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#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/hh_style/neuron/hocmodbuilders/mmwriter_leak.py | Python | bsd-2-clause | 4,602 | [
"Elk",
"NEURON"
] | 3b4361fba60e79cb81b1081525e7d4e44fb1dad0271a63407c5826fb81572c1c |
# -*- coding: utf-8 -*-
import json
import requests
import urllib3
from optparse import OptionParser
urllib3.disable_warnings()
def main(file, user, password, url):
ipa = IPAConnector(url, user, password)
print ipa.login()
input = open(file, "r").read()
decoded = json.loads(input, "utf-8")
# print "Get curre... | stavamichal/perun-services | slave/process-freeipa/lib/process-freeipa.py | Python | bsd-2-clause | 4,755 | [
"VisIt"
] | 526a02353d706dfae695ace1d6a37c3c6d184080b0e5fe9268caf33e086a0c7a |
'''
package docstring
author: Jyh-Miin Lin Cambridge University
address: jyhmiinlin at gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it under the terms of the... | jyhmiinlin/cineFSE | CsTransform/pynufft.py | Python | gpl-3.0 | 94,502 | [
"Mayavi"
] | e51b3d95852d312b47dc3f24acf9c4b928c2f1e2b10ab0455f1b9a6461e5b669 |
"""
NLTK DRT module extended with presuppositions
"""
__author__ = "Alex Kislev, Emma Li, Peter Makarov"
__version__ = "1.0"
__date__ = "Tue, 24 Aug 2010"
import re
import operator
from nltk.sem.logic import Variable
from nltk.sem.logic import EqualityExpression, ApplicationExpression, ExistsExpression, AndExpress... | napsternxg/nltk-drt | nltk-drt/src/presuppdrt.py | Python | apache-2.0 | 58,821 | [
"VisIt"
] | db7f8749182b76094660325456530875731060fc9e2b01feeda2a890b0c52353 |
"""This file contains code for use with "Think Bayes",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
"""This file contains class definitions for:
Hist: represents a histogram (map from values to integer frequencies).
P... | KECB/learn | thinkbayes.py | Python | mit | 44,250 | [
"Gaussian"
] | 9b931be9b95fa48be537e4512c381738510ee43abbf752d881c7a14eba0fff8e |
# -*- coding: utf-8 -*-
"""
Copyright (c) 2010-2014 Jennifer Ennis, William Tisäter.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any la... | Architektor/PySnip | venv/lib/python2.7/site-packages/pygeoip/const.py | Python | gpl-3.0 | 17,371 | [
"BWA",
"COLUMBUS"
] | e527b057bb976318b24ac49ea27ddd29465f538ea34a846f9ad48aa70cfb0c60 |
WEAPONS = {
"lewis gun low weight": "b79b965e-e080-475d-a1cc-2432de5f3bf5",
"sawtooth knife": "f9983578-e3e9-46fb-bcc5-6640825b7169",
"sjogren inertial factory": "5d89166e-58e1-46fd-b854-69641e9dcef7",
"survival knife": "5be36f02-de5e-4ddd-8e09-74fd16f39efc",
"m97 trench gun backbored": "ea7c6cf1-58... | Girbons/battlefield1-sdk | bf1/config/weapons.py | Python | mit | 11,137 | [
"FLEUR"
] | 3a6509768d880aea51db8f148039ca124edd7be9be083f817ef0191b1d368c20 |
# coding=utf-8
# Distributed under the MIT software license, see the accompanying
# file LICENSE or http://www.opensource.org/licenses/mit-license.php.
from unittest import TestCase
from mock import Mock, patch
from pyqrllib.pyqrllib import bin2hstr, hstr2bin
from qrl.core.misc import logger
from qrl.core.AddressStat... | randomshinichi/QRL | tests/services/test_WalletAPIService.py | Python | mit | 33,649 | [
"Jaguar"
] | 118e18728c205073794e0075b32a51e33c8c54b46cc068113c14a3a12d724962 |
# This is the config file for the VHF/UHF receiver.
from __future__ import print_function
import sys, struct, socket, traceback
from quisk_hardware_model import Hardware as BaseHardware
from n2adr import uhfrx_widgets as quisk_widgets
import _quisk as QS
DEBUG = 0
if sys.platform == "win32":
n2adr_sound_pc_capt ... | gonesurfing/Quisk_rpi_remote | n2adr/uhfrx_conf.py | Python | gpl-2.0 | 15,721 | [
"ADF"
] | 99c4a71a2da88ae5dc008b60c86663472708fe5631b3bdf0d928eb65e0d2b3b8 |
from pyscf.pbc.gto import Cell
from pyscf.pbc.scf import KRHF
from pyscf.pbc.tdscf import KTDHF
from pyscf.pbc.tdscf import krhf_slow_supercell, kproxy_supercell
from pyscf.tdscf.common_slow import eig
from test_common import retrieve_m, assert_vectors_close
import unittest
from numpy import testing
import numpy
de... | gkc1000/pyscf | pyscf/pbc/tdscf/test/test_kproxy_supercell_hf.py | Python | apache-2.0 | 7,379 | [
"PySCF"
] | eb604cd09622558d12c8cecb85e2ac27f95f6e265a313c8da66b4d473eefa4b1 |
import json
import os
from operator import lt, gt
from dateutil import parser
from django.apps import apps
from django.db import transaction
from rdflib import RDFS, Graph
from rdflib.namespace import DC, Namespace
from hs_core.hydroshare import utils, get_resource_file
from hs_file_types.models.base import AbstractL... | hydroshare/hydroshare | hs_file_types/utils.py | Python | bsd-3-clause | 17,852 | [
"NetCDF"
] | 9ec926a0464522bbdba1a40e4a8bcd862c5a8e1567f9d838f4ef4c2065265963 |
"""
Shared model and mapping code between Galaxy and Tool Shed, trying to
generalize to generic database connections.
