text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# $HeadURL$
__RCSID__ = "$Id$"
import types
import copy
import os
import string
import re
try:
import zipfile
gZipEnabled = True
except ImportError:
gZipEnabled = False
try:
from DIRAC.Core.Utilities import List, ThreadSafe
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
gCFGSyn... | coberger/DIRAC | Core/Utilities/CFG.py | Python | gpl-3.0 | 33,826 | [
"DIRAC"
] | 559848d5c6ddf08acd21206a4a62871dbd91ede4294f3f22e383e843b0354cac |
#!/usr/bin/env python
#JSON {"lot": "RKS/6-31G*",
#JSON "scf": "CDIISSCFSolver",
#JSON "linalg": "CholeskyLinalgFactory",
#JSON "difficulty": 4,
#JSON "description": "Basic RKS DFT example with GGA exhange-correlation functional (PBE)"}
from horton import *
# Load the coordinates from file.
# Use the XYZ file fro... | crisely09/horton | data/examples/hf_dft/rks_water_gga.py | Python | gpl-3.0 | 2,495 | [
"Gaussian"
] | 55ec9130ec4c001ce6c88fae67513e44913f816e9fc48176f1559b4dd9dcbd4a |
import copy
from .meta_parse import fbool, fint, fintlist, func_types, lcstr
#: All configuration keywords editable by the user
CFG_ANALYSIS = {
# filtering parameters
"filtering": [
["hierarchy parent", str, "Hierarchy parent of the dataset"],
["remove invalid events", fbool, "Remove events ... | ZellMechanik-Dresden/dclab | dclab/definitions/meta_const.py | Python | gpl-2.0 | 8,424 | [
"Gaussian"
] | 2ee091a6608c1723682c4243c57c991e67ee5f36bbfbb033b9a55ebd5a8c0ff1 |
#!/usr/bin/env python
##
# @file ctml_writer.py
#
# Cantera .cti input file processor
# @defgroup pygroup Cantera Python Interface
#
# The functions and classes in this module process Cantera .cti input
# files and produce CTML files. It can be imported as a module, or used
# as a script.
#
# script usage:
#
# python ... | imitrichev/cantera | interfaces/cython/cantera/ctml_writer.py | Python | bsd-3-clause | 87,633 | [
"CRYSTAL"
] | f8d5756548ad6fa058070aae1afeb8bd1377de195ca9478e6fedfc845a72477f |
"""
VOMS2CSAgent performs the following operations:
- Adds new users for the given VO taking into account the VO VOMS information
- Updates the data in the CS for existing users including DIRAC group membership
-
The following options can be set for the VOMS2CSAgent.
.. literalinclude:: ../ConfigTempla... | andresailer/DIRAC | ConfigurationSystem/Agent/VOMS2CSAgent.py | Python | gpl-3.0 | 8,324 | [
"DIRAC"
] | f27578cb9cf028f33baf7da1aaf91861dd5191572c3da905d9cc9846c57c22dc |
# -*- coding: utf-8 -*-
"""
Statistical measures of spike trains (e.g., Fano factor) and functions to estimate firing rates.
:copyright: Copyright 2014-2016 by the Elephant team, see AUTHORS.txt.
:license: Modified BSD, see LICENSE.txt for details.
"""
from __future__ import division, print_function
import numpy as ... | etorre/elephant | elephant/statistics.py | Python | bsd-3-clause | 42,361 | [
"Gaussian",
"NEURON"
] | baa43cc7d84d723b9ce8a3491ccafd021b728e62f5f0b90bbd2c20f1833aaf94 |
#!/usr/bin/env python
# encoding: utf8
"""Script to create a bunch of tarballs and montages, made available on the
/dex/downloads page.
"""
from __future__ import division
from glob import glob
import math
import os, os.path
import pkg_resources
import re
import subprocess
from subprocess import PIPE
import sys
import ... | veekun/spline-pokedex | bin/create-downloads.py | Python | mit | 18,338 | [
"CRYSTAL"
] | fd98f62d19aaf4c692de2a2091417c3c26333ae1d96333d0f4396c4de334adc7 |
# -*- coding: utf-8 -*-
#
# This file is a plugin for EventGhost.
# Copyright © 2005-2019 EventGhost Project <http://www.eventghost.net/>
#
# EventGhost is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation, either v... | topic2k/EventGhost | plugins/X10/__init__.py | Python | gpl-2.0 | 10,254 | [
"Firefly"
] | 658108862915845a9c1e29978d93ba76b4082c27962bb67c77eded016506c1df |
import json
from .visitor import Visitor, visit
__all__ = ['print_ast']
def print_ast(ast):
return visit(ast, PrintingVisitor())
class PrintingVisitor(Visitor):
__slots__ = ()
def leave_Name(self, node, *args):
return node.value
def leave_Variable(self, node, *args):
return '$' +... | wandb/client | wandb/vendor/graphql-core-1.1/wandb_graphql/language/printer.py | Python | mit | 5,888 | [
"VisIt"
] | 807f88fa089e597c3d15c088212697a312bfbff9b39a1cc03aac2246255b4d0f |
## \file
## \ingroup tutorial_roofit
## \notebook
## Basic functionality: interpreted functions and pdfs
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Generic interpreted pdf
# ------------------------------
# Declare observable x
x = ROOT.RooRealV... | root-mirror/root | tutorials/roofit/rf103_interprfuncs.py | Python | lgpl-2.1 | 3,103 | [
"Gaussian"
] | 9147aae81fcea97d40fa6998440f02f74fe200fdd431a31586a6fac8c4f73ed3 |
from __future__ import with_statement
import hashlib
import os
import stat
import tempfile
from fnmatch import filter as fnfilter
from fabric.state import output, connections, env
from fabric.utils import warn
class SFTP(object):
"""
SFTP helper class, which is also a facade for paramiko.SFTPClient.
