text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
import numpy as np
import os
from PyQt5.QtCore import QDir
from PyQt5.QtWidgets import (QApplication, QDialog, QFileDialog, QHBoxLayout, QLineEdit,
QPushButton, QStyle, QWidget)
from shapefile import ShapefileException
from pyteltools.conf import settings
from pyteltools.geom import BlueKe... | CNR-Engineering/PyTelTools | pyteltools/workflow/nodes_io.py | Python | gpl-3.0 | 51,557 | [
"VTK"
] | 5408b4fb4be3174630d06e8ebf24c82c527bb55def9add007d40f0ce92b63d9d |
#! /usr/bin/env python
import math
import scipy
import scipy.stats as stats
import numpy as np
import sys
import matplotlib.pyplot as plt
import csv
from argparse import ArgumentParser
from scipy.optimize import curve_fit
## from scipy.optimize import *
print "=========================================================... | MathiasGruber/plmd | src/PyReweighting/PyReweighting-1D.py | Python | gpl-2.0 | 18,772 | [
"Gaussian"
] | 9e8c33b04c3c8f4329901b81cf3d21ac8ae4cb5e4c29d4dddef4fcaeecb3f092 |
# ------------------------------
# Python Lists and Dictionaries
# ------------------------------
# Exercise 1
zoo_animals = ["pangolin", "cassowary", "sloth", "panda" ];
# One animal is missing!
if len(zoo_animals) > 3:
print "The first animal at the zoo is the " + zoo_animals[0]
print "The second animal at the z... | bensk/CS9 | _site/Code Examples/Python_Lists_Notes.py | Python | mit | 6,738 | [
"COLUMBUS"
] | 4e0ba54dbaf1d6aec46a20134db782eb16f0a88fd3c314a4193153cddc640044 |
# (C) British Crown Copyright 2015 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | ehogan/iris | lib/iris/tests/unit/fileformats/netcdf/test_parse_cell_methods.py | Python | lgpl-3.0 | 5,820 | [
"NetCDF"
] | de68aa093abc0782a68dccf2e4a3c410417c4943ef16d140b8a3934b3c960ad4 |
############################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundat... | VisTrails/vistrails-contrib-legacy | vtksnl/vtkviewcell.py | Python | bsd-3-clause | 38,676 | [
"VTK"
] | 957dd555c21d70f5bdc1f7ba13533cf243a76db6f4a8bbf18146e32a9529b6b5 |
# demo_gui.py ---
#
# Filename: demo_gui.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Jun 16 05:41:58 2010 (+0530)
# Version:
# Last-Updated: Tue Sep 11 14:26:13 2012 (+0530)
# By: subha
# Update #: 318
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
... | dilawar/moose-full | moose-examples/izhikevich/demogui_qt.py | Python | gpl-2.0 | 6,334 | [
"NEURON"
] | 73b8369201623577c956f3508818dab43f39c61b59827a4719aa7ff8e0de5860 |
#!/usr/bin/python
import pandas as pd
import numpy as np
import random
import sys
def main():
# initialize global variables
disable_pandas_warnings()
getUserInputFile()
setWeight()
setIdx()
random.seed()
# calculate sentiment for galaxy
galaxySentIdx = ['samsunggalaxy']
outputCol... | ggodreau/c3t2 | robolabel.py | Python | mit | 5,190 | [
"Galaxy"
] | 1ef7b00c7343603d59d31dff2bdbd11c10ded4ea500657e6dbb70dc6bddc3961 |
import os
from numpy import array,empty
from generic import obj
from machines import Job
from physical_system import generate_physical_system
from pwscf import generate_pwscf
from pw2qmcpack import generate_pw2qmcpack
from pw2casino import generate_pw2casino
from wfconvert import generate_wfconvert
from sqd import ge... | habanero-rice/hclib | test/performance-regression/full-apps/qmcpack/nexus/library/qmcpack_calculations.py | Python | bsd-3-clause | 33,931 | [
"QMCPACK"
] | 5c0de72c74146b5225c60c3149392524268f65463afe6d9a7761c70d00928662 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public Licens... | eustislab/horton | scripts/horton-esp-gen.py | Python | gpl-3.0 | 4,974 | [
"Gaussian"
] | 94fda320a04e1a24abe761766e54699fe0e26d87f497231910fc1f1a30716897 |
## JOHN URBAN (2015, 2016)
#info
import h5py, os, sys, tarfile, shutil
##import cStringIO as StringIO
from Bio import SeqIO
from glob import glob
import datetime
from random import randint
##class FastXMolecule(object):
## ## wraps over fasta/fastq files that may have 1 or many contents
## ## May want a separa... | JohnUrban/fast5tools | fast5tools/fxclass.py | Python | mit | 32,879 | [
"Biopython"
] | 6df5e3be4627633b1c1881097d32a50925cd88e681eba7a0805fa292c9f61eee |
"""The tests for the ASUSWRT device tracker platform."""
import os
from datetime import timedelta
import unittest
from unittest import mock
import socket
import voluptuous as vol
from homeassistant.setup import setup_component
from homeassistant.components import device_tracker
from homeassistant.components.device_tr... | persandstrom/home-assistant | tests/components/device_tracker/test_asuswrt.py | Python | apache-2.0 | 22,280 | [
"FEFF"
