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""" Given the FTPdetectinfo file (assuming FF files are available) and the stddev of Gaussian PSF of the image,
correct the magnitudes and levels in the file for saturation. """
from __future__ import print_function, division, absolute_import
import os
import datetime
import numpy as np
import matplotlib.pyplot... | apevec/RMS | Utils/SaturationCorrection.py | Python | gpl-3.0 | 5,479 | [
"Gaussian"
] | 7ca594de670b909f01749a375525277578e17f2cb7844f74d0994d29c35423a0 |
"""
Class for outlier detection.
This class provides a framework for outlier detection. It consists in
several methods that can be added to a covariance estimator in order to
assess the outlying-ness of the observations of a data set.
Such a "outlier detector" object is proposed constructed from a robust
covariance es... | ldirer/scikit-learn | sklearn/covariance/outlier_detection.py | Python | bsd-3-clause | 6,604 | [
"Gaussian"
] | fc8ec396cc4a1148aac228a34b21ef387b8be823f63a09932bf91dec8c5b7b35 |
"""Use Hydra to detect structural variation using discordant read pairs.
Hydra: http://code.google.com/p/hydra-sv/
Pipeline: http://code.google.com/p/hydra-sv/wiki/TypicalWorkflow
"""
import os
import copy
import collections
import subprocess
import pysam
from bcbio import utils, broad
from bcbio.pipeline.alignment... | a113n/bcbio-nextgen | bcbio/structural/hydra.py | Python | mit | 7,180 | [
"pysam"
] | c4f7195800aca57c26b127485e0ad9cc121005f72daa770e078c2d117f945b84 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##
# smc.py: Sequential Monte Carlo module
##
# © 2012 Chris Ferrie (csferrie@gmail.com) and
# Christopher E. Granade (cgranade@gmail.com)
#
# This file is a part of the Qinfer project.
# Licensed under the AGPL version 3.
##
# This program is free software: you can redi... | MichalKononenko/python-qinfer | src/qinfer/smc.py | Python | agpl-3.0 | 49,222 | [
"Gaussian"
] | 1149d3e8288a529e50553c1daacc70867b9c1d1e198709ebae55c184c51c8682 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | felipebetancur/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 96,319 | [
"Gaussian"
] | ec5e474c913e368d0e15ecea771915e31e4c5b92563fa2b189bc2508352cedfd |
# -*- coding: utf-8 -*-
"""Filters to supplement :mod:`pybel.struct.filters`."""
from .edge_filters import * # noqa: F401,F403
from .node_deletion import * # noqa: F401,F403
from .node_filters import * # noqa: F401,F403
| pybel/pybel-tools | src/pybel_tools/filters/__init__.py | Python | mit | 225 | [
"Pybel"
] | 21fab9091e235e532e676df1ba767b2298eb4cade2d2a5e2de5f6e71f9cae183 |
#!/usr/bin/env python
'''
Developer script to convert yaml periodic table to json format.
Created on Nov 15, 2011
'''
from __future__ import division
import json
from itertools import product
import ruamel.yaml as yaml
import re
from monty.serialization import loadfn
from pymatgen import Element
from pymatgen.core... | dongsenfo/pymatgen | dev_scripts/update_pt_data.py | Python | mit | 8,456 | [
"pymatgen"
] | 3f5ec1366eca567975455246ea652391eb9f3e59aaab9393235771d33dcb579d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import unittest
import os
from pymatgen.analysis.structure_analyzer import VoronoiCoordFinder, \
solid_angle, contains_peroxide, RelaxationAnalyz... | matk86/pymatgen | pymatgen/analysis/tests/test_structure_analyzer.py | Python | mit | 23,270 | [
"VASP",
"pymatgen"
] | 06bf0e37522b7a2f6fb55d88e9e832ab306910189a266753e102ae6541e4e5e2 |
# coding=utf-8
# Copyright 2022 The Balloon Learning Environment 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 require... | google/balloon-learning-environment | balloon_learning_environment/agents/random_walk_agent.py | Python | apache-2.0 | 3,650 | [
"Gaussian"
] | 92f0a6278b414587045ab5a5f6eb9da5a3e427f9a9071943b0bbc1786f6ad681 |
import os
import warnings
import numpy as np
from netCDF4 import Dataset
from cfmeta import Cmip5File
from pyclimate.nchelpers import nc_copy_atts, nc_copy_var
class DerivableBase(object):
"""Reprents a group of base variables.
Grouped base variables are used to initiate calculating derived variables.