"""... | malin1993ml/h-store | third_party/python/fabric/sftp.py | Python | gpl-3.0 | 10,790 | [
"VisIt"
] | d5cb590b53d6b5cc2e7e29c12e05ccc140d2df410a6e827332ede09c183b05c6 |
"""
Represent an operation to be performed on the elements of an object
structure. Visitor lets you define a new operation without changing the
classes of the elements on which it operates.
"""
import abc
class Element(metaclass=abc.ABCMeta):
"""
Define an Accept operation that takes a visitor as an argument... | tcp813/mouTools | design_patterns/visitor.py | Python | mit | 2,702 | [
"VisIt"
] | ac0d77b0baa165591e119af461ce23aadfb78b850e8167a4fb63ca163c2bd669 |
#
# Copyright (C) 2013,2014,2015,2016 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... | KonradBreitsprecher/espresso | testsuite/domain_decomposition.py | Python | gpl-3.0 | 1,968 | [
"ESPResSo"
] | 9a01ecb6ec21a20c921e162c262b7d891334461fdb3beb9757bb51f1336bf803 |
import py
import types
import sys
def checksubpackage(name):
obj = getattr(py, name)
if hasattr(obj, '__map__'): # isinstance(obj, Module):
keys = dir(obj)
assert len(keys) > 0
print (obj.__map__)
for name in list(obj.__map__):
assert hasattr(obj, name), (obj, name)
... | youtube/cobalt | third_party/web_platform_tests/tools/py/testing/root/test_py_imports.py | Python | bsd-3-clause | 1,983 | [
"VisIt"
] | 9cc83489ff2f333b26383df09210bf91b66b3415222fca34776d1537a2d07aac |
#*****************************************************************************
#* Copyright (c) 2014 Jonathan Wiedemann <wood.galaxy@gmail.com> (cutplan) *
#* Copyright (c) 2019 Jerome Laverroux <jerome.laverroux@free.fr> (cutline)*
#* *
#* ... | sanguinariojoe/FreeCAD | src/Mod/Arch/ArchCutPlane.py | Python | lgpl-2.1 | 8,639 | [
"Galaxy"
] | 9be4d8032446f29d15ee959b985f0273a0dee7ea439c1f7970cd178ea1db7dcf |
"""
Simple tools for plotting Neo-format data.
These tools are intended for quickly producing basic plots with simple
formatting. If you need to produce more complex and/or publication-quality
figures, it will probably be easier to use matplotlib or another plotting
package directly rather than trying to extend this m... | anupkdas-nus/global_synapses | pyNN-dispackgaes/utility/plotting.py | Python | gpl-3.0 | 12,674 | [
"NEURON"
] | 990b233b3f2be3fa67c171304725332eaad01dd8fd13d72d916e613e16c6d9b5 |
"""None"""
import time
import os
import numpy as np
from sklearn.grid_search import ParameterGrid
from sklearn.base import clone
from sklearn.gaussian_process import GaussianProcess
from scipy.stats import norm
from joblib import Parallel, delayed
from utils.state import _save
from utils.functions import gaussian... | ivannz/study_notes | year_15_16/thesis/notebooks/gaussian_exp_1d.py | Python | mit | 6,636 | [
"Gaussian"
] | 1a0418f2794621d87f38e24804e90d4009e4457c12cf63076f2120a1827adb43 |
# -*- coding: utf-8 -*-
"""The config functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import atexit
from functools import partial
import json
import os
import os.path as op
import platform
import shutil
import sys
import tempfile
import re
import numpy as np
from .check impor... | bloyl/mne-python | mne/utils/config.py | Python | bsd-3-clause | 20,862 | [
"Mayavi",
"VTK"
] | a60932d1fd722311baf7472bafba3fe5d7feeb6029d765e1f3eb23344e3b62bb |
import unittest
import pysal
import numpy as np
from scipy import sparse
#from pysal.spreg import error_sp_het as HET
from functools import partial
from pysal.contrib.handler import Model
GM_Error_Het = partial(Model, mtype='GM_Error_Het')
GM_Endog_Error_Het = partial(Model, mtype='GM_Endog_Error_Het')
GM_Combo_Het = ... | TaylorOshan/pysal | pysal/contrib/handler/tests/test_error_spet_sparse.py | Python | bsd-3-clause | 11,099 | [
"COLUMBUS"
] | 3e2419d78dbb905d6516ea1cd9d1b14720b3504daceb06a80fdf91cc9248d90c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/driver/qcdb/dbproc.py | Python | lgpl-3.0 | 3,856 | [
"Psi4"
] | cacfd102d9c2a3e5610df5b28ea682495765f62cef497d2029555140c244470a |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2013, 2014 CERN.
##
## Invenio 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 opt... | egabancho/invenio | invenio/modules/deposit/models.py | Python | gpl-2.0 | 47,429 | [
"VisIt"
] | 3c34e194bd9af2ecdc966d509ff1f6720b9f38f99c391de79e50b26f52402489 |
# -*- coding: utf-8 -*-
import json
import os
import time
from config import *
LETTER_Y = [[" _______________________________________________ "],
["| ___________________________________________ |"],
["| | | |"],
["| | ... | killerbat00/hncurses | src/utils.py | Python | mit | 4,389 | [
"Brian"
] | b301de9d5447bc9d2aa95e1f9854d0bf0beffb251970e77a90d8a2cbe89c031a |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""General functionality for mutations.
