text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""This module defines a linear response TDDFT-class.
"""
from math import sqrt
import sys
import numpy as np
from ase.units import Hartree
import _gpaw
import gpaw.mpi as mpi
MASTER = mpi.MASTER
from gpaw import debug
from gpaw.poisson import PoissonSolver
from gpaw.output import initialize_text_stream
from gpaw.lr... | qsnake/gpaw | gpaw/lrtddft/__init__.py | Python | gpl-3.0 | 14,822 | [
"ASE",
"GPAW"
] | e3e72d7b386a02b245556ef6a5a8f3738f743a47193c0582eeb5c8ae8433cf30 |
#!/usr/bin/env python
## /*=========================================================================
## Program: Visualization Toolkit
## Module: HeaderTesting.py
## Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
## All rights reserved.
## See Copyright.txt or http://www.kitware.com/Copyright... | ashray/VTK-EVM | Testing/Core/HeaderTesting.py | Python | bsd-3-clause | 17,257 | [
"VTK"
] | e0b3befc5f5cb81e4cbaee4bf8840f7e42cdafde03f6f6a03fc1514e3bde7308 |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
"""
Helper methods for generating gw input / and work flows.
"""
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel van Setten"
__email__ = "mjvansetten@gmail.com"
__date__ = "May 2014"
... | rousseab/pymatgen | pymatgen/io/abinitio/helpers.py | Python | mit | 6,823 | [
"pymatgen"
] | fcd0f0618054997c7ea2520c48397d59efe3e14a5f76d0b16446f23381f92fa3 |
## \example em/pdb2density.py
# A simple example showing how to simulate density from a protein.
# IMP uses a Gaussian smoothing kernel. see SampledDensityMap::resample for documentation.
#
import IMP.em
import IMP.core
import IMP.atom
import sys
IMP.setup_from_argv(sys.argv, "pdb2density")
m = IMP.Model()
# read pr... | shanot/imp | modules/em/examples/pdb2density.py | Python | gpl-3.0 | 851 | [
"Gaussian"
] | bffb4288bf22348151913d852d2e2ba19cdb7f32727b883b1ecfff8f6f0e1680 |
import ckan.plugins as plugins
import ckan.plugins.toolkit as toolkit
import ckanext.thredds.logic.action as action
from ckanext.thredds import helpers
import ckan.logic.validators as val
from pylons import config
import urllib
import json
import datetime
class ThreddsPlugin(plugins.SingletonPlugin):
plugins.impl... | ccca-dc/ckanext-thredds | ckanext/thredds/plugin.py | Python | gpl-3.0 | 10,660 | [
"NetCDF"
] | 57030de8c1062210a166a6e5f9222165b37c2f1c618cab72aa42bf2bada7eaa5 |
# Copyright (C) 2010-2014, Luis Pedro Coelho <luis@luispedro.org>
# vim: set ts=4 sts=4 sw=4 expandtab smartindent:
#
# License: MIT (see COPYING file)
import numpy as np
from . import _convolve
from . import morph
from .internal import _get_output, _normalize_sequence, _verify_is_floatingpoint_type, _as_floating_poi... | fabianvaccaro/pygums | pythonLibs/mahotas-1.1.0/mahotas/convolve.py | Python | gpl-2.0 | 18,219 | [
"Gaussian"
] | 7928c5721e3ba6cb7ba0f56dc1074250bbdaefb161ccb263005171328fa8ba63 |
"""Functions to plot epochs data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Si... | Odingod/mne-python | mne/viz/epochs.py | Python | bsd-3-clause | 19,613 | [
"Gaussian"
] | 4fca814025f5a96aa84fb8a14a9c859ecab1ca34f3cc734550f159ebe8d6594a |
# -*- coding: utf-8 -*-
import unicodedata
import json
import arrow
import scrapy
from scrapyproject.showingspiders.showing_spider import ShowingSpider
from scrapyproject.items import (ShowingLoader, init_show_booking_loader)
from scrapyproject.utils import TohoUtil
class TohoV2Spider(ShowingSpider):
"""
Toho... | gas1121/JapanCinemaStatusSpider | scrapyproject/showingspiders/toho_v2.py | Python | mit | 10,931 | [
"VisIt"
] | 90cc771a385cf9f40a4c0d38121951bedcee4fdb0e0c276fa1b240e94b180eec |
import tempfile
import unittest
import PIL.Image
import pillowfight
class TestGaussian(unittest.TestCase):
def test_gaussian(self):
with tempfile.NamedTemporaryFile(suffix='.jpg') as tmpfile:
in_img = PIL.Image.open("tests/data/crappy_background.jpg")
out_img = pillowfight.gaussi... | jflesch/libpillowfight | tests/tests_gaussian.py | Python | gpl-2.0 | 796 | [
"Gaussian"
] | 222f7d9beb56be1a84a1e9c9398e66bd21801bb1af004045a37ff5cf67b5e7b4 |
# mako/parsetree.py
# Copyright 2006-2020 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""defines the parse tree components for Mako templates."""
import re
from mako import ast
from ma... | chromium/chromium | third_party/mako/mako/parsetree.py | Python | bsd-3-clause | 19,411 | [
"VisIt"
] | 7a91a2e702ad640f0b729cddac45e5fe38cf18fbee3be223b834806282c0a786 |
"""
Basic image manipulation algorithms such as Gaussian smoothing and free rebinning.