... | pacificclimate/pyclimate | pyclimate/variables.py | Python | gpl-3.0 | 11,961 | [
"NetCDF"
] | 7da6ad1b3eec30e21aec7b428049947b8cf3d5f5c0444d7fb3be805870f147e2 |
# Generated by Django 2.2.4 on 2019-09-10 11:45
from django.db import migrations
PEOPLE_LIABLE_TO_VANDALISM = {
2811, # Theresa May
1120, # Jeremy Corbyn
4546, # Boris Johnson
6035, # Paul Nuttall
8372, # Nicola Sturgeon
737, # Ruth Davidson
34605, # Matt Furey-King (due to a vandal... | DemocracyClub/yournextrepresentative | ynr/apps/people/migrations/0017_set_vandalism_list.py | Python | agpl-3.0 | 10,823 | [
"Amber"
] | dbf7d06394e20cca6a3a53d2e8fdbe4d2592e15f362df0f7a3af7f871558663c |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from monty.json import MSONable
import numpy as np
import warnings
from pymatgen.core.spectrum import Spectrum
from copy import deepcopy
from veidt.elsie.preprocessing import Preprocessing
from veidt.elsie import si... | czhengsci/veidt | veidt/elsie/spectra_similarity.py | Python | bsd-3-clause | 17,366 | [
"pymatgen"
] | e58af651ce9dd88aa0e7ee494c1da831f1df38508594554392edf6dfcdbf1bc8 |
from PyQt4.QtGui import QGroupBox, QSizePolicy, QRadioButton, QHBoxLayout
class BasisTypeWidget(QGroupBox):
def __init__(self, parent=None):
super(QGroupBox, self).__init__(parent)
self.initUI()
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
def initUI(self):
se... | beangoben/toulouse_secretgui | cipsi/BasisTypeWidget.py | Python | gpl-3.0 | 844 | [
"Gaussian"
] | a447db40469128fd89118f2b51dce1d2124cfc0c3afc3aa714b9bac190e73a08 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 22 17:21:56 2018
.. codeauthor:: Jonas Svenstrup Hansen <jonas.svenstrup@gmail.com>
"""
import os
import numpy as np
import random
from astropy.io import fits
from astropy.table import Table, Column
from astropy.wcs import WCS
# Import stuff from ... | tasoc/photometry | simulation/simulateFITS.py | Python | gpl-3.0 | 13,921 | [
"Gaussian"
] | e364f3ba75bc0c6d1a236bb0780c9eb42862bfe58d696b74e957d29622383a4f |
#!/usr/bin/env python
import argparse
import random
words = ["a",
"a&p",
"a's",
"aa",
"aaa",
"aaaa",
"aaron",
"ab",
"aba",
"ababa",
"aback",
"abase",
"abash",
"abate",
"abbas",
"abbe",
"abbey",
"abbot",
"abbott",
"abc",
"abe",
"abed",
"abel",
"abet",
"abide",
"abject",
"ablaze",
"able",
"abner",
"abo",
"abode",
"abor... | changlinli/diceware-generators | diceware.py | Python | unlicense | 64,687 | [
"Amber",
"BLAST",
"Brian",
"DIRAC",
"Elk",
"GULP",
"Galaxy",
"MOE",
"MOOSE",
"NEURON",
"VisIt"
] | 0dd48547ba8856eda9eeaa8b4e3714c3c6e4e17f08dd06850f3a4fc2b944b25d |
#!/usr/bin/env python
from __future__ import division
import re
import os
import sys
from glob import glob
from getopt import getopt
blastdb=""
gi2taxid_file=""
do_psiblast=True
htaxid={}
taxhash={}
numOfIter=3
out=False
rm_psiblast=False
psi_path=""
try:
opts, args = getopt(sys.argv[1:], "hd:g:p:i:orl:", ["help", ... | agnmyk/simphypro | psi_parse.py | Python | mit | 4,537 | [
"BLAST"
] | 822f52bc986c43b2146157134fda850af91645918d54443a9b9131dbdc52b1dc |
""" SiteInspectorAgent
This agent inspect Sites, and evaluates policies that apply.
"""
__RCSID__ = '$Id$'
import math
import Queue
from DIRAC import S_OK
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.Core.Utili... | arrabito/DIRAC | ResourceStatusSystem/Agent/SiteInspectorAgent.py | Python | gpl-3.0 | 5,660 | [
"DIRAC"
] | 90f0b77cb9e6d77e2eca750cce166eff6abcf6be18863268812027521d8efa80 |
#PENDING TASKS FOR FURTHER OPTIMIZATION:
#1. hMat grows 2*int(radMax)+1 for all radiuses; i.e., all "radius" dimensions are growing to max radius size;
# Enlarge each matrix only by its corresponding radius size
#2. A given (a,b) point currently only votes for themselves; try voting for "neighboring" pixels and ev... | ashimb9/hough_transform | hough_circle.py | Python | gpl-3.0 | 4,167 | [
"Gaussian"
] | dfaa4e06f3f97999f745da99192e20639c42b3679658089a2399721d3c67634f |
""" ntsne.py
numpy wrapper for bh_tsne (https://github.com/lvdmaaten/bhtsne)
Brian DeCost bdecost@andrew.cmu.edu
"""
import os
import re
import shutil
import struct
import tempfile
import subprocess
import numpy as np
# vdM's bh_tsne reads and writes from/to these hardcoded paths
# in the directory from which ... | bdecost/ntsne | ntsne.py | Python | mit | 4,058 | [
"Brian"
] | 136b0a7ffc0925ea076de9b48785551f87f5df15b4aa5d78e14a8d1e6552cec7 |
import collections.abc
import warnings
from abc import abstractmethod
from collections import defaultdict
from datetime import datetime
from enum import Enum, EnumMeta
from textwrap import dedent
from typing import Any, Callable, Dict, Mapping, Optional, Set, Tuple, Union
from urllib.parse import urlencode
import ciso... | jeremyh/eo-datasets | eodatasets3/properties.py | Python | apache-2.0 | 25,006 | [
"NetCDF"
] | 3600bde7a618594421b8663241595f55e16cbb69f82295b1d7acab910bec6833 |
import json
import requests
import os
from settings import global_settings
_amino_acids_json_path = os.path.join(global_settings['package_path'], 'tools', 'amino_acids.json')
with open(_amino_acids_json_path, 'r') as inf:
amino_acids_dict = json.loads(inf.read())
water_mass = 18.01528
ideal_backbone_bond_length... | woolfson-group/isambard | isambard/tools/amino_acids.py | Python | mit | 15,990 | [
"Biopython"
] | e94df5a0f27765ba2f0c19bd3b478bb1b6a9faea2fc03094025a1c387c7237ed |
"""
:mod:`Mutators` -- mutation methods module
=====================================================================
In this module we have the genetic operators of mutation for each chromosome representation.