"""
# standard library
import random
# local stuff
from Bio.GA.Organism import Organism
class SafeFitnessM... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/GA/Mutation/General.py | Python | gpl-2.0 | 1,583 | [
"Biopython"
] | 1fbf3795cdc7d983c057a5df651b21ddc8209516b823dbd4daedbcb1d5b31579 |
# vim: tabstop=2 shiftwidth=2 softtabstop=2 expandtab autoindent smarttab
import abc
import collections
import copy
import hashlib
import json
import logging
import math
import os
import pickle
import random
from fn import _
import argparse
from datetime import datetime
import numpy
import inspect
import sys
log = log... | Sierangho/opentuner | opentuner/search/manipulator.py | Python | mit | 58,606 | [
"Gaussian",
"VisIt"
] | df218ddae6405046621df7b70cc405e934d7ad772284caf51af5838258c2f0aa |
"""
Core visualization operations based on Mayavi.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric... | Teekuningas/mne-python | mne/viz/backends/_pysurfer_mayavi.py | Python | bsd-3-clause | 20,456 | [
"Mayavi",
"VTK"
] | a6d22b7c966cf93d7295e69b48361d970a5835ce70bacb23a5f9a75a8c6be839 |
#!/usr/bin/env python
import sys, collections, itertools, os.path, optparse
optParser = optparse.OptionParser(
usage = "python %prog [options] <in.gtf> <out.gff>",
description=
"Script to prepare annotation for DEXSeq." +
"This script takes an annotation file in Ensembl GTF format" +
... | g1o/trinityrnaseq | trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py | Python | bsd-3-clause | 6,148 | [
"HTSeq"
] | 6296b47314e0e774ee8d446a24660a75832beacf79040d0f6c4e00a5a3bc80aa |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 the GNU Gen... | kkreis/espressopp | src/analysis/LBOutputScreen.py | Python | gpl-3.0 | 2,490 | [
"ESPResSo"
] | 955b3ea39c2803d7fb3b546ba82a59f6999f98efd6949df648562205444333d2 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | ConZ27/ansible-modules-core | cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,857 | [
"Dalton"
] | e7dba32494cf6a1c1ff0cc23c3ee2774475d2a861bb6ad27fe3ccebb72b69e87 |
from . import base
from .. import stats
from .. import items
from .. import dialogue
from .. import context
from .. import spells
from .. import invocations
from .. import effects
from .. import animobs
from .. import targetarea
from .. import aibrain
from . import animals
from . import treasuretype
from . import abili... | jwvhewitt/dmeternal | old_game/monsters/misc.py | Python | gpl-2.0 | 23,825 | [
"BLAST"
] | 5fcc74082b819b1c0afe9a6efe8460254395f2b22695c00ee64560929389a40d |
import pickle
import gzip
import os, sys, errno
import time
import math
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
#import gnumpy as gnp
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy itse... | bajibabu/merlin | misc/recipes/MGE/run_dnn_cm.py | Python | apache-2.0 | 42,653 | [
"NEURON"
] | 6ba5a764431219b56a3df6ce0a655a29b3e24b18db7e499494b7df1282e3a838 |
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
import director.applogic as app
import director.objectmodel as om
from director.timercallback import TimerCallback
from director import robotstate
from director import visualization as vis
from director import transformUtils
from director import ikconstraint... | mitdrc/director | src/python/director/teleoppanel.py | Python | bsd-3-clause | 60,475 | [
"VTK"
] | a5de9988f2b42842e9db02a4718e7257a2419e266bf7c81b69aea700c0eca05d |
from __future__ import unicode_literals
import re
from django.contrib import messages
from django.contrib.auth.models import User
from django.core.exceptions import ValidationError
from django.test.client import RequestFactory
from djblets.registries.errors import ItemLookupError, RegistrationError
from djblets.testi... | davidt/reviewboard | reviewboard/accounts/tests.py | Python | mit | 19,866 | [
"VisIt"
] | f65ed2b4eff13a72a36890ebe52d0fd8ba7964d98677991e08a63055892753cd |
"""
Tracking of rotating point.
Rotation speed is constant.
Both state and measurements vectors are 1D (a point angle),
Measurement is the real point angle + gaussian noise.
The real and the estimated points are connected with yellow line segment,
the real and the measured points are connected with re... | myboycrais99/Miscellaneous | Tracking/example_2.py | Python | gpl-3.0 | 3,288 | [
"Gaussian"
] | 711dce5d1c7b1beaca9363e035f0a0ec0235c42e9cce3adf5674c667b50bd4f5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/share/psi4/databases/S22.py | Python | lgpl-3.0 | 43,408 | [
"Psi4"
] | c8345a26bbe331f1d7e0a4333e869444165bfb3c462efe879578588cba4b8ab9 |
#!/usr/bin/env python
import unittest
import numpy as np
from pymatgen.core.lattice import Lattice
from pymatgen.symmetry.maggroups import MagneticSpaceGroup
from pymatgen.symmetry.groups import SpaceGroup
from pymatgen.util.testing import PymatgenTest
__author__ = "Matthew Horton"
__copyright__ = "Copyright 2017, Th... | mbkumar/pymatgen | pymatgen/symmetry/tests/test_maggroups.py | Python | mit | 7,489 | [
"pymatgen"