:requires: NumPy
:requires: SciPy
:author: Sami-Matias Niemi
:contact: sniemi@unc.edu
:version: 0.1
"""
import numpy as np
import scipy.signal as s
import scipy
def frebin(image, nsout, nlout=1, total=False):
"""
Shrink ... | sniemi/SamPy | image/manipulation.py | Python | bsd-2-clause | 9,087 | [
"Gaussian"
] | 52e1aea6cdcc76b41251ff9bdcaba28e9a8cb96eb6fb790190bc9b3b645b36fa |
"""
This package implements the No-U-Turn Sampler (NUTS) algorithm 6 from the NUTS
paper (Hoffman & Gelman, 2011).
Content
-------
The package mainly contains:
nuts6 return samples using the NUTS
test_nuts6 example usage of this package
and subroutines of nuts6:
build_tree ... | vhaasteren/piccard | outliers/nutstrajectory.py | Python | gpl-3.0 | 25,000 | [
"Gaussian"
] | 24443bff754687fc7c96c2f1310df9efa3435dd52b9ed2c0ac78f2688b17fc6f |
"""Loading icons."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import gtk
from logging import warn
import math
def load_icon(icon_path, icon_width=None, icon_height=None):
"""Load icon from path. Icon MUST be in PNG format.
@param... | pombredanne/zero-install | zeroinstall/gtkui/icon.py | Python | lgpl-2.1 | 1,367 | [
"VisIt"
] | ae77bf62cc6bc1a89398435e68bb5ebb904e09edaa097fc3c2081b1834ce1398 |
"""Example to solve 3D aqueous foam pipe flow using rheological
Herschel-Bulkley power law for bulk and wall shear stress dependent
slip velocity law for wall layer
"""
from simphony.core.cuba import CUBA
from simphony.api import CUDS, Simulation
from simphony.cuds.meta import api
from simphony.engine import EngineI... | simphony/simphony-openfoam | foam_internalwrapper/examples/aqueous_foam_pipe_flow_steady_state.py | Python | gpl-2.0 | 4,455 | [
"Mayavi"
] | f4f5c42afa6e36ff922ead784f7f1a5f9675329b995bdc0db21851b8af7a9dc3 |
import simtk.openmm.openmm as openmm
import wcadimer
system, _ = wcadimer.WCADimer()
temperature = wcadimer.temperature
collision_rate = wcadimer.collision_rate
timestep = 2.0 * wcadimer.stable_timestep
integrator = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
# Serialize openmm objects
with ope... | nrego/westpa | lib/examples/wca-dimer_openmm/we_exec/build_system.py | Python | gpl-3.0 | 495 | [
"OpenMM"
] | bf98ba8b60f06f3cc09368ff8f2386bb2319acb8c7c89ce07af41fd86e2f5f8b |
import string
import sys
from xml.sax import saxexts
from xml.sax import saxlib
from UserStack import UserStack
class XElement:
def __init__(self, name=None, attrs=None):
self.name = name
self.attrs = attrs
self.children = []
self.text = ''
def initialize(self):
pass
... | aarestad/gradschool-stuff | xml-class/python-xml/OutlineTool/outlinetool.py | Python | gpl-2.0 | 11,442 | [
"VisIt"
] | d44684a4cf1c20483e5ea78e87fbc8c2424b4c3263de5c2bc3a13934351df62c |
#============================================================================
#
# Copyright (c) Kitware Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses... | matthieuheitz/VesselView | Modules/Scripted/Workflow/Workflow.py | Python | apache-2.0 | 14,629 | [
"VTK"
] | 5ee5be125a272362b45539eb0089d2902278d63f7e15166594b34408ad17f683 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | samples/MDAnalysisIntegration.py | Python | gpl-3.0 | 3,536 | [
"ESPResSo",
"Gromacs",
"MDAnalysis"
] | dd189e72ce147148dbbdfcb7f455e157c2845bf25bd3e7a740f1ffc796e8e8d4 |
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Autodesk/molecular-design-toolkit | moldesign/forcefields/ffparams.py | Python | apache-2.0 | 7,010 | [
"Amber",
"CHARMM"
] | a4193fbde0dff1789ea1fc3d8dd2328eafc0e63cd7595abcbfd5d2e4d336d683 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RLumi(RPackage):
"""BeadArray Specific Methods for Illumina Methylation and Expression
... | LLNL/spack | var/spack/repos/builtin/packages/r-lumi/package.py | Python | lgpl-2.1 | 1,923 | [
"Bioconductor"
] | facdf3e4f2822887d0463317f855c58a083277e747f71af31b74f0ee07d792bc |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | uchidaknet/TiCustomBGService | build.py | Python | mit | 6,822 | [
"VisIt"
] | b3af31daa8f9371f60724e05b0f33d039d3bee141c5e01f0840d99f2ef96e233 |
#!/usr/bin/env python
# coding: utf-8
# # Basic ideas of the Principal Component Analysis (PCA)
#
# The principal component analysis deals with the problem of fitting a
# low-dimensional affine subspace $S$ of dimension $d$ much smaller than
# the total dimension $D$ of the problem at hand (our data
# set). Mathemati... | CompPhysics/MachineLearning | doc/LectureNotes/_build/jupyter_execute/chapter8.py | Python | cc0-1.0 | 36,331 | [
"MOE"
] | 867d4994f87875adc17a279e3ce7cd4bad8733c6cba0353c8cc2bdb9da875cf7 |
from ase import *
a = 2.70
c = 1.59 * a
h = 1.85
d = 1.10
slab = Atoms('2Cu', [(0., 0., 0.), (1/3., 1/3., -0.5*c)],
tags=(0, 1),
pbc=(1, 1, 0))
slab.set_cell([(a, 0, 0),
(a / 2, 3**0.5 * a / 2, 0),
(0, 0, 1)])
slab = slab.repeat((4, 4, 1))
slab.set_calculator(E... | freephys/python_ase | tutorials/N2Ru-relax.py | Python | gpl-3.0 | 879 | [