] | 514a0f7dd80c56dad3e952d13b49b4a41b49ec9971b50c627f4735d720f6c08c |
# Copyright 2013 by Iddo Friedberg idoerg@gmail.com
# Revision copyright 2013 by Peter Cock. 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.
"""Code for dealing with assorted Uni... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/UniProt/__init__.py | Python | gpl-2.0 | 582 | [
"Biopython"
] | 32125e7c1c11fa938db598740384e7e61d7106a0fc0f12f15cf85540e59a68d3 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | arunkgupta/gramps | gramps/gen/filters/rules/event/_hassourcecount.py | Python | gpl-2.0 | 1,726 | [
"Brian"
] | 8550265cff3c37c85021f64233cc6cae16fa0ad77d600a5d7f7e371c314adeee |
from aquests.protocols.http import request, response
from aquests.protocols.grpc import request as grpc_request
from aquests.protocols.ws import request as ws_request
from aquests.dbapi import request as dbo_request
import skitai
from ..backbone.http_request import http_request
from base64 import b64encode
import os
fr... | hansroh/skitai | skitai/testutil/client.py | Python | mit | 7,198 | [
"SIESTA"
] | 610cd41c2dfee96759705210bccab15115dccbb57101d53f93917c8d6083724e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0003_auto_20150428_0215'),
]
operations = [
migrations.AlterField(
model_name='student',
na... | koebbe/homeworks | visit/migrations/0004_auto_20150428_0224.py | Python | mit | 473 | [
"VisIt"
] | 1826d10fa791c5db410284303b8f0d15027f6b046afabc53e7ed26fa9565b382 |
from __future__ import unicode_literals
import click
COMMAND_HELP = 'Available commands:\n' \
'help - prints this message\n' \
'fields - show available form fields\n' \
'show {field_name} - show options for specified field\n' \
'select {field_name} {option_i... | jakubkbak/medicover-cli | medicover/cli/form.py | Python | mit | 2,999 | [
"VisIt"
] | 2b65fc693a0e27e5207aa211c7e9b520ec3ccfe2bace84310a5d047299074133 |
#!/usr/bin/env python
# File created on 14 Jul 2014
from __future__ import division
from qiime.util import parse_command_line_parameters, make_option
from qiime.differential_abundance import (DA_fitZIG, multiple_file_DA_fitZIG,
DA_DESeq2, multiple_file_DA_DESeq2, algorithm_list)
import os
__author__ = "Sophie We... | ssorgatem/qiime | scripts/differential_abundance.py | Python | gpl-2.0 | 9,308 | [
"Bioconductor",
"Gaussian"
] | 78c9c02ab09da3a4206fe8621717be7fa76a8e90f1c5bb8e3af217763cfbf5a0 |
#
# QAPI introspection generator
#
# Copyright (C) 2015 Red Hat, Inc.
#
# Authors:
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from qapi import *
# Caveman's json.dumps() replacement (we're stuck at P... | ehostunreach/qemu | scripts/qapi-introspect.py | Python | gpl-2.0 | 7,187 | [
"VisIt"
] | 7de8fb65c4156018aa75ac69139c3b629dde24122b6e5e27222b65d8729bf070 |
from ase.asec.run import RunCommand
class EOSCommand(RunCommand):
pass
EosCommand = EOSCommand
| conwayje/ase-python | ase/asec/eos.py | Python | gpl-2.0 | 103 | [
"ASE"
] | 3c13a57ca6f2425bec64e8a5a59e906ba95018902d37ec8128f6da4030d8f8ee |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import sys
import os
import shutil
import gzip
import pysam
import unittest
import subprocess
import glob
import re
import copy
import tempfile
from TestUtils impo... | kyleabeauchamp/pysam | tests/tabix_test.py | Python | mit | 41,519 | [
"pysam"
] | cba8273feba544b92eb0ebe5a822f32e81a2e7b15b240a701ee3d7df39732ecd |
#!/usr/bin/env python
#
# Wrapper script for invoking the VarScan JAR package.
#
# This script is written for use with the Conda package manager and is ported
# from a bash script that does the same thing, adapting the style in
# the peptide-shaker wrapper
# (https://github.com/bioconda/bioconda-recipes/blob/master/rec... | dmaticzka/bioconda-recipes | recipes/varscan/2.3.7/varscan.py | Python | mit | 2,313 | [
"Bioconda"
] | 1f176789c4ee19d0e58e12935356aaa6cfb66e04aaec0f7b6d05992bb554f73c |
#!/usr/bin/env python
import pdb
from kmos.io import *
from kmos.types import *
import kmos
import numpy as np
import kmos.utils
from ase.atoms import Atoms
import ase.io.castep
import os
DEFAULT_LAYER = 'Pd100'
class ModelBuilder(object):
def __init__(self):
self.pt = Project()
def standard_bui... | mieand/kmos | tests/complex_render_test/test_render_Pdsqrt5_process_list.py | Python | gpl-3.0 | 18,890 | [
"ASE",
"CASTEP"