"""
from sqlalchemy.orm import scoped_session, sessionmaker
from galaxy.util.bunch import Bunch
from inspect import getmembers, isclass
# TODO: Refactor this to be a proper class, not a bunch.
class ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/base.py | Python | gpl-3.0 | 1,177 | [
"Galaxy"
] | 069b5b39d58203f7c90fa8adee80f3b7f73a8511df5ee9b0553917999485d37a |
#!/usr/bin/env python
"""
openmoltools: Tools for Small Molecules, Antechamber, OpenMM, and More.
COPYRIGHT AND LICENSE
@author John D. Chodera <jchodera@gmail.com>
@author Kyle A. Beauchamp <kyleabeauchamp@gmail.com>
@author David L. Mobley <dmobley@mobleylab.org>
All code in this repository is released under the ... | andrrizzi/openmoltools | openmoltools/__init__.py | Python | gpl-2.0 | 1,083 | [
"Amber",
"Gromacs",
"OpenMM"
] | 5f49f1c3321381117b72ced775961ece1daa4e61f35b9522b101b9f21708c0d8 |
__script__.title = 'KKB Measurement Script'
__script__.version = '2.1 2017-07-11 saved as KKB_scan'
from gumpy.commons import sics
from org.gumtree.gumnix.sics.control import ServerStatus
from pickle import Pickler, Unpickler
import time
from math import log as ln
from math import exp, isnan, isinf, sin
... | Gumtree/Kookaburra_scripts | Internal/KKB_Scan.py | Python | epl-1.0 | 59,476 | [
"CRYSTAL"
] | ebd5ff9abbabc2b44f6757bb1302e4eea7eb08ef540d4cafb0bc0dd394ddc414 |
# Copyright (C) 2017,2018
# 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, either version 3 of the Licen... | espressopp/espressopp | src/interaction/SmoothSquareWell.py | Python | gpl-3.0 | 7,097 | [
"ESPResSo"
] | 15a53b427070a291997e32f8d50fc0f447e17b80dad146c23fb8e49802c0648a |
"""Perform streaming post-alignment preparation -- de-duplication and sorting.
Centralizes a pipelined approach to generating sorted, de-duplicated BAM output
from sequencer results.
samblaster: http://arxiv.org/pdf/1403.7486v1.pdf
biobambam bammarkduplicates: http://arxiv.org/abs/1306.0836
"""
import contextlib
impo... | a113n/bcbio-nextgen | bcbio/ngsalign/postalign.py | Python | mit | 16,296 | [
"BWA",
"pysam"
] | 8cb437ae94a803149c01848646f2636cb1f1ea177b4d1c6433e633f2bae6f2c4 |
import time
import traceback
class Gotchi:
def __init__(self):
self.birth = int(time.time())
self.lastcontact = self.birth
self.alive = True
self.awake = True
self.complaints = ''
self.complaints_list = list()
self.active_attrs = dict(food = Attribute(2000, ... | booski/booski_gotchibot | classes.py | Python | gpl-2.0 | 7,532 | [
"GULP"
] | 38fa91bf71224219115f10d84f012e592ab33d90de2cc5eb06e8d8d868af4b90 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkEnSightMasterServerReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkEnSightMasterServerReader.py | Python | bsd-3-clause | 528 | [
"VTK"
] | 257a405fa4f7bf4ffd6d577bf219f69c2fad9b92be346efbd6b86458f51c180b |
"""
Example of an elaborate dialog showing a multiple views on the same data, with
3 cuts synchronized.
This example shows how to have multiple views on the same data, how to
embedded multiple scenes in a dialog, and the caveat in populating them
with data, as well as how to add some interaction logic on an
ImagePlane... | srinituraga/caffe_neural_models | dataset_06/volume_slicer.py | Python | bsd-2-clause | 8,622 | [
"Mayavi",
"VTK"
] | 4d384b935faa5e0649f05076d1fc574fbb6b9236a28aa38d0206ab8a01b6ac5c |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2008 Tungsten Graphics, Inc., Cedar Park, Texas.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files ... | mxOBS/deb-pkg_trusty_chromium-browser | third_party/mesa/src/src/gallium/tools/trace/parse.py | Python | bsd-3-clause | 12,473 | [
"VisIt"
] | 52610155bed5b6bebc33ff2d21996c7a3d1982f3602c7eff944eb3555ec058cd |
# $Id$
import unittest
import numpy
from itcc.molecule import read
from itcc.ccs2 import sidechain
from itcc.core import tools
test_in = '''\
5 molden generated tinker .xyz (mm3 param.)
1 C 0.000000 0.000000 0.000000 1 2 3 4 5
2 H 0.000000 0.000000 1.089000 5 ... | lidaobing/itcc | tests/ccs2/sidechain.py | Python | gpl-3.0 | 1,440 | [
"TINKER"
] | e6ef0d2c64f679bced19b438ac936d95a63068faa2b9dc2dd2e4add918f2cf16 |
"""nanocrystalline.py - set up a nanocrystalline sample."""
from ase.lattice.cubic import BodyCenteredCubic, FaceCenteredCubic
from ase.visualize import view
from ase.optimize import FIRE
from ase import units
from asap3.md.nptberendsen import Inhomogeneous_NPTBerendsen
from asap3 import NeighborCellLocator
import num... | auag92/n2dm | Asap-3.8.4/Python/asap3/Setup/nanocrystalline.py | Python | mit | 9,207 | [
"ASE",
"CRYSTAL"
] | e26bc8616cfded8373863e146f7f70c8ecedda2aeface28ebd93ee735c409928 |
##############################################################################
# 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/exodusii/package.py | Python | lgpl-2.1 | 3,511 | [
"NetCDF"
] | 1e01f44776f040627339d5f0ebd5d27ae5f2f11ab22ba6c6212b3769ed5bca23 |
"""
This module implements basic kinds of jobs for VASP runs.
