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# 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... | psci2195/espresso-ffans | src/python/espressomd/constraints.py | Python | gpl-3.0 | 16,719 | [
"ESPResSo"
] | fe3b7c6062172f62cdeef04057cf58ab0522e294097bcd8a1f200af37358c40b |
from __future__ import absolute_import
import json
import os
import string
from collections import namedtuple
import paramiko
import logging
from dateutil import parser
from django.core.urlresolvers import reverse
from django.contrib.auth.models import Group, User
from django.contrib.contenttypes.models import Conten... | ResearchSoftwareInstitute/MyHPOM | hs_core/views/utils.py | Python | bsd-3-clause | 41,910 | [
"NetCDF"
] | d3b3a2df5245cc3170773e1e191eb453fca4ced0cd91900ddb2307d81c88e2eb |
"""
Adds a better Alt interface.
It includes a priority select and a fair select.
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
import inspect
from pycsp.parallel.a... | runefriborg/pycsp | pycsp/parallel/altselect.py | Python | mit | 14,371 | [
"Brian"
] | 61187c699c8b27afd40e00c7444fc8d52db394e82ef857589e90e2858ee1b82c |
#!/usr/bin/env python3
#
# Copyright (c) 2017 Weitian LI <weitian@aaronly.me>
# MIT license
#
"""
Convert the image (e.g., by WSClean) from units [Jy/beam] to [K]
by taking into account the telescope's beam size.
"""
import os
import sys
import argparse
import numpy as np
from astropy.io import fits
import astropy.... | liweitianux/atoolbox | astro/oskar/jybeam2k.py | Python | mit | 5,847 | [
"Gaussian"
] | 08bd3d0ea199428beb59826371c8755051a208cf0a1e530e75ffaa294fbdf619 |
try: paraview.simple
except: from paraview.simple import *
Glyph1 = GetActiveSource()
VirialRadius1 = VirialRadius( ProbeType="High Resolution Line Source" )
VirialRadius1.ProbeType.Point1 = [-0.010403109714388847, -0.061579469591379166, -0.11254894733428955]
VirialRadius1.ProbeType.Point2 = [-0.0036313242744654417, ... | corbett/parastro | ExamplePython/VirialRadius.py | Python | lgpl-3.0 | 1,591 | [
"ParaView"
] | c8e415501dc6d9d91fc1277edf57ca11d342fdd262c7dd9af40a12306becaf8c |
import numpy as np
from mdtraj.testing import eq, raises
import msmbuilder.featurizer
from msmbuilder.featurizer import subset_featurizer
from msmbuilder.example_datasets import fetch_alanine_dipeptide
def test_SubsetAtomPairs0():
dataset = fetch_alanine_dipeptide()
trajectories = dataset["trajectories"]
t... | rmcgibbo/msmbuilder | msmbuilder/tests/test_featurizer.py | Python | lgpl-2.1 | 3,904 | [
"MDTraj"
] | b3d423a9d275fcd3323b436d5f2f34b499eb00c3f8119effe70c51e5a8c66add |
#!/usr/bin/env python
from glob import glob
import numpy as np
import os
import sys
from horton import * # pylint: disable=wildcard-import,unused-wildcard-import
from horton.meanfield.test.common import check_cubic_wrapper
# log.set_level(log.high)
log.set_level(log.silent)
debug = True
def main(fns_fchk):
... | tovrstra/horton | data/examples/hf_compare/compare.py | Python | gpl-3.0 | 2,995 | [
"Gaussian"
] | 45f953aefb3aad06561d987acc1d2e77c9c34ee1f0d930279161ca86b08649ea |
# -*- coding: utf-8 -*-
import numpy as np
from ...Qt import QtCore, QtGui
from ..Node import Node
from . import functions
from ... import functions as pgfn
from .common import *
from ...python2_3 import xrange
from ... import PolyLineROI
from ... import Point
from ... import metaarray as metaarray
class Downsample(C... | mgraupe/acq4 | acq4/pyqtgraph/flowchart/library/Filters.py | Python | mit | 13,840 | [
"Gaussian"
] | 5f2309231fe418b65a3b01fe0fe1e12433ff284a67461325e9d4689c956262df |
import numpy as np
import numpy.linalg as la
class Kernel(object):
"""Implements list of kernels from
http://en.wikipedia.org/wiki/Support_vector_machine
"""
@staticmethod
def linear():
return lambda x, y: np.inner(x, y)
@staticmethod
def gaussian(sigma):
return lambda x, ... | Bin2015/ProjectBin | python-SVM-encryption/SVM/kernel.py | Python | apache-2.0 | 1,017 | [
"Gaussian"
] | 539b88f6079e005c70cb2f34ba49013b6c622da5849e0e16a7cd669dc7b72205 |
"""
Instructor Dashboard Views
"""
import datetime
import logging
import uuid
from functools import reduce
import beeline
import pytz
import six
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.http import Http404, HttpResponseServerError
from django.urls import ... | appsembler/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 39,151 | [
"VisIt"
] | 2e2355afdb139894d6dadce0ca8f7e2942480f42ed0b2396cdbe2cac7c437d84 |
#!/usr/bin/env python
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | terraform-google-modules/terraform-google-secret | test/verify_boilerplate.py | Python | apache-2.0 | 9,744 | [
"VisIt"
] | d91681d4ef9328ba5c6f9a672a48a7657281a77467a6384ee0fc481e0efd397f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
########### Attension
# [n] means n-dimension array
# [m x n] means (m x n)-dimension array
# no [] means 1-dimension data
import random as rand
import numpy as np
import numpy.linalg as nplnlg
import neuro_function as nf
class NeuroElement:
def __init__(self) : ... | WaterIsland/DLStudy | mln/CR/Mln.py | Python | mit | 14,196 | [
"NEURON"
] | f383446d671852f90cb152b826d40c19375da05a5e96afc2da7d348dc0b6e61c |
import torch
from torch.utils.data import DataLoader, TensorDataset
import torch.optim as optim
import torch.nn.functional as F
from torch.utils.tensorboard import SummaryWriter
from torch.optim.lr_scheduler import StepLR
import os
import os.path as osp
from tqdm import tqdm
import argparse
import time
import numpy as... | snap-stanford/ogb | examples/lsc/pcqm4m/main_mlpfp.py | Python | mit | 9,405 | [
"RDKit"
