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# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/awidgets/button.py | Python | gpl-3.0 | 1,420 | [
"Brian"
] | dc0ac0316a0c09997127fc8b468e6c46f84a3805d62fae06fc7beb822e1f0d6e |
#!/usr/bin/env python
"""
Given a BLAST or DIAMOND JSON output files, the corresponding FASTA (or FASTQ)
sequence files, and filtering criteria, produce a summary of matched titles
and (optionally) an alignment panel.
Run with --help for help.
"""
from __future__ import print_function
import os
import sys
import ar... | acorg/dark-matter | bin/alignment-panel-civ.py | Python | mit | 16,440 | [
"BLAST"
] | ef0d646acc4f5785bb296c744c6e588fd42f69c924fa1514f6269df254303c7e |
__author__ = 'ddeconti'
import sys
from rdkit.Chem import SDMolSupplier, MolToSmiles
def sdf_to_smile(sdf_filename):
sdf_struct = SDMolSupplier(sdf_filename)
for mol in sdf_struct:
try:
print MolToSmiles(mol)
except:
continue
def main(sa):
sdf_filename = sa[0]
... | dkdeconti/PAINS-train | training_methods/file_manipulation/sdf_to_smiles.py | Python | mit | 407 | [
"RDKit"
] | 171433a12b8bd9c3116dd6e823b76695005485094543d54817a1d7a71466357b |
import web
from web import form
render = web.template.render('templates/')
urls = ('/', 'index')
app = web.application(urls, globals())
myform = form.Form(
form.Textbox("boe"),
form.Textbox("bax",
form.notnull,
form.regexp('\d+', 'Must be a digit'),
form.Validator('Must be more tha... | urmyfaith/notes_web_py | basic/form/formV000.py | Python | apache-2.0 | 1,105 | [
"MOE"
] | 58fae6b20827b980345158ebe9caf273468dfe1ba1c355cfba925647171cfa2d |
import gaff2xml
m0 = gaff2xml.openeye.smiles_to_oemol("ClC(Cl)(Cl)Cl")
charged = gaff2xml.openeye.get_charges(m0)
trajectories, ffxml = gaff2xml.openeye.oemols_to_ffxml([charged])
f = open("./ccl4.xml", 'w')
f.write(ffxml.read())
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
import m... | kyleabeauchamp/DBayes | dbayes/build_ccl4.py | Python | gpl-2.0 | 1,088 | [
"MDTraj",
"OpenMM"
] | 4a508dca7943f85705c038fdf030dfa1068c67ec206cf364820be1f24e616c0b |
# -*- coding: utf-8 -*-
import sys
import os
# LIBRARY USED TO SUBMIT JOBS:
# - 'LSF' FOR IBM LSF WORKLOAD MANAGER (it uses 'sys_LSF.py')
# - 'LOCAL' FOR SEQUENTIAL RUN ON SINGLE MACHINE (it uses 'sys_single.py')
# - 'OTHER' FOR LIBRARIES ADAPTED TO OTHER WORKLOAD MANAGERS (it uses 'sys_OTHER.py')
mode = "LSF"
# PATH... | HudsonAlpha/aRNAPipe | lib/config.py | Python | mit | 4,161 | [
"HTSeq"
] | b3ec93b3baafebae19e88b62d70c0a2c613890bcf70689455ab89d382f684c63 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys, os, math, re, configparser, subprocess
from PyQt4 import QtCore, QtGui
ROOT = os.path.expanduser('~/.stardict-flashcard/')
CONFIG_PATH = os.path.join(ROOT, 'rc.ini')
ARCHIVE_DIR = os.path.join(ROOT, 'archive')
ACT_ICON_DIR = os.path.join(os.path.dirname(os.path... | kuanyui/stardict-flashcard | main.py | Python | gpl-3.0 | 42,485 | [
"VisIt"
] | f342aa30020a6f606bea04e952bde3d52fd19a46bdcf9c6b88cb22371bfada00 |
import os
import unittest
from ample import constants
from ample.modelling import octopus_predict
from ample.testing import test_funcs
INTERNET_AVAIL = test_funcs.internet_on()
@unittest.skip("Needs to be rewritten to avoid blocking read, but code is scheduled for removal")
# @unittest.skipUnless(INTERNET_AVAIL, "N... | linucks/ample | ample/modelling/tests/test_octopus_predict.py | Python | bsd-3-clause | 2,021 | [
"Octopus"
] | 90952dca4a0424a505a1454427160ff6720aa913b12e0f3574167e92d59b476f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Eric Nichols, <eric@ecei.tohoku.ac.jp>
################################################################################
import pymongo
import sys
import mongodb
from matrix2pmi import PMI
class Bootstrapper:
def __init__(self, host, port, db, matrix, rel,
... | underspecified/web-ka | tools/bootstrapper.py | Python | gpl-2.0 | 9,082 | [
"ESPResSo"
] | e152bc482409c67fa6ee85cbfa9dcc26e8ccec9e38694efd9c6cae899dca3719 |
from DIRAC.Core.Base import Script
Script.parseCommandLine()
import unittest
import itertools
from DIRAC.DataManagementSystem.DB.FileCatalogDB import FileCatalogDB
from DIRAC.Core.Security.Properties import FC_MANAGEMENT
seName = "mySE"
testUser = 'atsareg'
testGroup = 'dirac_user'
testDir = '/vo.formation.idgrille... | marcelovilaca/DIRAC | DataManagementSystem/DB/test/TestFileCatalogDB.py | Python | gpl-3.0 | 44,512 | [
"DIRAC"
] | bb579e51e282c4f1100adf31402a87b0173e5388ea9d0d4f09f18e8a1836ec52 |
"""
Test functions for stats module
"""
import warnings
import re
import sys
import pickle
from pathlib import Path
import os
import json
import platform
from numpy.testing import (assert_equal, assert_array_equal,
assert_almost_equal, assert_array_almost_equal,
as... | mdhaber/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 269,537 | [
"Gaussian"
] | dbc0b50ce9965f6288f2de9e5b1cf512da7ab829f633f7b11212bc0b9e26962d |
#!/usr/bin/env python
import sys
import argparse
import os.path
#Time of script execution and logging module
# import time
# import logging
import re
import itertools