"ASE"
] | 1818380e89eda8efd30fa7d7aaaaf069f4cf989bb37e7eb577a5933fb5dc3a7d |
from __future__ import print_function
import six
import bz2
from json import dumps, loads
from operator import itemgetter
from Bio.Blast import NCBIXML
from Bio.File import as_handle
from dark.hsp import HSP, LSP
from dark.score import HigherIsBetterScore
from dark.alignments import Alignment, ReadAlignments
from da... | bamueh/dark-matter | dark/blast/conversion.py | Python | mit | 12,742 | [
"BLAST",
"Biopython"
] | e844ea9ac8c36c68133c9e22a035f8f2025e4a30dacd75078b8aebe4ab1d57a6 |
## @package memonger
# Module caffe2.python.memonger
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import networkx as nx
import collections
import time
import heapq
import copy
from caffe2.python import workspace
fro... | bwasti/caffe2 | caffe2/python/memonger.py | Python | apache-2.0 | 38,744 | [
"VisIt"
] | e3eb7c5fc516a419d89e28fa657611876c42838ebdf80aee4c5f7b8d8f1cad8b |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/special/add_newdocs.py | Python | mit | 175,349 | [
"Gaussian"
] | fbce9e529ef258b59a986926491af8e1f11171c7c5fd8c670738d794b9a8b73b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Localization Compiler
#
import os, sys, codecs, shutil
from xml.dom.minidom import parse
template_dir = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
sys.path.append(os.path.join(template_dir,'../'))
from tiapp import *
ignoreFiles = ['.gitig... | hieupham007/Titanium_Mobile | support/common/localecompiler.py | Python | apache-2.0 | 5,732 | [
"VisIt"
] | 3f957950583b5cbfa86eb5711e623a88ce7ac8dda720474844134e7bbd720066 |
#!/usr/bin/env ipython
"""
Analisis of sheath-from-icme for Auger Low Energy data
IMPORTANT:
- Note that 'structure' argument refers to MC, sheath, ICME,
sheath-of-icme, taking the following possible values:
'i' : ICME
'mc' : MC
'sh.i' : sheath of ICME
'sh.mc' : sheath... | jimsrc/seatos | sheaths.icmes/src/sea_global.py | Python | mit | 5,255 | [
"NetCDF"
] | 0db9f055fa00ab77edb434ceab2d9b115fc706e99e2562b947be65ae608e04a3 |
import numpy as np
import theano
import theano.tensor as T
from smartlearner.tasks import stopping_criteria
from smartlearner.utils import sharedX
from smartlearner import Trainer
from smartlearner.optimizers import SGD, AdaGrad
from smartlearner.tasks import tasks
from numpy.testing import assert_array_almost_equ... | havaeimo/smartlearner | smartlearner/optimizers/tests/tests_optimizers.py | Python | bsd-3-clause | 4,539 | [
"Gaussian"
] | 2d6cee43446292e3a36a025d1b398b438bc92683123bc1fbc12aaaa97a8f1dbe |
# -*- coding: utf-8 -*-
"""
NACO AGPM/Saturated PSF real-time statistics module.
The main program here is run_and_process. Everything else is defined so the
code is easier to follow. It is intended to be run on the offline machine at
Paranal, and monitors a folder for incoming data.
You should exit and relaunch ... | AnthonyCheetham/naco_ispy | monitor.py | Python | gpl-3.0 | 22,177 | [
"Gaussian"
] | 78e799fa484f9e4dd7641b1e521ad25ef012d81932ef81f5d691d09aab7e0159 |
#
# Copied from VTK/Common/Testing/Python/PythonSmoke.py
#
import qt
try:
import vtk
except:
print "Cannot import vtk"
qt.QApplication.exit(1)
try:
print dir(vtk)
except:
print "Cannot print dir(vtk)"
qt.QApplication.exit(1)
try:
try:
try:
o = vtk.vtkLineWidget()
print "Using Hybrid"
... | finetjul/CTK | Applications/ctkSimplePythonShell/Testing/Python/vtkPythonSmoke.py | Python | apache-2.0 | 843 | [
"VTK"
] | 119ab5293b2df52c94ae8beac89d2430fd8f144c9cc41c3bf30426a717202ce0 |
import sys
import os
import glob
import distutils.util
import doctest
build_dir = "build/lib.%s-%s" % (distutils.util.get_platform(), sys.version[0:3])
sys.path.insert(0, os.path.join(os.getcwd(), build_dir))
import HTSeq
py_fdn = 'python'+str(sys.version_info[0])
def test_rst_file(filename):
print "Doctest of... | simon-anders/htseq | python2/test/test.py | Python | gpl-3.0 | 1,384 | [
"HTSeq"
] | e41d1eabc5c073141ae8b784cfc28b1568a1c8a30342d40b6537123da3cbc458 |
#!/usr/bin/python
"""
A simple routine to load in a LIGGGHTS hybrid dump file containing
contact and contact force data and convert into a .vtk unstructured
grid which can be used to visualise the force network. This routine
also writes the length of the connection between particles, in order
to be able to filter out i... | CFDEMproject/LPP | src/dump2force.py | Python | gpl-2.0 | 13,376 | [
"LAMMPS",
"ParaView",
"VTK"
] | f71a993bbafd9feca52d68e353f1b5d076566577712f8183fda5b39588df2947 |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 o... | NAMD/pypln.backend | pypln/backend/workers/spellchecker.py | Python | gpl-3.0 | 1,891 | [
"NAMD"
] | 3869b400dfccb0bbb8ca3ca2d8294e239f151e82f009fd15add58bdc30af2103 |
#!/usr/bin/env python3
import itertools
from collections import defaultdict
import logging
from operator import mul