] | ecd0cc4b48b490e95c6b69017b2746d59926d136adf1ed87e33ee7ada0b99317 |
# This file is part of CO𝘕CEPT, the cosmological 𝘕-body code in Python.
# Copyright © 2015–2022 Jeppe Mosgaard Dakin.
#
# CO𝘕CEPT 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 Lice... | jmd-dk/concept | src/linear.py | Python | gpl-3.0 | 216,106 | [
"Gaussian",
"VTK"
] | f47f4f0fe0a20ac6d83f36e2cf253eaaa98e6ab41c2dce2cee84fab58381c095 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 13 14:18:20 2017
@author: lracuna
"""
from pose_sim import *
from mpl_toolkits.mplot3d import Axes3D
from Rt_matrix_from_euler_t import R_matrix_from_euler_t
import itertools
from multiprocessing import Pool
from vision.camera_distribution import c... | raultron/ivs_sim | python/old_experiments/test_cam_distribution.py | Python | mit | 8,422 | [
"Gaussian"
] | dab38d3052ca32d896d0afd4aa01e6b5d39cfddd43c007da60e83d542d19811d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.test import TestCase, Client
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from django.contrib.auth.models import User
from django.test.utils import override_settings
import factory
from faker im... | kaka0525/Copy-n-Haste | CopyHaste/typing_test/tests.py | Python | mit | 4,660 | [
"VisIt"
] | c5e86ff106a04427ab91867a8102ab02a466d6522fd588e4036aa226926a1c1e |
# Regionalization script
# July 29, 2016
# Becky Davies, David Folch, Seth Spielman
#Depends on additional scripts: get_codes, acs_regionalization, extract_msas, data_prep_master, fullFunc
#Requires input docs: USA census tracts shapefile, MSA county crosswalk from OMB
import pysal as ps
import numpy as np
import pan... | co-ncrn/co-ncrn.github.io | code/full_script.py | Python | gpl-3.0 | 9,351 | [
"MOE"
] | 51b70e884b7a90b9b8d776f8d792aa6a863aa4cae675e30e9305bc80d050c7a5 |
# import libraries
import os
import numpy as np
import pandas as pd
import xarray as xray
import ftplib, wget, urllib
import dask as da
from dask.diagnostics import ProgressBar
from multiprocessing.pool import ThreadPool
import matplotlib.pyplot as plt
import shapely.ops
from shapely.geometry import box, Polygon
from m... | ChristinaB/Observatory | tutorials/ogh_xarray_landlab.py | Python | mit | 26,996 | [
"NetCDF"
] | 9c9df6582e2f97e4fd24d44d9341fd3cf88535c7a9abad9ee33762e01c800ba6 |
# Copyright (C) 2012 Olaf Lenz
#
# 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 version.
#
# ESPR... | icimrak/espresso | maintainer/check_features.py | Python | gpl-3.0 | 968 | [
"ESPResSo"
] | a331ccdce913964779e784eef702744be2255e02b1fbe7b030b6d46b252bc9d2 |
"""
# Copyright (C) 2007 Rob King (rob@re-mu.org)
#
# This library 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 2.1 of the License, or (at your option) any later version.