] | b274a925fe606c74e2880bd260a07592686081bd0a576f87bac92c7d1a51fa92 |
from distutils.core import setup, Extension
# To build files manually, run: python setup.py build_ext --build-lib ./
# extensions = [Extension(
# name="gsum.cutils",
# sources=["gsum/cutils.pyx"],
# # depends=['gsl/gsl_linalg.h', 'gsl/gsl_permutation.h'],
# # libraries=[*cython_gsl.get_libraries()],
#... | jordan-melendez/buqeyemodel | setup.py | Python | mit | 2,844 | [
"Gaussian"
] | acf9b5453088d5e2a0ffda9f3f674d10b79b239b661bb8bc1c1866931fcd0069 |
#!/usr/bin/env python3
import os
import json
import uuid
import subprocess
import unittest
from xml.etree import ElementTree as ET
from io import BytesIO
import urllib3 # type: ignore
import logging
logging.disable(logging.CRITICAL)
logger = logging.getLogger('pymisp')
from pymisp import PyMISP, MISPOrganisation, M... | SteveClement/MISP | tests/testlive_comprehensive_local.py | Python | agpl-3.0 | 29,299 | [
"Amber"
] | 909a4595687b467301d760323de34c4847288548fb33316c3f45d89bdd97a1a4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import numpy as np
from monty.serialization import loadfn
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import Element
from pymatgen.el... | richardtran415/pymatgen | pymatgen/electronic_structure/tests/test_dos.py | Python | mit | 32,388 | [
"pymatgen"
] | 3cfa1d1d86c57a9a8ba0cfa419410527d76c4ea0d52ff6ef928f4577a9c3218b |
from decimal import Decimal
from django.test import TestCase
from census.meta import ACSMeta, CensusMeta, Census2010Meta
from census.datasources import Census2000, Census2010
from census.data import Value
from census.management.commands import load_census
class MockDatasource(object):
def get_value(self, table,... | ProvidencePlan/Profiles | communityprofiles/census/tests.py | Python | mit | 5,287 | [
"MOE"
] | 11862958cd1524cfbc1564ea724fd265ba6ee03aa62eed0bac22918213ce36f6 |
import argparse
import math
import os
import pickle
import time
from collections import deque
from random import randint
import numpy as np
import pygame
from enum import IntEnum
from pygame.locals import *
from scipy.ndimage.filters import gaussian_filter
#############################################################... | EthanWelsh/Flappy-Bird | flappybird.py | Python | mit | 24,151 | [
"Gaussian"
] | cd48fc53f1c7e04e7b6c842de322038798700342992a3dd154f8d88e025f9024 |
import numpy as np
from asap3 import FullNeighborList
from asap3.MonteCarlo.Moves.Data import lattice as latticedata
from asap3.MonteCarlo.Moves.Base import Move, RandChoice
from ase.cluster.cluster import Cluster
class SurfaceMove(Move):
def __init__(self, debug=0):
self.debug = debug
self.surfac... | auag92/n2dm | Asap-3.8.4/Python/asap3/MonteCarlo/Moves/Surface.py | Python | mit | 15,210 | [
"ASE"
] | da12e8cb133c89e97195deb708497e08457c7cac951ad99a3bf8da9c2e77c5bf |
"""This demo program solves Poisson's equation
- div grad u(x, y) = f(x, y)
on the unit square with source f given by
f(x, y) = 10*exp(-((x - 0.5)^2 + (y - 0.5)^2) / 0.02)
and boundary conditions given by
u(x, y) = 0 for x = 0 or x = 1
du/dn(x, y) = sin(5*x) for y = 0 or y = 1
"""
# Copyright (... | wathen/PhD | MHD/FEniCS/Test/demo_poisson.py | Python | mit | 2,858 | [
"VTK"
] | 609b8096b4776b43f3102a23aa07fc531088a90b9a9845f2a8cb5b9b4bace881 |
# This script is used to filter polymorphism data in VA files according to a number of criteria determined by arguments from the workflow.
# The STEP argument is used to distinguish different types of filtering that are needed during the analysis
# STEP = 1: Normal argument-driven filtering
# STEP = 2: Candidate regio... | davidwilson-85/easymap | scripts_snp/variants-filter.py | Python | gpl-3.0 | 5,099 | [
"Biopython"
] | 2f8e49f089d0b0a1a41d9f5dd105d475f98a0d0e3af3c893dfcc406418b2653a |
# Copyright 2002 Gary Strangman. All rights reserved
# Copyright 2002-2016 The SciPy Developers
#
# The original code from Gary Strangman was heavily adapted for
# use in SciPy by Travis Oliphant. The original code came with the
# following disclaimer:
#
# This software is provided "as-is". There are no expressed or... | andyfaff/scipy | scipy/stats/_stats_py.py | Python | bsd-3-clause | 315,230 | [
"DIRAC"
] | 1d183588f52175dca307a48e58755955133517b925e1e448f6316aa315d01925 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
from pymatgen.core import Lattice
from pymatgen.electronic_structure.core import Orbital, Spin, Magmom
import numpy as np
class SpinTest(unittest.Test... | setten/pymatgen | pymatgen/electronic_structure/tests/test_core.py | Python | mit | 5,593 | [
"pymatgen"
] | a6c73a8387626c2d383d2e254c627539ad223ef2ae7a53e2f743598b33b7cef1 |
""" Parse Python source code.
This module provides a Parser class that may be used to parse Python source code
and retrieve various information from its abstract syntax tree.