"""
import logging
import math
import os
import shutil
import subprocess
import numpy as np
from monty.os.path import which
from monty.serialization import dumpfn, loadfn
from monty.shutil import decompress_dir
from pymatgen.core.structure import Structure... | materialsproject/custodian | custodian/vasp/jobs.py | Python | mit | 38,378 | [
"VASP",
"pymatgen"
] | 8e2d066e3efd892ec9830d9c783564c3b5f90cbc6ee15ce4a6751fad828916dd |
#!/usr/bin/env python
# Created: Thu Jul 13 11:09:00 2000
# Last changed: Time-stamp: <00/12/02 15:57:45 thomas>
# thomas@cbs.dtu.dk, http://www.cbs.dtu.dk/thomas
# File: xbbtools.py
# Copyright 2000 by Thomas Sicheritz-Ponten. All rights reserved.
# This code is part of the Biopython distribution and governed by its... | updownlife/multipleK | dependencies/biopython-1.65/Scripts/xbbtools/xbbtools.py | Python | gpl-2.0 | 759 | [
"Biopython"
] | e5f8823a08162ce3a745413aaabf34e27c9832b0215bd27055b3660bd3a2665f |
# -*- coding: utf-8 -*-
from time import sleep
url = "http://localhost:11111/"
def test_index(browser):
# Visit URL
browser.visit(url)
assert browser.is_text_present('about')
def test_404(browser):
# Visit URL
browser.visit(url + 'missing_link')
assert browser.is_text_present('Page not fou... | misnyo/searx | tests/robot/__init__.py | Python | agpl-3.0 | 2,212 | [
"VisIt"
] | e699a85a3d28adbfcf297a32248e9d9258fb6a74aab323d8adef633e3af0cf07 |
'''
Alex Crits-Christoph
License: GPL3
Identifies closest GenBank prokaryote genomes by euclidean distance between tetranucleotide frequencies of query sequences.
'''
import json
from scipy.spatial import distance
import sys
from Bio import SeqIO
from marker_genes import meta_marker
import operator
import argparse
im... | alexcritschristoph/CircHMP | identify_host.py | Python | gpl-2.0 | 11,633 | [
"BLAST"
] | ca43c3f8cb7b282383eb9b5d6718f89ffe05bda117bd20c1077937827d33c97a |
import unittest
import mock
from Tests.utils.utils import get_test_path
from kalliope import ResourcesManager
from kalliope.core.Models import Resources
from kalliope.core.Models.Dna import Dna
class TestResourcesmanager(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
... | kalliope-project/kalliope | Tests/test_resources_manager.py | Python | gpl-3.0 | 6,445 | [
"NEURON"
] | 31d71ff1ab95e246bf44883a3f08e7bf60eb6e4f63ff815ab3af484af0a2a102 |
"""
Utility functions for transcripts.
++++++++++++++++++++++++++++++++++
"""
import copy
import html
import logging
import os
from functools import wraps
import requests
import simplejson as json
import six
from django.conf import settings
from lxml import etree
from opaque_keys.edx.locator import BundleDefinitionL... | stvstnfrd/edx-platform | common/lib/xmodule/xmodule/video_module/transcripts_utils.py | Python | agpl-3.0 | 39,530 | [
"FEFF"
] | 103435f075a5bdef223fa8676b3d3d903948ec14a25f417f694957b14f7cfe85 |
#! /usr/bin/env python3
# -*- coding: utf8 -*-
##########################################################################
# #
# Program: va.py Version 1.2.2 Date: 18/07/2019 #
# ... | JohnKendrick/PDielec | PDielec/vibanalysis.py | Python | mit | 70,967 | [
"Gaussian",
"MOPAC",
"ORCA",
"VASP"
] | c4752d38b89992ab3079af797e7f5cc78dac2966d2db5197195a22da2a84f343 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import warnings
import numpy as np
from astropy.utils import isiterable
from astropy.utils.exceptions import AstropyUserWarning
try:
import bottleneck # pylint: disable=W0611
HAS_BOTTLENECK = True
from astropy.units import Quantity
except... | MSeifert04/astropy | astropy/stats/sigma_clipping.py | Python | bsd-3-clause | 30,864 | [
"Gaussian"
] | b5e43ade465458e0282347583577a412f88cb9d74b58c8ecf6443196fc1e46d9 |
import logging
import numpy as np
from neon.util.argparser import NeonArgparser
from neon.backends import gen_backend
from neon.initializers import Constant, Gaussian
from neon.layers import Conv, Pooling, GeneralizedCost, Affine, Dropout
from neon.optimizers.optimizer import MultiOptimizer, GradientDescentMomentum
fro... | cs-chan/fuzzyDCN | prune_neon/cifar10CNNfp.py | Python | bsd-3-clause | 3,178 | [
"Gaussian"
] | ea952e15621ebeb24dfdb4b81a6c7292217a288bc20ddc1fe13345de7ccba1cd |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2010 - 2011, University of New Orleans
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your o... | gblanchard4/viamics | framework/tools/blast.py | Python | gpl-2.0 | 12,084 | [
"BLAST"
] | 8ee36b786e2e73c657170dd6659eb6e35fe854b6ab35ec4212c6ea3bd39f24d9 |
#
# @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
#... | jturney/psi4 | psi4/driver/procrouting/dft/libxc_functionals.py | Python | lgpl-3.0 | 13,135 | [
"Psi4"
] | 542badbd3fd187e7f70cfdf43a35253a0499e8888b587958c6408eb22134a519 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | ghutchis/cclib | src/cclib/writer/cjsonwriter.py | Python | lgpl-2.1 | 4,465 | [
"Open Babel",
"cclib"
] | 5957f679e22dc9d4a15a7a33a4da56f13a0503e0e4d5854219cce57d72eacec7 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# first, create an image to warp
imageGrid = vtk.vtkImageGridSource()
imageGrid.SetGridSpacing(16,16,0)
imageGrid.SetGridOrigin(0,0,0)
imageGrid.SetDataExtent(0,255,0,255,0,0)
imageGr... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/TestGridWarpNearest.py | Python | gpl-3.0 | 2,678 | [
"VTK"
] | e5952926bd66761697a1d55359dbb4d55f2b9165f60b7581d5cd74cb14069a7c |
# 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... | dmlc/tvm | python/tvm/relay/backend/contrib/ethosu/tir/passes.py | Python | apache-2.0 | 33,840 | [
"VisIt"
] | dd8df924014daff2ffeea832f7f9e255f5a9b2a55eb14d25b7e7a11eebabbd38 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
Interface with command line GULP.
http://projects.ivec.org
WARNING: you need to have GULP installed on your system.
