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# ##### BEGIN GPL LICENSE BLOCK #####
#
# 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.
#
# This program is distrib... | nortikin/sverchok | nodes/logic/neuro_elman.py | Python | gpl-3.0 | 12,827 | [
"NEURON"
] | 25d6f9f9ebc0a683c429dc0041e3d728afac5120c2a4e01d1d97082dce88a275 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# Introduction: This script is used to fetch pairwise core genomes between each strain pair.
# It is better to put this script in ITEP directory.
# Created by galaxy on 2016/10/21 15:11
import os
import sys
import shutil
from collections import defaultdict
from ... | cvn001/RecentHGT | src/fetch_pairwise_genome.py | Python | mit | 3,100 | [
"Galaxy"
] | f7af669743e22b20d62719a34017f181e726a7aba1d0bf063c9652a59acb398c |
#!/usr/bin/env python
##############################################################################
#
# Usage example for the procedure PPXF, which
# implements the Penalized Pixel-Fitting (pPXF) method by
# Cappellari M., & Emsellem E., 2004, PASP, 116, 138.
# The example also shows how to include a library of templa... | moustakas/impy | lib/ppxf/ppxf_kinematics_example_sauron.py | Python | gpl-2.0 | 8,518 | [
"Galaxy",
"Gaussian"
] | f337d7ef1da2d1cdfe5c328243bfb52abb9063695b0d2825823e34d3e3411f6a |
#!/usr/bin/env python
import datetime
import shutil
from copy import deepcopy
from math import log, exp
try:
from math import inf
except ImportError:
inf = float("inf")
from argparse import ArgumentParser
import GetOrganelleLib
from GetOrganelleLib.seq_parser import *
from GetOrganelleLib.pipe_control_func imp... | Kinggerm/GetOrganelle | get_organelle_from_reads.py | Python | gpl-3.0 | 262,598 | [
"BLAST"
] | 9743c060a350421e38eb96137b5de8a6e4927d15fc8cf0300ef47891bc1c956e |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | trenton3983/Artificial_Intelligence_for_Humans | vol2/vol2-python-examples/examples/example_pso_iris.py | Python | apache-2.0 | 20,910 | [
"VisIt"
] | 832af39ad7f61bade0d07e76dd80addb7e2653204297beb3b28e9b65165a05f5 |
import numpy as np
from enthought.mayavi import mlab
import Image
def disp_odf(sph_map, theta_res=64, phi_res=32, colormap='RGB', colors=256):
pi = np.pi
sin = np.sin
cos = np.cos
theta, phi = np.mgrid[0:2*pi:theta_res*1j, 0:pi:phi_res*1j]
x = sin(phi)*cos(theta)
y = sin(phi)*sin(theta)
... | StongeEtienne/dipy | scratch/odf.py | Python | bsd-3-clause | 2,711 | [
"Mayavi"
] | 24b3c9472c959778b9242a99fa60a4b382af68e558cdef1f63a62fe980012dff |
# ===============================================
# MODULE STUDY: os
import os
reload(os)
print '*----------------------------------------*'
path = 'C:/' # nt
path = '/' # linux
print os.stat(path)
print '*----------------------------------------*'
print os.error # <type 'exceptions.OSError'>
print os.erro... | madoodia/codeLab | python/modules_os.py | Python | mit | 10,636 | [
"VisIt"
] | 43aa99dafa1ee0a7f5df3b32115342e213cfc49228a81693d97431cd5515e512 |
#!/usr/bin/python
# script extract a particular genome region and compute a z-score piRNA signature
# version 1 - 22-06-2012
# Usage bowtie_window_analysis.py <bowtie input> <geneID> <Upstream_coordinate> <Downstream_coordinate> <bowtie index> <output>
import sys, subprocess
from collections import defaultdict # requi... | JuPeg/tools-artbio | unstable/local_tools/bowtie_window_analysis.py | Python | mit | 1,514 | [
"Bowtie"
] | 3b412a3264ebf666530b3ea82b718be6d026d39c0a92b54add14a16a8e468ba1 |
"""
client_manual.py
Copyright 2016 Brian Romanchuk
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 ... | brianr747/Simple4Xpygame | clients/client_manual.py | Python | apache-2.0 | 1,507 | [
"Brian"
] | 11fade0adc6c7ccc54691e84aa91704d764db5e07cd570b2200954308bbde6de |
# Information about the IUPAC alphabets
protein_letters = "ACDEFGHIKLMNPQRSTVWY"
extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO"
# B = "Asx"; aspartic acid or asparagine (D or N)
# X = "Xxx"; unknown or 'other' amino acid
# Z = "Glx"; glutamic acid or glutamine (E or Q)
# http://www.chem.qmul.ac.uk/... | bryback/quickseq | genescript/Bio/Data/IUPACData.py | Python | mit | 7,553 | [
"BioPerl",
"PyMOL"
] | 97aa12dca31cb3eaa80b1d5aa9ab8382f992a70a3d7f19ded69ac75d0e300653 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
class Dealii(CMakePackage, CudaPackage):
"""C++ software library providing well-docum... | rspavel/spack | var/spack/repos/builtin/packages/dealii/package.py | Python | lgpl-2.1 | 21,842 | [
"NetCDF"