"""
import Util
from random import randint as rand_randint, gauss as rand_gauss, uniform as rand_uniform
f... | HyperloopTeam/FullOpenMDAO | lib/python2.7/site-packages/Pyevolve-0.6-py2.7.egg/pyevolve/Mutators.py | Python | gpl-2.0 | 27,943 | [
"Gaussian"
] | 003ed0cb026a3f9ecf532e8edb1efd55359c929c6f449650732912545ffcf612 |
"""
$Id: loggingrli.py,v 1.41 2006/04/24 14:49:23 jp Exp $
"""
import plastk.rl
from plastk.rl import RLI
from plastk.params import Parameter
from plastk import rand
#from Scientific.IO.NetCDF import NetCDFFile
from scipy.io.netcdf import netcdf_file as NetCDFFile
import time,sys,threading,os
NewColumn = 'new column'... | ronaldahmed/robot-navigation | neural-navigation-with-lstm/MARCO/plastk/rl/loggingrli.py | Python | mit | 16,837 | [
"NetCDF"
] | 341a18bf232268b8d44a9b50e7081e85fc80173c199d75573dc6fbb98f997cab |
#### PATTERN | DE | INFLECT ########################################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2012 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
######################################################... | EricSchles/pattern | pattern/text/de/inflect.py | Python | bsd-3-clause | 28,754 | [
"ASE"
] | 1019d722f0d1579e6367e28274bb6f9675a2b71a42fa657c0a548267022dff8c |
# -*- coding: utf-8 -*-
"""This module builds mutation functions that are bound to a manager."""
from typing import Callable
from pybel import BELGraph, Manager
from pybel.struct.mutation.expansion.neighborhood import expand_node_neighborhood
from pybel.struct.pipeline import in_place_transformation, uni_in_place_tr... | pybel/pybel-tools | src/pybel_tools/mutation/bound.py | Python | mit | 1,398 | [
"Pybel"
] | fb756b684f463593452abc97b7c5d9ca492983b96045a56e5119ec823b8d921f |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/gto/basis/parse_gaussian.py | Python | apache-2.0 | 3,951 | [
"Gaussian",
"NWChem",
"PySCF"
] | 16a74dea400a7a817238b067559121ec13764474256820d1ff5bd0e8dff5f176 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/fci/direct_uhf.py | Python | apache-2.0 | 14,488 | [
"PySCF"
] | 0eb1c5e46a86b7e137d60e524cacb648a7f0322e6eea1ef08a12da75b1f265d1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import time
import math
import espressopp
import mpi4py.MPI as MPI
import unittest
def vec_pbc(u,v,cell):
#vector u-v
dx = u[0] - v[0]
dy = u[1] - v[1]
dz = u[2] - v[2]
dx = dx - round(dx/cell[0])*cell[0]
dy = dy - round(dy/cell[1])*cell[1]
... | acfogarty/espressopp | testsuite/interaction_potentials/dihedral_harmonic/test_dihedralharmonic.py | Python | gpl-3.0 | 5,042 | [
"Gromacs",
"VMD"
] | 106dba4009cef3713639280bd7a156d0ccc0a55a07c71034b710b35abf16bc7e |
# -*- coding: utf-8 -*-
"""Transport functions for Amazon Web Services (AWS).
AWS has a cloud-based file storage service called S3 that can be programatically
accessed using the :mod:`boto3` package. This module provides functions for quickly
wrapping upload/download of BEL graphs using the gzipped Node-Link schema.
... | pybel/pybel | src/pybel/io/aws.py | Python | mit | 3,050 | [
"Pybel"
] | d45121418d73f022935b7eac4982b3bbf13ae0c136ffe8f5106591293900589d |
from .base import *
class diffusion(object):
"""
cytoscape session interface as shown in CyREST's swagger documentation for 'diffusion'.
:param url: an url of the type 'http://' + host + ':' + str(port) + '/' + version + '/'.
"""
def __init__(self, url):
self.__url = url + 'commands/diffu... | idekerlab/py2cytoscape | py2cytoscape/cyrest/diffusion.py | Python | mit | 2,230 | [
"Cytoscape"
] | 313a60b32f04e8d3ed0876920b5d44bc794f92b7a32faf5bf7c4c0a9cec82f5f |
'''Simulator independent grid cell network code.
.. currentmodule:: grid_cell_model.models.gc_net
Attractor network setup
-----------------------
This file is a module for the grid cell network. It allows you to create a
network of exponential integrate and fire neurons. There are two populations:
* Stellate cell... | MattNolanLab/ei-attractor | grid_cell_model/models/gc_net.py | Python | gpl-3.0 | 23,856 | [
"Gaussian",
"NEURON"
] | b6b4e05b69a1ff00e71643bea3488eff5e0a646569a4eb3b2d30f0b6b694c2f0 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=too-many-arguments
import sys
from scripts.writer import w... | neilswainston/PathwayGenie | scripts/strain_writer.py | Python | mit | 738 | [
"VisIt"
] | 6337092947f89c480b3ef17bef03e717a826bc0543046b523f5fb71db8965a13 |
# 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.
"""Use the DSSP program to calculate secondary structure and accessibility.
You need to h... | zjuchenyuan/BioWeb | Lib/Bio/PDB/DSSP.py | Python | mit | 15,902 | [
"Biopython"
] | bc3050270774554ccdd0665407b488663276699d80953bed22c794f4e5d37294 |
import os
import pytest
import logging
import numpy as np
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.utils import sct_test_path, sct_dir_local_path
from spinalcordtoolbox.scripts import sct_register_multimodal, sct_create_mask
logger = logging.getLogger(__name__)
def test_sct_register_multimo... | neuropoly/spinalcordtoolbox | testing/cli/test_cli_sct_register_multimodal.py | Python | mit | 5,959 | [
"Gaussian"
] | 9942bb0a18b7433bfa45d1207287745ac49458cc6e71668105bf1eb47c864dd0 |
import numpy as np
# Set the random seed for reproducibility
seed = np.random.randint(2**16)
print "Seed: ", seed
np.random.seed(seed)
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon
from optofit.cneuron.compartment import Compartment, SquidCompartment
from optofit.cneuron.channels import LeakC... | HIPS/optofit | examples/cython_demo.py | Python | gpl-2.0 | 4,626 | [
"Gaussian"
] | 73faa061f55809978f7ef560cc200b2cb514a77de717b46d9be62f0344c2f0a5 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
#File has been modified to check for endless data attack
import gtk, pango
from zeroinstall import _, translation
from zeroinstall.support import tasks, pretty_size
from zeroinstall.injector import model, reader, dow... | AlexanderRyzhko/0install-TUF | zeroinstall/0launch-gui/iface_browser.py | Python | lgpl-2.1 | 20,425 | [
"VisIt"
] | 0ff2436214edcdb87b8a586c869919cdb680b77a514b7586b5eaa754f4d8f4ea |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/dftd3/test/test_dftd3.py | Python | apache-2.0 | 1,865 | [
"PySCF"
] | 751e4ba5d402aa73c5a09c6a771551dbe3ae2b5894a59e77904d1fa039b2cddb |
# -*- coding: utf-8 -*-
"""Tests for graph operations."""