# from collections import *
# import random
import multiprocessing as mp
from Bio.Blast import NCBIXML
def main():
args = create_argparser()
#Get fi... | maubarsom/biotico-tools | python/parallel_blastxml_hitsort.py | Python | apache-2.0 | 7,755 | [
"BLAST"
] | 000d924037ab560749ee0f49e92a9dd40322f981b9f86af81dba101ca07580cf |
#! examine JK packing forms
import psi4
import numpy as np
from collections import OrderedDict
mol = psi4.geometry("""
0 2
H 0.0 2.0 0.0
H 0.0 4.0 0.0
H 0.0 6.0 0.0
H 0.0 8.0 0.0
H 0.0 10.0 0.0
""")
primary = psi4.core.BasisSet.build(mol, "ORBITAL", "cc-pVTZ")
aux = psi4.core.BasisSet.build(mol, "ORBITAL", "... | amjames/psi4 | samples/python/3-index-transforms/test.py | Python | lgpl-3.0 | 4,915 | [
"Psi4"
] | b712b86c9cfaea3e0c05b02cdd80f63b4e22fd230d7580e6e069fe7b0e836141 |
#!/usr/bin/env python
import sys
import pysam
import textwrap
import os
def print_header():
print textwrap.dedent("""\
##fileformat=VCFv4.1
##phasing=none
##INDIVIDUAL=TRUTH
##SAMPLE=<ID=TRUTH,Individual="TRUTH",Description="bamsurgeon spike-in">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Descript... | MischaLundberg/bamsurgeon | scripts/makevcf_indels.py | Python | mit | 2,715 | [
"pysam"
] | 7fc44dfb7e59868c1eea62f6ef00949f60b4e06163db82516eceb67ed01f845c |
""" :mod: RequestValidatorTests
=======================
.. module: RequestValidatorTests
:synopsis: test cases for RequestValidator
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
test cases for RequestValidator
"""
import unittest
from mock import MagicMock as Mock, patch
from DIRAC.RequestMana... | ic-hep/DIRAC | src/DIRAC/RequestManagementSystem/private/test/Test_RequestValidator.py | Python | gpl-3.0 | 3,896 | [
"DIRAC"
] | ac453d0185ba337dd244a71c0bffc152633477b471672e6471efd81b7018dfe9 |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-04-29 01:15:33
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-04-29 01:15:33 by Brian Cherinka
Last Modified On: 2016-04-29 01:15:33 by Brian
'''
from __future__ import print_function
from __future__... | bretthandrews/marvin | python/marvin/web/controllers/images.py | Python | bsd-3-clause | 2,080 | [
"Brian"
] | 0f6c4466f161409e7a6ff2671ffe492b2f96510cdc0af59cb1c4cf8a418d5a6a |
# shelve.py - save/restore working directory state
#
# Copyright 2013 Facebook, Inc.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
"""save and restore changes to the working directory
The "hg shelve" command saves changes made ... | hekra01/mercurial | hgext/shelve.py | Python | gpl-2.0 | 26,688 | [
"VisIt"
] | bfe7dd800108bd766ad4515d4379e97993a867f16406f043362cb50ed8943256 |
__all__ = ['smooth_image']
import math
from .. import utils
from ..core import ants_image as iio
def _smooth_image_helper(image, sigma, sigma_in_physical_coordinates=True, FWHM=False, max_kernel_width=70):
outimage = image.clone()
if not isinstance(sigma, (tuple,list)):
sigma = [sigma]
if ... | ANTsX/ANTsPy | ants/utils/smooth_image.py | Python | apache-2.0 | 2,480 | [
"Gaussian"
] | 576e42c594039d7fa6c4fa091b4c29df60c31574765e88d307ef4034690a6b81 |
# creates: diffusion-path.png
import os
from ase import *
if 1:
execfile('diffusion4.py')
images = [read('mep%d.traj' % i) for i in range(5)]
a = images[0] + images[1] + images[2] + images[3] + images[4]
del a.constraints
a *= (2, 1, 1)
a.set_cell(images[0].get_cell())
write('diffusion-path.pov', a, show_unit_cell... | freephys/python_ase | doc/tutorials/constraints/diffusion.py | Python | gpl-3.0 | 398 | [
"ASE"
] | 5dd46e6275ef523c539da9bf4d3fcc0de909430c3c25cce77d412fa20f1aa1ea |
# Copyright 2019 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/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/spectral-density | tf/lanczos_experiment.py | Python | apache-2.0 | 9,466 | [
"Gaussian"
] | daf65c4bc845bd30e851426110d7ca1541130e36b08bbb02dd018273d1fa1f59 |
import StringIO
import os
import sys
import componentinfo
import configutil
from util import *
###
def cmake_quote_string(value):
"""
cmake_quote_string(value) -> str
Return a quoted form of the given value that is suitable for use in CMake
language files.
"""
# Currently, we only handle e... | jeltz/rust-debian-package | src/llvm/utils/llvm-build/llvmbuild/main.py | Python | apache-2.0 | 36,219 | [
"VisIt"
] | b1d3b4e6f0fc5daa43c3815a036d7a83654947d215b27b19310a15ab5cdfde91 |
import glob,os,re,math,sys,random
# Should version this... 140813-16 TAW
# More flexible handling of residue/molecule names
# More extensive support for geometric operations
# In the context of this module, a residue is a list of atoms, where each atom/item
# is a list or tuple with at least 7 values:
#
# (atom nam... | Tsjerk/MartiniTools | Mapping/__init__.py | Python | gpl-2.0 | 22,248 | [
"GROMOS"
] | 8c59abc6b96b0ceba605d41c07be38210ffc1ac2550b630472aea5f7c0646b1a |
########################################################################
# File : ExecutorReactor.py
# Author : Adria Casajus
########################################################################
"""
DIRAC class to execute Executors
Executors are an active part of DIRAC.
