in '.html', ssi_server will
inline SSI (Server Side Includes) of the form:
<!-- #include virtual="fragment.html" -->
Run ./ssi_server.py in this directory and visit l... | sigstop/loomoe | tapestry/apps/tapestry/priv/www/bower_components/dygraphs/docs/ssi_server.py | Python | apache-2.0 | 1,938 | [
"VisIt"
] | e6b66bdee63b65b8ca9c184454a1fcf45841bf54fd670ce6ef543380d1ccbcd7 |
#!/usr/bin/env python
# file make_otu_network.py
__author__ = "Julia Goodrich"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Julia Goodrich"] # remember to add yourself
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Jose Clemente"
__email__ = "jose.clemente@gmail.com"
"""
This... | wasade/qiime | qiime/make_otu_network.py | Python | gpl-2.0 | 58,436 | [
"Cytoscape"
] | 4c928cb67861fa896fc2dd933673fc8308270cf396b31602e01493f046e1ed61 |
__author__ = 'Elahe'
import ephem
import numpy as np
import json
from numpy import *
import sqlite3 as lite
from calculations import *
import pandas as pd
class DataFeed(object):
def __init__(self, date, site, custom_episode = False):
self.Site = site
self.night_id = int(date - ephem.Date('20... | elahesadatnaghib/FB-Scheduler-v2 | FBDE.py | Python | mit | 24,163 | [
"VisIt"
] | 9bdd82cdcbafdb7f4377950bce4d054cd0a61b28f59cc876f6328c4fdf61cd0a |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkStructuredGridAlgorithm(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkStructuredGridAlgorithm.py | Python | bsd-3-clause | 519 | [
"VTK"
] | 99871f7539574c6996fa0d4554559407f76ae3cfdbe59839c6f2d8fa50cb925d |
#!/usr/bin/env python3
#
# Mimesis documentation build configuration file, created by
# sphinx-quickstart on Tue Oct 18 14:11:49 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | lk-geimfari/elizabeth | docs/conf.py | Python | mit | 10,540 | [
"Octopus"
] | a4410dc4283c6493a874c5014cb1725db7bff104d7f096bc4821c732cdd59395 |
from flask import render_template, request
import json
import lib.es as es
import web.util.tools as tools
def get(p):
host = p['c']['host']; index = p['c']['index'];
# keep pagination
p["q"] = tools.get('q', '*')
# pagination
p["from"] = int(tools.get('from', 0))
p["size"] = int(tools.get('siz... | unkyulee/elastic-cms | src/web/modules/post/controllers/post/view.py | Python | mit | 2,072 | [
"VisIt"
] | 2903f51d659a8260d794ed991d4933b67e3b2d243990a1799907fa939327af7c |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | 0k/odoo | addons/project/project.py | Python | agpl-3.0 | 73,303 | [
"VisIt"
] | ee52022e071c747614cf4ffe0710100ecb4128e5edc353c28c956b388451699d |
# Copyright (C) 2016, Davit Samvelyan
#
# This file is part of YouCompleteMe.
#
# YouCompleteMe 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 ... | oblitum/YouCompleteMe | python/ycm/buffer.py | Python | gpl-3.0 | 3,338 | [
"VisIt"
] | 9ef050631c244d62f9a1b641986337043ad6a03f031458dd96b6fecdc5d35197 |
#!/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/__init__.py | Python | apache-2.0 | 21,408 | [
"PySCF"
] | 30c9c8b55c5cd9c2eedd1fad3c686252dd486d36a05363105cf730376824b9b5 |
import pytest
from pysisyphus.io.pubchem import cid_from_name, sdf_from_cid, geom_from_pubchem_name
@pytest.mark.skip
def test_pubchem_cid_for_name():
name = "sodiumborohydride"
cid = cid_from_name(name)
assert cid == 4311764
@pytest.mark.skip
@pytest.mark.parametrize(
"name", [
"benzene",
... | eljost/pysisyphus | tests/test_pubchem/test_pubchem.py | Python | gpl-3.0 | 460 | [
"Jmol"
] | ee43421b41b76d49e7d07a84880d451d690d25bbf9a9a284a3d54e4afbeeeca6 |