"""
import __builtin__
import ast
import collections
import imp
import keyword
import string
##
# TODO
# - Handle global and nonlocal variabl... | liasis/introspector | Introspector/Parser/parse.py | Python | gpl-3.0 | 26,239 | [
"VisIt"
] | b838c12cd8ce892d6e744fd8ae968906b0dbfb1a2782326d5b74fbc663275cb2 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | racemidev/WMI_cmd | pysamba/ndr.py | Python | gpl-2.0 | 775 | [
"VisIt"
] | db482a009dcb6674cba39760df0857b6cf95838ae9842d1868e0926d957078bc |
import operator
import os
import math
import seqcluster.libs.logger as mylog
logger = mylog.getLogger(__name__)
REMOVED = 0
def get_distance(p1, p2):
if p1.strand == "+":
d = p1.start-p2.start
else:
d = (p1.end-(p1.end-p1.start)) - (p2.end-(p2.end-p2.start))
... | lpantano/seqcluster | seqcluster/libs/tool.py | Python | mit | 4,514 | [
"Bowtie"
] | 496ab4ed4a3bfd2d1b6633470366b474987cc8699c5ae40406595ef0f22f3624 |
# coding=utf-8
# Copyright 2022 The Tensor2Tensor 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... | tensorflow/tensor2tensor | tensor2tensor/models/image_transformer.py | Python | apache-2.0 | 37,900 | [
"MOE"
] | c9323106c139c8795ba1b62238723814620de0f95db3c44edf20467f9ac1affb |
# sql/elements.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | gdimitris/FleetManagerBackend | virtual_env/lib/python2.7/site-packages/sqlalchemy/sql/elements.py | Python | mit | 133,000 | [
"VisIt"
] | f91cd08116cfb4a31ba1631d597833d2dfb342b366d84b1f79a6a276ca8ad51c |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'castep'
tab.settings['Output file name'] = 'phonon.castep'
#
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'castep'
tab.settings['Output file name'] = 'phonon.castep'
tab.settings['Excel file name'] = ''
tab.settings['QM program'] = ''
#
#
t... | JohnKendrick/PDielec | Examples/Castep/Bubbles/script.py | Python | mit | 4,195 | [
"CASTEP"
] | 92d49e589ab91a40bf38bd4131e610e07e32cdb655a496bb253cec36c83f9ff6 |
import pytest
from pysisyphus.run import run_from_dict
from pysisyphus.testing import using
@pytest.mark.skip
@using("xtb")
def test_oniom_opt_big():
run_dict = {
"geom": {
"type": "redund",
# frag.py raffinose.xyz 21 14 33 10
"fn": "lib:birkholz/raffinose.xyz",
... | eljost/pysisyphus | tests_staging/test_oniom_opt/test_oniom_opt.py | Python | gpl-3.0 | 3,472 | [
"PySCF",
"xTB"
] | e286d71fc83e9b9b07ebe79ebd587bdc489b26ea37468e340d528c034070fe78 |
"""
Gaussian Convolution ipol demo web app
"""
from lib import base_app, build, http, image
from lib.misc import ctime
from lib.base_app import init_app
from lib.config import cfg_open
import shutil
import cherrypy
from cherrypy import TimeoutError
import os.path
import time
class app(base_app):
""" Gaussian Conv... | juan-cardelino/matlab_demos | ipol_demo-light-1025b85/app_available/87/app.py | Python | gpl-2.0 | 12,250 | [
"Gaussian"
] | acd6e1c1773d1eff5717c97954caee031cf3a68e958c3727beb567f98e9bd802 |
### hierarchical_clustering.py
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#t... | nsalomonis/AltAnalyze | import_scripts/multiBAMtoBED.py | Python | apache-2.0 | 19,538 | [
"pysam"
] | 5449b8e1f11c67316c6ed291ef6083744d5e622f8679005fb0d7259ce8836c18 |
from django.conf import settings
# When True ThumbnailNode.render can raise errors
THUMBNAIL_DEBUG = False
# Backend
THUMBNAIL_BACKEND = 'sorl.thumbnail.base.ThumbnailBackend'
# Key-value store, ships with:
# sorl.thumbnail.kvstores.cached_db_kvstore.KVStore
# sorl.thumbnail.kvstores.redis_kvstore.KVStore
# Redis re... | seedinvest/sorl-thumbnail | sorl/thumbnail/conf/defaults.py | Python | bsd-3-clause | 3,576 | [
"Gaussian"
] | ad92315694e0ad97a0ce1edba1315d29124b0b475beaa01827f27459d1f2a9bd |
# pylint: disable=W0622,R0903,R0902,R0913,W0633
"""Functions and objects to manipulate materials.
A material is an object with a refractive index function.
"""
from builtins import str
from builtins import object
from functools import partial
import numpy
from scipy.integrate import quad
from EMpy.constants import ... | DanHickstein/EMpy | EMpy/materials.py | Python | mit | 10,629 | [
"CRYSTAL"
] | 8bbbfcf8b6162e877b55b4089438c628fd8e30aeef6b7da6951fdb247eb66762 |
from compmod.models import RingCompression
from abapy import materials
from abapy.misc import load
from abapy.postproc import FieldOutput
import matplotlib.pyplot as plt
import numpy as np
import pickle, copy
import platform
from scipy import interpolate
#PAREMETERS
is_3D = True
inner_radius, outer_radius = 30 , 40
Nt... | lcharleux/compmod | doc/sandbox/laurent/ring_compression_voronoi.py | Python | gpl-2.0 | 3,955 | [
"VTK"
] | 458cdccec0e8ead58e791a92932d9229ef542946f99a321c6ee149022e656fc1 |
"""The Cauchy distribution."""
from equadratures.distributions.template import Distribution
from equadratures.distributions.recurrence_utils import custom_recurrence_coefficients
import numpy as np
from scipy.stats import cauchy
RECURRENCE_PDF_SAMPLES = 8000
class Cauchy(Distribution):
"""
The class defines a ... | psesh/Effective-Quadratures | equadratures/distributions/cauchy.py | Python | mit | 3,749 | [
"Gaussian"
] | f9231f292d54b10b2c1d15fed83182d1caa172191172ff4cec56982073b958be |
# -*- coding: utf-8 -*-
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleads/google-ads-python | google/ads/googleads/v9/common/types/user_lists.py | Python | apache-2.0 | 21,331 | [
"VisIt"
] | 18731d9edc5a5a51af6fd2a8e36c5ade59e0798925f100b03a382c50fbf1a604 |
"""
GSIServer - Contributed by Ivan R. Judson <judson@mcs.anl.gov>
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# ... | cmsdaq/hltd | lib/SOAPpy-py3-0.52.24/src/SOAPpy/GSIServer.py | Python | lgpl-3.0 | 5,218 | [
"Brian"
] | 5ceb737eb07b6679b49dceaa13f77a38270f430b112c9459c4b14bf3c646caec |
# Generated from UnitX.g4 by ANTLR 4.5.1
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by UnitXParser.