#
#... | shouldmakemusic/yaas | LiveOSC/LiveOSCCallbacks.py | Python | gpl-2.0 | 45,765 | [
"VisIt"
] | 7198cef0566c675839ca2db11a0050d9f150db62f77b45f34e317b5f308dfa8b |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/mobile/satfinder.py | Python | gpl-2.0 | 8,247 | [
"VisIt"
] | 5578bce42c74b26896b6bf51ac2b59dd3dd159a74e51905a29f78a1e176088f4 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or... | Forage/Gramps | gramps/gen/proxy/filter.py | Python | gpl-2.0 | 17,239 | [
"Brian"
] | a5d2aadabce0bed0daec059544375ca071dcfe696b55e29106c7c6a3303d2e0d |
import json
import math
import operator
import requests
from collections import OrderedDict
from django.conf import settings
from .utils import get_ratio, get_division, SUMMARY_LEVEL_DICT
class ApiClient(object):
def __init__(self, base_url):
self.base_url = base_url
def _get(self, path, params=None... | Ladaniels/censusreporter | censusreporter/apps/census/profile.py | Python | mit | 47,427 | [
"MOE"
] | 78cfc1530f8af87383cd4d44a4ef6e6e8d72400ca8c3a7edc16b43e1d8217746 |
# -*- coding: utf-8 -*-
from django.conf import settings
from selenium.webdriver.support.expected_conditions import visibility_of
from selenium.webdriver.support.wait import WebDriverWait
from selenium.webdriver.firefox.options import Options
from formfieldstash.tests.utils.django_utils import create_superuser
from fo... | benzkji/django-formfieldstash | formfieldstash/tests/test_admin.py | Python | mit | 5,957 | [
"Octopus"
] | 6279fe67f5649e5267c94addf51f09a8ca70e78886bcb561d4c2dffbe40d2055 |
import sys
sys.path.insert(1, "../../../")
import h2o
def offset_gaussian(ip,port):
# Connect to a pre-existing cluster
h2o.init(ip,port)
insurance = h2o.import_frame(h2o.locate("smalldata/glm_test/insurance.csv"))
insurance["offset"] = insurance["Holders"].log()
gbm = h2o.gbm(x=insurance[0:3], ... | ChristosChristofidis/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_offset_gaussianGBM.py | Python | apache-2.0 | 1,767 | [
"Gaussian"
] | 7cea86d63ef5347c2564930c195739f100c517af082b38c1781a6252cce90745 |
import itertools
from django.core.management.base import BaseCommand
from django.core.exceptions import ObjectDoesNotExist
from django.contrib.contenttypes.models import ContentType
from jsonattrs.models import Schema, Attribute, AttributeType
from exampleapp.models import Division, Department, Party
DATA = [
{... | Cadasta/django-jsonattrs | example/exampleapp/management/commands/loadtestdata.py | Python | agpl-3.0 | 9,626 | [
"ORCA"
] | 8c39b4941cc0c9e5bb70f181078e15a926813c9b01e2e21663c89463a4ec5b2b |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for Entrance exams in the LMS
"""
from textwrap import dedent
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.course_hom... | BehavioralInsightsTeam/edx-platform | common/test/acceptance/tests/lms/test_lms_entrance_exams.py | Python | agpl-3.0 | 3,170 | [
"VisIt"
] | fc251ca1fe803b2d3acdeb30152bd2b8bce117203d24416f653ade14a9f02234 |
#
# Author: Henrique Pereira Coutada Miranda
# Date: 18/10/2015
# Parallelize a GW calculation using Yambo
# In this example we take advantage of the fact that the q points of the dielectric function
# are totally independent calculations so its a good idea to calculate them in separate jobs
# These example runs local... | henriquemiranda/yambo-py | tutorial/bn/gw_pp_bn.py | Python | bsd-3-clause | 2,751 | [
"Yambo"
] | 9a3735d07f0ae01e763ab142594e03541c150e5b9d6452bf55863ccb37bee22f |
# Authors: Nicolas Goix <nicolas.goix@telecom-paristech.fr>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# License: BSD 3 clause
import numbers
import numpy as np
from scipy.sparse import issparse
from warnings import warn
from ..tree import ExtraTreeRegressor
from ..utils import (
chec... | shyamalschandra/scikit-learn | sklearn/ensemble/_iforest.py | Python | bsd-3-clause | 18,918 | [
"Gaussian"
] | 05eea1ebfc8b01176b8d0a596a12e4bf97aa1bbeee51371a39204b1b853f48a5 |
# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
# Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>,
# <d.desvillechabrol@gmail.com>
#
# Distributed un... | sequana/sequana | sequana/tools.py | Python | bsd-3-clause | 18,948 | [
"pysam"
] | 3e30c410979839a7373e94bc4c181dbbf0e031a903f9b01cf2f508d80afe902b |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | dnjohnstone/hyperspy | hyperspy/tests/samfire/test_samfire.py | Python | gpl-3.0 | 18,643 | [
"Gaussian"
] | 322a53ea81ded2cd10c131324147849ad589989d375b7e5fcdbf4839a0fc033d |
import re
import os
import shutil
import netCDF4
from django.dispatch import receiver
from django.core.files.uploadedfile import UploadedFile
from hs_core.signals import pre_create_resource, pre_add_files_to_resource, \
pre_delete_file_from_resource, pre_metadata_element_create, pre_metadata_element_update, \
... | RENCI/xDCIShare | hs_app_netCDF/receivers.py | Python | bsd-3-clause | 15,393 | [
"NetCDF"
] | 77f47c428b4d21b4927748c715781b6d35200fc47797d486de9396b78411d196 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | wesley1001/WeVoteServer | config/urls.py | Python | bsd-3-clause | 1,234 | [
"VisIt"
] | d4e46b2fd06f74d5aa2aa63ba08a965c90539f1922a65355e45ab36927c84d6a |
# Copyright 2004-2010 PyTom <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, mer... | MSEMJEJME/ReAlistair | renpy/display/text.py | Python | gpl-2.0 | 47,136 | [
"VisIt"
] | d1aefae828c27b78284129bc5f1aa40dfc454f826c823b91f628591d2fa0495b |