import logging
import sys
from optparse import make_option
from django.contrib.auth.models import User
from django.conf import settings
from django.core.mail import send_mail
from django.core.management.base import BaseCommand
from django.core.validators import email_re
from django_browserid.auth import default_usern... | chirilo/remo | remo/profiles/management/commands/create_users.py | Python | bsd-3-clause | 2,366 | [
"VisIt"
] | 4c6d4dc7b52904600c91e7b41896c35e69cce1cf98c6eb264fd6b839ecead6da |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | testsuite/python/lj.py | Python | gpl-3.0 | 2,545 | [
"ESPResSo"
] | b81983fd0f825b12cc2686764c8f2b4ef4d8fc092f55fc796f6225b7e1442f66 |
"""**************************************************************************
* out_proc_util.py *
* *
* Created on: April 18, 2015 *
* Autho... | yushakov/simulif | simulif/py_scripts/out_proc_util.py | Python | gpl-3.0 | 7,317 | [
"NEURON"
] | 87413cbeb23250c7238f2d0b43c26236d271b258f81afc24bd94b277f6ebeb07 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/exodus/blocks/all_nodesets.py | Python | lgpl-2.1 | 642 | [
"MOOSE"
] | 5c08e6c5fee2bcb10dcb0c195b122583aa40f3c0fc906e49e8ebe9bb77fa112a |
from Screens.Screen import Screen
from Components.Label import Label
from Components.Pixmap import Pixmap
from Components.ServiceEventTracker import ServiceEventTracker
from Components.config import config
from enigma import eTimer, iServiceInformation, iPlayableService, eDVBFrontendParametersSatellite, eDVBFrontendPar... | kakunbsc/enigma2.4 | lib/python/DB/dbpExtraInfoBar.py | Python | gpl-2.0 | 10,055 | [
"Galaxy"
] | 9be25fe59874595284c6ca227dfd0fa74ac90c4d45accd5839924d83e382dc64 |
from . import empty
from serializers import groups
def create_flat():
obj = groups.Group(FlatHeader(), FlatDescription(), FlatData())
return groups.Flat(obj)
def create_recursive():
obj = groups.Group(RecursiveHeader(), RecursiveDescription(), RecursiveData())
return groups.Recursive(obj)
class Fl... | alepulver/my-thesis | results-tables/serializers/stage/normal.py | Python | mit | 5,605 | [
"VisIt"
] | 674f2e88fa32e0a09ab65f695fc8524be8df969d80d9ff42e11c2872ebb39173 |
"""This file contains code for use with "Think Bayes",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
"""This file contains class definitions for:
Hist: represents a histogram (map from values to integer frequencies).
P... | jac2130/BayesGame | Betting/thinkbayes.py | Python | mit | 50,374 | [
"Gaussian"
] | b54283a04865b86618ae79a180f2c1f0211b952e4afb90c3a5cca057cf663094 |
"""
Test functions for multivariate normal distributions.
"""
from __future__ import division, print_function, absolute_import
import pickle
import numpy
import numpy as np
import scipy.linalg
from common_tests import check_random_state_property
from numpy.testing import (assert_allclose, assert_almost_equal,
... | DailyActie/Surrogate-Model | 01-codes/scipy-master/scipy/stats/tests/test_multivariate.py | Python | mit | 54,758 | [
"Gaussian"
] | d4451492231b6d9b952537848e6f4cbe6de3d682dee6117528b1d1989c3d49cc |
import numpy as np
from numpy.linalg import inv, solve
from scipy.special import gammaln
from scipy.misc import logsumexp
from pybasicbayes.abstractions import Distribution, GibbsSampling, Model
from pybasicbayes.distributions import Multinomial
from pgmult.utils import kappa_vec, N_vec, pi_to_psi, psi_to_pi, \
... | HIPS/pgmult | pgmult/distributions.py | Python | mit | 18,659 | [
"Gaussian",
"NEURON"