"""
__author__ = "Bharat Medasani, Wenhao Sun"
_... | aykol/pymatgen | pymatgen/command_line/gulp_caller.py | Python | mit | 26,888 | [
"GULP",
"pymatgen"
] | 5485a491f0d53e87fce1c4c38b5c933b6ee2513ee6a34bdfbe6ac373a8555fe3 |
import numpy as np
from ase.atoms import Atom, Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.calculators.singlepoint import SinglePointKPoint
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
def index_startswith(lines, ... | alexei-matveev/ase-local | ase/io/gpawtext.py | Python | gpl-2.0 | 5,331 | [
"ASE",
"GPAW"
] | 679a0ff7181c198b6f140cc4d6be490f8da593f38b08472452eb38e035af5f88 |
from __future__ import print_function
import numpy as np
from vtk import vtkPolyDataMapper, vtkPolyDataNormals, \
vtkLinearSubdivisionFilter, vtkSmoothPolyDataFilter, \
vtkDepthSortPolyData, vtkAlgorithm, vtkAlgorithmOutput
from ase.visualize.vtk.grid import vtkVolumeGrid
# ----------... | suttond/MODOI | ase/visualize/vtk/pipeline.py | Python | lgpl-3.0 | 6,964 | [
"ASE",
"VTK"
] | 61f4b9175539953986c6db24a19036501dcf224b5c35b8116218f1d15a622937 |
"""
@name: Modules/House/Family/Insteon/insteon_plm.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2010-2020 by D. Brian Kimmel
@note: Created on Feb 18, 2010
@license: MIT License
@summary: This module is for sending commands to and receiving responses from an Insteon ... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/insteon_plm.py | Python | mit | 18,308 | [
"Brian"
] | e87dea845bb7eeb81b287b4df28a99cc96e86dbae942e1fa54162c6e09a81ede |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | util.py | Python | mit | 15,220 | [
"VisIt"
] | ed1c33dedeb04d3852d5ecc1cd8a66e8aa5ee3548890a71d5854a1520bb05281 |
from frappe import _
def get_data():
return [
{
"label": _("Documents"),
"icon": "icon-star",
"items": [
{
"type": "doctype",
"name": "Lead",
"description": _("Database of potential customers."),
},
{
"type": "doctype",
"name": "Customer",
"description": _("Custome... | shitolepriya/Saloon_erp | erpnext/config/crm.py | Python | agpl-3.0 | 3,481 | [
"VisIt"
] | 7e62db5dc5880e092ba5a8fe45cfb2991a83035f95a3342939d7e1086691db60 |
"""
The Grizzled Utility Library is a general-purpose Python library with
a variety of different modules and packages. It's roughly organized into
subpackages that group different kinds of utility functions and classes.
"""
__docformat__ = "restructuredtext en"
__version__ = '1.0'
__author__ = 'Brian M. Clapper'
__e... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/grizzled/grizzled/__init__.py | Python | bsd-3-clause | 630 | [
"Brian"
] | 84d776ab085211ee07634f4611577cdafa7e669a2c1c13402560c587ca15878c |
"""
Phonon unfolding: Reciprocal space method. The method is described in
P. B. Allen et al. Phys Rev B 87, 085322 (2013).
This method should be also applicable to other bloch waves on discrete grid, eg. electrons wave function in wannier basis set, magnons, etc. Now only phonon istested.
"""
from ase.build import make... | mailhexu/pyDFTutils | pyDFTutils/unfolding/unfolding/phonon_unfolder.py | Python | lgpl-3.0 | 6,698 | [
"ASE"
] | 0a806548f572968fc6a5ef22e47c61b818c7b1c0d75953747d5ff8b2cf965da2 |
#!/usr/bin/env python
# B a r a K u d a
#
# Generate 2D plots and maps of the Mixed layer depth
#
# L. Brodeau, 2009
import sys
import numpy as nmp
from netCDF4 import Dataset
import barakuda_tool as bt
import barakuda_plot as bp
import barakuda_physics as bphys
venv_needed = {'ORCA','EXP','DIAG_D',... | brodeau/barakuda | python/exec/mld.py | Python | gpl-2.0 | 8,079 | [
"ORCA"
] | 4a9235826dc7d1cedb3af7654c82ad783451b545dabc537f3238ecedc152226c |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | devanshdalal/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 11,966 | [
"Gaussian"
] | 01bfd0029af6d696922b6d7b9217a2c5f828c67b1ca33ebb591d326f846e8fc1 |
#!/usr/bin/env python
#
# This file is part of Buildbot. Buildbot is free software: you can
# redistribute it and/or modify it under the terms of the GNU General Public
# License as published by the Free Software Foundation, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# A... | anish/buildbot | master/setup.py | Python | gpl-2.0 | 21,838 | [
"Brian"
] | 29a6adb0787ac989768f941694844fa3c014ca9bf71798a54f83841b901a5998 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
from distutils.vers... | HackFisher/depot_tools | git_cl.py | Python | bsd-3-clause | 105,244 | [
"VisIt"
] | 70c2e34f616f00261cec6c4212c6a5ab3e93b48d15aa95362e48cb67e41146b8 |
import os
import unittest
import pytest
from pymatgen.analysis.fragmenter import Fragmenter
from pymatgen.analysis.graphs import MoleculeGraph
from pymatgen.analysis.local_env import OpenBabelNN
from pymatgen.core.structure import Molecule
from pymatgen.util.testing import PymatgenTest
__author__ = "Samuel Blau"
__e... | materialsproject/pymatgen | pymatgen/analysis/tests/test_fragmenter.py | Python | mit | 6,728 | [
"pymatgen"