#! /usr/bin/env python
import db
import math
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sets import Set
from rdkit import Chem
from rdkit.Chem import Descriptors
from sklearn.feature_selection import VarianceThreshold
import pylab
data = db.getTarget_206_1977()
sicho_descriptors =... | PMitura/smiles-neural-network | baselines/sicho_csv.py | Python | bsd-3-clause | 1,850 | [
"RDKit"
] | d1bed036c2019a8277b5f1b67bcac5ac3fdb39dc27ef7bf1a3d91cbdee2d7ed3 |
#!/usr/bin/env python3
"""
This script is a python version of TimingAccuracyGLQC. 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():
TimingAccuracyGLQ... | MarkWieczorek/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyGLQC.py | Python | bsd-3-clause | 2,991 | [
"Gaussian"
] | 51312384ca10813fce40e7d92fbe82798a1d4e651d883817821ebb2ec3ff0c1e |
########################################################################
# $HeadURL $
# File: FTSStrategy.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/12 13:12:07
########################################################################
""" :mod: FTSStrategy
=================
.. module: FTSStrate... | calancha/DIRAC | DataManagementSystem/private/FTSStrategy.py | Python | gpl-3.0 | 18,283 | [
"DIRAC"
] | d57724d45fc87931287d2bb5e36953a2d9260161394f7f11e9260b116771a3ed |
# Copyright (C) 2011,2012,2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your... | KonradBreitsprecher/espresso | testsuite/ek_eof_one_species_y_nonlinear.py | Python | gpl-3.0 | 13,278 | [
"ESPResSo"
] | 5e2517b029cc01fb3f07d1987512df49b9b1c06d8678fc3aaf1d73e53d6ec506 |
# -*- coding: utf-8 -*-
# (c) 2016, Adrian Likins <alikins@redhat.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 License, or
# (at you... | 2ndQuadrant/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 52,042 | [
"Galaxy"
] | d846f449e77623058143d85098dd519db8cf1ff1e32fc4abcbff69301c4c4779 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018 Piero Dalle Pezze
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the ... | pdp10/sbpipe | sbpipe/pl/sim/sim.py | Python | mit | 14,826 | [
"COPASI"
] | 6045bba01d066e33145ce53d7b24e6aeab2f7b6300640f84899432798ab059fe |
# These tests are those of the deprecated GMM class
import unittest
import copy
import sys
import warnings
from nose.tools import assert_true
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_raises)
from scipy import stats
from sklearn impo... | imaculate/scikit-learn | sklearn/mixture/tests/test_gmm.py | Python | bsd-3-clause | 19,066 | [
"Gaussian"
] | 4f65f4f920fe3cecbf6116f91cb2f444f6efc532a31547f254a8a9df6e329169 |
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
#
# 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 b... | espressopp/espressopp | src/integrator/MinimizeEnergy.py | Python | gpl-3.0 | 4,426 | [
"ESPResSo"
] | 7983fc2a2ade275b23bf7ae2248e8122889fc72f54a7d70079ca1aa851ac5b24 |
# -*- coding: utf-8 -*-
# Copyright 2013 Pierre de Buyl
#
# This file is part of md_tools
#
# md_tools is free software and is licensed under the modified BSD license (see
# LICENSE file).
# This file contains code from the nMOLDYN project. The complete nMOLDYN license
# "CeCILL" is available at licenses/LICENSE_nMOLD... | pdebuyl/md_tools | md_tools/nmoldyn_code.py | Python | bsd-3-clause | 4,559 | [
"DIRAC"
] | ea6bd2904cd8ccd3afa87953a08c70503b2c118d40bcf3648004e9a78989e8ec |
#!/usr/bin/env python
from __future__ import division
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this soft... | squirrelo/qiita | qiita_ware/test/test_util.py | Python | bsd-3-clause | 17,567 | [
"scikit-bio"
] | 07f19ce8cde106c0bae7e2f6662e50ca37dfb0b4738ebdb1b8196a2778e04d52 |
#! /usr/bin/env python3
"""
Run QM calculations at multiple levels consecutively, using queuing system
Automate Multi-Level calculations
This should help with running a set of QM calculations at several levels (e.g.,
increasing basis set size), while intelligently using the queuing system such
as Sun Grid Engine.
It ... | thompcinnamon/QM-calc-scripts | gautools/aml.py | Python | apache-2.0 | 49,213 | [
"Gaussian",
"MDAnalysis"
] | b0a6e09dcb809e6c7396c6e77435cce91706d5d97df988a74b55963210824e69 |
'''
:Date: 27 Apr 2016
:Author: Public Health England
'''
import argparse
import glob
import os
from posix import wait
from subprocess import CalledProcessError
import subprocess
from time import sleep
def get_my_jobs(jobs, job_name=None):
cmd = ["qstat"]
current_jobs = set()
output = subprocess.check_... | phe-bioinformatics/PHEnix | test/submit_jobs.py | Python | gpl-3.0 | 2,463 | [
"BWA"
] | 3fa5425bfb2a3d27744da548413b9700b9955584c69eef3617a1167661f1c544 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import with_statement
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing decorator. It'll blo... | youtube/cobalt | tools/gyp/pylib/gyp/common.py | Python | bsd-3-clause | 16,339 | [
"VisIt"
] | 03d68545554cbc18f143caf0b2bc2836775540c997c6c5bc51a0edeb7e66fe55 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Licence: BSD 3 clause
from collections import Hashable
from sklearn.externals.funcsigs import signature
import numpy as np
from sklearn.gaussian_process.kernels import _approx_fprime
from sklearn.metrics... | ssaeger/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 11,602 | [
"Gaussian"
] | 8ef04ff356b49f0611b64664c18347ea176066c203053170210edcffe09bff6b |
from django.shortcuts import render