] | c502107416e4708308c1d306a1ecea3bc7de751e272b2586f0bbe28f41cdb51b |
__author__ = 'sebastians'
# PyMOL Animation Tutorials -- 01 - Movie Setup
# This tutorial will show you how to set up a python script for writing an PyMOL animation.
# To start PyMOL from a python script, import the pymol modules
import pymol
from pymol import cmd
# The next line is essential to prevent any threadin... | ssalentin/pymol-animations | tutorials/basics/01-moviesetup.py | Python | mit | 1,433 | [
"PyMOL"
] | fd286e97a707532139237b829d07ef8ce3c210228309f268b27b5f182ba3847c |
#
# Copyright 2018 Analytics Zoo 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 or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/chronos/detector/anomaly/test_th_detector.py | Python | apache-2.0 | 6,562 | [
"Gaussian"
] | 7486963ecb853adac3e563781167ecfda82f91291c87a8ecb8ab14145d9cceb8 |
###########################################################################
#
# 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
#
# https://www.apache.org/l... | google/starthinker | dags/twitter_dag.py | Python | apache-2.0 | 9,737 | [
"VisIt"
] | 6a1703e97021a8aa55d611901d09f73c1beba1ca5c721344c1e1dc25c6f76ab9 |
#!/usr/bin/python
#
# Copyright 2015 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 b... | coxmediagroup/googleads-python-lib | examples/adwords/v201506/error_handling/handle_policy_violation_error.py | Python | apache-2.0 | 4,209 | [
"VisIt"
] | 0a7af392ca6d10cb8225475011e1f5794ebe5122ada7400007b5c4df600ca25b |
"""
Project
FPGA-Imaging-Library
Design
Scale
Function
Scaling an image by your given scale.
Module
Software simulation.
Version
1.0
Modified
2015-05-28
Copyright (C) 2015 Tianyu Dai (dtysky) <dtysky@outlook.com>
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU ... | jaechoon2/FPGA-Imaging-Library | Geometry/Scale/SoftwareSim/sim.py | Python | lgpl-2.1 | 4,146 | [
"MOE"
] | 0e97724c8343b30dafdc654fd4dee371596ca2e83a01d4dfab8d7bac74747c69 |
### Refer to G. Kresse, Phys. Rev. B 73, 045112 (2006)
### for comparison of macroscopic and microscopic dielectric constant
### and absorption peaks.
import os
import sys
import numpy as np
from ase.units import Bohr
from ase.lattice import bulk
from ase.parallel import paropen
from gpaw.atom.basis import BasisMak... | robwarm/gpaw-symm | gpaw/test/big/response/silicon_ABS.py | Python | gpl-3.0 | 1,956 | [
"ASE",
"GPAW"
] | 12a9a3c9f729487781d9f782194387f9d397a35ba4af12c69b6cd341a1b105de |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License
# Version 1.1 (the "License"); you may not use this file except in
# compliance with the License. You may obtain a copy of the License at
# http://www.mozil... | SciViews/sciviewsk | pylib/codeintel_r.py | Python | lgpl-2.1 | 85,440 | [
"Gaussian"
] | f5bf500923c17bde83674488777febf85ecfdf64c598dd4068e9894d270bef84 |
# -*- coding: utf-8 -*-
"""
moe.paste.urls
~~~~~~~~~~~~~~
URL definitions.
:copyright: 2009 by tipfy.org.
:license: BSD, see LICENSE.txt for more details.
"""
from tipfy import get_config, Rule
def get_rules():
# Take the area name from the subdomain if they are in use. Otherwise
# assum... | ac001/moe | project/app/moe/paste/urls.py | Python | bsd-3-clause | 1,018 | [
"MOE"
] | 978a1f3b2a71eddf3ad5fe3875376529a82d85d577a91bdff175ce8ade629eb5 |
from ase import Atoms
from ase.units import Bohr
from gpaw import GPAW
from gpaw.tddft import TDDFT, photoabsorption_spectrum, \
LinearAbsorbingBoundary, P4AbsorbingBoundary, PML
from gpaw.test import equal
import os
# Sodium dimer, Na2
d = 1.5
atoms = Atoms(symbols='Na2',
positions=[( 0, 0, d),
... | robwarm/gpaw-symm | gpaw/test/td_na2.py | Python | gpl-3.0 | 2,589 | [
"ASE",
"GPAW"
] | 9402d54d0291845d86ca27ee818f7a368c84c0544b0a96266a4dd1e48d137660 |
#!/usr/bin/python
import MySQLdb
import sys
from connection import *
from utils import *
db = create_conn()
def has_type(name):
c = db.cursor()
sql = "SELECT id FROM taxonomy_name_type WHERE name = %s" % (sql_to_string(name))
c.execute(sql)
row = c.fetchone()
return row is not None
def add_type(name):
c... | flavioc/ibmc-bio-db | scripts/types.py | Python | gpl-3.0 | 1,099 | [
"BLAST"
] | ae6326e9ff6843751b166ace6712b863f163b2ce492911806b1a81bd80960d03 |
#!/usr/bin/env python
"""A simple example of how you can use Mayavi without
using Envisage or the Mayavi Envisage application.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2007, Enthought, Inc.