] | 51c3d2981b1282238e31c47e5d493d30ca3c260f1373ba8b6f45f27f52d3abb4 |
#!/usr/bin/env python
#
# Copyright 2008 Jose Fonseca
#
# 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 later version.
#... | hszer0/Explicator | xdot.py | Python | gpl-3.0 | 92,826 | [
"FLEUR"
] | 902c509d165d45a95cdd99d538a33706b3922bac415f8fa78549dc24ff18e75e |
#!/usr/bin/env python
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or with... | CMUSV-VisTrails/WorkflowRecommendation | scripts/system_info.py | Python | bsd-3-clause | 3,215 | [
"VTK"
] | e4ac7366187a57f132861786f8441d5c797d01cb0e2eae13c486d7ca4bc192ce |
#!/usr/bin/env python
from horton import *
import h5py as h5
import os
log.set_level(log.silent)
def store_wfn(fn_h5, mixing, name_case, exp):
with h5.File(fn_h5) as f:
name_mixing = '%08.5f' % (-np.log10(mixing))
grp = f.require_group(name_mixing)
grp = grp.require_group(name_case)
... | eustislab/horton | tools/convergence_tester/make_guesses.py | Python | gpl-3.0 | 4,368 | [
"Gaussian"
] | c4b47e73f213380d9a20f91eb7b13fa4a1cb960f1ef158eb44315b0a40a8b713 |
import re
import sys
import datetime
import AlphaSubstValidation
import AlphaSubstPrep
import AlphaSubstBaseMLBootstrap
import AlphaSubstScoring
import random
def stop_err(msg):
"Write the error message and exit"
sys.stderr.write(msg)
sys.exit()
#Retrieve Data
OutputFile = sys.argv[1]
AnalysisType = sys.a... | jmchilton/galaxy-central | tools/mdea/AlphaSubst.py | Python | mit | 9,343 | [
"Galaxy"
] | e91da56b9b9f66c082981016ea36231d366c2c47a15192491cebb17ddb71c5a8 |
#
# Copyright 2021 Lars Pastewka (U. Freiburg)
# 2018 Jacek Golebiowski (Imperial College London)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | libAtoms/matscipy | matscipy/calculators/mcfm/qm_cluster_tools/qm_flagging_tool.py | Python | lgpl-2.1 | 11,970 | [
"ASE",
"Matscipy"
] | a498c4af6b6f058cd179853dea6a101d031a733d4a4c3a9f626461156904b24b |
""" EC2Endpoint class is the implementation of the EC2 interface to
a cloud endpoint
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
import os
import json
import boto3
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.File import m... | ic-hep/DIRAC | src/DIRAC/Resources/Cloud/EC2Endpoint.py | Python | gpl-3.0 | 7,540 | [
"DIRAC"
] | 9ceaabd78a6cfffa20366908bac5f56f88b9c351a481e6a36567025b32b5069b |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import platform
import sys
import os
from spack import *
class Namd(MakefilePackage):
"""NAMDis a parallel molecular... | rspavel/spack | var/spack/repos/builtin/packages/namd/package.py | Python | lgpl-2.1 | 5,399 | [
"NAMD"
] | 0ac8b31a40d3c7e5b1312d9bf2a1079b5488b8b7bcf3c03b15102d35031e54c0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0092_remove_visit_improvementissues'),
]
operations = [
migrations.AddField(
model_name='visit',
... | koebbe/homeworks | visit/migrations/0093_visit_improvementissues.py | Python | mit | 497 | [
"VisIt"
] | b660e9f1063b20499a170da02d9e2c5d8858888c0397906b4de9003548a21ca0 |
"""
NeuroLearn Analysis Tools
=========================
These tools provide the ability to quickly run
machine-learning analyses on imaging data
"""
__all__ = ["Roc"]
__author__ = ["Luke Chang"]
__license__ = "MIT"
import pandas as pd
import numpy as np
from nltools.plotting import roc_plot
from scipy... | ljchang/nltools | nltools/analysis.py | Python | mit | 13,305 | [
"Gaussian"
] | 2716f7bedb2430e654457f85d90f34403782d4668bb2dc228ed15d0e0b2df0eb |
"""
Imageutils unit tests.
"""
from __future__ import division
import unittest
import numpy as np
from astraviso import imageutils as iu
class imageutilstests(unittest.TestCase):
"""
Imageutils unit test class.
"""
def setUp(self):
pass
def tearDown(self):
pass
class test_poisson_... | bradsease/astra-viso | astraviso/test/imageutils.py | Python | mit | 7,601 | [
"Gaussian"
] | 27219aa38f29f9e407231a6a73bfd7ed32aa7103ad3ae0dc5bff7e53a4355b99 |
#!/usr/bin/env python
# encoding: utf-8
"""description: Cororado PGEM models
"""
__version__ = "0.1"
__author__ = "@boqiling"
__all__ = ["PGEMBase", "DUT", "DUT_STATUS", "Cycle"]
from base import PGEMBase
from dut import DUT, DUT_STATUS, Cycle
class Crystal(PGEMBase):
pass
class Saphire(PGEMBase):
PGEM_ID ... | fanmuzhi/UFT | src/UFT/models/__init__.py | Python | gpl-3.0 | 564 | [
"CRYSTAL"
] | d4600926e9f5b6fb8c36df5d0186a38a6337b14d49b67944bbc25b3d14cb897e |
# Ask vnc text spoke
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed in the... | wgwoods/anaconda | pyanaconda/ui/tui/spokes/warnings_spoke.py | Python | gpl-2.0 | 2,529 | [
"Brian"
] | 4dacb6f0253d4a4f8c2613ca1ce3f50f7ce3fed2d683b49625a3ad7196caf767 |
#!/usr/bin/env python
"""Miscellaneous wrapper functions to Schrodinger's computational chemistry tools."""
import os
import sys
import csv
import shutil
import logging
import subprocess
import mdtraj
from openmoltools import utils
logger = logging.getLogger(__name__)
def run_and_log_error(command):
"""Run t... | choderalab/openmoltools | openmoltools/schrodinger.py | Python | mit | 11,742 | [
"MDTraj"
] | bcd858b882d840b989cc7b5089812644dd20adb03568ea76af05f6166726a482 |
__author__ = 'BisharaKorkor'
import numpy as np
from math import exp, pow, sqrt, pi, fmod
def movingaverage(a, w):
""" An array b of length len(a)-w is returned where b_n = (a_n + a_n-1 + ... + a_n-w)/w """
return [np.mean(a[i:i+w]) for i in range(len(a)-w)]
def gaussiankernel(sigma, width):
"""Generates... | BishKor/pyboon | arrayoperations.py | Python | mit | 2,659 | [
"Gaussian"
] | fe0ce18f4025cc1f6db9b26ef977ae1b2447a44fe7518dce36acc1b3453aab1f |
"""
expectmax.py
Implementation of the expectation-maximisation algorithm used to fit
a multivariate gaussian mixture model of moving groups' origins
to a data set of stars, measured in Cartesian space, centred on and
co-rotating with the local standard of rest.