] | c378ee1c46ddd1c346ec2ccbafb5436fbf17f62e710f9c3f465d1f34b1603f8e |
#!/usr/bin/env python
# =====================================================================
# This script builds a set of models, saves the models into an XML file
# and loads the models back into memory.
#
# Copyright (C) 2011-2015 Juergen Knoedlseder
#
# This program is free software: you can redistribute it and/or... | gammalib/gammalib | test/dev/example_model_xml_io.py | Python | gpl-3.0 | 2,799 | [
"Gaussian"
] | 31b7f6608b793b8b8c57d8849da9e800a6aa4c3732d2d4a6317cf94c7dde71a1 |
from __future__ import print_function
import numpy as np, pandas as pd
import regreg.api as rr
import nose.tools as nt
try:
import rpy2.robjects as rpy
rpy2_available = True
import rpy2.robjects.numpy2ri as numpy2ri
except ImportError:
rpy2_available = False
try:
import statsmodels.api as sm
... | selective-inference/selective-inference | selectinf/algorithms/tests/test_compareR.py | Python | bsd-3-clause | 34,392 | [
"Gaussian"
] | a36485b31fe4c39b5b5b2d072174582a6c0eba44539ce4a2f648d8e81eb79e1e |
"""Models of real-world locations
to be used with RoutingNode.worldObject"""
from SimPy.SimulationRT import Process, hold
import sys
import logging
__author__ = "B. Henne, P. Tute"
__contact__ = "henne@dcsec.uni-hannover.de"
__copyright__ = "(c) 2010-2012, DCSec, Leibniz Universitaet Hannover, Germany"
__license__ =... | bhenne/MoSP | mosp/locations.py | Python | gpl-3.0 | 5,389 | [
"VisIt"
] | 1817842a3525337163acaca45eb83fa3e2cee3ec789133df3b5b4227fc7c7df5 |
# 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... | KaiSzuttor/espresso | testsuite/python/observable_profile.py | Python | gpl-3.0 | 6,397 | [
"ESPResSo"
] | 5b0b615dac77e25193719fb94f3f81b1b0c6b9169c42269da0f7701f7b0f6d16 |
import unittest
import mock
from kalliope.core import LifoManager
from kalliope.core.Models import Brain, Signal, Singleton
from kalliope.core.Models.MatchedSynapse import MatchedSynapse
from kalliope.core.Models.settings.Settings import Settings
from kalliope.core.SynapseLauncher import SynapseLauncher, SynapseNameN... | kalliope-project/kalliope | Tests/test_synapse_launcher.py | Python | gpl-3.0 | 11,985 | [
"NEURON"
] | 27fb57ec440336747c77dd17894053cc1f6a83ffa8068ee6dcc065e6e486ce05 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/procrouting/sapt/fisapt_proc.py | Python | lgpl-3.0 | 7,370 | [
"Psi4"
] | e72694d6bfbc654ca85d3571b4b8ded16614bae59f7ae88df11bf21c3c3022c0 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | ghutchis/cclib | test/data/testScan.py | Python | lgpl-2.1 | 3,119 | [
"Jaguar",
"ORCA",
"cclib"
] | cbd5e611d060cb2a0fc568ab3d579d37c94d5f38300cf6f81e339799e955ab92 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/procrouting/proc_table.py | Python | lgpl-3.0 | 11,749 | [
"CFOUR",
"Gaussian",
"Psi4"
] | 1495a2a23af5e23de4123efb22cec641d0d7fbd515189d40bb38252c116fddc0 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO hmmer3-text indexing."""
import unittest
from search_tests_common ... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SearchIO_hmmer3_text_index.py | Python | gpl-2.0 | 18,717 | [
"Biopython"
] | 60ddb2effbab8180525609f495362a3685a0a86921168f4311e025f6fb283d9a |
""" This script submits a test prodJobuction with filter
"""
import time
import os
import json
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__.split( '\n' )[1],
'Usage:',
' %s test directory' % Script.scriptName... | hgiemza/DIRAC | tests/System/dirac-test-production.py | Python | gpl-3.0 | 4,565 | [
"DIRAC"
] | 3a78a761e219d92a9d7e1327ae80b093542a4ebe7921f35093e358a49b659cfc |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | millmanorama/autopsy | pythonExamples/dataSourceIngestModule.py | Python | apache-2.0 | 7,942 | [
"Brian"
] | 4940ae717198f840587e1aee56c224880b69fbebfc2fda6969a0983e5c6b896a |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | snippets/scriptKineticModel.py | Python | gpl-2.0 | 4,203 | [
"MOOSE"
] | ac1c10b2d3bd2c6fe8fbfd3ed38890253d6d2eb0fc93c4b1d7335de0f2311a86 |
import pandas as pd
# The Dataset comes from:
# https://archive.ics.uci.edu/ml/datasets/Optical+Recognition+of+Handwritten+Digits
# At face value, this looks like an easy lab;
# But it has many parts to it, so prepare yourself before starting...
def load(path_test, path_train):
# Load up the data.
# You probab... | jatraug/Dataclass | Module6/assignment2.py | Python | mit | 5,955 | [
"TINKER"
] | 8a5c902713e54370027d9a8ad4956af1e2044e802a07934afd40756793050bdb |
# SecuML
# Copyright (C) 2016 ANSSI
#
# SecuML 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.
#
# SecuML is distributed in the hope t... | ah-anssi/SecuML | SecuML/core/Tools/Plots/Density.py | Python | gpl-2.0 | 2,713 | [
"Gaussian"