# License: BSD Style.
from os.path import join, abspath
from pyface.api import GUI
# The core... | dmsurti/mayavi | examples/mayavi/standalone.py | Python | bsd-3-clause | 1,679 | [
"Mayavi"
] | e73805b4bf7837214035669a084e3cb7996cf0dd540fc48bf6492221cd2afca9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
from deepy.utils import global_rand
def get_fans(shape):
fan_in = shape[0] if len(shape) == 2 else np.prod(shape[1:])
fan_out = shape[1] if len(shape) == 2 else shape[0]
return fan_in, fan_out
class WeightInitializer(object):
"""
In... | ZhangAustin/deepy | deepy/utils/initializers.py | Python | mit | 4,086 | [
"Gaussian"
] | e99052484795645e4b32ef58b55d7d785f70b2a89134e9e3497343490d486312 |
"""Unit test for odbchelper.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.2 $"
__date__ = "$Date: 2004/05/05 21:57:19 $"
__co... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/odbchelpertest.py | Python | mit | 1,626 | [
"VisIt"
] | 55c11edaded109ece7853232259905c15d1adc089975481ecdd80509b1a52669 |
# -*- coding: utf-8 -*-
'''
Created on 3 juil. 2015
Toolbox for data obtained using G50 Automatique Ice Texture Analyser (AITA) provide by :
Russell-Head, D.S., Wilson, C., 2001. Automated fabric analyser system for quartz and ice. J. Glaciol. 24, 117–130
@author: Thomas Chauve
@contact: thomas.chauve@univ-grenoble-al... | ThomasChauve/aita | AITAToolbox/aita.py | Python | gpl-3.0 | 77,555 | [
"VTK"
] | 94912a42a6d0e73a29169e88d30fb79eecf05b2a0c8e1c2495cf658c24ce2c78 |
import sys
#QT imports
from PyQt5.QtWidgets import QApplication, QMainWindow, QInputDialog, QLineEdit, QFileDialog, QErrorMessage, QTableWidget, QTableWidgetItem,QTableWidgetItem
from PyQt5 import QtCore, QtWidgets, uic
from main_designer import Ui_MainWindow
# plotting
import matplotlib
matplotlib.use('Qt5Agg')
from m... | helgestein/XRDExplorer | main.py | Python | gpl-3.0 | 35,562 | [
"CRYSTAL"
] | 0b1e0199b70c9ba9fb3855f585ffcca7abe123b3c6d7f36bdceeb91973d9ae4b |
#! /usr/bin/env python3
import numpy as np
import shtns
import sys
class Spharmt(object):
def __init__(self,nlons,nlats,ntrunc,rsphere,gridtype='gaussian'):
"""initialize
nlons: number of longitudes
nlats: number of latitudes
"""
self._shtns = shtns.sht(ntrunc, ntrunc, 1... | schreiberx/sweet | local_software/tests/shtns_test_1.py | Python | mit | 1,453 | [
"Gaussian"
] | 41107ac7fb802d5290d8c3e11199930c6a89f146392d69bea239c4d0eab05650 |
from datetime import datetime, timedelta
import re
from wye.base.constants import WorkshopStatus
from tests import factories as f
def test_workshop_wrong_action(base_url, browser, outbox):
tutor_type = f.create_usertype(slug='tutor', display_name='tutor')
poc_type = f.create_usertype(slug='poc', display_name... | pythonindia/wye | tests/functional/workshop/test_workshop_flow.py | Python | mit | 6,679 | [
"VisIt"
] | afa94967439bd1a715ad4badcc0553aeeeb953eceb7c23564a072478ac7480f0 |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2020, Mostapha Sadeghipour Roudsari <mostapha@ladybug.tools>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU G... | mostaphaRoudsari/Honeybee | src/Honeybee_Generate Standard CIE Sky.py | Python | gpl-3.0 | 6,895 | [
"EPW"
] | 7725cb41cac6ff9eddeb52c9363540009fa508b09eb094c4431ff8d82428a5a7 |
input_name = '../examples/linear_elasticity/prestress_fibres.py'
output_name = 'test_prestress_fibres.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| RexFuzzle/sfepy | tests/test_input_prestress_fibres.py | Python | bsd-3-clause | 175 | [
"VTK"
] | f43a214d279f3b2528a7139f852dbda570024099a7d7e2869a9d8c5c79974b4c |
from pylab import *
# ###########################################
# Analysis functions
# ###########################################
def rate_from_spiketrain(spiket,spikei,fulltime,sigma,dt,nrnidx=None):