from django.http import HttpResponseBadRequest, HttpResponse
from .models import Project, ExperienceItem
from django.core.mail import EmailMessage
constant_values = {
'about_text':"Hello, everyone! Thanks for taking the time to visit my website. My name is Sean Dooher and I’m a s... | sean-dooher/website | mainpages/views.py | Python | mit | 2,350 | [
"VisIt"
] | 86723afcd4dce4217dd21a8a4ae852caa13c21d6bd7b5030693bd132b650e96d |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-variantannotation/package.py | Python | lgpl-2.1 | 2,532 | [
"Bioconductor"
] | fd3d73498665e03bb58922162dce3c41c080b9d73c7ec8ca50efd041af9b4b94 |
from __future__ import division
from __future__ import absolute_import
from builtins import range
import numpy as np
from numpy.random import random
na = np.newaxis
import scipy.stats as stats
import scipy.special as special
import scipy.linalg
from scipy.special import logsumexp
from numpy.core.umath_tests import inne... | mattjj/pybasicbayes | pybasicbayes/util/stats.py | Python | mit | 12,517 | [
"Gaussian"
] | d0c25fc558e2082955f77146101e5be2ff7fffc7bd3012f741b76f79255bb878 |
#!/usr/bin/env python3
"""
Copyright 2021 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/getLatestResources.py | Python | gpl-3.0 | 5,846 | [
"Galaxy"
] | 642d4f5a653d081feaf18a8c9eeea02a023a8aa201ae17142b9098b97afa6c3f |
# 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)
# adapted from official quantum espresso package
class QESirius(Package):
"""SIRIUS enabled fork of QuantumESPRESSO. ... | iulian787/spack | var/spack/repos/builtin/packages/q-e-sirius/package.py | Python | lgpl-2.1 | 12,663 | [
"EPW",
"ESPResSo",
"QMCPACK",
"Quantum ESPRESSO"
] | f7389ed287330d0c0b1cbbbc2db1997b5ef6bc7e0cae99becd00280fbddbe465 |
from setuptools import setup, find_packages
requires = [
'clldmpg>=1.0.0',
]
tests_require = [
'WebTest >= 1.3.1', # py3 compat
'mock',
]
setup(
name='cdk',
version='0.0',
description='cdk',
long_description='',
classifiers=[
"Programming Language :: Python",
"Frame... | clld/cdk | setup.py | Python | apache-2.0 | 763 | [
"CDK"
] | 98730645659719baa9912269af67fa5c91134652655843d169943536fb6dfddb |
#!/usr/bin/env python
import os,sys
import tables as tb
import numpy as np
from sklearn.neighbors.kde import KernelDensity
import cPickle as cp
deg = np.pi/180.
def add_image_points(rama, padding):
assert rama.shape == (rama.shape[0], 2)
assert np.all(np.abs(rama) < np.pi+1e-3) # must be in the range (-pi,p... | John-Jumper/Upside-MD | py/estimate_rama_distributions.py | Python | gpl-2.0 | 2,130 | [
"Gaussian"
] | d56e9ee2ff44c674e7804bb6c215e8834758751a0ce96f38b39932202d10fbe7 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
JK with analytic Fourier transformation
'''
import numpy
from pyscf.pbc.df import aft_jk
from mpi4pyscf.tools import mpi
comm = mpi.comm
rank = mpi.rank
get_j_kpts = mpi.call_then_reduce(aft_jk.get_j_kpts)
@mpi.parallel_call
def get_k_kpts(... | sunqm/mpi4pyscf | mpi4pyscf/pbc/df/aft_jk.py | Python | gpl-3.0 | 2,195 | [
"PySCF"
] | 55b4f8ca76560b120c2357c8dda440bef6e91696269ee351d8a322b618f19226 |
from dataclasses import field
from marshmallow import validate
from marshmallow_dataclass import dataclass, Optional, List
from .configuration import MikadoConfiguration
@dataclass
class ShortReads:
r1: List[str] = field(default_factory=lambda: [], metadata={
"metadata": {"description": "Array of left rea... | lucventurini/mikado | Mikado/configuration/daijin_configuration.py | Python | lgpl-3.0 | 9,527 | [
"BLAST"
] | d878f7d42d74a1618db775433311918f4807fb6027eb4678682f73b4a28fa053 |
from __future__ import unicode_literals
import os, re
from copy import copy
from sqlalchemy import *
from sqlalchemy.orm import *
from .model import *
from cgi import FieldStorage
from sprox._compat import unicode_text
try:
from tw import framework
framework.default_view = 'mako'
except ImportError:
class... | TurboGears/sprox | sprox/test/base.py | Python | mit | 7,653 | [
"VisIt"
] | 347367f601910c938ed5dbd971ddd0c241fc95a578b4e22cbd75cf4d63839a57 |
# preliminary road race announce 'stateful' terminal
# connects to IRC to receive UNT4 announce msg packs
#
# Notes:
# - does not _yet_ do live stream negotiation
# - server, port, channel, nick config via road_announce.ini
#
# TODO:
# - properly mark private vars/methods to avoid leak to other thread
# - configuratio... | gusgollings/scbdo | scbdo/rr_announce.py | Python | gpl-3.0 | 20,395 | [
"Amber"
] | e3efc89077c73be8df0c85c3d0cb754d169147bcda53d879af4eb77a01d6a534 |
# Copyright 2019 Open Source Robotics Foundation, 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... | ros2/launch | launch_xml/test/launch_xml/test_group.py | Python | apache-2.0 | 2,889 | [
"VisIt"
] | 9aeb816b3bc8cbbc8d8ec839e379454e295e0c71e1a3fd0b19909e2bfc92493c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# testtar - [insert a few words of module description on this line]
# 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 terms of t... | heromod/migrid | mig/unittest/testtar.py | Python | gpl-2.0 | 2,798 | [
"Brian"
] | a394d7589edaaf191857db21651de7c8e889808cc9104f4d9ca30961fe7ee845 |
#
# @file TestCompartmentVolumeRule.py
# @brief CompartmentVolumeRule unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by conver... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestCompartmentVolumeRule.py | Python | bsd-3-clause | 3,309 | [
"VisIt"