] | dbdce55b61890fa57e22c6932fa6ebc2a14454b539ff0b051a2b996d6ca6d3ed |
# Resource object code (Python 3)
# Created by: object code
# Created by: The Resource Compiler for Qt version 5.15.2
# WARNING! All changes made in this file will be lost!
from PySide2 import QtCore
qt_resource_data = b"\
\x00\x00\x00h\
\x89\
PNG\x0d\x0a\x1a\x0a\x00\x00\x00\x0dIHDR\x00\
\x00\x00 \x00\x00\x00 \x08\x0... | bdcht/amoco | amoco/ui/graphics/qt_/rc_icons.py | Python | gpl-2.0 | 478,751 | [
"xTB"
] | e38c4bc1760add4c8a1cfecb9d93d70cd1ecd6ca5174c4cc83fac597114ee46e |
import sys,os
keywords = ['PLPS_path', 'PDB2PQR_path', 'APBS_path', 'XLOGP3_path', 'ligand_file', 'BABEL_path',\
'n_conf', 'OMEGA_path']
def read_input(input_file):
file = open(input_file, 'r')
lig_file = []
for line in file:
key = line.split()[0]
if(key == keywords[0]):
... | avaidyam/Binoculars | bin/plps/scripts/prepare_ligands.py | Python | mit | 6,755 | [
"Amber"
] | 9d0bb7236d07157a15ea898510a305cf2fb96d2ce07dd3159f915d2f5fddd380 |
"""Cluster based on RMSD between conformations
{{header}}
Meta
----
depends:
- meta.pandas.pickl
- trajs
- top.pdb
"""
import mdtraj as md
from msmbuilder.cluster import MiniBatchKMedoids
from msmbuilder.io import load_meta, itertrajs, save_trajs, preload_top
## Set up parameters
kmed = MiniBatchKMedoids(
... | cxhernandez/msmbuilder | msmbuilder/project_templates/landmarks/featurize.py | Python | lgpl-2.1 | 784 | [
"MDTraj"
] | 8306dd756b548a094dbe0ca8e95e6d4a077bd1605ced7648837ff2146144c9c3 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2016-2020 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser 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 S... | t-wissmann/qutebrowser | qutebrowser/browser/browsertab.py | Python | gpl-3.0 | 39,585 | [
"VisIt"
] | 48caa08ad0c011a8047dd12c09b9a617f28889e44753c1ca57ed6e494818c0af |
#!/usr/bin/env python
import sys
sys.path.append("../")
import numpy as np
import pandas as pd
import scipy.io
from functions import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import neuroseries as nts
import sys
import scipy.ndimage.filters as filters
from sklearn.mixture import GaussianMixtu... | gviejo/ThalamusPhysio | python/figure_article_v4/main_article_v4_fig_supp_1.py | Python | gpl-3.0 | 9,337 | [
"Gaussian"
] | dc0ce2747decc3c2c2fc96888de9b38066482ff192a3535b518c682f0c4a6a80 |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import operator
import warnings
import numpy as np
from scipy import linalg, special, fft as sp_fft
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
'blackmanharris', 'flattop', ... | arokem/scipy | scipy/signal/windows/windows.py | Python | bsd-3-clause | 74,167 | [
"Gaussian"
] | de9e536962785b2854c2029c73cfeb168ec53d05c08aeedd6244929cf0252c10 |
# ----------------------------------------
# USAGE:
# python avg_structure.py config_file
# ----------------------------------------
# PREAMBLE:
import sys
import numpy as np
from numpy.linalg import *
import MDAnalysis
from MDAnalysis.analysis.align import *
from distance_functions import *
# ---------------------... | rbdavid/DENV-NS3h | Average_structure/avg_structure.py | Python | gpl-3.0 | 8,080 | [
"MDAnalysis"
] | 0f619c1e5f6cd2fb6f3fcb082875a2e78bd289d3820c7103dddafd4d9fc8309e |
# starting from CNTK/Examples/Image/Classification/AlexNet/Python/AlexNet_ImageNet_Distributed.py
# to make a local-only version
# Copyright (c) Microsoft. All rights reserved.
# Licensed under the MIT license. See LICENSE.md file in the project root
# for full license information.
# ===============================... | hjl/cntkdemo | AlexNetDemo/AlexNet-CNTK.py | Python | mit | 12,502 | [
"NEURON"
] | 5f8ea58230fb1e54e077630a606b64c83bd312a17f17e14128d5a9f0cd7613a9 |
"""
Browser set up for acceptance tests.
"""
# pylint: disable=E1101
# pylint: disable=W0613
from lettuce import before, after, world
from splinter.browser import Browser
from logging import getLogger
from django.core.management import call_command
from django.conf import settings
from selenium.common.exceptions impo... | geekaia/edx-platform | common/djangoapps/terrain/browser.py | Python | agpl-3.0 | 9,780 | [
"VisIt"
] | 6195fd39db2948695f0791382291a949ff492d3cc89b09d13aadad42cab28861 |
from __future__ import division, print_function
import numpy as np
from dipy.denoise.denspeed import nlmeans_3d
def nlmeans(arr, sigma, mask=None, patch_radius=1, block_radius=5,
rician=True, num_threads=None):
""" Non-local means for denoising 3D and 4D images
Parameters
----------
arr ... | StongeEtienne/dipy | dipy/denoise/nlmeans.py | Python | bsd-3-clause | 2,170 | [
"Gaussian"
] | e12c609eb34ee535811e2ed43828deec25d423e8bca784a258f42df9db1dfb98 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import ast
from odoo import api, models, _
class SurveyTemplate(models.Model):
"""This model defines additional actions on the 'survey.survey' model that
can be used to load a survey sample. The model defin... | jeremiahyan/odoo | addons/survey/models/survey_survey_template.py | Python | gpl-3.0 | 12,054 | [
"BLAST"
] | f24c48c3320b53900294252f15dacb30e44304b53b8102834071cc44b81167a4 |
"""Module for calculating phonons of periodic systems."""
import sys
import pickle
from math import sin, pi, sqrt
from os import remove
from os.path import isfile
import numpy as np
import numpy.linalg as la
import numpy.fft as fft
has_spglib = False
try:
from pyspglib import spglib
has_spglib = True
except ... | alexei-matveev/ase-local | ase/phonons.py | Python | gpl-2.0 | 27,283 | [
"ASE",
"GPAW"
] | a827c6627820892ef5190ccd1575c3ecb8dacd14ff233c06049bfae62a3ec2f7 |
# -*- coding: utf-8 -*-
"""
utils.py:
Utility functions for moose.
NOTE: Some function might break because unicode is default string in python3.