import unittest
from pybel import BELGraph
from pybel.dsl import protein
from pybel.struct.operations import (
left_full_join,
left_node_intersection_join,
left_outer_join,
node_intersection,
union,
)
from pybel.testing.utils import n
p1,... | pybel/pybel | tests/test_struct/test_struct_operations.py | Python | mit | 8,752 | [
"Pybel"
] | a49dbd7f44b835c17f6345677a5fe529e1f41a85e7d6c0d75d08f7f1f38fc8ac |
#!/usr/bin/env python
import argparse
import shutil
import icqsol_utils
# Parse Command Line.
parser = argparse.ArgumentParser()
parser.add_argument('--input', dest='input', help='Shape dataset selected from history')
parser.add_argument('--input_file_format_and_type', dest='input_file_format_and_type', help='Input f... | pletzer/galaxy-csg | tools/icqsol_add_surface_field_from_expression/icqsol_add_surface_field_from_expression.py | Python | mit | 3,070 | [
"VTK"
] | 3b07b52c9d91e052e220df85cbbd152b2674f3f268ef409b929f0c81574f0977 |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | illfelder/libcloud | libcloud/compute/drivers/azure.py | Python | apache-2.0 | 113,249 | [
"VisIt"
] | c6005998ac007ac4fbd04438589d2e0e1e7bae9702458d765ba0f97d993c0961 |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | zifeo/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 11,722 | [
"NEURON"
] | 9a0943f1258171c92e8b1e44814246ed714d43f14ca36546f543ce50d6dd5713 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/LennardJonesAutoBonds.py | Python | gpl-3.0 | 7,807 | [
"ESPResSo"
] | d9acd84347aa39b513379f03c724b092500d4f2b503e800aa5cf92de7bdba816 |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-gke-connect-gateway | scripts/fixup_gateway_v1beta1_keywords.py | Python | apache-2.0 | 6,237 | [
"VisIt"
] | aa17e8b517b7edaf7b00fd70f9141bf7bd56b55c0e8ae71a917e88789e05fd66 |
###############################################################################
# Name: s.py #
# Purpose: Define S and R syntax for highlighting and other features #
# Author: Cody Precord <cprecord@editra.org> #
... | garrettcap/Bulletproof-Backup | wx/tools/Editra/src/syntax/_s.py | Python | gpl-2.0 | 12,071 | [
"Gaussian"
] | 1d75aa1e5e706e6ef2475b544a2d93e496c10586c23ce79f34031d5aa4c62408 |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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.
#
# Seal is dis... | crs4/seal | tests/tseal/lib/aligner/bwa/test_bwa_memory.py | Python | gpl-3.0 | 4,962 | [
"BWA"
] | 2a087ac3bf5647732a66ab1bebb79ee6667ce9502a7a6090b9441bf9adb76b5f |
import torch
import numpy as np
from torch import nn
def identity(x):
return x
_str_to_activation = {
'identity': identity,
'relu': nn.ReLU(),
'tanh': nn.Tanh(),
'leaky_relu': nn.LeakyReLU(),
'sigmoid': nn.Sigmoid(),
'selu': nn.SELU(),
'softplus': nn.Softplus(),
}
def activation_fr... | vitchyr/rlkit | rlkit/torch/pytorch_util.py | Python | mit | 8,657 | [
"Gaussian"
] | c85164180ac091b0f962c28d4659b39afe5e2fd5f6765b6e7999b359099a8595 |
#!/usr/bin/env python
# This file is part of fast-tab and licensed under The MIT License (MIT).
import threading
import urllib
import re
import time
from config import *
class HttpError(BaseException):
def __init__(self, value):
self.value = value
def __str__(self):
return repr(self.value)
c... | Tie-fighter/fast-tab | CrawlerThread.py | Python | mit | 3,039 | [
"VisIt"
] | 5daf225f48ffd20ffd073cceb7d34557bde49b2c94de7506d04c98afcf955c12 |
""" Queries BDII for unknown CE.
Queries BDII for CE information and puts it to CS.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.Core.Utilities ... | coberger/DIRAC | ConfigurationSystem/Agent/CE2CSAgent.py | Python | gpl-3.0 | 21,288 | [
"DIRAC"
] | a9957a2f23f09b9aaf80b9c9f3a0d1e7e34a682429594d17810ef9dcbf18dd88 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Scour
#
# Copyright 2010 Jeff Schiller
# Copyright 2010 Louis Simard
# Copyright 2013-2014 Tavendo GmbH
#
# This file is part of Scour, http://www.codedread.com/scour/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this fil... | codedread/scour | scour/scour.py | Python | apache-2.0 | 178,584 | [
"VisIt"
] | ba723e8a69a43210c6ddab6a359e181245b8a4976505f41e7a789d895349b405 |
#!/usr/bin/env python
#
# LSST Data Management System
# Copyright 2012 LSST Corporation.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publishe... | LSST-nonproject/obs_omegacam | tests/getRaw.py | Python | gpl-3.0 | 4,058 | [
"VisIt"
] | 3e4622187211ba145830a0910c43a065f71dfacb4473009a5ae02bfdf2871b6e |
#!/usr/bin/env python
#
# Copyright 2002-2003 by Michael Hoffman. All rights reserved.
# 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.
"""Bio.DocSQL: easy access to DB API databases.
