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 |
|---|---|---|---|---|---|---|---|
from __future__ import division
from collections import defaultdict
from rdkit.Chem import HybridizationType
from rdkit.Chem.rdMolDescriptors import CalcFractionCSP3
from ._base import Descriptor
__all__ = ("CarbonTypes", "HybridizationRatio", "FractionCSP3")
class CarbonTypesBase(Descriptor):
__slots__ = ()
... | mordred-descriptor/mordred | mordred/CarbonTypes.py | Python | bsd-3-clause | 3,502 | [
"RDKit"
] | e36ade5a9ecd94b88102c6b938c46aff02634664b746029252640633cfc2bcce |
#!/usr/bin/env python
"""
Program to automatically print out CFS pager feeds.
Copyright 2010 - 2015 Michael Farrell <http://micolous.id.au/>
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 ver... | micolous/cfsprinter | src/pagerprinter/pagerprinter.py | Python | gpl-3.0 | 5,037 | [
"ASE"
] | eab89b31bc8bff6a5a149fef137b36f28c6d7b4d8c5dba1259e3cc09ee400c2f |
#!/usr/bin/env python3
import abc
import torch
from ..distributions import MultivariateNormal
from ..lazy import CholLazyTensor, TriangularLazyTensor
from ._variational_distribution import _VariationalDistribution
class _NaturalVariationalDistribution(_VariationalDistribution, abc.ABC):
r"""Any :obj:`~gpytorch... | jrg365/gpytorch | gpytorch/variational/natural_variational_distribution.py | Python | mit | 6,153 | [
"Gaussian"
] | 15b75665fd1af360a42a34e7d45712cf4bece1aebf73f60a5fa925a95cd3f531 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2005 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012,2017 Paul Franklin
# Copyright (C) 2014 Nick Hall
#
# This program... | dermoth/gramps | gramps/gui/plug/report/_styleeditor.py | Python | gpl-2.0 | 24,387 | [
"Brian"
] | bafd103e81250cd76b3eb41530a602a81beef3fb57d3ade1c5f978987043e9e2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# 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 Licen... | andreaso/ansible | lib/ansible/modules/system/runit.py | Python | gpl-3.0 | 9,044 | [
"Brian"
] | a10b0b94803d070adc09bb07705934c38f55c3858cb448b5a3f6292e6cef3aa1 |
"""
This is a procedural interface to the matplotlib object-oriented
plotting library.
The following plotting commands are provided; the majority have
MATLAB |reg| [*]_ analogs and similar arguments.
.. |reg| unicode:: 0xAE
_Plotting commands
acorr - plot the autocorrelation function
annotate - annotate som... | lthurlow/Network-Grapher | proj/external/matplotlib-1.2.1/lib/matplotlib/pylab.py | Python | mit | 11,780 | [
"Gaussian"
] | 62d0d331cba85beb2444d7befbfdae04ee2377c3c736200d8a95a7988fcf5333 |
import sys
import os.path
import argparse
import sqlite3
import ast
import locale
import codecs
TERM_ENCODING = locale.getdefaultlocale()[1]
VERSION = '0.4dev'
def execute_sql(conn, sql, params):
cur = conn.cursor()
try:
cur.execute(sql, params)
conn.commit()
except sqlite3.OperationalErr... | baverman/mpd-tag | mpd_tag.py | Python | mit | 8,783 | [
"VisIt"
] | 768a721783a9f85f0bdc3b8667232989fca8601051a8f75bc6bc201617393cde |
# -*- coding: utf-8 -*-
"""
E2E tests for the LMS.
"""
from unittest import skip
from .helpers import UniqueCourseTest, load_data_str
from ..pages.lms.auto_auth import AutoAuthPage
from ..pages.lms.find_courses import FindCoursesPage
from ..pages.lms.course_about import CourseAboutPage
from ..pages.lms.course_info im... | yokose-ks/edx-platform | common/test/acceptance/tests/test_lms.py | Python | agpl-3.0 | 15,062 | [
"VisIt"
] | fdd0bcaee02e6d641d8a63225e44cd9e04e2a874b41922c6f66a60e49953dd26 |
#!/usr/bin/env python
## category RNA-seq
## desc Finds regions of unusual deletions (CLIP-seq)
## experimental
"""
Finds regions of unusual deletions (CLIP-seq)
Given a set of BAM files, we search for areas where there are an unusual
amount of deletions. For CLIP-Seq, this can be an indicator of the location
of prot... | ngsutils/ngsutils | ngsutils/bam/cims.py | Python | bsd-3-clause | 8,325 | [
"pysam"
] | 8d92591c4ceb0369ace73beaf46cef313a0bf6e947a52b95bf636c4f353bc59f |
from __future__ import division, print_function
import abc
import numpy as np
from menpo.transform import Scale, AlignmentSimilarity
from menpo.model.pdm import PDM, OrthoPDM
from menpo.transform.modeldriven import ModelDrivenTransform, OrthoMDTransform
from menpo.fit.regression.trainer import (
NonParametricRegr... | jabooth/menpo-archive | menpo/fitmultilevel/sdm/trainer.py | Python | bsd-3-clause | 14,535 | [
"Gaussian"
] | 44ba0f9e25b9aea8b886f48980cd526d5bc0a74bfdc4ea7a58baad7d5865fb98 |
"""
IO for ADF files.