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.base import DirectedGraph
from pgmpy.factors.discrete import TabularCPD, JointProbabilityDistribution, DiscreteFactor
from pgmpy.... | sandeepkrjha/pgmpy | pgmpy/models/BayesianModel.py | Python | mit | 36,803 | [
"VisIt"
] | 2f2750e2cf865c64b1d29ece39eb8a3edca24d3b003996ee02a22465a32f5c6f |
import h5py
import os
#import ipdb
import pdb
import re
import numpy as npexit
from pylayers.antprop.channel import *
from pylayers.util.project import *
import pylayers.util.pyutil as pyu
import ConfigParser
import numpy.linalg as la
from numpy.linalg import svd
from numpy.fft import *
import time
"""
Module to hand... | dialounke/pylayers | pylayers/measures/exploith5.py | Python | mit | 38,000 | [
"BLAST",
"Gaussian"
] | 833adca3201bbf99f0b3dd714876cad26fbdca3deaef6345880ed99a3a50a365 |
from modules.basemodule import BaseModule
import collections
import json
import os
import pprint
import re
import shutil
import time
def log(*args, **kwargs):
print(*args, **kwargs)
def roomnr(x):
# CoffeeMud, Mob Factory exits are negative but room IDs are positive
return str(abs(x))
reverse = {
... | cizra/pycat | modules/mapper.py | Python | unlicense | 29,718 | [
"VisIt"
] | 6efb8e230de3b1ba349aaf052e831220c3d55c202e050fc5cc9f8e2b8c92e4a8 |
import pyspeckit
import numpy as np
from pyspeckit.spectrum.models import voigtfitter
# technically, the voigt fitter works as a singlefitter (i.e., you can fit the
# background level and the peak simultaneously)
# in practice, however, you need to fit the background independently except for
# gaussians. I don't kno... | keflavich/pyspeckit-obsolete | examples/multivoigt.py | Python | mit | 1,985 | [
"Gaussian"
] | 0ea2eb14e337a57e3a1b898a3261b5d9fba1ce69351a3138215957449d8d6607 |
import io
import os
from django.conf import settings
from django.contrib import messages
from django.http import FileResponse
from django.shortcuts import get_object_or_404, redirect
from django.template import loader
from django.urls import reverse, reverse_lazy
from django.utils import timezone
from django.utils.tex... | epcoullery/epcstages | candidats/views.py | Python | agpl-3.0 | 7,969 | [
"ASE"
] | 8ed645561a364df1460a5d9b39fe14a71224ded72ef50e59b4c7879cdbe80695 |
from kivy.app import App
from kivy.core.window import Window
from kivy.event import EventDispatcher
from kivy.logger import Logger
from kivy.metrics import Metrics
from kivy.properties import * # NumericProperty, ReferenceProperty...
from kivy.uix.screenmanager import ScreenManager, SlideTransition
''' Notes on lazy... | knappador/kivy-android-nativer | src/controllers.py | Python | mit | 9,416 | [
"Galaxy"
] | e6f570c0d1789d130d99e73d3d823187d27e36ebf36287a067da2e0728c634ce |
import logging
import os
from tool_shed.util import common_util
log = logging.getLogger( __name__ )
# String separator
STRSEP = '__ESEP__'
def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner,
changeset... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/container_util.py | Python | gpl-3.0 | 3,141 | [
"Galaxy"
] | 8c19195c89bf9e3aebbaf0d28ec501d78221541a7997ecf5f12f187229f1617a |
# ast.py
# Copyright (C) Mako developers
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise the compiler
module is used.
"""
from StringIO... | codendev/rapidwsgi | src/mako/pyparser.py | Python | gpl-3.0 | 17,291 | [
"VisIt"
] | 4fc462b220a69b0d65b416c447478102516caab743cf1bba67cc2d84f383e4e3 |
__all__ = ["install"]
from panda3d.core import *
from direct.directnotify.DirectNotifyGlobal import directNotify
from direct.showbase.PythonUtil import fastRepr
import sys
import traceback
notify = directNotify.newCategory("ExceptionVarDump")
reentry = 0
def _varDump__init__(self, *args, **kArgs):
global reentr... | grimfang/panda3d | direct/src/showbase/ExceptionVarDump.py | Python | bsd-3-clause | 6,999 | [
"VisIt"
] | e0bfd2d450cacf4f4d5043b90f51101bb4e6594ea0e103c15db2017557b7374a |
import pysam
import sys
def vcf_record_count(vcf):
v = pysam.VariantFile(vcf)
print(len(list(v.fetch())))
if __name__ == "__main__":
vcf_record_count(sys.argv[1])
| uc-cdis/cwl | genomel/docker/variant_calling/post_freebayes/pysam_vcf_check.py | Python | apache-2.0 | 177 | [
"pysam"
] | 765949f39593f344d1879602d6515bf9e25143b65c970a94db0482c711979712 |
import csv
import mapdamage
import pysam
import math
import logging
import time
class RescaleError(RuntimeError):
pass
def _phred_pval_to_char(pval):
""" Transforming error rate to ASCII character using the Phred scale"""
return chr(int(round(-10 * math.log10(abs(pval))) + 33))
def _phred_char_to_pval... | ginolhac/mapDamage | mapdamage/rescale.py | Python | mit | 13,609 | [
"pysam"
] | 8cb91050d17dfc608e3f4b7e4f927b701e62dedd5297080f349b6de87c481c09 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/MooseDocs/test/tree/test_html.py | Python | lgpl-2.1 | 1,407 | [
"MOOSE"