"""
from __future__ import print_function, division
from __future__ import absolute_import
__author__ = 'Subhasis Ray, Aditya Gilra, Dilawar Singh'
__copyright_... | dharmasam9/moose-core | python/moose/utils.py | Python | gpl-3.0 | 43,581 | [
"MOOSE",
"NEURON"
] | 933714eff707efbe75f1edd4a3fd63fc83e5fe1f28f401d632ca885db5b9faf8 |
#
# Copyright (C) 2003-2005 Rational Discovery LLC
# All Rights Reserved
#
""" Defines the class SigTreeNode, used to represent trees that
use signatures (bit vectors) to represent data. As inputs (examples),
SigTreeNode's expect 3-sequences: (label,sig,act)
_SigTreeNode_ is derived from _DecTree.DecTreeNode_... | adalke/rdkit | rdkit/ML/DecTree/SigTree.py | Python | bsd-3-clause | 1,768 | [
"RDKit"
] | 8a33c796c51b78f8e8d6f58c4cf19bc2c13c52683b436468c5975ef8857f3b09 |
# Py-BOBYQA example: minimize the noisy Rosenbrock function
from __future__ import print_function
import numpy as np
import pybobyqa
# Define the objective function
def rosenbrock(x):
return 100.0 * (x[1] - x[0] ** 2) ** 2 + (1.0 - x[0]) ** 2
# Modified objective function: add 1% Gaussian noise
def rosenbrock_noi... | numericalalgorithmsgroup/pybobyqa | examples/rosenbrock_noisy.py | Python | gpl-3.0 | 1,169 | [
"Gaussian"
] | 0bef94317ea3e82848fe29475b46943d201d079f6e7777bdd74013dcf83e10ae |
# 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... | glemaitre/scikit-learn | sklearn/ensemble/_iforest.py | Python | bsd-3-clause | 18,949 | [
"Gaussian"
] | 016b2f54e7313717f91dc5978372463d395e15a2636a5497528d9ef27090de1d |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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
... | alexandrul-ci/robotframework | src/robot/model/stats.py | Python | apache-2.0 | 6,395 | [
"VisIt"
] | 40ee1a10f3b18c5540d91b270c981948108e4c9b81ddaec5614a897a8d29c26a |
import copy
import numpy as np
from sklearn import datasets, preprocessing, model_selection
from neupy.utils import asfloat
from neupy.exceptions import LayerConnectionError
from neupy.algorithms.gd import objectives
from neupy import algorithms, layers, architectures
from base import BaseTestCase
class MixtureOfE... | itdxer/neupy | tests/architectures/test_mixtures_of_experts.py | Python | mit | 7,096 | [
"MOE"
] | 75282f1bea210d6862388ba89f3564f4c4518c34d56f54d0b507436dbe9e17aa |
import os
import pytest
from nikola.plugins.command.import_wordpress import (
modernize_qtranslate_tags,
separate_qtranslate_tagged_langs,
)
def legacy_qtranslate_separate(text):
"""This method helps keeping the legacy tests covering various
corner cases, but plugged on the newer methods."""
tex... | getnikola/nikola | tests/test_command_import_wordpress_translation.py | Python | mit | 5,515 | [
"VisIt"
] | dfcd7b525d486cedc6d567b94459fb82b5a8f7d58ca0c0ffd2c37643a602e2db |
#!/usr/bin/python2.7
import ntpath
import re
import time
import argparse
import swiginac
import listcreator
class TestGenerator():
in_D_dimensions = False
letter_i = 'i'
letter_j = 'j'
letter_k = 'k'
letter_l = 'l'
letter_m = 'm'
letter_n = 'n'
letter_o = 'o'
letter_p = 'p'
... | FeynCalc/pyfeyncalctester | src/pyfeyncalctester.py | Python | lgpl-3.0 | 26,063 | [
"DIRAC"
] | 38cec5cc76cc2a54f9d2d4082ec2443962bbe3c3003278a056498d9d13e4363d |
"""The CatPhan module automatically analyzes DICOM images of a CatPhan 504, 503, or 600 acquired when doing CBCT or CT quality assurance.
It can load a folder or zip file that the images are in and automatically correct for translational and rotational errors.
It can analyze the HU regions and image scaling (CTP404), t... | jrkerns/pylinac | pylinac/ct.py | Python | mit | 70,405 | [
"Gaussian"
] | f7629af37cce2a385a67eb6056a12b2f77044373dc4479e857ecb7cc9aa03b02 |
import cudamat as cm
import gpu_lock2 as gpu_lock
import h5py
import sys
import os
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
from time import sleep
import pdb
import datetime
import time
import config_pb2
from google.protobuf import text_format
class Param(object):
def __init__(self, w, config=Non... | udibr/unsup_video_lstm | util.py | Python | bsd-2-clause | 4,622 | [
"Gaussian"
] | 8b88c69f277e984fc7d34651c7e7b44f513e18c96c4c853a9f314dc637de97aa |
#!/usr/bin/env python3
import os
import requests
import time
import json
def getWeatherAsWords():
# Settings for your API key and location details read from environment strings, e.g. exports etc
appid = str(os.environ.get('apikey'))
locid = str(os.environ.get('locationkey'))
lat = str(os.environ.get(... | sjhawke/piface-cad | lib/writetheweather.py | Python | gpl-3.0 | 1,742 | [
"Amber"
] | 4ca12be4c6e1b546ee34e1fa200dee11dbe5c9506e6892f64f839d843e95804a |
"""
Tests the Gaussian quadrature rules.
"""
import numpy as np
import pytest
from pysofe.quadrature.gaussian import GaussQuadSimp
# set global shortcut and tolerance
fac = np.math.factorial
eps = 1e-8
class TestGaussQuadSimp(object):
order = 2
quad_rule = GaussQuadSimp(order, dimension=3)
def test_spe... | pysofe/pysofe | tests/test_quadrature/test_gaussian.py | Python | bsd-3-clause | 1,487 | [
"Gaussian"
] | 0d4dd7acb967489f160a1d047c3636a59b591cdc2d5e236721fe82fc5b77d392 |
# 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 ... | hzlf/openbroadcast | website/apps/ep/API/solr.py | Python | gpl-3.0 | 45,306 | [
"Brian"
] | ddb284a68d3b4edeb18389abfed5dd586a6fb56fc77e75f896f16b196b305aed |
import sys
try:
import numpy
except ImportError:
print("Numpy (http://numpy.scipy.org) not found.")
print("This test requires numpy!")
sys.exit(0)
import vtk
import vtk.numpy_interface.dataset_adapter as dsa
import vtk.numpy_interface.algorithms as algs
w = vtk.vtkRTAnalyticSource()
bp = vtk.vtkBrow... | sumedhasingla/VTK | Common/Core/Testing/Python/TestNumpyInterface.py | Python | bsd-3-clause | 6,292 | [
"VTK"
] | 0c1cdcbd210eb41484f74ae81be1ea5b7ff69f364ab6ef5f9313a6f5a5daa290 |
import os
import subprocess
from datetime import timedelta
from . import dispersion_file_utils as dfu
from .dispersiongrid import BSDispersionGrid, BSDispersionPlot, create_color_plot
class PolygonGenerator(object):
"""Generates polygon kmls from a NETCDF file representing smoke dispersion
time series.