All DIRAC executors must inherit fr... | yujikato/DIRAC | src/DIRAC/Core/Base/ExecutorReactor.py | Python | gpl-3.0 | 8,660 | [
"DIRAC"
] | c5a84b78636782d128ceae7a83687dfd676c3d84a5dc4ab3481ff3d1d0fb3cd1 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Block code for active space N-particle density matrices.
'''
from pyscf import gto
from pyscf import scf
from pyscf import mcscf
from pyscf.dmrgscf import dmrgci
b = 1.2
mol = gto.M(
verbose = 4,
atom = 'N 0 0 0; N 0 0 %f'%b,
basis... | gkc1000/pyscf | examples/dmrg/03-density_matrix.py | Python | apache-2.0 | 808 | [
"PySCF"
] | 6d2c19cd18d7be6ecd5787aa1506438f7f10a4003943539eea3f42bcd19d910b |
#-*- coding:utf-8 -*-
"""
This file is part of OpenSesame.
OpenSesame 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.
OpenSesame is distri... | eort/OpenSesame | libopensesame/sketchpad_elements/_gabor.py | Python | gpl-3.0 | 1,797 | [
"Gaussian"
] | 994754890374b875122849429427a58cf461afaf2981542bba2c063fab3532fa |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2017 Nervana Systems 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
#... | mas-dse-greina/neon | luna16/LUNA16_extract_patches_subset_HDF5.py | Python | apache-2.0 | 19,475 | [
"Gaussian"
] | bac89a1812515520e8c785a5a6615a193903c0f40147c6e76c1aecc8ae29e7d1 |
# -*- coding: utf-8 -*-
"""
Write EC and SMC Meshes in legacy VTK format as .vtk.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Relative import path for the DumpMeshToLegacyFormat script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__)... | BlueFern/DBiharMesher | meshes/c8000/Dump8000MeshLegacyFormat.py | Python | gpl-2.0 | 893 | [
"VTK"
] | a2fa187321825ec33b29ee3f8b78dfdad2547dca56ae878c8cde80658932c993 |
import hashlib
import os
import traceback
from typing import List, Set
from fsbc.paths import Paths
from fsgamesys.amiga.rommanager import ROMManager
from fsgamesys.archive import Archive, archive_extensions
from fsgamesys.filedatabase import FileDatabase
from .i18n import gettext
class FileScanner(object):
def... | FrodeSolheim/fs-uae-launcher | launcher/filescanner.py | Python | gpl-2.0 | 15,863 | [
"ADF"
] | e8c4f0011d853eb1dce11bf894a2e49ea47aa2a1bfe9b7040d39dd79c546354a |
from __future__ import absolute_import
import os
from sfepy import data_dir
from sfepy.base.base import nm
from sfepy.homogenization.micmac import get_homog_coefs_linear
from sfepy.homogenization.recovery import save_recovery_region,\
recover_micro_hook
def post_process(out, pb, state, extend=False):
from sfep... | vlukes/sfepy | examples/homogenization/linear_elastic_mM.py | Python | bsd-3-clause | 3,251 | [
"VTK"
] | a3f435a91321abe68fc1bc30faad7703d41453e38d212105b57fe3c6b6fc55aa |
#
# @BEGIN LICENSE
#
# QCDB: quantum chemistry common driver and databases
#
# Copyright (c) 2011-2017 The QCDB Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of QCDB.
#
# QCDB is free software; you can redistribute it and/or modify
# it ... | loriab/qcdb | qcdb/libmintsmolecule.py | Python | lgpl-3.0 | 127,084 | [
"Elk",
"Psi4"
] | 8537fe7628f91f8fe68f6078aaee354d765bec4d7d303b12fe63de6f96cc4a20 |
'''
Created on 10.11.2017
@author: stoll
'''
import csv
import os
from numpy import argwhere, transpose
import numpy
from apps.calc.tess_module.tess import helpers
from apps.calc.tess_module.tess import waterfalls
def tess(time,data,data2):
'''
TESS is a software project that is part of the OpenAdaptronics ... | IT-PM-OpenAdaptronik/Webapp | apps/calc/tess_module/tess/tess.py | Python | mit | 7,748 | [
"exciting"
] | c7564f3fd7d8dc0eeb87c367f3e5ba8f5d3d30bdc4d364cbafe6f74c80b2c45f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from datetime import datetime
import os
from unittest import TestCase
import warnings
from django.utils import html, safestring
from django.utils._os import upath
from django.utils.deprecation import RemovedInDjango18Warning
from django.utils.encoding im... | wfxiang08/django178 | tests/utils_tests/test_html.py | Python | bsd-3-clause | 9,468 | [
"ADF"
] | 47b39efcdb4c9bd7604e6580415954015b5adcc174b24285e6d32c4c569345c1 |
#!/usr/bin/env python
# File: dataset_kepler.py
# Author: James Bedell, 2014-06-27
#
# Kepler data set reader and plotter for light curves
#
# Copyright 2013-2015, by the California Institute of Technology. ALL
# RIGHTS RESERVED. United States Government Sponsorship
# acknowledged. Any commercial use must be negotiate... | wkiri/DEMUD | demud/dataset_mastcam.py | Python | apache-2.0 | 42,501 | [
"Gaussian"
] | 5c8ed0e909b6a3b55217dd3832deb1e50094ccfebec4159d00270cbd715565bf |
from abapy import materials
from abapy.misc import load
import matplotlib.pyplot as plt
from matplotlib import cm
import numpy as np
import pickle, copy, platform, compmod
# GENERAL SETTINGS
settings = {}
settings['export_fields'] = True
settings['compart'] = True
settings['is_3D'] = True
settings['lx'] = 1.