] | 33829c4e560d0da5d3fc7e7bfac2e310c860a53e7c3e730985bab24d21a29789 |
# Copyright 2001-2004 Brad Chapman.
# Revisions copyright 2009-2013 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.
"""General mechanisms to access applications i... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Application/__init__.py | Python | apache-2.0 | 30,870 | [
"BLAST",
"Biopython"
] | 6e4156ec8652798fabe19158003743cddbe34c10eb96ca64d53ddf8d6a4e2db6 |
import cv2
import numpy as np
import sys
def order_points(pts):
# initialzie a list of coordinates that will be ordered
# such that the first entry in the list is the top-left,
# the second entry is the top-right, the third is the
# bottom-right, and the fourth is the bottom-left
rect = np.zeros((4... | Hubert51/AutoGrading | Web/main.py | Python | mit | 20,714 | [
"Gaussian"
] | d0d1f1f843797365832fceaf383542824b229bf69071ef836010936467390538 |
import logging
from pytopol.parsers import blocks
lgr = logging.getLogger('mainapp.utils')
def build_res_chain(m):
# using a molecule object with atoms, builds residues and chains
R = None
residues = []
for i, a in enumerate(m.atoms):
if R is None or (a.resname != R.name or
... | resal81/PyTopol | pytopol/parsers/utils.py | Python | gpl-3.0 | 2,017 | [
"CHARMM",
"Gromacs"
] | b2e2ad5b4bb9af08417c77aec69321555270998404fa0fe811e80256d533a1d7 |
"""
==============
PopVis Example
==============
"""
# Authors: Mayank Agrawal <mayankagrawal96@gmail.com>
#
# License: MIT
########################################################
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from spykes.plot.neurovis import NeuroVis
from spykes.plot.popvi... | codekansas/spykes | examples/plot_popvis_example.py | Python | mit | 5,338 | [
"NEURON"
] | 9e195ede43901b5a3d7b00c5b5fe60eaea82984ee7bc5f5696dc5f03aebfb37f |
""" Code used for running the package directly from the Command Line """
import os.path
import logging
import argparse
import sys
from .db import AvailabilityDB
from .core import AvailabilityInfo
from .reports import ALL_REPORTS
from .settings import get_settings
def run():
# ----------------------... | supernathan23/dn_availability | dn_availability/cli.py | Python | mit | 13,300 | [
"VisIt"
] | 96494def86ae796a7b7d2b4709d12c470f738bcefec968ac9c06bf18e3cb6499 |
"""
The Grid module contains several utilities for grid operations
"""
import os
import re
from DIRAC.Core.Utilities.Os import sourceEnv
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DI... | andresailer/DIRAC | Core/Utilities/Grid.py | Python | gpl-3.0 | 15,874 | [
"DIRAC"
] | f3cac8a3db307ff3e51bf893255d839dc0dc8be0d081a3ff031d674a50a5cc0a |
# -*- encoding:utf-8 -*-
from __future__ import division, absolute_import, print_function
import sys, textwrap
from numpydoc.docscrape import NumpyDocString, FunctionDoc, ClassDoc
from numpydoc.docscrape_sphinx import SphinxDocString, SphinxClassDoc
from nose.tools import *
if sys.version_info[0] >= 3:
sixu = la... | AdaptiveApplications/carnegie | tarc_bus_locator_client/numpy-1.8.1/doc/sphinxext/numpydoc/tests/test_docscrape.py | Python | mit | 18,326 | [
"Gaussian"
] | 472280f74ebd9cca80d80caa85764c70465a63e5b9a18c07112c276461c05116 |
"""
Author: Remi Lafage <remi.lafage@onera.fr>
This package is distributed under New BSD license.