P... | pnwairfire/blueskykml | blueskykml/polygon_generator.py | Python | gpl-3.0 | 7,736 | [
"NetCDF"
] | b4ccc75bd2446435445a64aa8fb030d4b3f53c55e1d989b26a2abba6ae16e67a |
# $HeadURL $
''' ResourceStatusDB
Module that provides basic methods to access the ResourceStatusDB.
'''
from datetime import datetime
import sys
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.DB ... | Sbalbp/DIRAC | ResourceStatusSystem/DB/ResourceStatusDB.py | Python | gpl-3.0 | 15,471 | [
"DIRAC"
] | 3be9656d901a35386e9ed7dcdfe52d006b44e931dafa1d937b337d6abd26cf72 |
"""
SDSS Imaging
============
This example shows how to load the magnitude data from the SDSS imaging
catalog, and plot colors and magnitudes of the stars and galaxies.
"""
# Author: Jake VanderPlas <vanderplas@astro.washington.edu>
# License: BSD
# The figure is an example from astroML: see http://astroML.github.com... | astroML/astroML | examples/datasets/plot_sdss_imaging.py | Python | bsd-2-clause | 1,859 | [
"Galaxy"
] | efe67c4d1785d973d55d45ebbe1d710b32c3b3a18b5d6f9e3a6049c6c0f4938b |
# $HeadURL$
__RCSID__ = "$Id$"
import socket
import select
import time
import os
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTransport
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
class PlainTransport( BaseTransport ):
def... | Sbalbp/DIRAC | Core/DISET/private/Transports/PlainTransport.py | Python | gpl-3.0 | 4,006 | [
"DIRAC"
] | f91cdc106ce93c84a1a32a3fe4ed7c6a7fed6afe01b50d450cbc74e50465dff0 |
import discord
async def run(client, message, object_list=None):
player = None
in_list = False
# Checks if object is already in the object_list, then returns as a player object if true.
index = 0
for item in object_list:
# Checks if the object is for the current server, and has pl... | synlogic/kohaibot-for-discord | commands/moe.py | Python | gpl-3.0 | 1,982 | [
"MOE"
] | c31d46b82d9ba411e1246e8be7ede99778b1ecee294f19cc54450ec17e72bd5b |
import numpy as _np
from umbrella_potential import UmbrellaPotential as _up
import func
class UmbrellaIterator(object):
def __init__(self, umbrella,overlap) :
self.umbrella=umbrella
self.overlap=overlap
self.rejected=[]
self.accepted=None
self.check=0
r"""ov... | oacar/umbrella-sampling | umbrella_sampling/umbrella_iterator.py | Python | gpl-3.0 | 4,078 | [
"Gaussian"
] | ed1d8bfa79aaf4ecf581f14eda1cdfa9c1ae5994abf86714bb0b417ce4e68b1d |
# -*- coding: utf-8 -*-
'''
*******************************************************************
* File: chemConnectUtil.py
* Description:
* Author: HarshaRani
* E-mail: hrani@ncbs.res.in
********************************************************************/
/****************************... | dilawar/moose-core | python/moose/chemUtil/graphUtils.py | Python | gpl-3.0 | 4,605 | [
"MOOSE"
] | cff9e2c5ddd729541e1d60a5ad85f31f7251e62875c42466b81006afb262bbd2 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pordb_hauptdialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.2
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import Qt... | hwmay/pordb3 | pordb_hauptdialog.py | Python | gpl-3.0 | 105,874 | [
"VisIt"
] | 31493fcb6a9364c0ab4e0adfb8c38c31e87932277573cfe35011bd6872e8b471 |
#!/usr/bin/env python
''' Adds a bogus read group to a readgroup-less BAM file '''
import os
import sys
import pysam
from uuid import uuid4
def modhead(header, rgid, fn):
if 'RG' in header:
sys.stderr.write("RG found in header, this script is not what you want!\n")
sys.exit(usage())
header[... | adamewing/bamsurgeon | scripts/bsrg.py | Python | mit | 1,134 | [
"pysam"
] | 8acb985e2dfeeb4ed632ad8c963882e9d5d0e607a442ffe7b69f6cfdb5bc96f5 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'Video.flash_enclosure_url'
db.alter_column('localtv_video', 'flash_enclosure_url', self... | pculture/mirocommunity | localtv/migrations/0038_south_can_parse_bitly_field_type.py | Python | agpl-3.0 | 17,198 | [
"GULP"
] | 681ecf76c74339f9155e40837c09b06debf66987a39ee087833f2bd26bfde4c0 |
from jsRealBclass import jsRealB, N,A,Adv,V,D,P,C,DT,NO,Q, NP,AP,AdvP,VP,S,SP,PP,CP
from Realization.common import realize, jsrDayPeriod, jsrHour, get_max_term, get_min_term, get_term_at
precipitationTypes = {
"showers":{"en":N("shower").n("p"),
"fr":N("averse").n("p")},
"flurries":{"en":N("flu... | rali-udem/JSrealB | demos/Weather/Realization/Precipitation.py | Python | apache-2.0 | 4,874 | [
"CRYSTAL"
] | a1b8c7a6a9975caad4288567a59770b96ac407158459495478a40caf4dd40685 |
# -*- coding: utf-8 -*-
import skimage.io
import skimage.feature
import skimage.color
import skimage.transform
import skimage.util
import skimage.segmentation
import numpy
# "Selective Search for Object Recognition" by J.R.R. Uijlings et al.
#
# - Modified version with LBP extractor for texture vectorization
def _... | SelinaChe/Complex-Object-Detection-StackGAN | Region-to-Image_Matching/selectivesearch/selectivesearch.py | Python | mit | 8,757 | [
"Gaussian"
] | 7a8ef2e7d966b44ec165b9030bc4c4b082307266852cf70c1c42a28ca0375830 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.mail import send_mail
from django.core.urlresolvers import rev... | ak2703/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 53,068 | [
"VisIt"
] | c08b808c7f4887e6bfb1d18b1aa6adc0e2073d5d8e3f4341e80c7b7494a41640 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/management/commands/lock_training_accounts.py | Python | gpl-3.0 | 1,772 | [
"Brian"
] | 399a027d6379ad55c858060978965453327fbf049b2affb3c4d7338da434b5ce |
# -*- coding: utf-8 -*-
"""upload_docs
Implements a Distutils 'upload_docs' subcommand (upload documentation to
PyPI's pythonhosted.org).