This module is in desperate need of a tidy. The entry p... | mikeireland/chronostar | chronostar/expectmax.py | Python | mit | 73,596 | [
"Gaussian"
] | 73fc9717ff2fc33cda34118e7b948e92b1b7aa831b5fb3362a1e6d6e1ccaa7c6 |
# Copyright (c) 2015, Scott J Maddox. All rights reserved.
# Use of this source code is governed by the BSD-3-Clause
# license that can be found in the LICENSE file.
import os
import sys
fpath = os.path.abspath(os.path.join(os.path.dirname(__file__),
'../fdint/dgfd.pyx'))
with open... | scott-maddox/fdint | scripts/gen_dgfd_pyx.py | Python | bsd-3-clause | 1,395 | [
"DIRAC"
] | 2eb32b104ebbc0e847ac1bad9767f5fd648b508d946ae29c179b56331a41f7f6 |
########################################################################
#
# (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... | 2ndQuadrant/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 16,264 | [
"Brian",
"Galaxy"
] | b60fde4b79dd94672656d719e82ad13dd60d15f3c17672da9a20977d3e839ad1 |
#import warnings
#warnings.filterwarnings("ignore", message="using a non-integer number instead of an integer will result in an error in the future")
def template_names():
import glob as glob
template_files = glob.glob('miles_models/Mun*.fits')
return template_files
def choose_templates(templates, age_lim = 20.0,... | zpace/SparsePak-SFH | fake_galaxies.py | Python | mit | 17,002 | [
"Gaussian"
] | ad66898e3e988eec6a8fe718026c5f396cf8025fe2749e85ac6aea840b779f66 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Time Domain Electromagnetics (TDEM) functions and class"""
import sys
from math import pi
import numpy as np
import matplotlib.pyplot as plt
import pygimli as pg
from . vmd import VMDTimeDomainModelling
def rhoafromU(U, t, Tx, current=1.0, Rx=None):
r"""Apparent re... | gimli-org/gimli | pygimli/physics/em/tdem.py | Python | apache-2.0 | 16,310 | [
"VMD"
] | 213a7ac776868c9cd0a2151085ed7f32533d1dacb56531fd17bc39ff679fdb16 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.metrics.pairwise` submodule implements utilities to evaluate
pairwise distances or affinity of sets of samples.
This module contains both distance metrics and kernels. A brief summary is
given on the two here.
Distance metrics are a function d(a, b) such that d(a, b) < d(... | depet/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 29,572 | [
"Gaussian"
] | f5e773f18f469de1eb7f36a6e0b6bbc90aafc014c7bc7d1199cd1a1917d7b97a |
from __future__ import unicode_literals
from frappe import _
def get_data():
return [
{
"label": _("Sales Pipeline"),
"icon": "fa fa-star",
"items": [
{
"type": "doctype",
"name": "Lead",
"description": _("Database of potential customers."),
"onboard": 1,
},
{
"type": "... | Zlash65/erpnext | erpnext/config/crm.py | Python | gpl-3.0 | 4,679 | [
"VisIt"
] | 88bd9de5e23744164ecd7fedda95aebe7a103a18c03aa9026f1e3ed47550cb65 |
# 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... | pkreissl/espresso | testsuite/python/lb_boundary_volume_force.py | Python | gpl-3.0 | 3,425 | [
"ESPResSo"
] | a2bb68f022ca049df92ad49ad19f36a7653fc76e6327d5b34ed795da0af9259a |
# (c) 2014, Ovais Tariq <me@ovaistariq.net>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is dist... | ovaistariq/datadog-agent-checks | mysql_sys.py | Python | gpl-3.0 | 7,470 | [
"VisIt"
] | 19fb8af10eaa130e3b7cf17230e4b63d077e7b6961676beaec2b5f3748e0d77f |
"""
Codes for creating and manipulating gate filters. New functions: use of trained
Gaussian Mixture Models to remove noise and clutter from CPOL data before 2009.