>>> import os
... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/DocSQL.py | Python | gpl-2.0 | 6,126 | [
"Biopython"
] | a84f9ba6816192dad44bee4e785d205878b6c3ca626b1c3b01456b7ad4eba06c |
########################################################################
#
# (C) 2015, Chris Houseknecht <chouse@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 Fo... | azaghal/ansible | lib/ansible/galaxy/token.py | Python | gpl-3.0 | 5,736 | [
"Galaxy"
] | b6eada297fb0c43b903bdce96055d68d3d6e20122d673c92b8ad5c39032d77e1 |
import urllib
import requests
from requests import ConnectionError
from inbox.util.url import url_concat
from inbox.log import get_logger
log = get_logger()
from inbox.config import config
from inbox.basicauth import AuthError
# Google OAuth app credentials
GOOGLE_OAUTH_CLIENT_ID = config.get_required('GOOGLE_OAUTH_C... | abhishekgahlot/inbox | inbox/oauth.py | Python | agpl-3.0 | 6,163 | [
"VisIt"
] | d648ad9b618d5af7928102dd3e937c935c7dd15f66efb57682cadc2748bae660 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import zeroinstall
from zeroinstall import _
from zeroinstall.cmd import slave
from zeroinstall.support import tasks, unicode
from zeroinstall.injector.model import Interface
from zeroinstall.gtkui import help_box
im... | afb/0install | zeroinstall/gui/properties.py | Python | lgpl-2.1 | 14,097 | [
"VisIt"
] | 9cde02e313ac7aa19ee99e0095514500d26d08ea8bd2adf6b3be6f6c21cd1211 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | HackFisher/depot_tools | third_party/pylint/utils.py | Python | bsd-3-clause | 36,111 | [
"VisIt"
] | 3a6f4ff71e5f4b63dc01008f8aee7abde72caadda45fb78571ddfe89d3883531 |
(S'eb620a20b854ca69f2419f6edb7859f3'
p1
(ihappydoclib.parseinfo.moduleinfo
ModuleInfo
p2
(dp3
S'_namespaces'
p4
((dp5
S'Atom'
p6
(ihappydoclib.parseinfo.classinfo
ClassInfo
p7
(dp8
g4
((dp9
(dp10
S'__init__'
p11
(ihappydoclib.parseinfo.functioninfo
FunctionInfo
p12
(dp13
g4
((dp14
(dp15
tp16
sS'_exception_info'
p17
(dp... | pekkosk/hotbit | box/.happydoc.md.py | Python | gpl-2.0 | 15,727 | [
"Gaussian",
"VTK"
] | 551bcc91a2f2a3db00481f7a7d6eb68af1fa407a5843d1e64c2a08f4f653efaa |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | PeterLauris/aifh | vol1/python-examples/examples/example_anneal_disc_tsp.py | Python | apache-2.0 | 6,012 | [
"VisIt"
] | dd49133df65a51a400e1786c4d3d405b4a0a1091875d4945a7030803fca95b68 |
"""
This script runs an unbiased LAMMPS MD simulation, and stores the values of CVs along with
their corresponding potential and kinetic energies.
After that, the CVs are meshed at a given precision and the thermodynamical observables
such as F, E_min, TS and more are calculated from the values of PotEng.
"""
from __f... | marcocaccin/LearningMetaDynamics | MD_unconstrained/md_db0_build2.py | Python | gpl-2.0 | 7,243 | [
"ASE",
"LAMMPS"
] | 4806c1e46fe9155325857b3164b9e94cc8574a17ecc1aeac98d8a807a9e6426c |
'''
Copyright 2009, 2010 Brian S. Eastwood.
This file is part of Synctity.
Synctity 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.
Syncti... | beastwood/synctity | synctity.py | Python | gpl-3.0 | 22,018 | [
"Brian"
] | 8aed7fc913986f953df6cbf2204e9718ff13d5932d63699d3d7000c1638659e0 |
#!/usr/bin/python
# script for computing overlap signatures from a bowtie output
# Christophe Antoniewski <drosofff@gmail.com>
# Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target>
# <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedu... | drosofff/tools-artbio | deprecated/msp_sr_signature/signature.py | Python | mit | 5,451 | [
"Bowtie"
] | 83e6feb2f06ea1e7262787c9aaf3ef872a30f7227c0391236ce05d33ca54a0b5 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | corburn/scikit-bio | skbio/stats/distance/_base.py | Python | bsd-3-clause | 32,394 | [
"scikit-bio"
] | a9c0fdec1e7481973d388cd1070bb191f4ecb45970ea6b12cfd4f654ee001c7f |
#!/usr/bin/env python
# Translated from Hanoi.cxx.
import vtk
class GV(object):
"""
Used to store global variables.