"""
from pymatgen.core.structure import Molecule
from monty.json import MSONable
import re
import os
from monty.itertools import chunks
from monty.io import reverse_readline
__author__ = 'Xin Chen, chenxin13@mails.tsinghua.edu.cn'
def is_numeric(s):
"""
Return True is the string ``s``... | gVallverdu/pymatgen | pymatgen/io/adf.py | Python | mit | 31,771 | [
"ADF",
"Gaussian",
"NWChem",
"pymatgen"
] | babd8eb46b751c4c2bd4d9412072357ea05432f3f70eb73cd5018c096d0a478a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# lsresowners - simple list of resource owners for a resource with access
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the term... | heromod/migrid | mig/shared/functionality/lsresowners.py | Python | gpl-2.0 | 3,190 | [
"Brian"
] | 49769199ac604e8ba0a9a03e20cc32d8ba64a2ce0ca4b93e7217815b1f9246c0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | pmghalvorsen/gramps_branch | gramps/gen/plug/menu/_enumeratedlist.py | Python | gpl-2.0 | 4,029 | [
"Brian"
] | e029e68b33dd13ca4187bbfc5d4bb599eefcbce7ddffe8ae3d554ca10c03191d |
# Copyright (C) 2007-2011 Franco M. Luque
# URL: <http://www.cs.famaf.unc.edu.ar/~francolq/>
# For license information, see LICENSE.txt
# util.py: Some utilities, mainly for serialization (pickling) of objects.
import os
import pickle
import sys
import nltk
obj_basedir = 'lq-nlp-commons'
def write_file(filename,... | davidswelt/dmvccm | lq-nlp-commons/util.py | Python | gpl-3.0 | 5,462 | [
"VisIt"
] | a7af99a335557ccfc992f09eb3bc24d4ca332894eb2a2f2cb1c6ed3d44cecb38 |
##
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/d/dirac.py | Python | gpl-2.0 | 5,945 | [
"DIRAC"
] | 29bc5602596cc7e468a76b2a3a1ef33fc04ec7eab6434a40d7a7d32eb71b9c63 |
# This file contains all the possible names used in toon name generation.
# Each name has a unique id and a category:
# 0 - boyFirst
# 1 - girlFirst
# 2 - neutralFirst
PETNAMES = '''0*0*Achilles
1*0*Adolfo
2*0*A... | silly-wacky-3-town-toon/SOURCE-COD | toontown/pets/PetNamesEnglish.py | Python | apache-2.0 | 38,924 | [
"Bowtie",
"ESPResSo",
"Galaxy",
"Jaguar",
"MOE",
"MOOSE",
"NEURON"
] | 67b8bd3d3d09e8522b5bfbfb9635fb5f98d8f2d2d952d6820d7eb872f7f97478 |
"""
Save per-interface and per-feed configuration information.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from xml.dom import minidom, XMLNS_NAMESPACE
from zeroinstall.support import basedir
from zeroinstall.injector import model
from zeroinst... | timdiels/zeroinstall | zeroinstall/injector/writer.py | Python | lgpl-2.1 | 2,305 | [
"VisIt"
] | 93c93c9df4853d6945576bcf7205cee99b0e1e0164afc650842c49f938b7ee10 |
from cardboard import types
from cardboard.ability import (
AbilityNotImplemented, spell, activated, triggered, static
)
from cardboard.cards import card, common, keywords, match
@card("Hidetsugu's Second Rite")
def hidetsugus_second_rite(card, abilities):
def hidetsugus_second_rite():
return Ability... | Julian/cardboard | cardboard/cards/sets/saviors_of_kamigawa.py | Python | mit | 37,555 | [
"VisIt"
] | ef2043c4b93cc50649e65aace12b2a9ec70459cb5b1913d27d29cce7872361c7 |
#!/usr/bin/env python
#
# Perform PRS calculations given and MD trajectory and a final state
# co-ordinate file
#
# Script distributed under GNU GPL 3.0
#
# Author: David Penkler
# Date: 17-11-2016
import sys, argparse
import numpy
import mdtraj as md
from math import log10, floor, sqrt
from lib import sdrms
from ... | RUBi-ZA/MD-TASK | prs.py | Python | gpl-3.0 | 9,080 | [
"MDTraj"
] | 42ca1a0f147e25af1c5b6a76ce2c7a4da3428483a6c8b027809c9b849905f27f |
"""
:copyright: (c) 2014 Building Energy Inc
:license: see LICENSE for more details.
"""
import random
from django.contrib.webdesign import lorem_ipsum
import datetime
import base64
from decimal import getcontext, Decimal
getcontext().prec = 7
from localflavor.us.us_states import STATE_CHOICES
from seed.test_helpers.fa... | buildingenergy/buildingenergy-platform | seed/test_helpers/factory/helpers.py | Python | apache-2.0 | 21,921 | [
"Amber",
"Brian",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Desmond",
"FLEUR"
] | 902ae5e00919a02254fe01b1c14ccace5ead2beb5b06bb2dfe6f4ec3c1576161 |
#!/usr/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Pipeline
========
Utility functions to help setting up Yank configurations.