@title: filtering.py
@author: Valentin Louf <valentin.louf@bom.gov.au>
@institutions: Monash University and the Australian Bureau of Meteorology
@created: ... | vlouf/cpol_processing | cpol_processing/filtering.py | Python | mit | 9,055 | [
"Gaussian"
] | b57a3c97ef1879760983ef025c83f50b5884c630ae133a1382359ef6b453fe50 |
# -*- coding: UTF-8 -*-
"""
Data literal storing emoji names and unicode codes
"""
__all__ = ['EMOJI_UNICODE', 'UNICODE_EMOJI', 'EMOJI_ALIAS_UNICODE', 'UNICODE_EMOJI_ALIAS']
EMOJI_UNICODE = {
u':1st_place_medal:': u'\U0001F947',
u':2nd_place_medal:': u'\U0001F948',
u':3rd_place_medal:': u'\U0001F949',... | vjmac15/Lyilis | lib/emoji/unicode_codes.py | Python | gpl-3.0 | 195,719 | [
"FLEUR",
"Octopus"
] | dd76adca880b1b9adfd0a41932b616907deedc6e65320e1550ebf6ec93e756a2 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import hrl_lib.mayavi2_util as mu
impor... | tapomayukh/projects_in_python | sandbox_tapo/src/AI/Code for Project-3/HMM Code/hmm_crossvalidation_force_20_states.py | Python | mit | 17,322 | [
"Gaussian",
"Mayavi"
] | b1e9cfcecfed31467178823a43308c87b7dce1060ced4db82d5dbee7236b8078 |
#!/usr/bin/python -O
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
#################################################... | INNUENDOWEB/INNUca | src/SPAdes-3.11.0-Linux/share/spades/spades_pipeline/corrector_logic.py | Python | gpl-3.0 | 2,484 | [
"BWA"
] | 6b6ec537f80ab43597839f31a0e961f78926ae2570dfba648e7124652cc68ec5 |
"""
LMS Course Home page object
"""
from collections import OrderedDict
from bok_choy.page_object import PageObject
from .bookmarks import BookmarksPage
from .course_page import CoursePage
from .courseware import CoursewarePage
from .staff_view import StaffPreviewPage
class CourseHomePage(CoursePage):
"""
... | miptliot/edx-platform | common/test/acceptance/pages/lms/course_home.py | Python | agpl-3.0 | 8,981 | [
"VisIt"
] | 7a19d9ad11514dd4e2bf90521d831b820c1c9ccfaf26785cadb5b1f78b5fe0d4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# unit - some simple unit tests against migfs
# Copyright (C) 2003-2011 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 terms of the GNU General Public ... | heromod/migrid | mig/migfs-fuse/unit.py | Python | gpl-2.0 | 7,325 | [
"Brian"
] | 66bde0b2d3850e36f93cb9c8b6b73382902ce403f6fe3b298c9278e8bd8f2f04 |
"""Predictor classes."""
from abc import ABC, abstractmethod
import logging
from typing import Iterable, Sequence
import acton.database
import acton.kde_predictor
import GPy as gpy
import numpy
import sklearn.base
import sklearn.linear_model
import sklearn.model_selection
import sklearn.preprocessing
from numpy.rando... | chengsoonong/acton | acton/predictors.py | Python | bsd-3-clause | 26,833 | [
"Gaussian"
] | 8e74b5c356cca0328f890651985ad1d9cf9c69dc3b7a0daf3ff6a79d1c17e143 |
from com.im.lac.types import MoleculeObjectIterable
from com.im.lac.util import StreamProvider
from com.im.lac.util import CloseableMoleculeObjectQueue
from com.im.lac.types import MoleculeObject
from java import lang
import sys
from java.util import ArrayList
from java.util.stream import Stream
from java.lang import T... | InformaticsMatters/squonk | components/rdkit-camel/src/main/python/molecule_objects.py | Python | apache-2.0 | 1,872 | [
"RDKit"
] | 0c8549ccdd15ffb166410271570764996f1dfac64c254834bcc3081fc068dd88 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and
from frappe import _
from frappe.model.mapper import get_m... | gangadharkadam/office_erp | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 13,651 | [
"VisIt"
] | ba33e2822bc032ac031c391d693465f49b2585e7acefa20a143be5dd6b1f7dfd |
"""Defines the HTTPError class.
Copyright 2013 by Rackspace Hosting, 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 applicab... | openilabs/falconlab | env/lib/python2.7/site-packages/falcon/http_error.py | Python | mit | 4,535 | [
"VisIt"
] | f66705aac4080dbb357cb770bd244edab68fdd49a57ac10f44ff75eda9de9819 |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
from django.db.models import Q, F
import py... | chrisndodge/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 91,666 | [
"VisIt"
] | 3b7af1650888bb1fe1a2cbd573afb1292221ec53c27b8d5d178172a6e21c70e0 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Multiple_Contact_Classification/Final_New_classify_2_objects_2_categories_1200ms_scaled.py | Python | mit | 12,548 | [
"Mayavi"
] | 868422c64d90bb8372c8fafb374d28438b00f7af70edbebf7654a4825b626fbc |
import numpy as np
import scipy.special as sps
def wixi(x):
""" Complex Error Function (Faddeeva/Voigt).
w(i*x) = exp(x**2) * ( 1-erf(x) )
This function is called by other functions within this module.
We are using the scipy.special.wofz module which calculates
w(z) = exp(-z**2) * ... | paulmueller/PyCorrFit | pycorrfit/models/MODEL_TIRF_gaussian_1C.py | Python | gpl-2.0 | 8,849 | [
"Gaussian"
] | 610f5ae1cff88e7c3be41ea5417bdf3b831e0abb9b0a9319d59e25a86d4f229c |
# Lint as: python3
# Copyright 2018 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 ... | tensorflow/lingvo | lingvo/core/optimizer_test.py | Python | apache-2.0 | 8,526 | [
"Gaussian"
] | 065511a319388c9dbe05cb11bb5be7c0f695856aad60cbf9cee8b85caf11dc72 |
#! /usr/bin/env python
"""Generate Java code from an ASDL description."""
# TO DO
# handle fields that have a type but no name
import os, sys, traceback
import asdl
TABSIZE = 4
MAX_COL = 100
def reflow_lines(s, depth):
"""Reflow the line s indented depth tabs.
Return a sequence of lines where no line exte... | alvin319/CarnotKE | jyhton/ast/asdl_antlr.py | Python | apache-2.0 | 37,458 | [
"VisIt"
] | 8671e63ad5752a5adac68d78838260b503191ab4f6c21f2fd174891c2444384d |
"""
Basic visualization of neurite morphologies using matplotlib.