Mixture of Experts
"""
# TODO : support for best number of clusters
# TODO : implement verbosity 'print_global'
# TODO : documentation
import numpy as np
import warnings
OLD_SKLEARN = False
try: # scikit-learn < 0.20.... | relf/smt | smt/applications/moe.py | Python | bsd-3-clause | 24,509 | [
"MOE"
] | d76eea468a68aed612afcde83145bcf00622d9b41ada42f6526dda8ce67cda9a |
#!/usr/bin/python
#
# Copyright (C) 2018-2019 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... | mkuron/espresso | maintainer/gh_post_style_patch.py | Python | gpl-3.0 | 3,132 | [
"ESPResSo"
] | b772a298f2dc7899e33d5911f3c9a126ef1776bbab07a12a8341bc234233f521 |
import discord, asyncio, logging, time, threading, markovify, psutil, posixpath, platform, re, requests, os, time, shutil, glob, textwrap, datetime, json
from pprint import pprint
import random
from random import randint
import PIL
from PIL import ImageFont
from PIL import Image
from PIL import ImageDraw
from pyfiglet ... | ZerataX/ebooks | ebooks.py | Python | gpl-3.0 | 39,538 | [
"VisIt"
] | c7903bde6ffad2aa94048c4e127a9344306f57ef4ace190a7dbbe849f1ecc072 |
# Copyright 2015, Kay Hayen, mailto:kay.hayen@gmail.com
#
# Part of "Nuitka", an optimizing Python compiler that is compatible and
# integrates with CPython, but also works on its own.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complianc... | tempbottle/Nuitka | nuitka/nodes/NodeBases.py | Python | apache-2.0 | 41,638 | [
"VisIt"
] | 2e8565e712e458882539bd9cc523eb5400de8b7a57649e9c5e9fd88502a390a5 |
########################################################################
# File : FC_Scaling_test
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Test suite for a generic File Catalog scalability tests
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base impor... | Andrew-McNab-UK/DIRAC | tests/Integration/DataManagementSystem/FC_scaling_test.py | Python | gpl-3.0 | 10,751 | [
"DIRAC"
] | 54ef00daf22d0e615f9a37b5817e1cbd612e65ce08ca6af1eab9bbbb38836814 |
# First pass at loading and running a cell model
import os
os.environ['NUMPTHREADS'] = '1'
import moose
import proto18
def dumpPlots( fname ):
if ( os.path.exists( fname ) ):
os.remove( fname )
tab.xplot( fname, 'soma.Vm' )
catab.xplot( fname, 'soma.Ca' )
library = moose.Neutral( '/library' )
moose.setCwe( '/l... | dilawar/moose-full | moose-examples/snippets/MULTI/runcell18.py | Python | gpl-2.0 | 1,706 | [
"MOOSE"
] | ffde5db0038db9eb5f9c1ba23e36fe0d8cb6d400f98984693d8cea1fcd6e5c6e |
# coding: utf8
{
' Quotas: %(quotas)s x%(quota_amount).2f': ' Quotas: %(quotas)s x%(quota_amount).2f',
' Transaction number: %s': ' Transaction number: %s',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" je voliteľný výraz ako "field1=\'newv... | reingart/gestionlibre | languages/sk-sk.py | Python | agpl-3.0 | 16,860 | [
"VisIt"
] | d793213d63e43ae7c0f95d85412ca2f6fc65f01604d678fa180e61b76eff95f5 |
from __future__ import division
from collections import defaultdict
from math import sqrt, log
import numpy as np
from scipy.spatial.distance import cdist, pdist
from sklearn.utils import check_random_state
def inertia(X, labels, metric='sqeuclidean', p=2):
"""
Given data and their cluster assigment, comp... | sarajcev/nowcasting | cluster_metrics.py | Python | gpl-3.0 | 24,358 | [
"Gaussian"
] | 3bfc4925a5d928e740f535bb08286b95a3125586658006758396f4c5e32b18cc |
# -*- encoding: utf-8 -*-
"""
synthetic.py : To obtain the characteristic size of the point spread function
(PSF) of a microscope system, and to generate simulated images containing one
or multiple spots (PSF's).
Copyright (C) 2021 Andries Effting, Delmic
This program is free software; you can redistribute it and/or... | pieleric/odemis | src/odemis/util/synthetic.py | Python | gpl-2.0 | 4,092 | [
"Gaussian"
] | cc00b73e1a04b9ddbcb1f2e6194af2833f5f9f0b9395456d556731367adfd370 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree_check.py
The original template file format supports any... | SGenheden/lammps | tools/moltemplate/src/lttree_check.py | Python | gpl-2.0 | 133,762 | [
"LAMMPS"
] | 280ab7443fcdcd5528d31e8f198bbf3cc53fc2309cc9f457308d2667e30e94bc |
#!/usr/bin/env python
"""
Save polynomial basis on reference elements or on a mesh for visualization into
a given output directory.
"""
from __future__ import absolute_import
import sys
from six.moves import range
sys.path.append('.')
import os
from argparse import ArgumentParser
import numpy as nm
from sfepy.base.bas... | vlukes/sfepy | script/save_basis.py | Python | bsd-3-clause | 10,029 | [
"VTK"
] | 286d683e764b4ea846b6c897f7aae6a75723cf1d52495c1f1f7c3a241aede96d |
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('third_party_auth', '0009_auto_20170415_1144'),
]
operations = [
migrations.AddField(
model_name='ltiproviderconfig',
name='skip_hinted_login_dialog',
fie... | eduNEXT/edunext-platform | common/djangoapps/third_party_auth/migrations/0010_add_skip_hinted_login_dialog_field.py | Python | agpl-3.0 | 1,526 | [
"VisIt"
] | 68413ca10327e98fd81b75a6414e00b6514936ea74236c1f12f1530f5fbfe0c2 |
import matplotlib.pyplot as plt
import numpy as np
import time
from matplotlib.path import Path
pi=np.pi
# "dirac_sheet.py" is an object class that defines a 2D discretized sheet for calculating solutions to the
# time-domain solutions of the Dirac equation. It implements a staggered time and staggered space d... | arthurbarnard/Dirac_simulation | dirac_sheet.py | Python | gpl-3.0 | 12,611 | [
"DIRAC"
] | 5289ed6196fee181bf7369c87eb00c6478b99bc0fc6c031b721efe913d610b54 |
import numpy as np
from mayavi import mlab
from BDQuaternions import Conventions, EulerAngles
from BDSpace.Coordinates import Cartesian
import BDSpaceVis as Visual
# Create cartesian coordinate system
convention = Conventions().get_convention('Bunge')
# if you don't pass arguments the basis coincide with 'Absolute'... | bond-anton/Space_visualization | demo/03_euler_angles_precession.py | Python | apache-2.0 | 1,473 | [
"Mayavi"
] | a391af9cb6d4351e253b83c32bef09f4661534bd6d86e38eb04587f8014aa2a6 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vt... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/constrainedDelaunay.py | Python | bsd-3-clause | 4,603 | [
"VTK"
] | 296496da2c7ecfc67fa591175632ddc511b12f8c843afde6d2d65c576bcbdcc1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes for plotting Pourbaix objects.