"""
Returns a rate series of spiketimes convolved with a Gaussian kernel;
all times must be in SI unit... | h-mayorquin/camp_india_2016 | tutorials/EI networks/data_utils.py | Python | mit | 1,848 | [
"Gaussian",
"NEURON"
] | 8375016b9147d0278249cb5b439cb14223071c63d427c315206c3903c01f7603 |
#!/usr/bin/env python
'''
DCS Filter
Version 2.0
By Brendan Kohrn, Scott Kennedy(1), and Mike Schmitt(1)
(1) Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195
Based on work by Scott Kennedy, Mike Schmitt
December 17, 2013
Written for Python 2.7.3
Required modules: Pysam, Samtools... | loeblab/Duplex-Sequencing | Nat_Protocols_Version/DuplexMaker.py | Python | bsd-3-clause | 9,412 | [
"Biopython",
"pysam"
] | b34c7580d4fec8243ee1d511d6b4d884a480c7bf23f039f1caff5c655ebd7cc2 |
"""GSIFTP module based on the GFAL2_StorageBase class."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger
from DIRAC.Core.Utilities.Pfn import pfnp... | yujikato/DIRAC | src/DIRAC/Resources/Storage/GFAL2_GSIFTPStorage.py | Python | gpl-3.0 | 2,073 | [
"DIRAC"
] | 0e66bd11f252b7c570c3ea87a1ccc2b40652876baa2988e8e58805879e6038a0 |
# Copyright (C) 2012 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
# self.option) any later version.
#
# This program is distributed in ... | hagabbar/pycbc_copy | pycbc/events/events.py | Python | gpl-3.0 | 32,066 | [
"Gaussian"
] | 1b1298bf480a111e5b9bac39a58b51552a5d6ae9e9cd1a24ba07ac96724b86f3 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-get-jdl
# Author : Stuart Paterson
########################################################################
"""
Retrieve the current JDL of a DIRAC job
"""
from __future__ import print_function
__... | fstagni/DIRAC | Interfaces/scripts/dirac-wms-job-get-jdl.py | Python | gpl-3.0 | 1,482 | [
"DIRAC"
] | 51fda810771664d6e45fabb6d79f1e06bd535abb2d91aa07db894076d3cd5dc9 |
from django.db import models
class CrfModelManager(models.Manager):
"""A manager class for Crf models, models that have an FK to
the visit model.
"""
def get_by_natural_key(self, subject_identifier, visit_schedule_name,
schedule_name, visit_code, visit_code_sequence):
... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/managers.py | Python | gpl-2.0 | 2,877 | [
"VisIt"
] | dbe5b0dd9dbd3dbff7bcc75c4eb9d67642e1358c262cd22774d44c185df0af08 |
# -*- coding: utf-8 -*-
#
# plot_connections.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 Licens... | INM-6/nest-git-migration | topology/doc/old_doc/plotting_tools/plot_connections.py | Python | gpl-2.0 | 3,755 | [
"Mayavi"
] | 69475cf33a96b8601adf7413ac8cf5226432ff9228824457c5a8997de9b8b673 |
"""
Find runs that match crAssphage with a minimum number of runs, a minimum alignment length, and a minimum percent
identity
"""
import os
import sys
import argparse
import pysam
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Count hits in a bam file")
parser.add_argument('-d', hel... | linsalrob/crAssphage | bin/bam/count_bam_hits.py | Python | mit | 1,853 | [
"pysam"
] | 97cad19e6b7e5a5a893fe65d2539d89fedb68ef925e945ee6b2229c7d1e84838 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import os
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf, skip
from selenium.webdriver.common.by import By
from selenium.webdriver.common.action_chains import ActionChains
from ..helpers import UniqueCourseTest, is_yo... | 10clouds/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 51,712 | [
"VisIt"
] | d158e125faa0fbdf1da48371f631b95cf09eeadcd66eeffb90ffae7dcae5617c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
It finds a list of genes that might homologous (there is a short read which maps on both genes).
Author: Daniel Nicorici, Daniel.Nicorici@gmail.com
Copyright (c) 2009-2021 Daniel Nicorici
This file is part of FusionCatcher.