Usage is restricted to morphologies in the sWC format with the three-point soma `standard <http://neuromorpho.org/neuroMorpho/SomaFormat.html>`_
"""
import sys,time
import os, sys
from matplotlib.cm import get_cmap
from Crypto.Protocol.AllOrNothing imp... | RoozbehFarhoodi/McNeuron | McNeuron/visualize.py | Python | mit | 27,682 | [
"NEURON"
] | b640b872edf49cbc4df887a0bcef83d9dda96b431f00aefbe4ecb68113ce3791 |
from brian import (NeuronGroup, Network, StateMonitor,
second, ms, volt, mV)
import numpy as np
import matplotlib.pyplot as plt
network = Network()
XT = -50*mV
DeltaT = 0.05*mV/ms
eqs = "dX/dt = DeltaT*exp((X-XT)/DeltaT) : volt"
neuron = NeuronGroup(1, eqs, threshold="X>=XT", reset=-65*mV)
neuron.X... | achilleas-k/brian-scripts | expo_iaf.py | Python | apache-2.0 | 502 | [
"Brian",
"NEURON"
] | 43eb5fd95b8637b06b93fbd00933a9ff2d60c341fb8e7eb983d2427561fb5877 |
"""Tests for setendings.py.
Checks that `end_lineno` and `end_col_offset` node properties are set.
"""
import unittest
from python_ta.transforms.setendings import *
PATH = 'examples/ending_locations/'
class TestEndingLocations(unittest.TestCase):
"""The method, ending_transformer.visit(module) walks the given a... | RyanDJLee/pyta | tests/test_setendings.py | Python | gpl-3.0 | 20,344 | [
"VisIt"
] | 84a783ceb6ee6b2ff135d03c7ace6c0573bda29753868e85d3d8a6e5393c05cc |
from brainiak.eventseg.event import EventSegment
from scipy.special import comb
import numpy as np
import pytest
from sklearn.exceptions import NotFittedError
def test_create_event_segmentation():
es = EventSegment(5)
assert es, "Invalid EventSegment instance"
def test_fit_shapes():
K = 5
V = 3
... | lcnature/brainiak | tests/eventseg/test_event.py | Python | apache-2.0 | 5,227 | [
"NEURON"
] | b32f7bf02849be47ef7bbad46cedb9f54875ce89d97389945246672ed50284f0 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | flavioamieiro/pypln.web | pypln/web/core/tests/views/test_corpus.py | Python | gpl-3.0 | 8,500 | [
"NAMD"
] | 7528066fa3a7f70c7efb8f4ac3f2981336da19d1919f2ac7ddc490cffcfc61b2 |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
Sphinx-Gallery Generator
========================
Attaches Sphinx-Gallery to Sphinx in order to generate the galleries
when building the documentation.
"""
from __future__ import division, print_function, absolute_import
import codecs
import ... | Eric89GXL/sphinx-gallery | sphinx_gallery/gen_gallery.py | Python | bsd-3-clause | 32,422 | [
"Mayavi"
] | 703555067397bb99ccb2896386b3a4e46233489e2eff8a9e7143891c435b9f36 |
"""
Taken from https://github.com/brentp/pyfasta/blob/452d1ce5406ed73c4149b6d201bc65e4aa8afc27/tests/bench.py
"""
from itertools import islice
from tempfile import NamedTemporaryFile
import pyfaidx
import pyfasta
import pysam
from Bio import SeqIO
import time
import random
import os
import sys
from subprocess import c... | mattions/pyfaidx | scripts/benchmark.py | Python | bsd-3-clause | 8,301 | [
"pysam"
] | e8c6c4449758f2ee3407c5b212293cf27c9699c0976718764e1dc92a1c7c8caf |
# 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 agreed ... | google-research/ott | ott/tools/gaussian_mixture/fit_gmm_pair.py | Python | apache-2.0 | 12,305 | [
"Gaussian"
] | 72b723ff337f69cad94b1009ed9d64b0d0d8deac4fa64cfcddc8177d0b9e2848 |
from cached_property import cached_property
from pathlib import Path
from qgis.PyQt.QtCore import pyqtSignal
from qgis.PyQt.QtCore import Qt
from ThreeDiToolbox.datasource.threedi_results import ThreediResult
from ThreeDiToolbox.models.base import BaseModel
from ThreeDiToolbox.models.base_fields import CheckboxField
fr... | nens/threedi-qgis-plugin | tool_result_selection/models.py | Python | gpl-3.0 | 8,337 | [
"NetCDF"
] | f6ac1d0fae3c7eba5414fa24481ebe40589204375d03b3383dc823c05904f0a5 |
import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
from ase.test import NotAvailable
# if CMR_SETTINGS_FILE is mis... | grhawk/ASE | tools/ase/test/cmr/ase_rw.py | Python | gpl-2.0 | 1,194 | [
"ASE"
] | 5034f5449c418ea81a7da4e44d22c8085a441a9679edc2a5405df1cb7247f8bb |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
star... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t31_rlvps07_hn16_clr0p003.py | Python | mit | 7,660 | [
"NEURON"
] | 7086f8113b0f47b01ceccc69170064eaf7ea64d22d9a0666f8c5867e5aeb65ef |
#!/usr/bin/env python3
"""
This script is a python version of TimingAccuracyDHC. We use numpy functions to
simplify the creation of random coefficients.