] | 19bb9ab976f43e7e228dc910c47bb8179eac6517082d5d3972dcf8bdd658645a |
# Print embeddable python library, as well as other libs it requires.
# Will prefer static linkage unless invoked with "shared" argument.
# -JGG, 8/4/04, rev. 7/21/05 for OS X Tiger
import sys, os.path, distutils.sysconfig
static_link = 1
nargs = len(sys.argv)
if nargs == 2 and sys.argv[1] == "shared":
static_link... | RTcmix/RTcmix | src/parser/python/print_libpython.py | Python | apache-2.0 | 2,353 | [
"Jaguar"
] | 839bb2d442b7623c4ee47a0a44249990ecb932ba8d41e2e0a8818a8ca459598a |
from django import forms
from ..models import MaternalInterimIdcc
from edc_constants.constants import YES, NO
from .base_maternal_model_form import BaseMaternalModelForm
class MaternalInterimIdccForm(BaseMaternalModelForm):
def clean(self):
cleaned_data = super(MaternalInterimIdccForm, self).clean()
... | botswana-harvard/tshilo-dikotla | td_maternal/forms/maternal_interim_idcc_form.py | Python | gpl-2.0 | 3,361 | [
"VisIt"
] | 37b35ba6e541526e55647e703f0452cb68c102df4df781f3ff53047a3b573681 |
"""Hilbert spaces for quantum mechanics.
Authors:
* Brian Granger
* Matt Curry
"""
from __future__ import print_function, division
from sympy import Basic, Interval, oo, sympify
from sympy.core.compatibility import u, range
from sympy.printing.pretty.stringpict import prettyForm
from sympy.physics.quantum.qexpr imp... | drufat/sympy | sympy/physics/quantum/hilbert.py | Python | bsd-3-clause | 19,514 | [
"Brian"
] | 0cea0f62d2937a03a3ae0790f58c641e4b6252763a7222d269246ed58afaca1d |
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
zeros, arange, sort, amin, amax, any, atleast_1d,
sqrt, ceil, floor, a... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/scipy/stats/morestats.py | Python | gpl-3.0 | 93,860 | [
"Gaussian"
] | 71b010b87f426c1cf1edd69239e1fe6aecfdd3d5c831c8c55bd00159ec834961 |
# Copyright 2019 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tpu | models/official/detection/dataloader/maskrcnn_parser_with_copy_paste.py | Python | apache-2.0 | 25,872 | [
"Gaussian"
] | 55ebcb19404baddc72743c811d8338c7c80c085727ef330d802fd1b4106e33fb |
#!/usr/bin/env python
#
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to start and stop Android emulator.
Assumes system environment ANDROID_NDK_ROOT has been set.
Emulat... | espadrine/opera | chromium/src/build/android/pylib/utils/emulator.py | Python | bsd-3-clause | 12,504 | [
"Galaxy"
] | 24965886121375eba54017187be6fea043f5c5567c6a8be8b16f3794daa875a1 |
# -*- coding: utf-8 -*-
"""Functions for building graphs that use both expansion and induction procedures."""
import logging
from typing import Iterable, Union
from .expansion import expand_all_node_neighborhoods
from .expansion.upstream import expand_downstream_causal, expand_upstream_causal
from .induction.neighbo... | pybel/pybel | src/pybel/struct/mutation/induction_expansion.py | Python | mit | 2,477 | [
"Pybel"
] | 789faef2e3b24675dee538de7efd997c6be2076834962429d17d46f2133517da |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | snlds/examples/tensorboard_utils.py | Python | apache-2.0 | 6,652 | [
"Amber"
] | 97d971568e55a8344a3268250b47ff7a55032ca58b0f43252c5b4614b8443e85 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=========================================================
Logit function
=========================================================
Show in the plot is how the logistic regression would, in this
synthetic dataset, classify values as either 0 or 1,
i.e. class one or two, us... | seckcoder/lang-learn | python/sklearn/examples/linear_model/plot_logistic.py | Python | unlicense | 1,389 | [
"Gaussian"
] | 04fab5c697c5f4b311aa9b5d97860ac81b9b702b9bfe1cac239be281f8ff0fc3 |
import asyncio, discord, time, parsedatetime, os, json
from datetime import datetime
from operator import itemgetter
from discord.ext import commands
from Cogs import Settings, Message, UserTime
try:
from igdb_api_python.igdb import igdb
LOADED = True
except:
# Missing the api
LOADED... | corpnewt/CorpBot.py | Cogs/GameLookup.py | Python | mit | 6,774 | [
"Jaguar"
] | 2d6b4331d40b110b6753c7f605684d4e551c3cf6ba1124d6822e34d11fdcd7b2 |
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 17 15:13:23 2015
@author: sm1fg
Use to plot 1D and 2D slices of gdf formatted data.
Dictionaries are used so appropriate labels and line colors can be extracted
from the data name lists.
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.axes as ... | SWAT-Sheffield/pysac | pysac/mhs_atmosphere/plot/mhs_plot.py | Python | bsd-2-clause | 24,757 | [
"Mayavi"
] | 036dc27998ef0085390448545e1672d1fbd95c4f72d5edfdbd025119e230f6da |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
This example shows how to generate the analytical gradients for DF integrals.