"""
def __init__(self, numberOfPucks=5, numberOfSteps=5, puckResolution=48, configuration=0):
self.numberOfPucks = numberOfPucks
self.numberOfSteps = numberOfSteps
... | lorensen/VTKExamples | src/Python/Visualization/Hanoi.py | Python | apache-2.0 | 12,641 | [
"VTK"
] | dd47338e91fbe40981ef0c44db4ad027e5c44bf8bf515fda4259e609355d5d20 |
# -*- coding: utf-8 -*-
# Copyright (C) 2014 Daniele Simonetti
#
# 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.
#
# Thi... | Kaniabi/l5r-character-manager-3 | l5r/main.py | Python | gpl-3.0 | 100,415 | [
"VisIt"
] | f132151bfc50ae2409b8829bf17141604d96ade3d2b7bbeb8fad9989aee4093f |
# Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree. An additional grant
# of patent rights can be found in the PATENTS file in the same directory.
task_config = {}
"""A sh... | calee88/ParlAI | parlai/mturk/tasks/model_evaluator/task_config.py | Python | bsd-3-clause | 2,630 | [
"CASINO"
] | 8c63c44dc7146dcc97d866aaf11d63708724a9261ca67330de82b53c79ad131e |
import unittest
from octopus.server.shell_mananger import ShellManager
class TestShellManager(unittest.TestCase):
def testUnreachableServer(self):
self.hostname = 'localhost'
self.port = '1337'
shell_manager = ShellManager(self.hostname, self.port)
shells = shell_manager.list()
... | octopus-platform/octopus-tools | tests/orientdb_shell_manager.py | Python | lgpl-3.0 | 383 | [
"Octopus"
] | 687dfe2c320848738afbb77dffcb18bf30831a0e7241bf158b6dcb1acbe5ae6c |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawLoops(myscreen,loops,loopColor):
# draw the loops
nloop = 0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
i... | JohnyEngine/CNC | opencamlib/scripts/waterline/waterline_8_tux_adaptive.py | Python | apache-2.0 | 2,739 | [
"VTK"
] | 9b96e53963ff4f3943b74bee2e5b93ec8e6acca807fde324eba1f0781b714e96 |
"""
===========================================
===========================================
Author: Shujia Huang & Siyang Liu
Date : 2014-05-20 08:50:06
"""
import sys
import numpy as np
from sklearn import mixture
from sklearn.utils.extmath import logsumexp
# My own class
import VariantDatum as vd
import VariantRecal... | ShujiaHuang/AsmVar | src/AsmvarVarScore/modul/VariantRecalibratorEngine.py | Python | mit | 5,602 | [
"Gaussian"
] | 17dc68fbd6dd03692b4343f6efe316064e919cc015fd2fc1aa7d5640e3927138 |
# Copyright (c) 2015-2016 Cisco Systems, Inc.
#
# 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, merge... | rgreinho/molecule | molecule/command/dependency.py | Python | mit | 2,997 | [
"Galaxy"
] | 1cc2395234bdf8f7ae9ad7d1dea43892325e25b2625544c8c8eb6282b6ebf987 |
########################################################################
# $HeadURL $
# File: RegisterOperation.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/19 13:55:14
########################################################################
""" :mod: RegisterFile
==================
.. module: R... | sposs/DIRAC | DataManagementSystem/Agent/RequestOperations/RegisterFile.py | Python | gpl-3.0 | 3,599 | [
"DIRAC"
] | 4168366998290cfcf420db21cc137683b399503791ecef8522ec5b70e61a5328 |
# Starts Gevent which runs Flask
from gevent.pywsgi import WSGIServer
from neuron.app import app
def start_gevent(app_port):
http_server = WSGIServer(('', app_port), app)
http_server.serve_forever()
if __name__ == "__main__":
start_gevent(5000)
| Andrew-Shay/Neuron | neuron/start_gevent.py | Python | mit | 262 | [
"NEURON"
] | e38e6d3a9680f9e6d0ad8de4c5ddda5f2b1e54be67fb6bad4ac2dfa16445b2a4 |
from ....interfaces import utility as util # utility
from ....pipeline import engine as pe # pypeline engine
from ....interfaces import camino as camino
from ....interfaces import fsl as fsl
from ....interfaces import camino2trackvis as cam2trk
from ....algorithms import misc as misc
from ...misc.utils imp... | sgiavasis/nipype | nipype/workflows/dmri/camino/diffusion.py | Python | bsd-3-clause | 10,837 | [
"ParaView",
"VTK"
] | 5ca9d2fb2e23bbb0d0d4de54e66503e0171b1fd211cf3b8114f7a980140158ce |
#!/usr/bin/env python
"""Modules for calculating thermochemical information from computational
outputs."""
import os
import sys
import numpy as np
from ase import units
def rotationalinertia(atoms):
"""Calculates the three principle moments of inertia for an ASE atoms
object. This uses the atomic masses from... | slabanja/ase | ase/thermochemistry.py | Python | gpl-2.0 | 14,410 | [
"ASE"
] | 7fa5edc9d586f0c1f8f35402150fbec51406d6714b027a76b5c1a95e956a8b44 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, getopt
import re
import os
import csv
import shlex, subprocess
import pickle
import html2text
import time, datetime
import math
import json
from json import encoder
encoder.FLOAT_REPR = lambda o: format(o, '.2f')
from operator import itemgetter, attrgetter
relo... | ychahibi/ntnu-trondheim-igem | igem_matchmaker/backend/downloadAllTeamsInfos.py | Python | apache-2.0 | 14,769 | [
"VisIt"
] | 5484bdbe8c90d2492465375282574bf99d0949aba2be0c3ab28fab93c079fb53 |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import gw as gw_c
class KnowValues(unittest.TestCase):
def test_rf0_ref(self):
""" This is GW """
mol = gto.M( verbose = 1, atom = '''H 0 0 0; H 0.17 0.7 0.587''', basis = 'cc-pvdz',)
... | gkc1000/pyscf | pyscf/nao/test/test_0052_gw_rf0_ref.py | Python | apache-2.0 | 1,018 | [
"PySCF"
] | 5bc3705a7e74a61f1ecf238aa3d4caa8e6db2ebec7cc4aa14f9ada98e919297c |
"""
Test functions for models.GLM
"""
import os
import numpy as np
from numpy.testing import *
import statsmodels.api as sm
from statsmodels.genmod.generalized_linear_model import GLM
from statsmodels.tools.tools import add_constant
from statsmodels.tools.sm_exceptions import PerfectSeparationError
from nose import Sk... | pprett/statsmodels | statsmodels/genmod/tests/test_glm.py | Python | bsd-3-clause | 17,451 | [
"Gaussian"
] | ffe620636f45a8211d20bf2e2aa52724e9bea56fbe0df4ff908518ce4d5f14a7 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | testsuite/python/lb_boundary.py | Python | gpl-3.0 | 4,708 | [
"ESPResSo"
] | e09a595e41d9367dab5037369a227e2bf43879f02ad741ed0b803790c6dbd319 |
#!/bin/env python
import time
import simtk.openmm as mm
from simtk.openmm import app
from simtk.openmm import Platform
from simtk.unit import *
import numpy as np
from mdtraj.reporters import NetCDFReporter
from smarty import *
import sys
import numpy as np
molname = [sys.argv[1]]
mol_filename = ['Mol2_files/'+m+'.mo... | bmanubay/open-forcefield-tools | single-molecule-property-generation/run_molecule_v3.py | Python | mit | 3,988 | [
"MDTraj",
"OpenMM"
] | 3516becb5d13e76198d514e551c9980aca77d08faa760f6ecd69421f2598b94a |
# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# 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.