"""... | choderalab/yank | Yank/pipeline.py | Python | mit | 116,266 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NetCDF",
"OpenMM"
] | ab34eaadcf4e3dccc17851771253c3560e6c3e405ecdce54e713cbd5ac4977ac |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Classes and tools for storing and handling parsed data"""
import logging
from collections import namedtuple
... | berquist/cclib | cclib/parser/data.py | Python | bsd-3-clause | 23,991 | [
"Gaussian",
"cclib"
] | 8b762136df15b0e133b07cc1a1069dc99f02fa4703cc9a1c0647204ca64c55e2 |
MIME_TYPE_DEFAULT = 'text/html'
MIME_TYPE_DICT = {
'.3gp': 'video/3gpp',
'.aab': 'application/x-authoware-bin',
'.aam': 'application/x-authoware-map',
'.aas': 'application/x-authoware-seg',
'.ai': 'application/postscript',
'.aif'... | ycroft/XPHENIX | source/ant/controller/mime_type.py | Python | gpl-3.0 | 18,867 | [
"Gaussian",
"MOPAC",
"NetCDF",
"VMD"
] | 8ef0738df7d329eb56afce806fd7719e47dea103a58a009e2eee7ee5526628b6 |
#!/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 | python/peacock/Execute/TerminalTextEdit.py | Python | lgpl-2.1 | 2,291 | [
"MOOSE"
] | 30b25b632db412a8f67185a853b0591bd75c0005d5659a1878367d8befece529 |
# from matplotlib.colors import LogNorm
# import matplotlib.pyplot as plt
# import numpy as np
import pandas as pd
from root_pandas import read_root
import sys
# from itertools import islice
# MY LIBS
import mie_utils as my
file_name = sys.argv[1]
crystal_name = sys.argv[2]
run_number = sys.argv[3]
particle_name = s... | f-forcher/crystal-channeling-analysis | save_as_hdf_goniocut.py | Python | gpl-3.0 | 2,407 | [
"CRYSTAL"
] | 7f1fd30181f5a271791e938b8764d29cba88a11e39ccd8cf50098b90bf702b3c |
"""
Sample Mayavi customization file.
This code is not to be executed as `mayavi2 -x user_mayavi.py` or
`python user_mayavi.py`.
Put this file in ~/.mayavi2/user_mayavi.py and rerun mayavi2 to see what
it does -- the worker view may not show up by default so you will have
to go to View->Other and in the Show View dia... | dmsurti/mayavi | examples/mayavi/user_mayavi.py | Python | bsd-3-clause | 9,815 | [
"Mayavi"
] | 22abdcd9f3b9f4bd889b6f60da1acecd6b4c7c8b5bf20b245a23d5608b97ef4c |
########################################################################
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/12/11 18:04:25
########################################################################
""" :mod: SubprocessTests
=======================
.. module: SubprocessTests
:synopsis: uni... | yujikato/DIRAC | src/DIRAC/Core/Utilities/test/Test_Subprocess.py | Python | gpl-3.0 | 1,565 | [
"DIRAC"
] | ce0dfef92e278b2c564c1adb48c6b8f6761a9ed6592739981c76623e3c6672a7 |
import collections
import copy
import warnings
import numpy
import six
from chainer import cuda
from chainer import link as link_module
from chainer import serializer as serializer_module
from chainer import variable
def _sum_sqnorm(arr):
sq_sum = collections.defaultdict(float)
for x in arr:
with cu... | ysekky/chainer | chainer/optimizer.py | Python | mit | 26,435 | [
"Gaussian"
] | 302aff72da7906a77dbe5770f33963ab77865008137562b5f0e5187d549cce2f |
""" demixed Principal Component Analysis
"""
# Author: Wieland Brendel <wieland.brendel@neuro.fchampalimaud.org>
#
# License: BSD 3 clause
from __future__ import print_function
import numpy as np
from collections import OrderedDict
from itertools import combinations, chain
from scipy.sparse.linalg import svds
from s... | machenslab/dPCA | python/dPCA/dPCA.py | Python | mit | 40,570 | [
"NEURON"
] | feb9d0408371729a58d519b13483f80e0788df70e1230e56f84514359be1e64c |
from bs_utils.utils import *
import re
BAM_MATCH = 0
BAM_INS = 1
BAM_DEL = 2
BAM_SOFTCLIP = 4
CIGAR_OPS = {'M' : BAM_MATCH, 'I' : BAM_INS, 'D' : BAM_DEL, 'S' : BAM_SOFTCLIP}
def N_MIS(r,g):
mismatches = 0
if len(r)==len(g):
for i in xrange(len(r)):
if r[i] != g[i] and r[i] != "N" and g[... | BSSeeker/BSseeker2 | bs_align/bs_align_utils.py | Python | mit | 13,972 | [
"Bowtie"
] | bc8bdd0e938b2846bb8241a9aee9e34a92ed180fd5d2637f838ccfb21358c849 |
# -*- coding: utf-8 -*-
import mds.math
import mds.ordered_set
class Convention(object):
@staticmethod
def convention_names(
dataset):
result = []
for attribute_name in ["Conventions", "conventions"]:
if hasattr(dataset, attribute_name):
names = getattr... | jfrygeo/solutions-geoprocessing-toolbox | suitability/toolboxes/scripts/MultidimensionSupplementalTools/MultidimensionSupplementalTools/Scripts/mds/netcdf/convention/convention.py | Python | apache-2.0 | 9,216 | [
"NetCDF"
] | 267f93361ff2e89ed511d35f2d05234d6a6db93d3f1697ca8025723aa4d6d228 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/interaction/PotentialUniqueDist.py | Python | gpl-3.0 | 4,000 | [
"ESPResSo"
] | 73360e5ef89890df541a9a594d43133b17902b83ecf5b768d807fb6dd08ebb1c |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import copy
import json
import os
import py... | s-hertel/ansible | test/units/galaxy/test_collection_install.py | Python | gpl-3.0 | 43,229 | [
"Galaxy"
] | 20f7d78462c72319aa4942702803aafc3efc5c8a308072941171f9dd870e9f92 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | huikang/vCSIMx86_qemu | scripts/qapi-types.py | Python | gpl-2.0 | 6,861 | [
"VisIt"
] | e18cff55adbf9e1c072942cafddac401477f9ba7fd44b75013b566f452369b58 |
# -*- coding: utf-8 -*-
# Copyright 2017 Zachary Marv (马子昂)
#
# 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... | pkumza/LibRadar | LibRadar/dex_tree.py | Python | apache-2.0 | 17,703 | [
"VisIt"
] | e98a2f69929b929010d52ee5668966d91e76878339551f535aa07ac9aa3218b1 |