'''
import numpy
from pyscf import gto, df, lib
mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='ccpvdz')
# Generate auxmol to hold auxiliary basis.
# One g shell is adde... | gkc1000/pyscf | examples/df/41-df_integrals_gradients.py | Python | apache-2.0 | 2,307 | [
"PySCF"
] | 19d1413fbf5cd97e1e83506fc5ba145d91539e6e629625cbeaaa8ed968555563 |
#These functions use another python class call "matfun.py" which has matrix and vector operations. Available at http://users.rcn.com/python/download/python.htm
#mean wind for a layer AGL
#this algorith uses lists of wind direction and speed, heights and the top and
#bottom of the layer
#the key to finding the mean w... | rhurkes/sigtor.dusty | src/etc/bunkers.py | Python | mit | 5,442 | [
"Brian"
] | 4de17360988e1c3ff3ae17dd7922e39f119a1f33efa0283a17bcf7e3e3acd50c |
import collections
import glob
import logging
import os
import pandas
import shutil
import subprocess
from grocsvs import step
from grocsvs import utilities
from grocsvs.stages import collect_reads_for_barcodes
from grocsvs.stages import cluster_svs
class AssemblyStep(step.StepChunk):
@staticmethod
def get_... | grocsvs/grocsvs | src/grocsvs/stages/assembly.py | Python | mit | 7,424 | [
"BWA"
] | 170c1f2655e9b5eccd7bc06effc8db6394ec80dc5f0b75dd7d8ee195f4b30d8a |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | haohonglin/tornado | tornado/websocket.py | Python | apache-2.0 | 38,365 | [
"VisIt"
] | a62ce8057bd9fa1e0a77a9682647bb2061728ec43bf9b58e6f3e4c849b0789e8 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | google/yapf | yapf/pytree/split_penalty.py | Python | apache-2.0 | 24,502 | [
"VisIt"
] | 9e9d9bf663089f96a63ab4058dcb1ab23a23373c2bb087b2e17266227b979114 |
"""
Bok choy acceptance tests for conditionals in the LMS
"""
from capa.tests.response_xml_factory import StringResponseXMLFactory
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.lms.... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/lms/test_conditional.py | Python | agpl-3.0 | 4,837 | [
"VisIt"
] | 21012038f05d449ba8bdd0e46ebe939f12ede1611ab8bcc98fb9d4477e04906d |
#!/usr/bin/env python
import sys
import subprocess
from math import floor, ceil, log10
import numpy
try:
from pyx import *
except:
pass
from ..hic import HiC
from ..plotting import plot_compact_array, plot_upper_array, plot_diagonal_from_compact_array
from ..plotting import plot_full_array, plot_diagonal_fro... | bxlab/HiFive_Paper | Scripts/hifive-1.1.3/hifive/commands/get_hic_interval.py | Python | bsd-3-clause | 13,537 | [
"Galaxy"
] | 87b01c8173ec1a156218e3798b574e298b294a264f2576d90910c0066bd12240 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
__author__ = "Handong Ling"
__version__ = "0.1"
__maintainer__ = "Handong Ling"
__email__ = "handongling@berkeley.edu"
__status__ = "Development"
__date__ = "4/23/19"
import os
import unittest
import numpy as... | gVallverdu/pymatgen | pymatgen/symmetry/tests/test_site_symmetries.py | Python | mit | 1,260 | [
"pymatgen"
] | 67cb190d1aa5825a00711f3c9624c5166528447bea2d0d867e8a621bd9403690 |
import numpy as np
from gpaw.utilities.blas import gemm
from gpaw.utilities.lapack import general_diagonalize
from gpaw.utilities import unpack
from gpaw.hs_operators import reshape
from gpaw.eigensolvers.eigensolver import Eigensolver
class Davidson(Eigensolver):
"""Simple Davidson eigensolver
It is expect... | robwarm/gpaw-symm | gpaw/eigensolvers/davidson.py | Python | gpl-3.0 | 8,419 | [
"GPAW"
] | 9f77dfe03dedeff544160c703dab77f1f7aeb8ee45a02c79526aa7d2d650ba9f |
# -*- coding: utf-8 -*-
#
# test_regression_issue-1034.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of ... | lekshmideepu/nest-simulator | testsuite/pytests/test_regression_issue-1034.py | Python | gpl-2.0 | 13,081 | [
"NEURON"
] | 2758ee53b9216e617e0b29a11ac0537dc6457f2915fff6fd6fe07b94bc4eb596 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Jul 26, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | aykol/pymatgen | pymatgen/core/tests/test_bonds.py | Python | mit | 1,635 | [
"pymatgen"
] | 8e94a8cfddad463adffcb98edc08849d90e36d9fc81c528932ed200ef63f612c |
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1417442133.491906
_template_filename='templates/webapps/galaxy/workflow/run_complete.mako'
_template_uri='workflow/run_complete.mako'
_te... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/database/compiled_templates/workflow/run_complete.mako.py | Python | gpl-3.0 | 3,697 | [
"Galaxy"
] | a392a408350f00db7d586033a7b14312728660d52ed783b14abfc05065b3ab3a |
#!/usr/bin/python
#Jonathan Pritchard
"""
This code provides options for visualising a 21cmFast box.
"""
import os
import re
import sys
import math
import string
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from mpl_toolkits.mplot3d import Axes3D
import mayavi.mlab as mlab
import time
import commands
imp... | yunfanz/ReionBub | tocmfastpy/box_visual.py | Python | mit | 7,439 | [
"Mayavi"
] | bfdb791e8504c1d427a1487f080bc98f8db46cd53b17e0ef984f72c623424413 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | modules/level_set/examples/vortex/viewer.py | Python | lgpl-2.1 | 621 | [
"MOOSE",
"VTK"
] | c90c3aca879e41976fd72f9c402636422deb2ab8335f2b83b76069e1cb7158c1 |
"""
GPoFM: Gaussian Process Training with
Optimized Feature Maps for Shift-Invariant Kernels
Github: https://github.com/MaxInGaussian/GPoFM
Author: Max W. Y. Lam [maxingaussian@gmail.com]
"""
import os, sys
import numpy as np
import numpy.random as npr
import matplotlib.pyplot as plt
from GPoFM import *
BEST_... | MaxInGaussian/GPoFM | examples/mnist/mnist.py | Python | bsd-3-clause | 6,279 | [
"Gaussian"
] | d86b7794a30bdf0844b7f97c3ef0c697ed7dfbc99d1b649b707898412226166d |
# -*- coding: utf-8 -*-
"""
Default Django settings. Override these with settings in the module pointed to
by the DJANGO_SETTINGS_MODULE environment variable.