s... | lcharleux/compmod | doc/sandbox/ludovic/cuboidTest_bimodal.py | Python | gpl-2.0 | 3,184 | [
"VTK"
] | 880964879fd0f67e3c460825e0454f806ca68a97228390e0fb14ad7f1c366995 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/repeatmasker/package.py | Python | lgpl-2.1 | 3,210 | [
"BLAST"
] | 95eeb5dd3b66a0ddb6f09c340bfeb8c96ed094e9d1fb7efcfcf4042e7264efda |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageIdealHighPass(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkImageIdealHighPass.py | Python | bsd-3-clause | 499 | [
"VTK"
] | 2d6fc799e6d0fd99e1ae8f34ee0ba3abf1713603e1ddb735ce60eb1d92b16ab8 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-cpu-normalization
# Author : Ricardo Graciani
########################################################################
"""
Determine Normalization for current CPU
"""
__RCSID__ = "$Id$"
import DIRAC
f... | marcelovilaca/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-cpu-normalization.py | Python | gpl-3.0 | 2,138 | [
"DIRAC"
] | be76b229cf380618fc0021813e8c039b1d85d52df67a4aea4909c6b1f7851e77 |
import httplib
import os
import urlparse
from urlparse import urljoin
from xml.etree import cElementTree
import netCDF4 as nc
import requests
import wx
from gui.controller.NetcdfDetailsCtrl import NetcdfDetailsCtrl
from gui.views.OpenDapExplorerView import OpenDapExplorerView
import threading
from sprint import *
c... | Castronova/EMIT | gui/controller/NetcdfCtrl.py | Python | gpl-2.0 | 9,743 | [
"NetCDF"
] | ae554ec33a2c0f48f36598b9c318025fe2657cbecab2e133d51772bf94eed80e |
""" This is a test of the chain
ProductionClient -> ProductionManagerHandler -> ProductionDB
It supposes that the ProductionDB, TransformationDB and the FileCatalogDB to be present
It supposes the ProductionManager, TransformationManager and that DataManagement/FileCatalog services running
"""
from __futur... | yujikato/DIRAC | tests/Integration/ProductionSystem/Test_Client_TS_Prod.py | Python | gpl-3.0 | 10,220 | [
"DIRAC"
] | 891340039a146dfdc1afb662f5a7c8289116b44fd99a8a8f953b828a83bf5f91 |
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 25 14:02:59 2015
by LW March 2015
set of utility functions for beamline alingment and commissioning
v 0.0.1 (this version): might have created a typo in E-calibration!!!
added dcm_roll for calculating DCM Roll correction
"""
############
... | NSLS-II-CHX/ipython_ophyd | startup/96-util_funcs.py | Python | bsd-2-clause | 44,614 | [
"Gaussian"
] | ca45b57a7ca8e84677c8acf40eb2694ac4f55441871a3bbf403baba14ac90fa2 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.common.action_chains import ActionChains
from .course_p... | sbalde/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 25,523 | [
"VisIt"
] | 4b63043c00897d104ef47adf8abeaf9a482bc840352b0726c52387e201800556 |
# -*- coding: utf-8 -*-
"""
Created on Tue Nov 1 16:17:59 2016
@author: Pedro
"""
# git tag -a v1.1 -m 'Version 1.1'
# git push origin --tags
# build with: python setup.py bdist_wheel sdist
# upload with: twine upload dist/* --skip-existing
# install locally with: pip install --upgrade --no-deps --force-reinstall ... | pedvide/simetuc | setup.py | Python | mit | 5,173 | [
"ASE"
] | ceae7a35690cc52031d9be2dc5cc0a3f218c71dc54e1458676c4b5f6e145668e |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <d.engemann@fz-juelich.de>
#
# License: BSD 3 clause
from math import log, sqrt
import warnin... | B3AU/waveTree | sklearn/decomposition/pca.py | Python | bsd-3-clause | 25,539 | [
"Gaussian"
] | f879e936f480985369a17180325bc9453aaa2893a92e677094cd2a1f38722248 |
def itemTemplate():
return ['object/tangible/item/quest/force_sensitive/shared_fs_crystal_health.iff'] # needs correct iff still
def customItemName():
return "Biological Focus Crystal"
def requiredLevelForEffect():
return 80
def biolink():
return 1
def lootDescriptor():
return 'rarebuffitem'
def i... | agry/NGECore2 | scripts/loot/lootItems/legendarylootchest/biological_focus_crystal.py | Python | lgpl-3.0 | 561 | [
"CRYSTAL"
] | 5f43b1299d2c41c201a8ae075ca4bb0ab200c623631267460c1c5b10f4156b67 |
"""
Data-driven tests for references.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import glob
import hashlib
import json
import os
# TODO it may be a bit circular to use pysam as our interface for
# accessing reference information, since this is th... | srblum/server | tests/datadriven/test_references.py | Python | apache-2.0 | 7,572 | [
"Biopython",
"pysam"
] | 5f3562341a642181dd3f531d2291f602c568bb1a639f395cf73508e667b54673 |
#!/usr/bin/env python
import logging
logger = logging.getLogger(__name__)
import argparse
import copy
import io
import os
import sys
import time
import traceback
import pyexiv2
import numpy as np
from numpy.f2py.auxfuncs import throw_error
import matplotlib as mpl
from logging import exception
if os.environ.get... | stevemarple/AuroraWatchNet | software/server/bin/make_awn_plots.py | Python | gpl-2.0 | 33,954 | [
"Amber",
"VisIt"
] | f6b0e4d3cb5bfddc92da684528aca8cf71db2dc343d720a0b6d72e74d1c27074 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/pmi.py | Python | gpl-3.0 | 49,194 | [
"ESPResSo"
] | 21a2dfdf8f703c39e5ee36a5897a2530c7e49071dbf9b8a101b6db394080536e |
# ftests/base.py
import sys
import os
import time
from unittest import skip
from datetime import datetime
from django.conf import settings
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from selenium import webdriver
from selenium.common.exceptions import WebDriverException
from selenium.webdr... | thomec/tango | ftests/base.py | Python | gpl-2.0 | 5,278 | [
"VisIt"
] | 336a1725b75f32ee0bf8c96ae23525f5613bce506ac2ee91e23fb3520dc9ba58 |
"""Polynomial factorization routines in characteristic zero. """
from __future__ import print_function, division
from sympy.polys.galoistools import (
gf_from_int_poly, gf_to_int_poly,
gf_lshift, gf_add_mul, gf_mul,
gf_div, gf_rem,
gf_gcdex,
gf_sqf_p,
gf_factor_sqf, gf_factor)
from sympy.poly... | ojengwa/sympy | sympy/polys/factortools.py | Python | bsd-3-clause | 33,927 | [
"Gaussian"
] | 78e5cba0b52d33aa252958bd6e40d3256e39a27b1dc29dbd3d04ad9ccb75b04a |
# -*- coding: utf-8 -*-
"""
generator.py is a simple script that creates a sqlite database of Android
device models and its corresponding user-friendly names, e.g.:
SM-N910W8, Samsung Galaxy Note4.