"""
import os
import socket
import zipfile
import tempfile
import sys
import shutil
from base64 import standard_b64encode
from pkg_resources import iter_entry_points
from distuti... | timohtey/mediadrop_copy | mediacore_env/Lib/site-packages/distribute-0.7.3/setuptools/command/upload_docs.py | Python | gpl-3.0 | 6,871 | [
"VisIt"
] | 80444031b529315d750a42d8f5f8409f516e3f5d3bbb30c5ac748ab87b45c8a6 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=no-init
"""These are more i... | mganeva/mantid | Testing/SystemTests/tests/analysis/VesuvioCommandsTest.py | Python | gpl-3.0 | 19,361 | [
"Gaussian"
] | e488e27bf74c4454f929026ef2cc6437f37633764515e8304238eea998c81422 |
# (c) 2014, Brian Coca, Josh Drake, et al
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
DOCUMENTATION = '''
cache: memcached
short_description: Use ... | vmindru/ansible | lib/ansible/plugins/cache/memcached.py | Python | gpl-3.0 | 6,917 | [
"Brian"
] | 822553ef59d64cba609340c4e69e35771e018535bd70146150f733e9ec2595a0 |
# Modified to work with Exaile - Brian Parma
#
# Copyright (C) 2008 Erik Hetzner
# This file is part of Spydaap. Spydaap 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 (... | sjohannes/exaile | plugins/daapserver/server.py | Python | gpl-2.0 | 6,352 | [
"Brian"
] | 215dc07a219814db7098785b04d28ea10a41d43e1c209c30f841d93c3430d0a7 |
#!/usr/bin/env python2
#
# Copyright (C) 2020(H)
# Jozef Stefan Institute
# Max Planck Institute for Polymer Research
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify... | govarguz/espressopp | testsuite/minimize_energy/test_minimize_energy.py | Python | gpl-3.0 | 3,062 | [
"ESPResSo"
] | 97a9c51ae94845ef1b68b95aa440b19fd11aa5e6b79d66b77a8f219b6c47a498 |
# coding: utf-8
'''
Authors: Tyler Reddy and Anna Duncan
The purpose of this Python module is to provide utility functions for analyzing the diffusion of particles in molecular dynamics simulation trajectories using either linear or anomalous diffusion models.'''
import numpy
import scipy
import scipy.optimize
def f... | tylerjereddy/diffusion_analysis_MD_simulations | diffusion_analysis.py | Python | mit | 18,518 | [
"Gromacs",
"MDAnalysis"
] | ec60c3b6025c51d158aba4acfb96c5dfec9d41bb77f7ef28135febf07fd77525 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, microprot development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------... | biocore/microprot | setup.py | Python | bsd-3-clause | 2,303 | [
"scikit-bio"
] | bf0570c56eb3e4112b260ae77aeb01871a00b41a523cf0d8b7e7345eb7526130 |
# ICE Revision: $Id$
"""
Application class that implements pyFoamSurfacePlot.py
"""
import sys,string
from os import path
from optparse import OptionGroup
from copy import copy
from math import sqrt
from .PyFoamApplication import PyFoamApplication
from PyFoam.RunDictionary.SurfaceDirectory import SurfaceDirectory
f... | Unofficial-Extend-Project-Mirror/openfoam-extend-Breeder-other-scripting-PyFoam | PyFoam/Applications/SurfacePlot.py | Python | gpl-2.0 | 20,314 | [
"VTK"
] | 890e1268cd57d3d8e06d1d333e6aa2a93c3da3e7bd53cdf2e880f32a32270e7f |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Hard particle Monte Carlo integrators."""
from hoomd import _hoomd
from hoomd.data.parameterdicts import TypeParameterDict, ParameterDict
from hoomd.data.typ... | joaander/hoomd-blue | hoomd/hpmc/integrate.py | Python | bsd-3-clause | 76,701 | [
"HOOMD-blue",
"OVITO"
] | 14a7f3768805f268fed379fc9b9474e3b20648e0b2d7c0ed412076c257217ef8 |
"""
Utility functions to mimic the template support functions for vtkVariant
"""
import vtk
import sys
_variant_type_map = {
'void' : vtk.VTK_VOID,
'char' : vtk.VTK_CHAR,
'unsigned char' : vtk.VTK_UNSIGNED_CHAR,
'signed char' : vtk.VTK_SIGNED_CHAR,
'short' : vtk.VTK_SHORT,
'unsigned short' : v... | SimVascular/VTK | Wrapping/Python/vtk/util/vtkVariant.py | Python | bsd-3-clause | 7,045 | [
"VTK"
] | cb7a47784cd185f102e5f0e8c3ba8bdd993834910e2464caed46ac955baf8061 |
# Copyright 2015 gRPC 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 writing... | nicolasnoble/grpc | src/python/grpcio/grpc_core_dependencies.py | Python | apache-2.0 | 80,830 | [
"ORCA"
] | de8a63b67c6dc7c53f4184a93b801e27a219d17242695b567cb68dc17447cfe2 |
from abc import ABCMeta, abstractmethod, abstractproperty
import math
import numpy as np
class RF(object):
__metaclass__ = ABCMeta
def __init__(self, grid):
"""
grid: a meshgrid list with arrays for 2 coordinates
represents the screen coordinates
"""
i... | neurokernel/retina | retina/vrf/vrf_no_gpu.py | Python | bsd-3-clause | 7,190 | [
"Gaussian"
] | d338906301802cebb5da584c79ead8dea74f507abbcf7ad93742ff92fe13cebe |
#!/usr/bin/python
# Copyright (C) 2014 Brian J. Stucky
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | openpaul/DNApy | ztr.py | Python | gpl-3.0 | 14,307 | [
"Brian"
] | 17b76c7afea85df79de33710afddcaed956ca60406a434f27670844dba385687 |
"""
iterative_machine_generator.py
Set up a system of equations, generates the Python module to
solve it.