#
# @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
#... | susilehtola/psi4 | psi4/driver/diatomic.py | Python | lgpl-3.0 | 11,347 | [
"Psi4"
] | 1d83271db4cf5c5c6967b7331becc68df056db30cec2574a871bffad4ca4c801 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/Parameter.py | Python | gpl-3.0 | 4,672 | [
"ORCA"
] | 3e5a0d3462f1a94c73321cf25db1bcef24996b8f1ba4d54137091325345d73d1 |
# -*- coding: utf-8 -*-
"""URLs for geomat project"""
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.contrib.staticfiles.storage import staticfiles_storage
from django.views import defaults as default_vi... | GeoMatDigital/django-geomat | config/urls.py | Python | bsd-3-clause | 3,181 | [
"VisIt"
] | bfa5e1b6e4fa9ddbc2ebdfe40cce0794553253755d1d709391cb728210274296 |
from collections.abc import Sized, Iterable
from . import ast
class Selection(Sized, Iterable):
def __init__(self, nodes):
self.selection = nodes
def __iter__(self):
return iter(self.selection)
def __len__(self):
return len(self.selection)
def __getitem__(self, item):
... | kyouko-taiga/tango | tango/utils.py | Python | apache-2.0 | 1,562 | [
"VisIt"
] | 1c80a0486cae2a4b03c144b4bc7a843a08be5d38f40004d6f1e3fb2bc3dc8ccf |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | samples/h5md.py | Python | gpl-3.0 | 1,917 | [
"ESPResSo"
] | 31f0f930338821f0c6fb06d19e7b5bedc11238f278c6662c36454fac1037a47e |
#!/usr/bin/env python
# encoding: utf-8
'''
Word transformation.
Transforms words from singular to plural, class names to table names,
modularized class names to ones without, and class names to foreign keys.
Inflection is language specific and the default `inflection` handles English
language inflection. You can ac... | rsms/smisk | lib/smisk/inflection/__init__.py | Python | mit | 11,020 | [
"Octopus"
] | 6c62df1a71937736779868e24deffcb2fdc2face4eced7e8d0c87512ec61203d |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, cint, nowdate, add_days, get_link_to_form
from frappe import ... | StrellaGroup/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | gpl-3.0 | 37,262 | [
"VisIt"
] | be47042e4601e6dd73736994545c66eada945b644a6c36e1533e2294318c3ab6 |
# -*- coding: utf-8 -*-
##############################################################################
# 2014 E2OpenPlugins #
# #
# This file is open source software; you can redistribute... | mickeyreg/e2openplugin-OpenWebif | plugin/controllers/models/owibranding.py | Python | gpl-3.0 | 19,849 | [
"Galaxy"
] | bdb283cfa907df12491fe4b6002b02dd169f245b22055ea9942b35e333bbb2d7 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor-common | remindor_common/database.py | Python | gpl-3.0 | 21,951 | [
"Brian"
] | 25073b18441c7922defba4c10aadafce643e91135d336cead528c7992948b669 |
from copy import deepcopy
from block import Block
from comment import Comment
from filter import Filter
from helpers.base_types_and_classes import atlas_bases, gg_es_bases, gg_spell_bases, jewellery, good_spell_bases, \
good_armour_bases, gg_phys_bases, good_phys_bases, gg_atlas_bases, other_atlas_bases, melee_onl... | teuneboon/PoEFilter | examples/new_xai_filter.py | Python | mit | 32,201 | [
"Amber",
"CRYSTAL"
] | cb342ab3d8db191411e44f738c4716dfb636589a47a4ccef8b2bb0808f52f809 |
#!/usr/bin/env python -Es
"""
Script to set up a custom genome for bcbio-nextgen
"""
from __future__ import print_function
from argparse import ArgumentParser
import collections
import gzip
import os
from Bio import SeqIO
import toolz as tz
from bcbio.utils import safe_makedir, file_exists, chdir, is_gzipped
from bcb... | a113n/bcbio-nextgen | scripts/bcbio_setup_genome.py | Python | mit | 15,182 | [
"Galaxy"
] | 3ee490fe80f04c973d03cc6c7ac922eca6e8bc0dfec8ef526240f0f8e755074e |
""" A generic client for creating productions
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.API import API
class Production(API):
""" Contains methods to build a production on the client, before it's actually added to the Production System
"""
def __init__(self, **kwar... | petricm/DIRAC | ProductionSystem/Client/Production.py | Python | gpl-3.0 | 1,095 | [
"DIRAC"
] | c8a4d1ef65d84093df4eb79f5188e2c45a2486e21e396d40ccf5a72087e601d1 |
# Monte Carlo Localisation
import prob_motion_model as pmm
#import hokuyo
import random
import numpy as np
import matplotlib.pyplot as plt
import time
import socket
import copy
import ttest
import math
from serial.tools import list_ports
import serialWrapper
import packetBuilder
import packetParser
import traceback
#... | redarmy30/Eurobot-2017 | old year/RESET-master/CommunicationWithRobot/localisation2.py | Python | mit | 9,722 | [
"Gaussian"
] | 353431dfcea443108fe36a2822266f5a71e4bb5daeb607d34db9ac68cfe7dfc7 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | R-Lefebvre/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 60,196 | [
"CRYSTAL"
] | c4bbc7359d834386a868d216870702cd4e0d4ffabe110489a50ecd439dfad69d |
#!/usr/bin/python
# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | google/myelin-acorn-electron-hardware | cpu_socket_expansion/pcb/cpu_socket_expansion.py | Python | apache-2.0 | 17,964 | [
"CRYSTAL"
] | d53dcfdab4813cc9f9f7048ba17bbcecbd8c72aceb1a5d89af2d7268685f02cb |
# Copyright 2018 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 agreed to in writing, ... | mlperf/training_results_v0.5 | v0.5.0/intel/intel_minigo_submission_public_tensorflow/code/minigo/tensorflow/minigo/strategies.py | Python | apache-2.0 | 10,535 | [
"VisIt"
] | baa8f55dfb3a2d521404aef4b0c25b52a7291468b4ca89788fb1a721bc9fbf5a |
#!/usr/bin/env python
####################################################################################