This is part of AndroidDeviceNames library:
https://github.com/tslamic/AndroidDeviceNames
:copyright: (c) 2017 by Tadej... | corcoran/AndroidDeviceNames | generator/generator.py | Python | apache-2.0 | 3,671 | [
"Galaxy"
] | 9bd3033d02cebc35e064f959603e7f2917bfa4bab1acf4a91e3840ee3f4e3d57 |
#!/usr/bin/env python
#
# @file example1.py
# @brief SBML Groups example
# @author Akiya Jouraku
# @author Frank Bergmann (python port)
#
# $Id: example1.py 11938 2010-09-20 02:04:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/branches/libsbml-5/examples/groups/example1.py $
#
... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/examples/python/groups/example1.py | Python | bsd-3-clause | 3,168 | [
"VisIt"
] | a723a9552c3e55b819b7b32808ed10895865ee5e2e7242391996b52910a69698 |
#!/usr/bin/env python
import glob
from setuptools import setup
setup(
name='cargo-port',
version='1.0',
description='Python Distribution Utilities',
author='Intergalactic Utilities Commission',
maintainer='Helena Rasche',
url='https://github.com/erasche/community-package-cache',
packages=[... | erasche/community-package-cache | setup.py | Python | mit | 679 | [
"Galaxy"
] | bf7493177ce4737169c49d6fa10823e1c123d20abdf49f6bc1f0f935ddee42f2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###########################################################################
# #
# ESPResSo++ Python script for tabulated GROMACS simulation #
# ... | BackupTheBerlios/espressopp | examples/polystyrene_gromacs/polystyrene.py | Python | gpl-3.0 | 9,024 | [
"ESPResSo",
"Gromacs"
] | cab7b6a5ad4c84451804c3e896f70a28eb0741ce21042403566a77c9067ea825 |
import os
from pywps.Process import WPSProcess
import logging
from flyingpigeon.log import init_process_logger
logger = logging.getLogger(__name__)
class FetchProcess(WPSProcess):
def __init__(self):
WPSProcess.__init__(self,
identifier="fetch",
ti... | KatiRG/flyingpigeon | flyingpigeon/processes/wps_fetch.py | Python | apache-2.0 | 2,170 | [
"NetCDF"
] | 4e573ac0c54a35fd44aa38fa52f01e6fa97c647062ed78afebfdbea4b883b560 |
##
# title: BreadInterface.ButtonLayout
# by: Brian Kim
# description: the class that defines the content
# and functionality of BreadInterface buttons
#
import pygtk
pygtk.require('2.0')
import gtk
class ButtonLayout():
@staticmethod
def gtk_button( text, scale=1 ):
""" returns a properly styled gtk butto... | briansan/BreadInterface | py/BreadInterface/ButtonLayout.py | Python | bsd-2-clause | 1,964 | [
"Brian"
] | 57f8c7a37796b4fcb6145abfb3b1a6a0a346b0a2ad6b8efb8e24b3e56475dd5f |
import numpy as np
import sys
import time
from ase.units import Bohr
from ase.structure import bulk
from gpaw import GPAW, FermiDirac
from gpaw.atom.basis import BasisMaker
from gpaw.response.df import DF
from gpaw.mpi import serial_comm, rank, size
from gpaw.utilities import devnull
if rank != 0:
sys.stdout = dev... | ajylee/gpaw-rtxs | gpaw/test/diamond_absorption.py | Python | gpl-3.0 | 1,311 | [
"ASE",
"GPAW"
] | 81c2c9c8d9e85e8514742447bbd77800a965f2a6d4649edcca5b4dfcf22d10ed |
# 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 RAffyplm(RPackage):
"""Methods for fitting probe-level models
A package that exten... | LLNL/spack | var/spack/repos/builtin/packages/r-affyplm/package.py | Python | lgpl-2.1 | 1,572 | [
"Bioconductor"
] | 776fe0dfaa85d443fb38077fcfdd482120e4c0535980360b100639642b0d9998 |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum
#
# @@ 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.
#
"""basic unit testing code for SMILES:
- canonic... | bp-kelley/rdkit | rdkit/Chem/UnitTestSmiles.py | Python | bsd-3-clause | 8,714 | [
"RDKit"
] | 68d1c2516ca2abfb0f2ad54ad217b292268a7415f7ac137b93683431aead8ad7 |
"""
Climate contour/vector plots using cf-python, matplotlib and cartopy.