This module is going to be replaced with the less crazy equation_solver.py
Copyright 2016 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in comp... | brianr747/SFC_models | sfc_models/deprecated/iterative_machine_generator.py | Python | apache-2.0 | 14,865 | [
"Brian"
] | 1d6cb50796bde52488d71f63f78fb8bb95bdc63bade1da74345e6f6d12b119b7 |
# Copyright (c) 2003-2010 Sylvain Thenault (thenault@gmail.com).
# Copyright (c) 2003-2010 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 t... | mattjmorrison/Pylint | utils.py | Python | gpl-2.0 | 19,795 | [
"VisIt"
] | 9da06fdaa6a08eedbee7cfb5ba7f08e49b2c4610db8282cf1940b6afa63701e5 |
# UIHeart.py
# Aaron Taylor
# Moose Abumeeiz
#
# When you take a Heart, it will create a UI heart.
# It will show isaacs current health
#
from pygame import *
class UIHeart:
"""Class for a UI heart"""
# HEART VARIANTS:
#
# 0 - Red heart
# 1 - Soul heart
# 2 - Black heart
# 3 - Eternal heart
# NOTE: After ... | ExPHAT/binding-of-isaac | UIHeart.py | Python | mit | 1,818 | [
"MOOSE"
] | 8194e9ef7ad244a8774b44f47170e2be54a3916782ff6f18813574f5229bec1b |
"""
New version of bioconductor? This script goes through each current Bioconductor
recipe, finds the corresponding dependencies that are also in this repo, and
reports the [reverse toplogically sorted] set of Bioconductor packages should
be updated using bioconductor-scraper.py.
In other words, the first items in the... | JingchaoZhang/bioconda-recipes | scripts/bioconductor/update_bioconductor_packages.py | Python | mit | 1,990 | [
"Bioconda",
"Bioconductor"
] | 880ebc2abb4eaaf7e18e66787dd1a87f3676cb94337d082b25f24045bc10f48c |
# Copyright (C) 2020 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 versio... | KaiSzuttor/espresso | testsuite/scripts/samples/test_reaction_ensemble_complex_reaction.py | Python | gpl-3.0 | 1,720 | [
"ESPResSo"
] | 173655f5982f877ad10bd9fc5cc4d85f9228c58b0f46adc5a0037fa8e1073f4c |
import wx
import wx.grid
import wx.lib.scrolledpanel
import os
import os.path
import sys
import time
import platform
import multiprocessing
import Bio.PDB
import webbrowser
import datetime
import gzip
from threading import Thread
from tools import *
class EnsembleGenPanel(wx.lib.scrolledpanel.ScrolledPanel):
def _... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/ensemblegen.py | Python | gpl-2.0 | 50,590 | [
"PyMOL"
] | 8517b700cc8e4e3898b98b32079dafdb0f916d7ba30ac0641b15467aa9c0eb9b |
"""
Implements the Kalman filter for a linear Gaussian state space model.
References
----------
https://lectures.quantecon.org/py/kalman.html
"""
from textwrap import dedent
import numpy as np
from scipy.linalg import inv
from quantecon.lss import LinearStateSpace
from quantecon.matrix_eqn import solve_discrete_ricc... | QuantEcon/QuantEcon.py | quantecon/kalman.py | Python | bsd-3-clause | 9,620 | [
"Gaussian"
] | 01930e0031a33d6e1b6edf0d81d5b8c4aa3e5ed5098153d0b2b7f4d1ae57ce22 |
"""
Django-specific extensions for use with aloe_django_.
.. _aloe_django: https://github.com/aloetesting/aloe_django
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
# pylint:disable=redefined-builtin,unused-wildc... | koterpillar/aloe_webdriver | aloe_webdriver/django.py | Python | mit | 1,027 | [
"VisIt"
] | b0e9d9cbcbdf9055b29f2e7bf425c3b34e63963f1395aaeb1a0577c4f3902863 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/tensorflow/python/ops/distributions/normal.py | Python | bsd-2-clause | 9,211 | [
"Gaussian"
] | 9ea189395aaeb3b3785227db4d7c0ad24995c6dd9492b56f2e6312fef812addb |
"""Very basic example of a simulation without a resampler or boundary
conditions"""
from copy import copy
import sys
import logging
## Logging
from eliot import start_action, to_file
from eliot.stdlib import EliotHandler
logger = logging.getLogger()
# logger.setLevel(logging.DEBUG)
logger.addHandler(EliotHandler)
... | ADicksonLab/wepy | jigs/eliot/source/stdout_log.py | Python | mit | 2,764 | [
"OpenMM"
] | e353ff06d200aff6795ef45c20b7d3ac0534c9f89d8375b10136b3e41b65e068 |
# coding=utf-8
import os
from fabric.colors import blue, cyan, green, magenta, red, yellow
from fabric.decorators import task
from fabric.operations import local
from fabric.state import env
from fabric.utils import puts
env.version = '0.7.7'
env.colorize_errors = True
env.proxy = '127.0.0.1:1087'
# env.pypi_mirror ... | nypisces/Free | fabfile.py | Python | mit | 7,780 | [
"GULP"
] | 7eeb3cf3ec54b47aa8735a2fcdcd5ad22f1ad05a8c61197a5686b267619aca5c |
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