] | 319182f5dba1cb1aad650a34cb862a51ab03e03e7f1e9eb391e09f38ed6f28ab |
# gearring_macro.py
# the macro to generate a gearring.
# created by charlyoleg on 2013/10/03
#
# (C) Copyright 2013 charlyoleg
#
# This file is part of the Cnc25D Python package.
#
# Cnc25D is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... | charlyoleg/Cnc25D | cnc25d/tests/gearring_macro.py | Python | gpl-3.0 | 8,182 | [
"VisIt"
] | 94719933c145dd992b6620686d4e20414af26044439a49ab9de9a7e009fb669a |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | eleftherioszisis/NeuroM | neurom/io/tests/test_utils.py | Python | bsd-3-clause | 12,060 | [
"NEURON"
] | a0c2d236f469742dfdd3cc0be76e1eafe639e02d64178ea5e328d66afe41e3db |
#!usr/bin/python
# -*- coding: utf-8 -*-
# Far West 1798, a shooter multi player network game
# (C) Jean Ingrasciotta 2015 ginoingras@gmail.com
# licencied under GPLV3
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | ginoingras/FarWest1789 | FW1789_V001.py | Python | gpl-3.0 | 22,116 | [
"Dalton"
] | 1b5bd86e09e9f8d8e5e957467ad4f03a1f6c4940126fdc5bfe6797d4e09e6969 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/utils/test_qcprot.py | Python | gpl-2.0 | 6,678 | [
"MDAnalysis"
] | 266043dcf25c800075c54c31de7f79ae3a0213c25294f0519669f42e2844f5e5 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/sequence/_rna.py | Python | bsd-3-clause | 12,748 | [
"scikit-bio"
] | 4f8290f8080b8e3de16cf9a91ddf203b911a5f52e41230749d6f05eaff78215b |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | KonradBreitsprecher/espresso | testsuite/exclusions.py | Python | gpl-3.0 | 6,649 | [
"ESPResSo"
] | 51e3cc1d79f156c0f8e05ede517ab3c003d1d39c33fd45603e7af6479da638bd |
#!/usr/bin/env python
"""
Get summary informations of all productions
"""
import DIRAC
from DIRAC.Core.Utilities.PrettyPrint import printTable
from DIRAC.Core.Base.Script import Script
@Script()
def main():
Script.parseCommandLine()
from DIRAC.ProductionSystem.Client.ProductionClient import ProductionClient
... | DIRACGrid/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_get_all.py | Python | gpl-3.0 | 1,259 | [
"DIRAC"
] | db710b938dccc1740722067559ad7610c942e4c68f0a4f11c1a135003b688e3f |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/commoncode/test_ignore.py | Python | apache-2.0 | 8,496 | [
"VisIt"
] | 12dec42eb3e58506e8019ef2b30565b18ac9ad1e0a62e27984ebbf901118f753 |
import ROOT as R
f = R.TFile("histograms.root", "recreate")
funcs = ["gaus", "landau", "expo", "pol1"]
titles = ["Gaussian", "Landau", "Exponential", "First order polynomial"]
limits = [(-5, 5), (-5, 10), (0, 10), (0, 10)]
for idx in range(4):
h_name = "histogram_{0}".format(idx)
low, high = limits[idx]
h ... | alexpearce/example-monitoring-app | monitoring_app/static/files/generate_histograms.py | Python | mit | 439 | [
"Gaussian"
] | 35949f7aa99e828cd832f6e765afaf71d25ff254bf8a776662be08364d9b8bcb |
# Following tutorial on XML from https://docs.python.org/2/library/xml.etree.elementtree.html
# recommended by http://www.rdegges.com/quickly-extract-xml-data-with-python/
# Tracking on github in project https://github.com/rcoridan/NSF_History
from xml.etree import ElementTree as ET
import os, glob
import pandas as ... | rcoridan/NSF_History | 20140515_nsf-funding_pandas.py | Python | gpl-3.0 | 1,498 | [
"ADF"
] | cffdb9460032d31bc78f9b34d0589be50cb9ce41a6e16e032551d8b98d56d5f5 |
# coding: utf8
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN',
'# of International Staff': '# of International Staff',
'# of National ... | waidyanatha/sambro-eden | languages/ar.py | Python | mit | 288,112 | [
"VisIt"
] | fd0a9e530323007b0c88ff717a0a85a3b3f4d74702ade24dd44e8b5f8ede160f |
#
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may n... | gouravshenoy/airavata | sandbox/simstream/example/openmm_example/openmm_streamer.py | Python | apache-2.0 | 4,719 | [
"MDTraj",
"OpenMM"