"""
import time
import numpy as np
from pyshtools import expand
from pyshtools import spectralanalysis
# ==== MAIN FUNCTION ====
def main():
TimingAccuracyDHC(... | MarkWieczorek/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyDHC.py | Python | bsd-3-clause | 2,762 | [
"Gaussian"
] | ed9e8c9bf85bd8224001d776abeee511ce00243901770ac82d3ff91b6e40d758 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/diversity/alpha/tests/test_faith_pd.py | Python | bsd-3-clause | 8,646 | [
"scikit-bio"
] | fee044def915af522e9ef2c110f12e70e84faf2cc0e386507f16d7faa12c53b6 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','license','co... | arnaudsj/titanium_mobile | support/module/iphone/templates/build.py | Python | apache-2.0 | 5,924 | [
"VisIt"
] | 5e22d195b1cb3abff0461e2ab393108ce3d4c11a9303c67d0fb6288f433ba72b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Program to compare models using different compute engines.
This program lets you compare results between OpenCL and DLL versions
of the code and between precision (half, fast, single, double, quad),
where fast precision is single precision using native functions for
tr... | SasView/sasmodels | sasmodels/compare.py | Python | bsd-3-clause | 62,003 | [
"Gaussian"
] | 75732db330232b971f5a0d228969683fed7d7cc8e0b5902e2794e822bf256c13 |
# -*- coding: utf-8 -*-
'''
diacamma.event package
@author: Laurent GAY
@organization: sd-libre.fr
@contact: info@sd-libre.fr
@copyright: 2016 sd-libre.fr
@license: This file is part of Lucterios.
Lucterios is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as... | Diacamma2/asso | diacamma/event/tests.py | Python | gpl-3.0 | 12,538 | [
"Dalton"
] | 771c40f0d4852a640c9780290855fcca414f4b1afd758add88cc64cfdf68b7dc |
#!/bin/bash
"""This file hold the function run_mcmc, which takes a trained emulator and a set of truth data and runs
and MCMC analysis with a predefined number of steps and walkers."""
from time import time
from multiprocessing import cpu_count, Pool
import warnings
from itertools import izip
from os import path
... | mclaughlin6464/pearce | pearce/inference/run_mcmc.py | Python | mit | 26,088 | [
"Gaussian"
] | 0d6cf0a4c03cae33b8f16f1993d5b6482ff6e802acd7034f4e1d7d20a32b5db2 |
#
# 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/_note.py | Python | gpl-2.0 | 1,777 | [
"Brian"
] | 2b38d31c86a1156f0c9ea41b8853f99e977908e537ab2a94cc00e8a041d88092 |
#!/usr/bin/env python
########################################################################
# File : dirac-agent
# Author : Adria Casajus, Andrei Tsaregorodtsev, Stuart Paterson
########################################################################
"""
This is a script to launch DIRAC agents. Mostly internal.
""... | DIRACGrid/DIRAC | src/DIRAC/Core/scripts/dirac_agent.py | Python | gpl-3.0 | 1,520 | [
"DIRAC"
] | bb5335a5da0676c83f9bb1a023111c05424bc3527768153d1ea72f5ed752a2ea |
# Cycles Mineways setup
# Version 1.3.0, 5/28/16
# Copyright © 2016
# Please send suggestions or report bugs at https://github.com/JMY1000/CyclesMineways/
# 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 Foundat... | JMY1000/CyclesMineways | CyclesMineways.py | Python | gpl-3.0 | 46,368 | [
"VisIt"
] | 7d316a43271c6b09b3e043d667c085be0d35833751c765b0632e076aaa33300d |
import os
from datetime import datetime
from django.test import SimpleTestCase
from django.utils.functional import lazystr
from django.utils.html import (
conditional_escape, escape, escapejs, format_html, html_safe, json_script,
linebreaks, smart_urlquote, strip_spaces_between_tags, strip_tags, urlize,
)
from... | nesdis/djongo | tests/django_tests/tests/v22/tests/utils_tests/test_html.py | Python | agpl-3.0 | 11,720 | [
"ADF"
] | e71fdab3a5bc021e61386024fc8bbaa18e1c4a7038144047a58378845ca58bb3 |
import copy
import numpy as np
import numpy.random as rng
from utils import randh
from numba import jit
# How many parameters are there?
num_params = 3
# Some data
data = np.loadtxt("road.txt")
N = data.shape[0] # Number of data points
# Plot the data
import matplotlib.pyplot as plt
plt.plot(data[:,0], data[:,1], "o... | eggplantbren/NSwMCMC | python/straightline.py | Python | gpl-2.0 | 1,954 | [
"Gaussian"
] | 5aad979a4ab8fa1847dfedb05a05cad5dc0df920fb62c7ff63cd116159e45b6c |
from threading import Lock
class ResponsibleGenerator(object):
"""A generator that will help clean up when it is done being used."""
__slots__ = ["cleanup", "gen"]
def __init__(self, gen, cleanup):
self.cleanup = cleanup
self.gen = gen
def __del__(self):
self.cleanup()
... | RDFLib/rdflib | rdflib/plugins/stores/concurrent.py | Python | bsd-3-clause | 2,709 | [
"VisIt"
] | 9badfedfb8716ec1d997cbccb6e0dbd4fb4a01dc8762577229cc25023ac02b23 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
import numpy
from math import sin,cos
from SceneObject import SceneObject
class LIDAR(SceneObject):
'''
A template for drawing a LIDAR point cloud.
Ref: http://stackoverflow.com/questions/7591204/how-to-display-point-cloud-in-vtk-in-different-colo... | GearsAD/semisorted_arnerve | sandbox/bot_vis_platform_post3b/scene/LIDAR.py | Python | mit | 3,811 | [
"VTK"
] | a42f29b85d56782e946c279a7912cf8cbc884f52105cba11251596c03508a4bc |
"""
==========================
FastICA on 2D point clouds
==========================
This example illustrates visually in the feature space a comparison by
results using two different component analysis techniques.
:ref:`ICA` vs :ref:`PCA`.