#
# This script reads the input src free image and put fake galaxies and point sources on it.
# This script heavily relies on the demo provided in GalSim package.
#
###############################################... | inonchiu/ComEst | comest/SrcPlacer.py | Python | mit | 78,803 | [
"Galaxy",
"Gaussian"
] | e3a6496d58a5efede203e3cb09c0e9725e6944cd1d3434ddeb71a421f8ca9e90 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/esutil/UniformOnSphere.py | Python | gpl-3.0 | 1,464 | [
"ESPResSo"
] | b681cd48c900af33c72979e35fdfc2458f1bcf66163b6e8dca5ecf0260be7f76 |
"""
Light Actors
~~~~~~~~~~~~
Positional lights in PyVista have customizable beam shapes, see the
:ref:`ref_light_beam_shape_example` example. Spotlights are special in
the sense that they are unidirectional lights with a finite position,
so they can be visualized using a cone.
This is exactly the purpose of a ``vtk.... | akaszynski/vtkInterface | examples/04-lights/actors.py | Python | mit | 2,810 | [
"VTK"
] | 5c0bcfb596cd9a2ca3d4ee5dc8791817000b9eb2fe579132dda94f66f3cfcee5 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0001_nao.py | Python | apache-2.0 | 2,947 | [
"PySCF"
] | ae0b261f84e922e2849d88115dc686f1a48f2f11c3d9e24992b992914f80f3fc |
"""Learn to estimate functions from examples. (Chapters 18-20)"""
from .utils import (
removeall, unique, product, argmax, argmax_random_tie, isclose,
dotproduct, vector_add, scalar_vector_product, weighted_sample_with_replacement,
weighted_sampler, num_or_str, normalize, clip, sigmoid, print_table, DataFi... | andres-root/AIND | Therm1/Planning/Project/aimacode/learning.py | Python | mit | 35,994 | [
"NEURON"
] | 7dacb8892de3ce6f4c861c98ffcaea3b326168374c844c6be19dd2a84a1b44e1 |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
A Neurongrouper
"""
#<DefineAugmentation>
import ShareYourSystem as SYS
BaseModuleStr="ShareYourSystem.Specials.Simulaters.Simulater"
DecorationModuleStr="ShareYourSystem.Standards.Classors.C... | Ledoux/ShareYourSystem | Pythonlogy/draft/Simulaters/Neurongrouper/__init__.py | Python | mit | 7,319 | [
"Brian"
] | 47fcd492b9d3c07994c8e4f753d6e49434ee7dff848dd8266055c6b3ff2dc431 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008-2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/gui/editors/paymentcategoryeditor.py | Python | gpl-2.0 | 4,450 | [
"VisIt"
] | b7321b7a80b9a86a3d0339eff4dcfd6ff96564305824917cde5fec1bdafc0fd4 |
#! /usr/bin/env python
"""
Module containing functions for cubes frame registration.
"""
__author__ = 'C. A. Gomez Gonzalez, V. Christiaens, G. Ruane, R. Farkas'
__all__ = ['frame_shift',
'cube_shift',
'frame_center_radon',
'frame_center_satspots',
'cube_recenter_satspots'... | vortex-exoplanet/VIP | vip_hci/preproc/recentering.py | Python | mit | 72,782 | [
"Gaussian"
] | 5d5d5baf5efe413e7bf991c1d5694fe919e281ae4a65a0d65173f37829e35c45 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/navpane2.py | Python | gpl-2.0 | 8,619 | [
"VisIt"
] | b2114f74e15e636a1b82fd99ebdf56e4607a75b29da9973abd0c308e0fdeccc3 |
# Copyright 2016 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... | mengxn/tensorflow | tensorflow/contrib/factorization/python/ops/gmm_ops.py | Python | apache-2.0 | 20,164 | [
"Gaussian"
] | adafd6a94af81db61f8361075262b6b96431a1024036c25abc3e3a8d384529eb |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | maintainer/benchmarks/p3m.py | Python | gpl-3.0 | 8,176 | [
"ESPResSo"
] | b3e7a65c2d008f4dc8c9ab3c1fb8f08240fd123fa892a310eec6cfd06cd8cfb6 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/gui/editors/producteditor.py | Python | gpl-2.0 | 20,617 | [
"VisIt"
] | b4ecdfb741cbefb6a2bf60a10e81620930b422eb9467502f4b13c3c5a0b0cc1d |
# coding: utf8
Paises=(
(4, 'AF', 'AFG', 93, 'Afganistán', 'Asia', '', 'AFN', 'Afgani afgano'),
(8, 'AL', 'ALB', 355, 'Albania', 'Europa', '', 'ALL', 'Lek albanés'),
(10, 'AQ', 'ATA', 672, 'Antártida', 'Antártida', '', '', ''),
(12, 'DZ', 'DZA', 213, 'Argelia', 'África', '', 'DZD', 'Dinar algerino'),
(16, 'AS', 'ASM', ... | jredrejo/bancal | web2py/applications/bancal/modules/paises.py | Python | gpl-3.0 | 18,468 | [
"BWA"
] | 8a44c74b8b79dd6dd5871e988c54df637a6b7ce55741004d6e1c03c9fd543307 |
#!/usr/bin/env python
import sys
import http.client
import requests
import glob, os
import os.path, time, datetime
import re
class CodeSync:
ErrorCounter = 0
Executed = []
def query(server, port, uri, projects):
conn = http.client.HTTPConnection(server, port)
conn.request("bGET", uri)
... | alessandromaggio/codesync | client/codesync.py | Python | gpl-3.0 | 11,269 | [
"VisIt"
] | e3629db03eef3af8b377711f451f26b0058f8efcac1feba00c2909a41e7e1c38 |
import scipy.stats
import numpy
def poly_transform(u):
v = numpy.copy(u)
v[0] = 10**(v[0]*10 - 5)
v[1:] = 20*v[1:] - 10
return v
class PolyModel(object):
"""
A gaussian (or other) distribution of width 'syserror' around a polynomial
of the given degree.