class UnitXVisitor(ParseTreeVisitor):
# Visit a parse tree produced by UnitXParser#program.
def visitProgram(self, ctx):
return self.visitChildren(ct... | 0ED/UnitX | unitx/UnitXVisitor.py | Python | mit | 4,699 | [
"VisIt"
] | 7bd2ec3d1c4d3d9b1faf6715a4dbe2ae177e239c407da3c0e990697004b66038 |
"""
.. module:: graph
:synopsis: Graph related stuffs
.. moduleauthor:: Ken Sugino <ken.sugino@gmail.com>
"""
# system imports
from collections import Counter
import subprocess
import multiprocessing
try:
import cPickle as pickle
except:
import pickle
import gzip
import os
import time
from functools imp... | kensugino/jGEM | jgem/graph.py | Python | mit | 24,694 | [
"VisIt"
] | 935195e66569d28dd37c2981038889fc2d0d2ca1cd8d86b59fcd6a9cdb55e1b1 |
#!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | govarguz/espressopp | examples/analyze_during_integration/analyze_during_integration.py | Python | gpl-3.0 | 2,404 | [
"ESPResSo"
] | 93119c0160b23f1b023ee8b79edf299d62f8adb8e52e095ce5a1de52bd58e530 |
# 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 RBumphunter(RPackage):
"""Bump Hunter
Tools for finding bumps in genomic data"""
... | LLNL/spack | var/spack/repos/builtin/packages/r-bumphunter/package.py | Python | lgpl-2.1 | 1,783 | [
"Bioconductor"
] | ff08f4770f57a405a15c6d835e7c5f5b56cd4cffda9f2b5973671547b81466fb |
"""
A module to manage all transcations with the metmask database.
How to use this module
======================
1. Get a connection to your database (just a file location or possible
':memory:' if you do intend to keep the information
``mm = dbi.db('/home/user/metmask.db')``
2. Insert with `setMask` (see... | kozo2/metmask | metmask/dbi.py | Python | gpl-3.0 | 39,416 | [
"Bioconductor"
] | 643c55e74b738dae1d8d4c57f1d0102595c472d5681fc7f51390a8a2428f8a74 |
import math
import re
import collections
import numpy as np
import skimage.measure
from IPython.display import display
from pythreejs import *
from .atom_data import *
from collections import defaultdict
def rgb2hex(r, g, b):
r = max(0, min(r, 255))
g = max(0, min(g, 255))
b = max(0, min(b, 255))
re... | evangelistalab/forte | forte/utils/py3js_renderer.py | Python | lgpl-3.0 | 43,790 | [
"Psi4"
] | d5300c837bdc733c562ba3879910a7eced279801645dfd582fd087f724dce436 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project Compiler
#
import os, sys, re, shutil, time, base64, run, sgmllib, codecs
template_dir = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
sys.path.append(os.path.join(template_dir,'../'))
sys.path.append(os.path.join(template_dir,'../modul... | arnaudsj/titanium_mobile | support/iphone/compiler.py | Python | apache-2.0 | 19,432 | [
"VisIt"
] | 04c85ca508d36cebcf74ed88d8c5263a7e1fa24f651e220d3741e856669fa4a9 |
__author__ = 'AT'
import gzip
import os
import cPickle
import pandas
from ExtRBF import ExtRBF
import GPy
import numpy as np
class DataSource:
"""
Loading and preparing data for experiments. Some of the datasets are generated using the Matlab code
(see data/matlab_code_data), in order to ensure they are
... | adezfouli/savigp | GP/data_source.py | Python | apache-2.0 | 13,003 | [
"Gaussian"
] | 37845f9dd4db2bbc8dd2aacdb37f4768d29e2098fd931f077d0012241667d598 |
'''
This scripts takes care of postprocessing and reorganizing/correcting
data after Molcas scan...
'''
from collections import namedtuple
from argparse import ArgumentParser
import glob
from itertools import repeat
import multiprocessing
import numpy as np
import os
from shutil import copy2
from quantumpropagator i... | acuzzio/GridQuantumPropagator | Scripts/PostProcessing3dData.py | Python | gpl-3.0 | 19,928 | [
"MOLCAS"
] | ad2975b4acda4644d52dc9b1eb2210e6c738fb7ef5662a423affe74e90559f96 |
"""
@name: PyHouse_Install/src/Install/private.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2016 by D. Brian Kimmel
@license: MIT License
@note: Created May 13, 2016
@Summary: Create .private
Create the /etc/pyhouse/.private.yaml file that will hold the secret i... | DBrianKimmel/PyHouse_Install | src/Install/private.py | Python | mit | 1,018 | [
"Brian"
] | 5821a80e647083756533f85084c7aa5fc0fa0d2ac5e14c103dca7d3cebbc71c8 |
# $Id: TemplateExpand.py 1053 2008-07-30 12:03:29Z landrgr1 $
#
# Created by Greg Landrum August, 2006
#
#
from rdkit import RDLogger as logging
logger = logging.logger()
logger.setLevel(logging.INFO)
from rdkit import Chem
from rdkit.Chem import Crippen
from rdkit.Chem import AllChem
from rdkit.Chem.ChemUtils.AlignDe... | rdkit/rdkit-orig | rdkit/Chem/ChemUtils/TemplateExpand.py | Python | bsd-3-clause | 14,044 | [
"RDKit"
] | 9bfa50a2641bd54f35e3fc2317fffaa7cb5b7d73e9c5b666457e753056c55079 |
import os
import numpy as np
from scipy.io.netcdf import netcdf_file
from netCDF4 import Dataset
def file2dict(filename):
if not os.path.isfile(filename):
raise ValueError("ERROR: Could not read %s" % filename)
nc = netcdf_file(filename, 'r', mmap=False)
ret = {}
for ikey in nc.variables.keys... | MaterialsDiscovery/PyChemia | pychemia/utils/netcdf.py | Python | mit | 1,924 | [
"NetCDF"
] | 2d337a3fe78efeaeebb78fe627fada8c1f559ba57424b39d7315170f8aa9dfd3 |
import pysam
import time
import scipy as sp
import sys
import os
import warnings
import pdb
from sets import Set
def get_counts_from_single_bam(fn_bam, regions):
"""This function extracts read counts from a given bam file spanning
a set of given intervals."""
if not os.path.exists(fn_bam + '.bai'):
... | KjongLehmann/m53 | libs/bam.py | Python | mit | 3,463 | [
"pysam"
] | 785f9702e29d54ebb44492a586aabb57387157f36931087eb70f21ee25f56908 |
#! /usr/bin/env python
"""Assembly execution drivers.