# get set abstraction for graph representation
from functools import reduce
# TODO - Sub... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Pathway/Rep/MultiGraph.py | Python | gpl-2.0 | 6,743 | [
"Biopython"
] | 4885b9325aff6f2bf470883981dc74d88f209a0d6ad5043fd98a7abe483893a6 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/utils.py | Python | gpl-2.0 | 9,298 | [
"VisIt"
] | a2b9d760e7c4d0db16b320e85413ddf56e6001420f1b9cc30df89f1b824a0295 |
# $HeadURL$
__RCSID__ = "$Id$"
import types
import threading
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.FrameworkSystem.Client.Logger import gLogger
gEventSync = Synchronizer()
class EventDispatcher:
def __init__( self ):
sel... | sposs/DIRAC | Core/Utilities/EventDispatcher.py | Python | gpl-3.0 | 2,888 | [
"DIRAC"
] | 5446f8ab0da22ff68d1e43c0f4f0c839afa6e93333d0255393b9cb4b99b7c1e4 |
#!/usr/bin/env python
import os
import numpy as np
if __name__ == '__main__':
from pyscf.pbc import gto
from pyscf.pbc.scf import RHF
from qharv.cross import pqscf
import sys
sys.path.insert(0,'../basis')
from basis import bfd_basis
mygs = 16 # grid density
# grid density for visualization
myvgs =... | Paul-St-Young/share | algorithms/iso3d/hf/obj_from_chf.py | Python | mit | 2,691 | [
"PySCF"
] | 91365799fe3cc974a8d3fc06b882c0d561614388aa109db5f6a81ff3cc79724d |
import os, sys
import logging
from optparse import OptionParser
import matplotlib
matplotlib.use('PDF')
from hiclib import mapping
from mirnylib import h5dict, genome, plotting
from hiclib import fragmentHiC, binnedData
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import numpy ... | aehrc/ngsane | tools/hiclibMapping.py | Python | bsd-3-clause | 14,871 | [
"Biopython",
"Bowtie"
] | da6aedcf37787bf1b520f89f6b8c34144768bea5a0c086c2a56b3588dcaac726 |
# -*- coding: utf-8 -*-
#
# test_growth_curves.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Lice... | weidel-p/nest-simulator | pynest/nest/tests/test_sp/test_growth_curves.py | Python | gpl-2.0 | 14,529 | [
"Gaussian"
] | 2a196bb3a1b336d226cc81d0278e632f12ba921f4055e172f80fddee190f5d28 |
# Copyright 2002 Gary Strangman. All rights reserved
# Copyright 2002-2016 The SciPy Developers
#
# The original code from Gary Strangman was heavily adapted for
# use in SciPy by Travis Oliphant. The original code came with the
# following disclaimer:
#
# This software is provided "as-is". There are no expressed or... | jamestwebber/scipy | scipy/stats/stats.py | Python | bsd-3-clause | 257,732 | [
"DIRAC"
] | 1ff33fd8e2ed92246bfbd9a74068149b121a6c2f452cc0f98145532394886102 |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | nervous-laughter/q2-demux | q2_demux/tests/test_demux.py | Python | bsd-3-clause | 35,140 | [
"scikit-bio"
] | bec51178e83bc3f61780cd91d0b468ab065e438c1d1d28146a7dc91e2f8e1f5a |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import tensorflow as tf
import numpy as np
from tf_sparsenet import Sparsenet as snet
try:
import matplotlib.pyplot as plt
except ImportError:
print("Can't import matplotlib. No plotting.")
def block_diag(*ar... | emdodds/DictLearner | tf_toposparse.py | Python | mit | 9,336 | [
"Gaussian"
] | dae03b509a2e669647bcd097e017232275bba8903d72471c868016d71896105c |
"""
This module module is used to generate the CAs and CRLs (revoked certificates)
Example::
from DIRAC.Core.Security import Utilities
retVal = Utilities.generateRevokedCertsFile()
if retVal['OK']:
cl = Elasticsearch( self.__url,
timeout = self.__timeout,
us... | fstagni/DIRAC | Core/Security/Utilities.py | Python | gpl-3.0 | 3,245 | [
"DIRAC"
] | fe6c65a92443538f7a6938dd6c7e2a7fb469eed55f63924b9c406827e53b7532 |
# Copyright 2018 the GPflow 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 writi... | GPflow/GPflow | tests/gpflow/expectations/test_expectations.py | Python | apache-2.0 | 12,037 | [
"Gaussian"
] | 36fe23867e7bf64bfe41e88e2ab43c97819434e74cf9ed3cdcde3f964dfbf0ce |
#! /usr/bin/env python
''' Generic utilities.'''