Representing ICA in the feature space gives the view of 'geometric ICA':
ICA... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/decomposition/plot_ica_vs_pca.py | Python | mit | 3,329 | [
"Gaussian"
] | f80535f5f58450012442742aaa57ec546ec732ed8e66083f8b75428ae4dd2fe9 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'ArticleMetaDataMap'
db.create_table('neuroelectro_articlemetadatamap', (
... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0061_auto__add_articlemetadatamap.py | Python | gpl-2.0 | 31,187 | [
"NEURON"
] | 8ea1459809ae5ff787e215297f558e0a732a24dbce2063d0d4ba696e2f19b908 |
#!/usr/bin/env python
#coding=utf-8
import urllib
import base64
import hmac
import time
from hashlib import sha1 as sha
import os
import md5
import StringIO
from threading import Thread
import threading
import ConfigParser
from oss_xml_handler import *
#LOG_LEVEL can be one of DEBUG INFO ERROR CRITICAL WARNNING
LOG_LE... | matrixorz/justpic | justpic/third/oss/oss_util.py | Python | mit | 36,295 | [
"NetCDF"
] | 72b1c935d75386f248e53e632489e5c4a592e9b9026ddb9c94985446d478fdaf |
# -*- coding: utf-8 -*-
# MDclt.primary.amber.log.py
#
# Copyright (C) 2012-2015 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
Classes for transfer of AMBER simulation logs to h5
"""
##########... | KarlTDebiec/MDclt | primary/amber/log.py | Python | bsd-3-clause | 14,006 | [
"Amber"
] | 5bb9e215fb008c31708d60e32ebc7ebe577f03d41bb877645159cf7959048277 |
import os, sys, re
from Bio import pairwise2
from Bio.Blast import NCBIXML
from Bio.SubsMat.MatrixInfo import blosum62
import gzip
import optparse
import subprocess
from jaspar.settings import BASE_DIR
'''
The original code is available in motif_inferrer.py.
This is modified by Aziz Khan <azez.khan@gmail.com> on May ... | asntech/jaspar | utils/motif_inferrer/inferrer.py | Python | bsd-3-clause | 9,890 | [
"BLAST"
] | 8ffceed2e45f33254a1c90f55fe565979ca3fafd8592bc98a29f9ec1d783400f |
import argparse
import inspect
import logging
import json
import base64
from docstring_parser import parse
from flask import Flask, request
from flask_restx import Api, Resource, fields, abort
from flask_cors import CORS
from indra import get_config
from indra.sources import trips, reach, bel, biopax, eidos
from indr... | johnbachman/indra | rest_api/api.py | Python | bsd-2-clause | 39,694 | [
"Cytoscape"
] | 6346c02f370f7d9eaf532dbbde371c84ea3d5dd3c70a81cdde8ad3c07c754a96 |
from openmm_systems.test_systems import (
LennardJonesPair,
LysozymeImplicit,
)
import simtk.openmm.app as omma
import simtk.openmm as omm
import simtk.unit as unit
from wepy.runners.openmm import gen_sim_state
import time
def create_sim():
test_sys = LysozymeImplicit()
integrator = omm.LangevinInt... | ADicksonLab/wepy | jigs/trio_mapper/source/sync_openmm.py | Python | mit | 1,288 | [
"OpenMM"
] | 4165b3ae598bfb555f85e9b45100d96f06a8ccd926eb84c2445328656ca6145e |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd.
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import webnotes
from webnotes import session, msgprint
from webnotes.utils import today,add_days,cint,nowdate,formatdate
sql = webnotes.conn.sql
from utilities.t... | gangadhar-kadam/sapphire_app | support/doctype/customer_issue/customer_issue.py | Python | agpl-3.0 | 3,002 | [
"VisIt"
] | 06076fffe95317533a114c001eb777f6cee22616a8fba9dbaece22b4100efa91 |
"""
Loads synthetic reaction datasets from USPTO.
This file contains loaders for synthetic reaction datasets from the US Patenent Office. http://nextmovesoftware.com/blog/2014/02/27/unleashing-over-a-million-reactions-into-the-wild/.
"""
import os
import csv
import logging
import deepchem
import numpy as np
from deepc... | lilleswing/deepchem | deepchem/molnet/load_function/uspto_datasets.py | Python | mit | 3,783 | [
"RDKit"
] | f645712ea5bad992601456acedee6efd2a72c942a869c5b3699a1c94968f4ee1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from functools import reduce
try:
# New Py>=3.5 import
from math import gcd
except ImportError:
# Deprecated import from Py3.5 onwards.
from fra... | matk86/pymatgen | pymatgen/core/surface.py | Python | mit | 55,689 | [
"pymatgen"
] | 6f2c3212a24b5087b890fd4ef8085f46e86c726c27f4a5f71dcb24a838db53e0 |
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import contextlib
import functools
import os
import pkgutil
import sys
import warnings
import attr
import py
import six
import _pyt... | hackebrot/pytest | src/_pytest/main.py | Python | mit | 25,480 | [
"VisIt"
] | 111fe939298b33c18d54f44b9d328e22b9a1bf92aa940a38cf016ee8921e40e3 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010-2012 Gary Burton
# GraphvizSvgParser is based on the Gramps XML import
# DotSvgGenerator is based on the relationship graph
# report.
# ... | gramps-project/addons-source | GraphView/graphview.py | Python | gpl-2.0 | 167,934 | [
"FLEUR"
] | 3f99aca903a0b50b1d80f3debf66565020209cefc2608e51100384479ca9e83f |
# Copyright (c) Mathias Kaerlev 2012.
# This file is part of Anaconda.
# Anaconda is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# ... | joaormatos/anaconda | mmfparser/player/extensions/LacewingServer/__init__.py | Python | gpl-3.0 | 47,484 | [
"BLAST"
] | abd126338ea562f2ac6fe152ebe1e10190b49e61b108b1f8f54023bf84c0e832 |
''' CacheFeederAgent
This agent feeds the Cache tables with the outputs of the cache commands.