"""
from __future__ import unicode_literals
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module d... | koniiiik/django | django/conf/global_settings.py | Python | bsd-3-clause | 22,073 | [
"VisIt"
] | 2e49afbd831815e0be20fe3719d804b56050cd33d3d0eb9abbf6abce996c0bf5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative sampling [1]_ [2]_.
The train... | akutuzov/gensim | gensim/models/word2vec.py | Python | lgpl-2.1 | 80,409 | [
"VisIt"
] | e23f76ea4c58d4ee0e4b819b26f05d8f0dc955a795762351c32459b1d46438a3 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import webapp2
import jinja2
import re
from google.appengine.ext import ndb
from google.appengine.ext import blobstore
from google.appengine.api import users
from google.appengine.ext.webapp import blobstore_handlers
import logging
import parsers
import headers
import os
... | westurner/schemaorg | api.py | Python | apache-2.0 | 40,150 | [
"VisIt"
] | 43b93ec7efd9e8a56626478cac80c77ba86b5d0316e35315b03524035bf85e61 |
import numpy as np
import glob
import os
import matplotlib.pyplot as plt
import corner
def load_summary(filename):
dtype=[('minr', 'f8'),
('maxr', 'f8'),
('ca_ratio', 'f8'),
('ba_ratio', 'f8'),
('a', 'f8'),
('center', 'f8'),
('width', 'f8'),
... | astroandes/AlineacionesSatelitesLG | code/asphericity_stats.py | Python | mit | 35,777 | [
"Gaussian"
] | 1511f32a392d9a5f43fe183c11493c95b390a5ebcd8b468d2a8576687a674e6c |
# -*- coding: utf-8 -*-
"""Implementation of execution-related magic functions.
"""
from __future__ import print_function
#-----------------------------------------------------------------------------
# Copyright (c) 2012 The IPython Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# ... | mattvonrocketstein/smash | smashlib/ipy3x/core/magics/execution.py | Python | mit | 51,853 | [
"VisIt"
] | e497a6297e4111a2adc6cf2b534cd2112b8d9eeb9a1626801c956832160bf3eb |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD 3 clause
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_rand... | Titan-C/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 19,173 | [
"Brian",
"Gaussian"
] | fd70ee16fc2a753bbd9fe3fd78d9d3c76f020c79b762dd6ce72d93d0e30d3680 |
#!/usr/bin/env ipython
from pylab import *
import numpy as np
import console_colors as ccl
from scipy.io.netcdf import netcdf_file
import os, sys
import matplotlib.patches as patches
import matplotlib.transforms as transforms
from numpy import array
from matplotlib.gridspec import GridSpec
import matplotlib.pyplot as p... | jimsrc/seatos | mixed/figs/sheaths.paper/src/together4.py | Python | mit | 11,024 | [
"NetCDF"
] | 740a9d178c844ff167f815016e0480b8a8791784c1e66b73058aadc95f467978 |
import logging
logger = logging.getLogger(__name__)
import operator
import os
import copy
import bisect
import pybedtools
import vcf
import json
import base64
svs_of_interest = ["DEL", "INS", "DUP", "DUP:TANDEM", "INV" ,"ITX", "CTX"]
sv_sources = ["Pindel", "BreakSeq", "HaplotypeCaller", "BreakDancer", "CNVnator",
... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/MetaSV-0.5-py2.7.egg/metasv/sv_interval.py | Python | apache-2.0 | 16,097 | [
"BWA"
] | ae3397f8d14fb91903c848fb415f1ae8406ca072b6d5c6f89bc838d72c25ff69 |
import collections
import functools
import json
import logging
import math
import typing
from pathlib import Path
from random import Random
from typing import Optional, Dict, Set, List, Tuple, Iterator, Union
import matplotlib.pyplot as plt
import networkx
from PySide2 import QtWidgets
from PySide2.QtCore import Qt
fr... | henriquegemignani/randovania | randovania/gui/tracker_window.py | Python | gpl-3.0 | 38,307 | [
"BLAST"
] | 26172f0d6a0f2a6e4079a37e5cd60576bea317bbc448eb7b6380b1ff78c3d982 |
# vi:sts=4:sw=4:et
"""Code for parsing OpenEmbedded license strings"""
import ast
import re
from fnmatch import fnmatchcase as fnmatch
def license_ok(license, dont_want_licenses):
""" Return False if License exist in dont_want_licenses else True """
for dwl in dont_want_licenses:
# If you want to excl... | Brainbuster/openpli-buildumgebung | openembedded-core/meta/lib/oe/license.py | Python | gpl-2.0 | 7,781 | [
"VisIt"
] | 058c3c496c15143a3a121964720a768a2a576501ec71b2b2f9059d90867dcd8b |
#!/usr/bin/env python
#from sumatra.projects import load_project
#from sumatra.parameters import build_parameters
#from sumatra.decorators import capture
from ruffus import *
import sys
import os
import time
import datetime
import drmaa
from omics_pipe.utils import *
from omics_pipe.parameters.default_parameters imp... | adammaikai/OmicsPipe2.0 | omics_pipe/WES_GATK_report.py | Python | mit | 3,854 | [
"BWA"
] | cbfd551fe468d4c83fe87d189f0fe6db7d79e69be9853d4976f55fdba1f6a0a6 |
"""
Data structure for 1-dimensional cross-sectional and time series data
"""
from __future__ import annotations
from io import StringIO
from shutil import get_terminal_size
from textwrap import dedent
from typing import (
IO,
TYPE_CHECKING,
Any,
Callable,
Hashable,
Iterable,
Literal,
S... | gfyoung/pandas | pandas/core/series.py | Python | bsd-3-clause | 169,090 | [
"Elk"
] | 09e85904d66d8027a38e7a5e799db78785b805865cc70cf78d962358c02f0ac3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# we set up default information for our locale.