degree = 1:
y is distributed independently of x.
... | JohannesBuchner/syscorr | syscorr/poly.py | Python | agpl-3.0 | 1,405 | [
"Gaussian"
] | 62ca768bf40662b0066c94a5010faf4db4ecc319a79a558346d7ca1ef8b0b621 |
import json
import requests
from django.conf import settings
from django.db.models.signals import post_save, pre_delete, post_delete
from django.dispatch import receiver
from karrot.conversations.models import Conversation
from karrot.groups import roles, stats
from karrot.groups.emails import prepare_user_became_edi... | yunity/yunity-core | karrot/groups/receivers.py | Python | agpl-3.0 | 4,447 | [
"VisIt"
] | a776caa2a6a0c03650cc380fb83bfc5edc66fb9d2385ea0d5afabe9c40dd8eff |
# -*-python-*-
#
# Copyright (C) 1999-2006 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | foresthz/fusion5.1 | www/scm/viewvc/lib/idiff.py | Python | gpl-2.0 | 5,475 | [
"VisIt"
] | 07b26cc410fd10a707d66313e639697858fbc589509e44b59e397d6dd87ce07f |
# -*- 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-datastream | tests/unit/gapic/datastream_v1/test_datastream.py | Python | apache-2.0 | 295,710 | [
"Octopus"
] | 7ccb006918d32b21f2f7b5a76f662c58fe0378e01ca3017f515a46d043749d20 |
# -*- coding: utf-8 -*-
"""Tests for PyBEL-Tools."""
| pybel/pybel-tools | tests/__init__.py | Python | mit | 54 | [
"Pybel"
] | a9981d19a53a9bba2d376711fa9016aa6e878f7d0ccae04ed685bd1ec3725d36 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 4 20:44:24 2016
@author: ddboline
"""
from __future__ import (absolute_import, division, print_function, unicode_literals)
import os
import re
import datetime
from subprocess import call, Popen, PIPE
HOMEDIR = os.getenv('HOME')
HOSTNAME = os.uname... | ddboline/movie_collection_app | movie_collection_app/util.py | Python | mit | 6,774 | [
"EPW"
] | 66a6c30d9540d054b65b4365f4c5f2aef659cf821da565f12939b7e999813984 |
#! /usr/local/bioinfo/python/3.4.3_build2/bin/python
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
import pandas as pd
import argparse
def importBlastOutput():
'''
Import Blast output using pandas read_csv.
Pandas dataframe will used to make a lis... | 3nrique0/Tools_for_Bioinformatics | extract_fasta_from_blast/4_extract_genomic_sequences.py | Python | gpl-3.0 | 7,728 | [
"BLAST"
] | 4ec169490930af23490ca9935c55207e8149c4418262745455f1e63201dfd9b7 |
# -*- test-case-name: xmantissa.test -*-
# Copyright 2008 Divmod, Inc. See LICENSE file for details
"""
Public interfaces used in Mantissa.