This module provides the default parameters and handling of
assembler-specific configurations.
Assembler defaults are set in the 'arast.conf' file
"""
import logging
import os
import re
import subprocess
import shutil
import glob
import metadata as meta
from C... | cbun/assembly | lib/assembly/assembly.py | Python | mit | 7,846 | [
"BWA"
] | 64129e204620fa9eea49a5d292df86378c43bc7b654dd4ac962ba255ab20c5d4 |
#!/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/pbc/df/ft_ao.py | Python | apache-2.0 | 6,876 | [
"PySCF"
] | f9681443bedb96a9bfb3052981719e9046ef5b9060e1b58f38fb777bd4de6c59 |
import new, sys
import galaxy.util
import parameters
from parameters import basic
from parameters import grouping
from elementtree.ElementTree import XML
class ToolTestBuilder( object ):
"""
Encapsulates information about a tool test, and allows creation of a
dynamic TestCase class (the unittest framework... | dbcls/dbcls-galaxy | lib/galaxy/tools/test.py | Python | mit | 2,997 | [
"Galaxy"
] | 06b06591f5793691f23800da59fdecf7d6f1d897864227b9ea38d9dd3b23e2e4 |
"""A backend request handler process.
This file uses zmq.web to implement the backend logic for load balanced
Tornado request handlers.
This version uses a streaming message protocol to enable the backend to send
the HTTP body back to the frontend/browser in multiple asynchronous chunks.
To enable streaming mode, you... | ellisonbg/zmqweb | examples/backend_stream.py | Python | bsd-3-clause | 3,064 | [
"Brian"
] | 9bfab99f1b0c1f6de1894e29b43121cadaf07f94a94c57a9de66d7c8d42db67e |
from erukar.system.engine import MaterialGood
class SalericiteCrystal(MaterialGood):
BaseName = "Salericite Crystal"
BriefDescription = "a chunk of crystalline salericite"
BasePricePerSingle = 118
WeightPerSingle = 0.6
| etkirsch/legends-of-erukar | erukar/content/inventory/materials/raw/SalericiteCrystal.py | Python | agpl-3.0 | 236 | [
"CRYSTAL"
] | 74ba7bec0b41e452696a7049ad685cb1053fdaa7583255de8786e204f146ec32 |
import cv
from math import atan2, sqrt, ceil, pi, fmod
import sys, getopt, os
from location import TripLoader
from pylibs import spatialfunclib
from itertools import tee, izip
import sqlite3
##
## important parameters
##
cell_size = 1 # meters
gaussian_blur = 17
trips_path = "trips/trips_1m/"
def pairwise(iterable):... | Vanuan/gpx_to_road_map | biagoni2012/kde.py | Python | apache-2.0 | 5,391 | [
"Gaussian"
] | 8dd01698322f62506528116e0c7284e70a6c32e09b33e1ced9712c2891b120c5 |
"""
usage: dist-scramble.py <egg_name> [platform]
egg_name - The egg to scramble (as defined in eggs.ini)
platform - The platform to scramble on (as defined in
dist-eggs.ini). Leave blank for all.
Platform-inspecific eggs ignore this argument.
"""
import os, sys, logging
root = logging.g... | dbcls/dbcls-galaxy | scripts/dist-scramble.py | Python | mit | 1,160 | [
"Galaxy"
] | 88bc4b5c77c18dace29df039c17f41e8938728a80989776b8f6777402134d4f8 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-tasks | tests/unit/gapic/tasks_v2beta2/test_cloud_tasks.py | Python | apache-2.0 | 219,688 | [
"Octopus"
] | 67844a2758a5b04043be0997d28fe1ae5aa25755ef5f6806c7bc99af4b956522 |
'''OpenAnything: a kind and thoughtful library for HTTP web services
This program is part of 'Dive Into Python', a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
This library has been slightly modified by Mike Miller, 2005.
- changed function name
- rea... | Recaiden/pysh | lib/openanything.py | Python | gpl-2.0 | 3,377 | [
"VisIt"
] | 8b91585cf41b46028428f2da61b319edff6c4ed08f50adb68fe27149c4a7a689 |
#!/usr/bin/env python
"""
Summarize ultimate fantasy scores and results.
"""
from __future__ import print_function
import argparse
import numpy as np
import pandas as pd
from usau import markdown, reports
def compute_fantasy_picks(captain_multiplier=2, from_csv=False, fantasy_input=None):
"""Con... | azjps/usau-py | usau/fantasy.py | Python | mit | 11,294 | [
"Dalton"
] | e496e894d078bb7f014a05bfa625d62f3bcb23daa6f693fb7bb06496fbce66bf |
################################################################################
# $Id$
# $Date$
# $Revision$
################################################################################
# #
# LICENSE ... | epsylon3/torrentflux | html/bin/clients/fluazu/fluazu/TransferFile.py | Python | gpl-2.0 | 5,394 | [
"VisIt"
] | b5aa9a48f4d7c4a9548675504be5c68a5e307c15b7005b1ccdc78b65bd0f80a3 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-few-public-methods
import sys
from Bio.Alphabet import generic_dna
from Bio.Seq impor... | neilswainston/PathwayGenie | scripts/pross.py | Python | mit | 3,559 | [
"VisIt"
] | f4b91a264e6367bc7d7cc782e944ef57e79db749be7649adebb4bb8d52274362 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jH0ward/psi4 | psi4/driver/qcdb/libmintsbasissetparser.py | Python | lgpl-3.0 | 16,141 | [
"Gaussian",
"Psi4"
] | 764cca97cba4b2b7725ad088c26931ad5c546a8485996eac8b71bc4ce87ecfb3 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-yarn/package.py | Python | lgpl-2.1 | 2,596 | [
"Bioconductor"
] | e8ffc74e1b7ddbe4d17a227513246d618512f005862fa6a2c48890a798a22104 |
'''
Created on Oct 9, 2014
@author: dusenberrymw
'''
import math
class Logistic(object):
"""The Logistic (Sigmoid) activation function, which is one of the
possibilities that can be used by the network
"""
def __init__(self):
self.name = "logistic"
def activate(self, input_value):
... | dusenberrymw/Pine | pine/activation.py | Python | mit | 5,768 | [
"NEURON"
] | fe2a0ab2a3ac3bd48d0196f05490a5f4e46ea3c441fb4209d5bbe276c0491e6d |
#!/usr/bin/env python
"""
Real-time time encoding and decoding algorithms. These algorithms
can process signals of arbitrarily long length without the memory
limitations of the functions in the asdm and iaf modules.