] | 4f3245d692fdec496f5af285262a10060dd86ae524b2818a5b4aee48d9e54afd |
#!/usr/bin/env python
# A python script to remove outdated dependency files and associated objects. It operates from any
# directory within the herd. It cleans out the moose directory and any herd animials included in the
# Makefile.
#
# The script requires one input parameter, the root directory of MOOSE (e.g., ~/pro... | Chuban/moose | framework/scripts/rm_outdated_deps.py | Python | lgpl-2.1 | 4,850 | [
"MOOSE"
] | b67dc633b4f8442cad3e2529e3e2d1f6f22da940916ec5ef6f729d329c8d4290 |
#!/usr/bin/env python
# initial translation from the tcl by VTK/Utilities/tcl2py.py
# further cleanup and fixes to the translation by Charl P. Botha
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example demonstrates how to use the vtkImageTracerWidget
# to trace on a sli... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/GUI/Python/ImageTracerWidget.py | Python | gpl-3.0 | 7,773 | [
"VTK"
] | 72fef5ca257fd44dac68f5703f8460575cf8046a497e71386316872de0e424f6 |
#
# 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/tf2/callbacks.py | Python | apache-2.0 | 12,083 | [
"ORCA"
] | 4fae6585df8214a72d4c5d10a5ca6b3d5a0580b117768843cf7068535fa6a1e8 |
#!/usr/bin/env python
#
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
#... | YueLinHo/Subversion | tools/dev/graph-dav-servers.py | Python | apache-2.0 | 5,467 | [
"Brian"
] | 88e4ff63e44da1b2f249f92900f90353cb4c87c2838fd6d2cbd5accf01554785 |
import os, cv2
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from matplotlib.widgets import Slider, Button
def _changeThreshold(val):
global _percentThreshold
global _threshold
_percentThreshold = _slider.val
_threshold = _percentThreshold / 100 * 255
_chan... | userdw/RaspberryPi_3_Starter_Kit | 08_Image_Processing/Thresholding/adaptiveGaussianThresholding/adaptiveGaussianThresholding.py | Python | mit | 2,125 | [
"Gaussian"
] | 53a280bd1a20c759c7532b326e1fdbf17608b432a1765bdf8d2efb53ef112170 |
# Copyright (c) 2018 PaddlePaddle 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 app... | luotao1/Paddle | python/paddle/fluid/tests/unittests/test_gaussian_random_op.py | Python | apache-2.0 | 11,246 | [
"Gaussian"
] | f64c7886e11089ad2471bdfe6e43ebe2e2de500b9de07beccf58a0b4c1059d54 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
""" Twitter bot based on libturpial that reads RSS feeds and post them on
microblogging accounts """
# Authors:
# * Wil Alvarez (aka Satanas)
# Organization: ArepaDev <http://github.com/arepadev>
# Jan 26, 2012
import os
import sys
import time
import Queue
import shutil
... | arepadev/twitrss | twitrss.py | Python | gpl-3.0 | 29,494 | [
"VisIt"
] | 863fd26ab2bf3f99d7fb3a88937be77b14f4a425bf910ef41bf80bb9dd8df97e |
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
# create a new 'XDMF Reader'
periodic_solitary_wavesxmf = XDMFReader(FileNames=['/home/cekees/proteus/proteus/tests/periodic/hp025-new-weight/peri... | erdc/proteus | proteus/tests/periodic/hp025-new-weight/plot_soliton.py | Python | mit | 32,154 | [
"ParaView"
] | 18d4858fc76248c0b0475fbb08d22c89f65e414cf8f45e5d36691b2050b82ce3 |
# Lint as: python3
# Copyright 2020 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/tensorflow | tensorflow/python/eager/gradient_input_output_exclusions.py | Python | apache-2.0 | 12,622 | [
"VisIt"
] | 94c8d49b62e398f63e34ec98d89856907b865d41ddcad80ce06e176ab42fb227 |
import unittest
from StringIO import StringIO
from itcc.molecule import read
from itcc.tinker import tinker
test_in = ''' 5 molden generated tinker .xyz (mm3 param.)
1 C 0.000000 0.000000 0.000000 1 2 3 4 5
2 H 0.000000 0.000000 1.089000 5 1
3 H 1.0267... | lidaobing/itcc | tests/tinker/tinker.py | Python | gpl-3.0 | 695 | [
"TINKER"
] | ac6df67f868063450f45256221698df7a696a17b301c6df613b23bb27fb05e83 |
import os
import subprocess
import sys
from GpdbBuildBase import GpdbBuildBase
class GpBuild(GpdbBuildBase):
def __init__(self, mode):
self.mode = 'on' if mode == 'orca' else 'off'
def configure(self):
return subprocess.call(["./configure",
"--enable-orca",
... | lintzc/gpdb | concourse/scripts/builds/GpBuild.py | Python | apache-2.0 | 1,432 | [
"ORCA"
] | ee5f66a636f69531223be4faf7a37ffd50e77834ce1bead5639c25762580b740 |
from datetime import datetime, timedelta
from django.db import models
from django.db.models import F
from django.core import signing
from django.conf import settings
from django.core.exceptions import ImproperlyConfigured
from django.contrib.auth.models import User
from theme.models import UserProfile
from .utils imp... | hydroshare/hydroshare | hs_tracking/models.py | Python | bsd-3-clause | 11,384 | [
"VisIt"
] | 053b9febc550bac1c818a7a6400689c04dec4b2c19d4fb41b47c68e2ab543347 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/coulomb_mixed_periodicity.py | Python | gpl-3.0 | 3,986 | [
"ESPResSo"
] | a2e4c23180633c6eb057c9e875892c487e4b736d7c6f8c6816592eaea7910ba4 |
def printHSP(hsp, indent=''):
for attr in ['bits', 'expect', 'frame', 'query_end', 'query_start',
'sbjct', 'query', 'sbjct_end', 'sbjct_start']:
print('%s%s: %s' % (indent, attr, hsp[attr]))
def normalizeHSP(hsp, readLen, blastApplication):
"""
Examine an HSP and return informatio... | bamueh/dark-matter | dark/blast/hsp.py | Python | mit | 7,644 | [
"BLAST",
"Biopython"
] | c14929ad57ea903ad764c7490236526e28fbcbab2e7a69512c30759ffa0de07c |
#!/usr/bin/env python
from cvxpy import *
import numpy as np
import random
from math import pi, sqrt, exp
def gauss(n=11,sigma=1):
r = range(-int(n/2),int(n/2)+1)
return [1 / (sigma * sqrt(2*pi)) * exp(-float(x)**2/(2*sigma**2)) for x in r]
np.random.seed(5)
random.seed(5)
DENSITY = 0.1
n = 1000
x = Variabl... | riadnassiffe/Simulator | src/tools/ecos/cvxpy/examples/expr_trees/helloworld.py | Python | mit | 791 | [
"Gaussian"
] | bf9dabc6e6cfafbdaab4fb47133aba9d6a09687995c4decd2a88365c5ca4de76 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
It converts a FASTQ file from one PHRED quality score to another one.