Andy Heaps NCAS-CMS April 2021
"""
import numpy as np
import subprocess
from scipy import interpolate
import matplotlib
from copy import deepcopy
import os
import sys
import matplotlib.pyplot as plot
from matplotlib.collections import PolyCollect... | ajheaps/cf-plot | cfplot/cfplot.py | Python | mit | 340,274 | [
"ORCA"
] | 6022c8c449647291b92aa5f613b3024db0c8830ed1912d463ec1274eaeaf20f0 |
from __future__ import division
from PyQt4 import QtCore
from numpy import *
from scipy import optimize
from scipy import constants as scipycsts
import pylab
from filter import savitzky_golay
# Define some global variables
DEBUG=0 # Debug mode can take values (0,1,2). 0 plots no intermediary results. 1 plots interme... | timrae/pylase | hakkipaoli.py | Python | gpl-2.0 | 13,524 | [
"Gaussian"
] | 5c2f1095af94830f9ad1e91e8b84b4b18df04f1fd918426c394cb658e9ff6dd9 |
#!/usr/bin/python
import os, sys # low level handling, such as command line stuff
import string # string methods available
import re # regular expressions
import getopt # comand line argument handling
from low import *
OUTPUTHASH = {
'q' : 'query',
'h' : 'hitid',
'd' : 'hitdescr',
... | lotharwissler/bioinformatics | python/blast/parse_blast_out2.py | Python | mit | 9,699 | [
"BLAST"
] | 45d40d930b138af261fb1d905194726b1d68138b33a1b9c17121ea392d695f80 |
""" Actual implementation of the FMCS algorithm
This code should be used by importing rdkit.Chem.MCS
"""
from rdkit.Chem.fmcs.fmcs import *
| ptosco/rdkit | rdkit/Chem/fmcs/__init__.py | Python | bsd-3-clause | 141 | [
"RDKit"
] | 9855d044bec3a35ef07b84a9ce1a5cef1d11d830c78590aeae5a298085766f5c |
#!/usr/bin/env python
""" This template will become the job wrapper that's actually executed.
The JobWrapperTemplate is completed and invoked by the jobAgent and uses functionalities from JobWrapper module.
It has to be an executable.
The JobWrapperTemplate will reschedule the job according to certain cri... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/JobWrapperTemplate.py | Python | gpl-3.0 | 11,404 | [
"DIRAC"
] | 580dfcd8f2d2baa6c61abdbb296bf725543566749703dd3a41cb63f953cf9350 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Laurawly/tvm-1 | python/tvm/tir/stmt_functor.py | Python | apache-2.0 | 2,383 | [
"VisIt"
] | 9d75fb0024f162f215e36098b157942392bbde24d6dc359292c1fa825451c20a |
# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanReadable
from Tools.Ge... | Franc1/Enigma2-Skin-SkyHD | usr/lib/enigma2/python/Components/Converter/MetrixExtraInfo.py | Python | mit | 24,129 | [
"Galaxy"
] | 64957042a92316c6ec4a5a36ee641f2a2ba3d677eb63c4418b07f90dc8eb5898 |
"""
The Grid module contains several utilities for grid operations
"""
import os
from DIRAC.Core.Utilities.Os import sourceEnv
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.ConfigurationSystem.Client.Helpers import Local
from... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Grid.py | Python | gpl-3.0 | 4,538 | [
"DIRAC"
] | 990c1d3ed28a6e90e8785e6267f6c2e49d803be788067967c69aa6ac19e6a4bf |
#!/usr/bin/env python
#Copyright (C) 2014 by Glenn Hickey
#
#Released under the MIT license, see LICENSE.txt
import unittest
import sys
import os
import argparse
import logging
import itertools
import copy
import numpy as np
from teHmm.common import runShellCommand
from teHmm.common import runParallelShellCommands
fr... | glennhickey/teHmm | bin/naiveTrackCombine.py | Python | mit | 6,448 | [
"Gaussian"
] | 346713f7cdf97f2074fde3f512e6bf053c730eef5ea032710a554b0c18dae85c |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import combinations
from itertools import product
import numpy ... | ltiao/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 40,416 | [
"Brian"
] | f5f2a8eb55069fb45832250aa31475827e0fe9350079afac1f6bca2732609a9b |
#!/usr/bin/env python
from ase.dft.kpoints import special_paths, special_points, parse_path_string, bandpath
import numpy as np
def cubic_kpath():
special_path = special_paths['cubic']
points = special_points['cubic']
paths = parse_path_string(special_path)
special_kpts = [points[k] for k in paths[0]... | mailhexu/pyDFTutils | resource/phonon_ana/pyFA/kpoints.py | Python | lgpl-3.0 | 452 | [
"ASE"
] | ec7509561b23737c212bfe411c9083dbf439ecac615438ff64ea249f5777dca0 |
# coding: utf-8
from __future__ import unicode_literals, division
__author__ = "Chen Zheng"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Chen Zheng"
__email__ = "chz022@ucsd.edu"
__date__ = "Oct 18, 2017"
import unittest
import os
from monty.os import cd
from monty.te... | specter119/custodian | custodian/feff/tests/test_jobs.py | Python | mit | 1,751 | [
"FEFF",
"pymatgen"
] | c82bc1e2532814bf8c3928da5bc4c9ba549868866559b81a9364aa0774533576 |
"""
Classes and functions for easier management of the InstalledComponents database
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
import re
import datetime
from sqlalchemy import MetaData, Column, Integer, String, DateTime, create_engine, te... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/DB/InstalledComponentsDB.py | Python | gpl-3.0 | 40,316 | [
"DIRAC"
] | 84d04a45f5da801a89b81c1dd0a2eeedaea438ab5169f02687c0358bbeffe83c |
# -*- coding: utf-8 -*-
# Copyright 2009 James Hensman and Michael Dewar
# Licensed under the Gnu General Public license, see COPYING
import numpy as np
import node
from scipy import special #needed for calculating lower bound in Gamma, Wishart
class ConjugacyError(ValueError):
def __init__(self,message):
ValueErro... | jameshensman/pyvb | src/pyvb/nodes/nodes_todo.py | Python | gpl-3.0 | 7,789 | [
"Gaussian"
] | 56340c26218b6b07e77731479d49f69378a1da9da5e0a254d681284a7b3aecad |
# Copyright (c) 2012 - 2014 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
# Written by Mike Smith. michaeltsmith.org.uk
import numpy as np
from ..core import GP
from .. import likelihoods
from .. import kern
from ..core import Param
class GPOffsetRegression(GP):
""... | mikecroucher/GPy | GPy/models/gp_offset_regression.py | Python | bsd-3-clause | 4,059 | [
"Gaussian"
] | 250b6acfff76d07ff08a0b15cc13f9b0e669a3ffb6745cb4e651ba674f74e304 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Example using the iohub Wintab Pen device. Demo requires a properly
installed Wintab compatible device running on Windows.