FusionCatcher is free software: you can ... | ndaniel/fusioncatcher | bin/find_homolog_genes.py | Python | gpl-3.0 | 20,372 | [
"Bowtie"
] | d2af7f2a9ff20df77342a8bb1f3d641178c0ad85151379fd17d109036498952f |
#!env/bin/python
from twython import Twython
import config
import string
twitter = Twython(config.app_key, config.app_secret)
auth = twitter.get_authentication_tokens(callback_url='oob')
print "Visit\n\n{url}\n\nand enter the PIN here: ".format(url=auth['auth_url'])
pin = raw_input('> ')
twitter = Twython(config.ap... | plaidfluff/fluff_ebooks | auth.py | Python | apache-2.0 | 647 | [
"VisIt"
] | 9ebd29b2a161b840786411d58aa068eddf0059b25ea46422a319f474cad9cf76 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 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 General Public License as published by
## the Free Sof... | tiagocardosos/stoq | stoqlib/net/calendarevents.py | Python | gpl-2.0 | 12,181 | [
"VisIt"
] | 5d6eeca8a1577073b7814eed7f9363b361fb7feac6023dc20a352159e3ca105b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen import Structure, Lattice, Specie, DummySpecie
import numpy as np
"""
Classes for reading/writing mcsqs files following the rndstr.in format.
"""
__author__ = "Matthew Horton"
__copyright__ = "C... | blondegeek/pymatgen | pymatgen/io/atat.py | Python | mit | 4,455 | [
"CRYSTAL",
"pymatgen"
] | 12e345c5302bc0cf14756e1fac2474b85de47c1ba90e088636eaad23400e8065 |
'''
Example of a spike receptor (only receives spikes)
In this example spikes are received and processed creating a raster plot at the end of the simulation.
'''
from brian import *
import numpy
from brian_multiprocess_udp import BrianConnectUDP
# The main function with the NeuronGroup(s) and Synapse(s) must be na... | ricardodeazambuja/BrianConnectUDP | examples/OutputNeuronGroup_multiple_outputs_2.py | Python | cc0-1.0 | 2,836 | [
"Brian",
"NEURON"
] | 13e4a9d48b7d18268ca247c6b76007c0f0f5ee88ca97da5679bc6e94de936daf |
# -*- coding: utf-8 -*-
"""Collection of physical constants and conversion factors.
Physical constants
==================
=============================== ==============================================
``g`` Earth standard gravity in :math:`\sf ms^{-1}`
``h`` Planck ... | atmtools/typhon | typhon/constants.py | Python | mit | 4,982 | [
"Avogadro"
] | c04d9df1364da30c7da730d7ffceaf5d57736b955af56a03db0658d4d9bac2dd |
# -*- coding: utf-8 -*-
#
# hpc_benchmark.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 License, ... | sdiazpier/nest-simulator | pynest/examples/hpc_benchmark.py | Python | gpl-2.0 | 16,231 | [
"NEURON"
] | 154d3d5c915612eaf6678740d14c97020ee5114c083efd905cd1515c7f9c4f3e |
# sourceclientgui.py: new for version 0.7 this provides the graphical
# user interface for the new improved streaming module
# Copyright (C) 2007-2012 Stephen Fairchild (s-fairchild@users.sourceforge.net)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | radiocicletta/idjc-x | python/sourceclientgui.py | Python | gpl-2.0 | 129,563 | [
"Amber"
] | 656871eb5becdd195753528285959ce7d6ab524540a83f8e0c795f31b9182b60 |
from jobman import DD, expand, flatten
import pynet.layer as layer
from pynet.model import *
from pynet.layer import *
from pynet.datasets.mnist import Mnist, Mnist_Blocks
import pynet.datasets.spec as spec
import pynet.datasets.mnist as mnist
import pynet.datasets.transfactor as tf
import pynet.datasets.mapping as m... | hycis/Pynet | hps/deprecated/MLP.py | Python | apache-2.0 | 7,256 | [
"Gaussian"
] | 9cd1cdc53ef0f18d8916419e6d92c07bf67b2648a2aa2ea84e909b5dad0fd8eb |
# This is a small script for reweighting molecular simulations using
# the Bayesian/MaxEnt (BME) approach
# Copyright (C) 2018 Sandro Bottaro (name . surname @ iit . it)
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License V3 as publishe... | PPKE-Bioinf/consensx.itk.ppke.hu | consensx/bme_reweight.py | Python | mit | 18,356 | [
"Gaussian"
] | a98a814f8ee437851c213d144f33e953869824745dd436ea2d17e0f1b859e6d3 |
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