Author: Daniel Nicorici, Daniel.Nicorici@gmail.com
Copyright (c) 2009-2021 Daniel Nicorici
This file is part of FusionCatcher.
FusionCatcher is free software: you can redistribute it and/or modi... | ndaniel/fusioncatcher | bin/phred.py | Python | gpl-3.0 | 10,921 | [
"Biopython"
] | 0084a67774941aa4a26bc75d0c8876a29f2746ddcc83ad45d05bb0ed48789834 |
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
# pyeq2 is a collection of equations expressed as Python classes
#
# Copyright (C) 2013 James R. Phillips
# 2548 Vera Cruz Drive
# Birmingham, AL 35235 USA
#
# email: zunzun@zunzun.com
#
... | burkesquires/pyeq2 | Models_2D/Logarithmic.py | Python | bsd-2-clause | 40,156 | [
"CRYSTAL"
] | bdc616fb1375414027aa4bc93e639c797b06066689210bf2faa07ea5d061071f |
#!/usr/bin/python
# Copyright 2017 SuperDARN Canada
#
# brian.py
# 2018-01-30
# Communicate with all processes to administrate the borealis software
import sys
import os
import time
from datetime import datetime
import threading
import argparse
import zmq
sys.path.append(os.environ["BOREALISPATH"])
if __debug__:
... | SuperDARNCanada/borealis | brian/brian.py | Python | gpl-3.0 | 11,734 | [
"Brian"
] | 00c81ee45a0198541ce6dfd52c64be9df6521c567de823a13122de386600e309 |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | panmari/tensorflow | tensorflow/contrib/distributions/python/ops/gaussian_conjugate_posteriors.py | Python | apache-2.0 | 4,476 | [
"Gaussian"
] | be94e6f2d0a1991e2665a5ccbb840e2aee6554325924522f8c94c8e224763b60 |
# -*- coding: utf-8 -*-
#
# gap_junctions_inhibitory_network.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version... | stinebuu/nest-simulator | pynest/examples/gap_junctions_inhibitory_network.py | Python | gpl-2.0 | 5,989 | [
"NEURON"
] | 2a27151825874216258d8dc2e83b51ea6179eba69116450346e292b24892f229 |
import numpy as np
class GaussianMoments(object):
"""
This class creates an object that returns the higher order
moments, of an non-central Gaussian, up to the 8-th order.
https://en.wikipedia.org/wiki/Normal_distribution
"""
__slots__ = ("m_arr", "v_arr", "n_size")
def __init__(se... | vrettasm/VGPA | code/src/gaussian_moments.py | Python | gpl-3.0 | 6,505 | [
"Gaussian"
] | ccc085b18e9a27e98bfb40a73e1106f7042c331f44f3221035de83c9d004c86b |
# -*- coding: utf-8 -*-
'''
Created on 2011/11/03
@author: tn10
'''
import exceptions
import multitask #@UnresolvedImport
from timeit import itertools
import itertools
from functools import wraps
def main():
pass
#if __name__ == '__main__': main()
def _treatment(pos, element):
return '%d: %s' % (pos, eleme... | t10471/python | practice/src/exclass/exclass.py | Python | mit | 6,118 | [
"Brian"
] | 6b71534fc70cc40c61e71889604ea1b7d7c27238deaf9c7468d1d77e8aebd938 |
'''
Utilities for generating sound.
'''
__id__ = "$Id$"
__version__ = "$Revision$"
__date__ = "$Date$"
__license__ = "LGPL"
import pyatspi
import orca.debug as debug
import orca.settings_manager as settings_manager
import orca.generator as generator
_settingsManager = settings_manager.getManager()
cl... | chrys87/orca-beep | src/orca/sound_generator.py | Python | lgpl-2.1 | 2,212 | [
"ORCA"
] | 814c2951aaef12d64972bc5ec3b5d9516196c78091f055d100c6f4d961b1f73d |
"""
.. _point_spread:
Corrupt known signal with point spread
======================================
The aim of this tutorial is to demonstrate how to put a known signal at a
desired location(s) in a :class:`mne.SourceEstimate` and then corrupt the
signal with point-spread by applying a forward and inverse solution.
"... | jniediek/mne-python | tutorials/plot_point_spread.py | Python | bsd-3-clause | 6,578 | [
"Gaussian"
] | 9087e85a93807e8a8b3960115bf54a6840933545bcd0def8d481c42b730a5adf |
"""Scraper for United States District Court for the District of Columbia
CourtID: dcd
Court Short Name: D.D.C.
Author: V. David Zvenyach
Date created: 2014-02-27
Substantially Revised: Brian W. Carver, 2014-03-28
"""
from juriscraper.opinions.united_states_backscrapers.federal_district import dcd_2013
class Site(dcd_... | brianwc/juriscraper | opinions/united_states_backscrapers/federal_district/dcd_2011.py | Python | bsd-2-clause | 507 | [
"Brian"
] | 631bbbc63c15d8d7727e848e282c1ae0c5b9bbf8ba56f9eeb5c0f15160c55202 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | Huawei-PaaS/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 38,108 | [
"CDK"
] | 08d47d76509f564fa99b89d45fc3814cdb8ff549bce25ee306ba2a804336e911 |
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