"""
from zope.interface import Interface, Attribute
from nevow.inevow import IRenderer
class IColumn(Interface):
"""
Represents a column that can be viewed via a scroll... | twisted/mantissa | xmantissa/ixmantissa.py | Python | mit | 43,809 | [
"VisIt"
] | b49c26cb40051a861b8e9cc3b24141edb0d1f30fc60e605ac04bfb6b9ea0af9c |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy.misc.doccer import inherit_docstring_from
from scipy import optimize
from scipy import integrate
impor... | matthewalbani/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 140,183 | [
"Gaussian"
] | 8c3f85ea94f477859b74c4f10f16f96640efcb7d4ad8ea94a81998be34ed900b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from contextlib import contextmanager
from datetime import datetime
from unittest import skip
import pytest
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutP... | ahmedaljazzar/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 30,502 | [
"VisIt"
] | 64edae34943cbcf7360b480fd5a0c0ff86c83691ad7272bdca885e7a7880a645 |
"""
Tests for array_handler.py.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
import unittest
import vtk
import numpy
from tvtk import array_handler
from tvtk import tvtk_base
# FIXME: test_tvtk_base.py is in the local directory so just doi... | dmsurti/mayavi | tvtk/tests/test_array_handler.py | Python | bsd-3-clause | 16,704 | [
"VTK"
] | 0952bf2b6d78138912365fac1c40abb9d065cc414102ba7d99d284166119eb5d |
extensions = dict(
required_params=['training_frame', ('cols', "NULL")],
validate_required_params="",
set_required_params="""
parms$training_frame <- training_frame
if(!missing(cols))
parms$ignored_columns <- .verify_datacols(training_frame, cols)$cols_ignore
""",
set_params="""
# Check if user_y i... | michalkurka/h2o-3 | h2o-bindings/bin/custom/R/gen_glrm.py | Python | apache-2.0 | 6,624 | [
"Gaussian"
] | 8a28d0fe324e268f4529dc6ca1bba1b3b511f35bb2d3cf55b51c0523e6916c77 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | godfryd/pylint | lint.py | Python | gpl-2.0 | 47,174 | [
"VisIt"
] | 8e14b90c68b4a95dd3a12d9026519118bc10a5f9a7b05192484aa29b46b0b838 |
"""
Tests for Shopping Cart views
"""
import pytz
from urlparse import urlparse
from decimal import Decimal
import json
from django.http import HttpRequest
from django.conf import settings
from django.test import TestCase
from django.test.utils import override_settings
from django.core.urlresolvers import reverse
from... | UQ-UQx/edx-platform_lti | lms/djangoapps/shoppingcart/tests/test_views.py | Python | agpl-3.0 | 86,720 | [
"VisIt"
] | b448b41d3dd8de32c43e5055c10f6b3fdb35d67f63b26d2ea511155a40843c59 |
# Functions removed from main code that MAY still be useful somewhere.
# From Analyse Object
# def save_ranges(self):
# """
# Saves signal/background/transition data ranges for each sample.
# """
# if os.path.isfile(self.param_dir + 'bkg.rng'):
# f = input(('Range files al... | oscarbranson/latools | latools/latools_graveyard.py | Python | mit | 9,555 | [
"Gaussian"
] | c7ce87abb3ed43c308a49b67f8288938e2a04d0527f47dbd56c3b4e96a976b80 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013, 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public L... | Freeseer/freeseer | src/freeseer/tests/framework/config/options/test_choice.py | Python | gpl-3.0 | 2,916 | [
"VisIt"
] | 7d6d835c86b2e4dd680909c0e2a80ad678a20c06df5aecfd08b38a7f2295bc95 |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Example script that generates FEFF input files from a cif file
Remove comment # on write line to actually write files to disk
"""
import os
import argparse
from pymatgen.io.feff.se... | tschaume/pymatgen | pymatgen/cli/feff_input_generation.py | Python | mit | 2,139 | [
"FEFF",
"pymatgen"
] | 7c682ee96b3b7e03544dc3d9a07999f916340da0b0889021cf63b667318cd8ab |
import sys, numpy as np, hashlib, copy, cPickle, ctypes, os, os.path as osp
from collections import defaultdict,namedtuple
import __builtin__
import traceback
import cgt
from . import utils
# ================================================================
# Datatypes
# ================================================... | briancheung/cgt | cgt/core.py | Python | mit | 122,529 | [
"Gaussian",
"VisIt"
] | c130844a5b805239320b24d22a31038e7415bb442dc0971a63e50c9e73bbdfc6 |
import os
import sys
import errno
import argparse
from subprocess import call, PIPE, Popen
HOME_DIR = os.environ.get('HOME')
def install_pysimm(prefix):
os.chdir(prefix)
if os.path.isdir('pysimm'):
print('pysimm directory already exists...assuming it is the pysimm repository and continuing...')
e... | polysimtools/pysimm | complete_install.py | Python | mit | 4,322 | [
"Amber",
"LAMMPS"
] | 4a0f47535b7c57b0853b74850e80d8e49f1f07eb7be9dd34e37a1af9a373cf00 |
#
# @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
#... | psi-rking/psi4 | psi4/driver/p4util/python_helpers.py | Python | lgpl-3.0 | 43,894 | [
"Psi4"
] | 1e8912996e9a6580d881d8e17e269d4dc98a510c2e5478a79fcdfe28ba342126 |
# -*- coding: utf-8 -*-
#
# phonopy documentation build configuration file, created by
# sphinx-quickstart on Mon Apr 13 15:11:21 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All... | anttikarttunen/ajk-test | doc/conf.py | Python | bsd-3-clause | 8,914 | [
"phonopy"
] | 0dbd7201027c9e7b0f67eee0932d3bae75c6e317a6619f3915d3d5f274d2c974 |
"""Functions to plot epochs data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Si... | effigies/mne-python | mne/viz/epochs.py | Python | bsd-3-clause | 16,323 | [
"Gaussian"
] | ac0d3ee0679fa430bd0b6b3523baa7077d434cf06e8030481a3d4271c45f53e4 |
# multi2.py ---
# Upi Bhalla, NCBS Bangalore 2014.
#
# Commentary:
#
# This loads in a medium-detail model incorporating
# reac-diff and elec signaling in neurons. The reac-diff model is
# psd_merged31d.g which has only Ca in the dendrites, but is quite
# interesting in the PSD and spine head. Problem is lots of
#... | dilawar/moose-full | moose-examples/snippets/MULTI/multi2.py | Python | gpl-2.0 | 14,932 | [
"MOOSE"
] | 989342392922d941808ca2b27a0fff0b25363f3c67f3ae914b5cba018e26beed |
from __future__ import absolute_import
import collections
import os
import sqlite3
from mercurial.i18n import _
from mercurial.node import sha1nodeconstants
from mercurial import (
encoding,
error,
pycompat,
)
from . import gitutil
pygit2 = gitutil.get_pygit2()
_CURRENT_SCHEMA_VERSION = 1
_SCHEMA = (... | jwren/intellij-community | plugins/hg4idea/testData/bin/hgext/git/index.py | Python | apache-2.0 | 11,645 | [
"Octopus",
"VisIt"
] | d1c2192e58842c1efab7297b5c8e7fd9cc52538b88b3581492ac880490d4a5c8 |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for QgsRasterFileWriter.