"""
import six
from six.moves import map
from six.moves import zip
__author__ = "Sai Jayarama... | sonium0/pymatgen | pymatgen/analysis/pourbaix/plotter.py | Python | mit | 24,142 | [
"pymatgen"
] | 43472bcd65dac1448988b34ccc25e8930541096bd82504a9f9af30e55607a8f4 |
# Orca
#
# Copyright (C) 2013-2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (... | chrys87/orca-beep | src/orca/scripts/toolkits/GAIL/script.py | Python | lgpl-2.1 | 5,302 | [
"ORCA"
] | fc74a08f12daee81d78b2c4df43ff0d4f63446043bb058ab1b6d65fd168fcbdd |
#
# Copyright 2014, 2018 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | libAtoms/matscipy | scripts/fracture_mechanics/run_ideal_brittle_solid.py | Python | lgpl-2.1 | 6,486 | [
"ASE",
"CRYSTAL",
"Matscipy"
] | 77dfaf298b340c9eec76184b23c02ea268c80572a708bdc83d8fa6bef22a9b5d |
from lib_spm import *
from scipy.stats import norm
#out_dir = os.path.join('/data42s/comparat/firefly/v1_1_0/figures', 'mass-redshift-presentation')
out_dir = os.path.join(os.environ['HOME'], 'wwwDir', 'firefly')
def plotDIFF(imf_ref, imf_1, imf_2, m_bins = n.arange(-10., 10., 0.1)):
print('eboss')
stellar_mass = im... | JohanComparat/pySU | spm/bin_SMF/plot_differences_age.py | Python | cc0-1.0 | 6,094 | [
"Firefly",
"Galaxy"
] | f0abc5d41ea1a3c4c95b423ebb9aa9de6ac369b7d7bf124de9fbdda4b1e64271 |
#!/usr/bin/env python
from __future__ import division
import unittest
import numpy as np
import warnings
from pymatgen.core.lattice import Lattice
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.groups import PointGroup, SpaceGroup
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The ... | tallakahath/pymatgen | pymatgen/symmetry/tests/test_groups.py | Python | mit | 6,002 | [
"pymatgen"
] | ca0d5c1901692e0e7febab0add29a3222ad9d0e6fb1e5aa569e493d02323767b |
# -*- coding: utf-8 -*-
#
## we set up default information.
## first, easy to maintain lists which can eventually be moved to
## files.
from typing import Collection, List, Mapping
from .abstractLang import AbstractLanguage
class Language(AbstractLanguage):
# TRANSLATOR WARNING: DO NOT TRANSLATE THE FIELD NAME... | kirienko/gourmet | src/gourmet/defaults/defaults_nl.py | Python | gpl-2.0 | 25,199 | [
"Octopus"
] | dc03a825f4102be070f57918b210c13ccf704ba23eed83f06c04ac366cb17c55 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
from __future__ import print_function
import h2o
import sys
sys.path.insert(1,"../../../") # allow us to run this standalone
from h2o.estimators.random_forest import H2ORandomForestEstimator
from h2o.estimators.gbm import H2OGradientBoostingEstimator
from h2o.estimato... | spennihana/h2o-3 | h2o-py/tests/testdir_algos/stackedensemble/pyunit_stackedensemble_gaussian.py | Python | apache-2.0 | 7,384 | [
"Gaussian"
] | c4c752d86a627ef2f90d4eeef59d225fcb38ea1c1214bf42151b6b522b9f2505 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2007 Philippe LAWRENCE
#
# This file is part of pyBar.
# pyBar 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 Licens... | wood-galaxy/pyBarEC | pyBar.py | Python | gpl-2.0 | 93,060 | [
"FLEUR"
] | e0ebe0fc3fcf2f2a60f1f97c6c1b092d399398f567e349be35fed12fc7acceff |
"""
.. module:: components
:platform: Unix
:synopsis: module containing definitions of component objects in pysm.
.. moduleauthor: Ben Thorne <ben.thorne@physics.ox.ac.uk>
"""
from __future__ import absolute_import, print_function
import numpy as np
import healpy as hp
import os, sys, time
import scipy.constant... | bthorne93/PySM_public | pysm/components.py | Python | mit | 51,029 | [
"Gaussian"
] | b94c987b6bdfb44cda6c68d2435e4bd2e3cf8149a4ed16d088479f8831ef6478 |
import logging
import os
import shutil
import sys
from string import Template
from galaxy.util import unicodify
from galaxy import eggs
eggs.require( 'MarkupSafe' )
import markupsafe
log = logging.getLogger( __name__ )
CHUNK_SIZE = 2**20 # 1Mb
INSTALLATION_LOG = 'INSTALLATION.log'
# Set no activity timeout to 20 m... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/basic_util.py | Python | gpl-3.0 | 5,198 | [
"Galaxy"