(Wacom digital pen, MS Surface v1 or v2, ...)
"""
import os
import time
import _wintabgraphics as wintabgraphics
from psychopy import core, visual... | psychopy/psychopy | psychopy/demos/coder/iohub/wintab/pen_demo.py | Python | gpl-3.0 | 9,638 | [
"Gaussian"
] | 7acdaf9b79224004c4c09c600a52e13e8a3ce831070ec3e06fe55d3a10299622 |
from __future__ import annotations
import random
import pytest
from cctbx import sgtbx
from dials.algorithms.symmetry.cosym._generate_test_data import generate_intensities
from dials.array_family import flex
from dxtbx.model import Beam, Crystal, Experiment, Scan
from dxtbx.model.experiment_list import ExperimentLis... | xia2/xia2 | tests/Modules/Scaler/test_DialsScalerHelper.py | Python | bsd-3-clause | 14,996 | [
"CRYSTAL"
] | 51a24471243970fbdc3e5b3e42cbabf2f150c6cd7f9e6e664b447ac42925f4f5 |
#########################################################################################
# $HeadURL$
# Torque.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" Torque.py is a DIRAC independent class representing Torque batch system.
Torque... | vmendez/DIRAC | Resources/Computing/BatchSystems/Torque.py | Python | gpl-3.0 | 6,321 | [
"DIRAC"
] | 526ac241e80dd765413af4a1aca6df1e0bc6f017b51748b301a400d954f0a852 |
'''Base table class.'''
import abc
import typing
from typing import Iterator, Optional
from wpull.pipeline.item import URLRecord, URLProperties, URLData, Status, \
URLResult
class DatabaseError(Exception):
'''Any database error.'''
class NotFound(DatabaseError):
'''Item not found in the table.'''
Ad... | chfoo/wpull | wpull/database/base.py | Python | gpl-3.0 | 4,136 | [
"VisIt"
] | ad21cba51136c927e35a4476666bc7bcf83b7163d5f7c98f850a623de831d175 |
#!/usr/bin/python
#
# Copyright 2015 John Kendrick
#
# This file is part of PDielec
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the MIT License
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied wa... | JohnKendrick/PDielec | PDielec/UnitCell.py | Python | mit | 23,459 | [
"CASTEP",
"VASP"
] | 4f7117ebd2347899760c2dd1067a7359835926c8489a3c952d3f45285d0f2775 |
#
# Copyright 2014, 2020 James Kermode (Warwick U.)
# 2016 Punit Patel (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Li... | libAtoms/matscipy | scripts/fracture_mechanics/make_crack_thin_strip.py | Python | lgpl-2.1 | 9,912 | [
"ASE",
"Matscipy"
] | d4c012898ba8789d64c61287893f8aeff2466fa3e94729745d85f152f3212edd |
__author__ = 'amarch'
# -*- coding: utf-8 -*-
from numpy import *
import matplotlib.pyplot as plt
from scipy.optimize import *
import scipy
from scipy.special import *
import math
import inspect
from utils import strutils as infoutils
from utils.bcolors import *
from RotationCurveHandler import *
from VelocityDispersi... | Amarchuk/2FInstability | core/Galaxy.py | Python | gpl-3.0 | 5,786 | [
"Galaxy"
] | a79f03653716cf16815eb4352050463ea2628fab9c7b7217669a1ded274aaa47 |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d, transpose
from numpy.core.numeric import (
ones, zeros, arange, concatenate, a... | dwillmer/numpy | numpy/lib/function_base.py | Python | bsd-3-clause | 156,505 | [
"Gaussian"
] | 9aa81a25a915c87fd0b974e20a63f79487feeeb3303145128cbf578eb9f76900 |
# Copyright (c) 2011 Brian Beach
# All rights reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, ... | CapOM/ChromiumGStreamerBackend | tools/telemetry/third_party/gsutilz/third_party/boto/tests/integration/s3/test_pool.py | Python | bsd-3-clause | 8,255 | [
"Brian"
] | a9e3ce670358240da6ed639462e98b4a1eede9e723fefff3a468d3c585fe3d36 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
""" Inspired from https://gist.github.com/RichardBronosky/454964087739a449da04
See http://www.python.org/dev/peps/pep-0008/ for more PEP-8 details
This module's docstring summary line.
This is a multi-line docstring. Paragraphs are separated with blank lines.
Normally... | fstagni/DIRAC | tests/formatting/pep8_bad.py | Python | gpl-3.0 | 3,680 | [
"DIRAC"
] | 0ba7ffe4f1cfd87cfde1bfc81dc0451f3d55c034e13331f7ccb0bc89589ed366 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Jan 24, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__da... | gmatteo/pymatgen | pymatgen/io/tests/test_cssr.py | Python | mit | 1,813 | [
"VASP",
"pymatgen"
] | c222175812db838fa775ced6b44079121d14cc71ec581222ede1705e541a3a55 |
configfile: "config.json"
rule indexing_bowtie2:
input:
ref='{sample}.assembly.out/contigs.fasta'
output:#index='{sample}.pilon/{sample}.index',
outdir='{sample}.pilon',
fwd='{sample}.pilon/{sample}.index.1.bt2'
# fwd=expand('{sample}.pilon/{sample}.index.{index}.bt2', sample=config[... | marbl/MetaCompass | workflows/prepare_correction.py | Python | artistic-2.0 | 2,073 | [
"Bowtie"