# Translators should use this file as the basis of their translation.
# Copy this file and rename it for you locale.
#
# For example, Spanish uses:
# defaults_es.py
#
# British English uses:
# defaults_en_GB.py
#
# Please fill in ... | Linutux/Gourmet | gourmet/defaults/defaults_fr.py | Python | gpl-2.0 | 68,262 | [
"FLEUR",
"Octopus"
] | a511816655987b746a9b62e49dd5d3cf60508c3525e293d52af3c26d245a97ce |
"""Python wrapper for Google web APIs
This module allows you to access Google's web APIs through SOAP,
to do things like search Google and get the results programmatically.
Described here:
http://www.google.com/apis/
You need a Google-provided license key to use these services.
Follow the link above to ge... | mikemintz/neutron | modules/google.py | Python | gpl-2.0 | 17,239 | [
"VisIt"
] | 610c0d443d34d46c83f6a45a91f99e45fe594e5ade2ae9144562480579fbc3c0 |
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
import requests
BASE_URL = "http://espncricinfo.com"
SUMMARY_URL = BASE_URL + "/netstorage/summary.json"
MATCH_URL = lambda match_url: BASE_URL + match_url[:-5] + ".json"
class espn_scrap:
def __init__(self):
# for maintaing list of... | Steindi01/handball-score-applet | cricket_score_indicator/espn_scrap.py | Python | gpl-3.0 | 14,270 | [
"BLAST"
] | a1e3f879eaba740ecb441fa81391b17b096a3a85d7e37e5faf39891c0194e0f6 |
# Copyright 2010 - 2013, Qualcomm Innovation Center, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | dpauls/OpenMAMA | site_scons/site_tools/javadoc.py | Python | lgpl-2.1 | 5,204 | [
"VisIt"
] | c8a6a6c92e99712616af7dbbce4d451baa3f555126b8b3a3ff4a2fe61d91d17b |
# Copyright (c) 2013-2015 Siphon Contributors.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""Test parsing of metadata from a TDS client catalog."""
import logging
import xml.etree.ElementTree as ET # noqa:N814
from siphon.metadata import _ComplexTypes, _SimpleT... | Unidata/siphon | tests/test_metadata.py | Python | bsd-3-clause | 24,339 | [
"NetCDF"
] | 01b974e39dfa9767237d37044e932a7e95380725a80b90f63942974861c95c73 |
#!/usr/bin/env python
#
# Copyright 2012 the V8 project authors. 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 code must retain the above copyright
# noti... | zero-rp/miniblink49 | v8_5_1/tools/presubmit.py | Python | apache-2.0 | 16,193 | [
"VisIt"
] | 1ff6fb81c0e38ad4af9d4bbd504958424912f84fdfbc75b180f17346f72d24a0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
en = pylid.PyLID(3)
en.total_ngrams = 276465487
en.lang = 'en'
en.ngrams = Counter({
u'#th': 5558910,
u'the': 4533496,
u'he#': 3711446,
u'on#': 1965108,
u'ion': 1964537,
u'#of': 1785037,
u'#to': 1782... | dmort27/pylid | pylid/langs/en.py | Python | mit | 245,654 | [
"ADF",
"ASE",
"BWA",
"EPW",
"Elk",
"MOE",
"xTB"
] | 49bb4a068e14f58dee8ffd3713f668baa45f1806b1df5011afe3361093b9a525 |
"""
Created on 14 Aug 2013
@author: thom
"""
from rdkit.Chem import AllChem as Chem
class DefaultChemistry(object):
"""A simple Chemistry based on real-world chemistry."""
def __init__(self, parameters=None):
""":param parameters: Parameters object"""
# Single : 77.7 = 777.1/10 = 104.2 + ... | th0mmeke/toyworld | chemistry_model/default_chemistry.py | Python | gpl-3.0 | 5,522 | [
"RDKit"
] | 12937cf28d808c1c1b31b049943437f21f6e9178c3b4487d42ed50f1bf8d4fa2 |
"""The loans database.
This module manages saving the loans into files and reading them back.
"""
import datetime
import pathlib
import json
import firefly
def get_loans():
"""Returns all the existing loans.
"""
path = pathlib.Path("loans")
path.mkdir(exist_ok=True)
loans = []
for p in path.g... | amitkaps/full-stack-data-science | credit-risk-deploy/webapp/loansdb.py | Python | mit | 1,768 | [
"Firefly"
] | 2d789894cbb8c5ce9f5e4ce8fa71697e6c6a74e523f8356f9477f206c3ce31c5 |
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import numpy as np
import numpy.polynomial.polynomial as poly
from scipy.special import erf
import warnings
def erfint(x):
"""
Integral of the error function.
Parameters
----------
x : float or array
Argument.
Returns
------... | MassimoCimmino/pygfunction | pygfunction/utilities.py | Python | bsd-3-clause | 24,189 | [
"Gaussian"
] | 563a1c033dc29e5b04327d10f1da62fe81f8e715f144be99e8f7fb07320fb14a |
"""
Support code for the freedesktop.org basedir spec.
This module provides functions for locating configuration files.
@see: U{http://freedesktop.org/wiki/Standards/basedir-spec}
@var home: The value of $HOME (or '/' if not set). If we're running as root and
$HOME isn't owned by root, then this will be root's home ... | dabrahams/zeroinstall | zeroinstall/support/basedir.py | Python | lgpl-2.1 | 5,002 | [
"VisIt"
] | 6a015bbe9d84fe5827f414c2ec643469163bb04986688bbe90c0bf4b3b56b63e |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/shortstack/package.py | Python | lgpl-2.1 | 1,944 | [
"Bowtie"
] | 5eb69b0c2ec79dd57367750655ec1cfeaa85f803c6c4835b75649976e4550154 |
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