#from numpy import *
#from pylab import *
from datetime import time, datetime
from math import sqrt
__metaclass__ = type
datetimeFormat = "%Y-%m-%d %H:%M:%S"
#########################
# Enumerations
#########################
def inverseEnumeration(l):
'Returns t... | Transience/tracker | utils.py | Python | mit | 23,493 | [
"Gaussian"
] | 4afb44cdb0966ec1c49e791ca8b5376f8b2110ea36903d439b5e42aa1e03588f |
"""Tools for signal processing."""
import numpy as np
from scipy.ndimage.filters import gaussian_filter1d
__all__ = ['smooth', 'canoncorr', 'participation_ratio', 'stable_rank']
def smooth(x, sigma=1.0, axis=0):
"""Smooths a 1D signal with a gaussian filter.
Args:
x: array_like, The array to be smoothed
... | nirum/jetpack | jetpack/signals.py | Python | mit | 2,118 | [
"Gaussian"
] | 0dab99395949a1876d7c17ee1eb1cb3767b78ac916d17fd9f2511da53155988b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing QRNAS.
https://github.com/sunandanmukherjee/QRNAS
Output::
(...)
Missing atom added: ATOM 34 H3T RA3 A 77 39.444 67.315 58.412 1.00 0.00 H
Missing atom added: ATOM 23 OP3 G A 1 ... | mmagnus/rna-pdb-tools | rna_tools/tools/mq/QRNAS/QRNAS.py | Python | gpl-3.0 | 5,902 | [
"Amber"
] | 23656ab174ec375affc46fcd576ce954ccf10c2b27062b4aa9734bec8388cf37 |
# an integer number as compartment identifier
# type of neuronal compartment
# 0 - undefined
# 1 - soma
# 2 - axon
# 3 - basal dendrite
# 4 - apical dendrite
# x coordinate of the compartment
# y coordinate of the compartment
# z coordinate of the compartment
# radius of the compartment
# parent compartm... | dilawar/moogli | moogli/parser/swc.py | Python | gpl-2.0 | 3,318 | [
"NEURON"
] | 5921889973d6cb4efffaf31e52b71ec072d3e1e5c3b5e784748d5998715e89c0 |
import Constants
import os
import glob
import sys
import h5py
import StringIO
from PIL import Image
import numpy as np
import binascii
# XRF JOB ARGS KEYS
JOB_IS_LIVE_JOB = 'Is_Live_Job' # INTEGER
JOB_STANDARDS = 'Standards' # TEXT
JOB_DETECTOR_LIST = 'DetectorList' # TEXT
JOB_MAX_FILES_TO_PROC = 'MaxFilesToProc' ... | aglowacki/Taskington | modules/mapspy.py | Python | mit | 6,145 | [
"NetCDF"
] | 387320ad65debf732784b5766c2073eb476772e479656cbc8cfb96a1da1ecb69 |
"""
Tools for making FSPS templates
"""
import os
from collections import OrderedDict
import numpy as np
import astropy.units as u
from astropy.cosmology import WMAP9
FLAM_CGS = u.erg/u.second/u.cm**2/u.Angstrom
LINE_CGS = 1.e-17*u.erg/u.second/u.cm**2
try:
from dust_attenuation.baseclasses import BaseAttAvModel... | gbrammer/eazy-py | eazy/sps.py | Python | mit | 59,521 | [
"Gaussian"
] | fd4b8a5d31406aa2ab0f970d0dbb0fe50f0cc7c57adf79ce536c8729602436d6 |
from netpyne import specs, sim
import matplotlib.pyplot as plt
import numpy as np
# Network parameters
netParams = specs.NetParams() # object of class NetParams to store the network parameters
## Cell types
PYRcell = {'secs': {}}
PYRcell['secs']['soma'] = {'geom': {}, 'mechs': {}}
PYRcell['secs']['soma']['geom'] =... | Neurosim-lab/netpyne | examples/subConn/subConn_DistanceBased.py | Python | mit | 5,269 | [
"NEURON"
] | f5ad11829b202fbdadf36e648938fdd56129f8c585ad332b71e90314888493e4 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/MOL2.py | Python | gpl-2.0 | 13,100 | [
"MDAnalysis",
"RDKit"
] | 7476f7ef03f3c672f9d74fb47aa89cc18bcebb025ccf16a35d876dd795070f4f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2007-2009 Stephane Charette
# Copyright (C) 2009 Gary Burton
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Paul Franklin
#
# This ... | Forage/Gramps | gramps/gui/plug/report/_graphvizreportdialog.py | Python | gpl-2.0 | 10,828 | [
"Brian"
] | da0c7056934f21b05893d94f76358b874ba4788a0806324ab19316244f150847 |
# (C) 2012, Michael DeHaan, <michael.dehaan@gmail.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 your option) any la... | qrkourier/ansible | lib/ansible/plugins/callback/osx_say.py | Python | gpl-3.0 | 3,032 | [
"exciting"
] | 48976026b81ad2239392878583ac874c89169e575ca84ed4253432cd166ff316 |
# dmd_image.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import os
import sys
from optparse import OptionParser
import pygame
import pygame.locals
... | spierepf/mpf | tools/dmd_image.py | Python | mit | 13,830 | [
"Brian"
] | 820ecda710c74685e89a22980aae7e49e2caa12b85afe0a3cc21f2d15d1e5d5e |
# common.py - shared symbols and globals
import os, errno
# exception class so you know where exception came from
class FsDriftException(Exception):
pass
NOTOK = 1
OK = 0
BYTES_PER_KiB = 1 << 10
BYTES_PER_MiB = 1 << 20
KiB_PER_GiB = 1 << 20
MiB_PER_GiB = 1 << 10
USEC_PER_SEC = 1000000
FD_UNDEFINED = -1
class ... | bengland2/fsstress | common.py | Python | apache-2.0 | 2,836 | [
"Gaussian"
] | 60867200973d808e1c87c6eb79dea0b6cd964497f0b210edd5fc2438d482d002 |
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