] | 901091255eb63f36ab1563084f61d6f5395722f9c8fff895bd5dc44513fd456e |
# -*- coding: utf-8 -*-
# Copyright(C) 2008-2011 Romain Bignon
#
# This file is part of weboob.
#
# weboob is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at you... | eirmag/weboob | modules/aum/contact.py | Python | agpl-3.0 | 12,643 | [
"exciting"
] | c53fde703120df929435a2d529c4111cca801e28459ae424c64e4ed31d01da64 |
#!/usr/bin/env python
# _*_ coding:utf-8 _*_
import boto
import json
import os
import subprocess
import webbrowser
from datetime import datetime
from distutils.spawn import find_executable
from fabric.api import local, require, task
from fabric.state import env, output
from oauth import get_document, get_credentials
f... | nprapps/dailygraphics | fabfile/__init__.py | Python | mit | 18,729 | [
"VisIt"
] | 434f82619ad88335bb605b65fadc3b621c8d4f6d81285885cdcb3eb2d71b7447 |
# -*- coding: utf-8 -*-
# Copyright (c) 2020 Ansible Project
# 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
from ansible.cli.galaxy import _display_role
def test_display_role(mocker, c... | Shaps/ansible | test/units/cli/galaxy/test_display_role.py | Python | gpl-3.0 | 913 | [
"Galaxy"
] | d632b9e4e110f887ac22a7f5fe31d143d3b5635ffb15791447a31643c05a5ee5 |
import os
import sys
import re
import time
import tempfile
import subprocess
# GitPython
import git
from git import InvalidGitRepositoryError, NoSuchPathError, GitCommandError
# settings, including lookaside uri and temporary paths
from pyskein import SkeinError
# github api and token should be kept secret
from gith... | gooseproject/skein | skein/githubremote.py | Python | gpl-3.0 | 13,825 | [
"VisIt"
] | ce250a4c86c9ccb9037bf72445f456cf5d86599fddfe7df0f65a37da3d2182c7 |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.7 on 2016-11-08 01:10
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('visit', '0117_auto_20160804_1909'),
]
operations = [
migrations.AddField(
... | koebbe/homeworks | visit/migrations/0118_staff_is_active.py | Python | mit | 450 | [
"VisIt"
] | 963a9b0a5b9a55440e7f27fc803dafd253d784001b8a68c5c6500bb49c132c93 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
__author__ = 'ajain'
| sonium0/pymatgen | pymatgen/analysis/hhi/__init__.py | Python | mit | 131 | [
"pymatgen"
] | 2c9496a91a0dbbfa9f9c8f465290d8678465573dcf69af449f1f7ad844d475fe |
#
# QAPI helper library
#
# Copyright IBM, Corp. 2011
# Copyright (c) 2013-2018 Red Hat Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from __futu... | marioli/qemu | scripts/qapi/common.py | Python | gpl-2.0 | 84,040 | [
"VisIt"
] | f3bfc0d42047d986a70eae97e7f91adbe742db37444a431a39e6000674b3c96a |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2015 Gerald Kunzmann <gerald@gkunzmann.de>
# Copyright (C) 2013-2016 Paul Franklin
#
# This program is free software; yo... | sam-m888/gprime | gprime/plugins/textreport/familygroup.py | Python | gpl-2.0 | 37,964 | [
"Brian"
] | 9efee83e546cc6b1a1ce6ee51a53639d9e7fe4e77a9d6a3f38519d8fc04e839c |
##############################
# #
# Instructions #
# #
##############################
# To run, use the following command:
# $ python shortest_distance.py <input_file>
# where <input_file> is the filename with the question's input
import sys
import ... | joseph-roque/advent-of-code | day_09/shortest_distance.py | Python | mit | 2,702 | [
"VisIt"
] | 2bff08363fa7eadae905ae9027e963bf4ce241b512a342e460cbd79152d39cab |
# Author: Kyle Kastner
# License: BSD 3-clause
import numpy as np
from theano import tensor
import theano
from ..utils import concatenate
def binary_crossentropy(predicted_values, true_values):
"""
Bernoulli negative log likelihood of predicted compared to binary
true_values
Parameters
----------... | dribnet/dagbldr | dagbldr/nodes/penalties.py | Python | bsd-3-clause | 7,872 | [
"Gaussian"
] | 882bf65bae79b000ab6c6ad8dfa1f887f42fb00d54711518b11ab69c1ff1a639 |
#!python
# encoding: utf-8
# ***** 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.... | dostavro/dotfiles | sublime2/Packages/SublimeCodeIntel/libs/codeintel2/util.py | Python | mit | 28,696 | [
"VisIt"
] | 27eb2ef364587d6ecd9caae9a0f164aa157777a2772a4796926c6820b0018bcd |
"""
Calculate dumb and brute force consensus sequences from MSAs.
Currently requires that the MSA has no entire gap columns.
"""
# 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... | jrjhealey/bioinfo-tools | Consensus.py | Python | gpl-3.0 | 6,946 | [
"Biopython"
] | ef2998c064696d3604557d442bf0825aa9f9601361ad557969d92078b6dbbefe |
# -*- coding: utf-8 -*-
# This file is part of beets.
# Copyright 2015, Adrian Sampson.
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation t... | kelvinhammond/beets | beetsplug/discogs.py | Python | mit | 14,498 | [
"VisIt"
] | 5eb1e780c5deb02ce7a8e473746cc2b4c98bc128e03e319525861113054efa97 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | prculley/gramps | gramps/plugins/webreport/statistics.py | Python | gpl-2.0 | 11,054 | [
"Brian"
] | ce419ccb2ecb4278e555f6d86b125f8386eb76b8264b8663686786b2e687910a |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from __future__ import with_statement
import os.path
import re
import time
import sys
import lxml.html
from lxml.cssselect import CSSSe... | lrowe/splinter | splinter/driver/djangoclient.py | Python | bsd-3-clause | 14,054 | [
"VisIt"
] | 6bcca316ab0deef58a9129926ef360642ae29671008ed7eca0c4ee9569cbd71c |
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