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
"... | dwadler/QGIS | tests/src/python/test_qgsrasterfilewriter.py | Python | gpl-2.0 | 9,364 | [
"NetCDF"
] | 13c8f86548928ee866b526ad1ad80183778a46eba2a4906a5d0e1a51179faf84 |
# proxy module
from __future__ import absolute_import
from mayavi.filters.wrapper import *
| enthought/etsproxy | enthought/mayavi/filters/wrapper.py | Python | bsd-3-clause | 91 | [
"Mayavi"
] | 27f7f889b321f6717b06bc560df4cace10921e4843f977a71dcbb83c368492c6 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from textwrap import dedent
from flaky import flaky
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...page... | chauhanhardik/populo | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 13,347 | [
"VisIt"
] | 1885e641a7b92e51d9b817242392cd5f9e3486f8e5df0c0c5c86d9da4763fce9 |
from allensdk.model.biophys_sim.config import Config
from allensdk.model.biophys_sim.neuron.hoc_utils import HocUtils
class Utils(HocUtils):
def __init__(self, description=None):
description = Config().load('manifest.json')
super(Utils, self).__init__(description)
self.generate_cell()
... | Neurosim-lab/netpyne | examples/saveLoadV1/AA/active_cell_utils.py | Python | mit | 3,092 | [
"NEURON"
] | da38db3c6ecdb81cca53f638f8ae4c504730da88abd04fb3a6f98ce5b598566a |
#!/usr/bin/env python
#
# SchoolTool - common information systems platform for school administration
# Copyright (c) 2003 Shuttleworth Foundation
#
# 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... | lxml/lxml | test.py | Python | bsd-3-clause | 21,306 | [
"VisIt"
] | 919868ff05ae43f6440c50f6e2c9f2212281f944da7d35c68fc4a4154be28f58 |
# -*- coding: utf-8 -*-
'''
Python wrapper for the the python requests package
It is a convienience lib of common code used by
several gentoo utilities.
Copyright:
(c) 2013 Brian Dolbec
Distributed under the terms of the GPL-2 license
Author(s):
Brian Dolbec <dolsen@gentoo.org>
'''
__vers... | dol-sen/ssl-fetch | sslfetch/__init__.py | Python | gpl-2.0 | 334 | [
"Brian"
] | 393727a4d074766103bba30df7f6965c8f405aa171a874ec0724d8b020ed4867 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/mxnet/estimator.py | Python | apache-2.0 | 14,442 | [
"ORCA"
] | a98f90cc0ad0907612800e579ad302ff0bed912ff0cce9e633cdc1ad487836c7 |
"""
This class is used to define the plot using the plot attributes.
"""
from DIRAC import S_OK
from DIRAC.MonitoringSystem.Client.Types.PilotSubmissionMonitoring import PilotSubmissionMonitoring
from DIRAC.MonitoringSystem.private.Plotters.BasePlotter import BasePlotter
class PilotSubmissionMonitoringPlotter(BaseP... | DIRACGrid/DIRAC | src/DIRAC/MonitoringSystem/private/Plotters/PilotSubmissionMonitoringPlotter.py | Python | gpl-3.0 | 3,909 | [
"DIRAC"
] | bb5ea7102efc3598d01b6fb7fadf971bdbadfb4b35e74f007571e4edc7483c73 |
import numpy as np
from ase import Atoms
from gpaw import GPAW, FermiDirac
from gpaw.test import equal
calc = GPAW(nbands=1)#, txt=None)
atoms = Atoms('He', pbc=True, calculator=calc)
atoms.center(vacuum=3)
e0 = atoms.get_potential_energy()
niter0 = calc.get_number_of_iterations()
try:
calc.get_fermi_level()
exc... | qsnake/gpaw | gpaw/test/fermilevel.py | Python | gpl-3.0 | 1,024 | [
"ASE",
"GPAW"
] | 43ae76d73da9f70a058cc5fe78a020e7239a907aa31ea0ac978ed1b96d78127a |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Perform DNA-DNA alignment using BLAST, NUCMER and BLAT. Keep the interface the
same and does parallelization both in core and on grid.
"""
import os.path as op
import sys
import shutil
import logging
from jcvi.utils.cbook import depends
from jcvi.apps.base import (
... | tanghaibao/jcvi | jcvi/apps/align.py | Python | bsd-2-clause | 15,771 | [
"BLAST"
] | 92b91427409bfd5ccffed8647b92cb3aa22bffddeae4063884b316b070477937 |
""" This fixer changes all occurrences of the form 'module.member' from the
global dictionary MAPPING's keys and replaces them with the corresponding
value. It adds the proper imports to make it available in the script.
For example this code::
import orange
import orngSVM
data = orange.ExampleTable("iris"... | yzl0083/orange | Orange/fixes/fix_changed_names.py | Python | gpl-3.0 | 47,037 | [
"Gaussian"
] | 37f08df11745c6cada261cc677ba8c4baeb0d9adf06a46a5769c968fe348e0bd |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.