'''
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.Core.Base.AgentModule ... | vmendez/DIRAC | ResourceStatusSystem/Agent/CacheFeederAgent.py | Python | gpl-3.0 | 5,763 | [
"DIRAC"
] | e115257f90adcfe146e690a56844951d8473ef1d4f140af1e8552564c186dcff |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/qcdb/jajo.py | Python | lgpl-3.0 | 17,941 | [
"Avogadro",
"CFOUR",
"Psi4"
] | 512bd1ce1f0e12904193b7288c716d912d79cf2b995eb5f68bf4708a5f694c9c |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Polypeptide-related classes (construction and representation).
Simple example with mul... | bryback/quickseq | genescript/Bio/PDB/Polypeptide.py | Python | mit | 14,402 | [
"Biopython"
] | f67968d3f43e9e44dc0c942d4d39cf962b096d09afba6829431d2a046caf6095 |
"""
TESTS is a dict with all you tests.
Keys for this will be categories' names.
Each test is dict with
"input" -- input data for user function
"answer" -- your right answer
"explanation" -- not necessary key, it's using for additional info in animation.
"""
TESTS = {
"Basics": [
{
... | Bryukh-Checkio-Tasks/checkio-mission-family-gifts | verification/tests.py | Python | mit | 5,048 | [
"Amber"
] | ff7be966cb866c0045324dbe55ed68151b1f4427c2554f6a3e0b59c2d02c489f |
# -*- coding: utf-8 -*-
# pylint: disable=line-too-long
import os
import sys
import glob
import numpy
import string
from collections import Counter
import anvio
__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license... | meren/anvio | anvio/constants.py | Python | gpl-3.0 | 25,794 | [
"pysam"
] | 5ad9a220852e715dd3a58d35fac6f94ec81326bed043bbc3a0e1664bbcb408f6 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/lib/openlyricsexport.py | Python | gpl-2.0 | 4,641 | [
"Brian"
] | 8e68a0e2a3f63e9a63004412ce1d0c8ce0e6141c692df6755f337f9e0a13f132 |
''' Test_RSS_Policy_JobRunningMatchedRatioPolicy
'''
import unittest
import DIRAC.ResourceStatusSystem.Policy.JobRunningMatchedRatioPolicy as moduleTested
################################################################################
class JobRunningMatchedRatioPolicy_TestCase( unittest.TestCase ):
def setUp( ... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Policy/test/Test_RSS_Policy_JobRunningMatchedRatioPolicy.py | Python | gpl-3.0 | 4,283 | [
"DIRAC"
] | f4c21000ca49684c76fde1b0aacc70e062d6c9a7da3bd9d1404ecdf6775adb05 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | QuantumElephant/horton | horton/constants.py | Python | gpl-3.0 | 1,499 | [
"Avogadro"
] | 70f086f8f1643bee145f8ad88bb70d4d07c7084ee555aa8b5570d6ad15fad31c |
# File: subst.py
# Author: Brian A. Vanderburg II
# Purpose: A generic SCons file substitution mechanism
# Copyright: This file is placed in the public domain.
##############################################################################
# Requirements
##########################################... | salilab/mdt | tools/subst.py | Python | gpl-2.0 | 5,887 | [
"Brian"
] | 80ee8e2a82d64704fd80050c6802603d0bc9fb625ddbed2fadb7434fe51627da |
# global imports
import cython
import logging
import itertools
import sys
# local imports
try:
import openbabel
except:
pass
from rdkit import Chem
from .molecule import Atom, Bond, Molecule
from .pathfinder import compute_atom_distance
from .util import partition, agglomerate, generate_combo
import rmgpy.m... | chatelak/RMG-Py | rmgpy/molecule/generator.py | Python | mit | 21,132 | [
"RDKit"
] | f7a9dd043a7e4214bf1c07384e85e40770d59afba3fe54c747bb5b7ae40fee73 |
"""
Defines the plugin to take storage space information given by WLCG Accounting Json
https://twiki.cern.ch/twiki/bin/view/LCG/AccountingTaskForce#Storage_Space_Accounting
https://twiki.cern.ch/twiki/pub/LCG/AccountingTaskForce/storage_service_v4.txt
https://docs.google.com/document/d/1yzCvKpxsbcQC5K9MyvXc-vBF... | DIRACGrid/DIRAC | src/DIRAC/Resources/Storage/OccupancyPlugins/WLCGAccountingJson.py | Python | gpl-3.0 | 4,466 | [
"DIRAC"
] | c3db8d71eefba20e8da0feacef044190224e169d8fa5c49b1aaceb1b5ac0c61e |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, John D. Cho... | daviddesancho/mdtraj | mdtraj/formats/mol2.py | Python | lgpl-2.1 | 7,865 | [
"MDTraj",
"OpenMM"
] | be67b84cdb3386ff4242a90072c388b8279d073369798d72033050bd6c94ab0d |
# Copyright 2014 PerfKitBenchmarker 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 appli... | syed/PerfKitBenchmarker | perfkitbenchmarker/benchmarks/speccpu2006_benchmark.py | Python | apache-2.0 | 10,962 | [
"GAMESS",
"Gromacs",
"NAMD"
] | 43ef63c6f1f7fce6f8b0251566421cf90a11f260df345d446a3a3f51db4208e1 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 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 Software F... | andrebellafronte/stoq | stoqlib/gui/search/salespersonsearch.py | Python | gpl-2.0 | 3,025 | [
"VisIt"
] | fb9010329b369c15d127ccfc0007475c04765cb81026a0c7513f269de1016077 |
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