- ASDMRealTimeDecoder - Real-time ASDM decoder.
- ASDMRealTimeDecoderIns - Parameter-insensitive re... | bionet/ted.python | bionet/ted/rt.py | Python | bsd-3-clause | 32,939 | [
"NEURON"
] | 318491809d7a7bcdb9d5028fe7ebdf1e2fa81622b9fcb8e2cfde297a9e95acab |
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# Copyright (c) 2021, Greg Landrum
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source... | greglandrum/rdkit | rdkit/Chem/Draw/SimilarityMaps.py | Python | bsd-3-clause | 17,614 | [
"RDKit"
] | 3edd3595ccdb0238034b36308c2b05c1f815f198856c919ee97df57d77af2dd6 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | brianmay/python-tldap-debian | tldap/backend/base.py | Python | gpl-3.0 | 5,414 | [
"Brian"
] | 391c5b395e631dd7fb3cebc5400b56533b678d0ba4348d74f4488999773915fa |
"""A biologically-inspired model of visual perception."""
from math import exp, hypot
import logging
import numpy as np
import cv2
import cv2.cv as cv
from collections import OrderedDict, deque
from itertools import izip
#import pyNN.neuron as sim
from lumos.context import Context
from lumos.util import Enum, getNorm... | napratin/nap | nap/vision/visual_system.py | Python | mit | 62,141 | [
"NEURON"
] | ac79d2d39dd90b62cb00d6e232ad765e8cf214dcdaa13d897fbb0f449f99ebdc |
from ase.io import read
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize import BFGS
# read the last structures (of 5 images used in NEB)
images = read('neb.traj@-5:')
for i in range(1, len(images) - 1):
images[i].set_calculator(EMT())
neb = NEB(images)
qn = BFGS(neb, trajectory='neb... | misdoro/python-ase | doc/tutorials/neb/diffusion4.py | Python | gpl-2.0 | 355 | [
"ASE"
] | 8dd5764c47321dbf7071d0eb5197b7e255bccd567c4341cdb01ec65139e33817 |
import os
import re
import sys
import os.path
import tempfile
import functools
import ase.db
from ase.db.table import Table, all_columns
from ase.visualize import view
from ase.io.png import write_png
from ase.db.summary import Summary
from flask import Flask, render_template, request, send_from_directory
app = Fla... | askhl/ase | ase/db/app.py | Python | gpl-2.0 | 5,037 | [
"ASE"
] | b08e29f7eef6e1f3ec15270c61ed0664c8bf10eb405d53e41e6621a53a0e4f7d |
# 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 RTxdbHsapiensUcscHg19Knowngene(RPackage):
"""Annotation package for TxDb object(s)
Ex... | LLNL/spack | var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py | Python | lgpl-2.1 | 962 | [
"Bioconductor"
] | a10b7579580a79c784e2178c19251e118ef4a96adeb4abdac8c741ddd792ba54 |
import json
import os
import time
from pychemia import pcm_log
from pychemia.crystal import KPoints
from ..dftb import DFTBplus, read_detailed_out
class StaticCalculation:
def __init__(self, structure, workdir, slater_path, waiting=False, kpoints=None, output_file='results.json',
max_scc_iteratio... | MaterialsDiscovery/PyChemia | pychemia/code/dftb/task/static.py | Python | mit | 3,066 | [
"CRYSTAL"
] | e90e36e010ba28b4a8e4e3c4d0d7f9bcf999ef25b143c10776080b87964d86d5 |
from backdoors.backdoor import *
class Web(Backdoor):
prompt = Fore.RED + "(web) " + Fore.BLUE + ">> " + Fore.RESET
def __init__(self, core):
cmd.Cmd.__init__(self)
self.intro = GOOD + "Using Web module"
self.core = core
self.options = {
"port" : Option("port"... | sovaa/backdoorme | backdoors/shell/web.py | Python | mit | 2,308 | [
"VisIt"
] | 8288a3e54348bf5126478b654ca4d775727d720b1510ed5683ca83013aa7ce0b |
# ----------------------------------------------------------------------------
# Copyright 2015 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
#
# http://www.apache.o... | jfsantos/neon | tests/test_recurrent.py | Python | apache-2.0 | 10,800 | [
"Gaussian"
] | 41bbb5146720ca5a61cda73b220df99afdc13c2021788f76e277129503ea39d0 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2014 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import codecs
import contextlib
import cookielib
import copy
import getpass
import hashlib
import httplib
import inspect
import json
import logging
import ntpath
import os
imp... | goofwear/raspberry_pwn | src/pentest/sqlmap/lib/core/common.py | Python | gpl-3.0 | 126,017 | [
"VisIt"
] | 287b09412f707b06a0fa06a1329b5312061d9a8b43081a7ead7ddeb5ac2bcfdd |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for
# license information.
#
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes ... | lmazuel/azure-sdk-for-python | azure-mgmt-web/azure/mgmt/web/models/app_service_environment_resource.py | Python | mit | 13,994 | [
"ASE"
] | 9198f9702a17d17c406e87c7d3f7e38f4040deff371ed6254a0755ab723f6525 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.