] | 324fb61b55cf6e16e7b410565ec65161fe172d3adbeac0743ac91a6fad5e7efe |
# Copyright (c) 2006-2011, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2011, 2013-2014 Google, Inc.
# Copyright (c) 2013-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Steven Myint <hg@stevenmyint.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/g... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/pylint/checkers/exceptions.py | Python | apache-2.0 | 16,120 | [
"VisIt"
] | 2bd1cfbefcaa5e2af8a9a3a0e9ca7a96fc3dbdf802876ee61ad710604eae7472 |
#!/usr/bin/env python
#
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# A... | mitya57/debian-buildbot | setup.py | Python | gpl-2.0 | 8,524 | [
"Brian"
] | 8adb0cae5384f176ede467425e51a4672e100fd17eccc110683b87f4b6a2ddd1 |
from __future__ import absolute_import, division, print_function
import contextlib
import itertools
import os.path
import pickle
import shutil
import sys
import tempfile
import unittest
import warnings
from io import BytesIO
import numpy as np
import pandas as pd
import pytest
import xarray as xr
from xarray import ... | jcmgray/xarray | xarray/tests/test_backends.py | Python | apache-2.0 | 121,213 | [
"NetCDF"
] | 1cff333ed4a0093b5c44fe6878cf88d2f80409fb35599e7c20ff659d3a5b26fa |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
from builtins import object, dict, str
import os
import json
import logging
import networkx as nx
from indra.statements import Influence
# Python 2
try:
basestring
# Python 3
except:
basestring = str
logger = logg... | pvtodorov/indra | indra/assemblers/cag/assembler.py | Python | bsd-2-clause | 12,390 | [
"Cytoscape"
] | 2dd5f7cb6d2b9da981886903434a9ae65f49a868c3ff94d63f12a3c12cbe73df |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
import sys
from rdkit import six
from rdkit.VLib.Node import VLibNode
class TransformNode(VLibNode):
""" base class for nodes which filter their input
Assumptions:
- transform function takes a number of arguments equal to th... | jandom/rdkit | rdkit/VLib/Transform.py | Python | bsd-3-clause | 1,971 | [
"RDKit"
] | 432d541534fd1caeb2c1a938244cd33144536604178bef85f45f7ae48f65ee6e |
from ._MultiNEAT import *
def Scale(a, a_min, a_max, a_tr_min, a_tr_max):
t_a_r = a_max - a_min
if t_a_r == 0:
return a_max
t_r = a_tr_max - a_tr_min
rel_a = (a - a_min) / t_a_r
return a_tr_min + t_r * rel_a
def Clamp(a, min, max):
if a < min:
return min
elif a > max:
... | peter-ch/MultiNEAT | MultiNEAT/viz.py | Python | lgpl-3.0 | 13,883 | [
"NEURON"
] | 730d7403255204a41e8b0142cc684a89686fed4c16a0407f5c99dc7ad18a7c2f |
from ase import *
atoms = Atoms('H7',
positions=[(0, 0, 0),
(1, 0, 0),
(0, 1, 0),
(1, 1, 0),
(0, 2, 0),
(1, 2, 0),
(0.5, 0.5, 1)],
constraint... | freephys/python_ase | ase/test/example.py | Python | gpl-3.0 | 627 | [
"ASE"
] | bcb75adf627f93fe7d0005c0f47acf782d255d59b5f6d224ef0867bb7c06e14f |
#!/usr/bin/env python
#from sumatra.projects import load_project
#from sumatra.parameters import build_parameters
#from sumatra.decorators import capture
from ruffus import *
import sys
import os
import time
import datetime
import drmaa
from omics_pipe.utils import *
from omics_pipe.parameters.default_parameters imp... | adammaikai/OmicsPipe2.0 | omics_pipe/ChIPseq.py | Python | mit | 3,774 | [
"Bowtie"
] | a05fa93fcf195e639cb875810cfd0cdb54179efb39cc7a1bbcf1b5c27ad3f9b1 |
#!/usr/bin/env python2
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2015, Kovid Goyal <kovid at kovidgoyal.net>'
import httplib, hashlib, zlib, string, time
from io import BytesIO
from temp... | ashang/calibre | src/calibre/srv/tests/http.py | Python | gpl-3.0 | 17,003 | [
"MOOSE"
] | 935ff2fbd919ff606fda17408e4aaab63b148154d0a822c12397411713b2c3df |
import warnings
import numpy as np
import pandas as pd
import xarray
import scipy.stats as st
import numba
try:
import pymc3 as pm
except:
pass
import arviz as az
import arviz.plots.plot_utils
import scipy.ndimage
import skimage
import matplotlib._contour
from matplotlib.pyplot import get_cmap as mpl_get_c... | justinbois/bebi103_utils | bebi103/viz.py | Python | mit | 91,620 | [
"Gaussian"
] | 499f89c0d03a6a665e152e44adee807e8f26c94fc66b0fa06405ee1e701cda3e |
#===============================================================================
# This file is part of TEMPy.
#
# TEMPy is a software designed to help the user in the manipulation
# and analyses of macromolecular assemblies using 3D electron microscopy maps.
#
# Copyright 2015 Birkbeck Colleg... | OniDaito/ChimeraXTempy | TEMPy/Consensus.py | Python | mit | 24,096 | [
"Gaussian"
] | 94340f6d31d3c47b29a5052713cc8aa463393b29e13eada40e1eb449f43407a9 |
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_base.form.forms import BaseModelForm
from microbiome.apps.mb.choices import VISIT_REASON, VISIT_INFO_SOURCE, MATERNAL_VISIT_STUDY_STATUS, INFO_PROVIDER
from ..models import MaternalVisit, MaternalConse... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/forms/maternal_visit_form.py | Python | gpl-2.0 | 1,637 | [
"VisIt"
] | 9708c0feb088fdd3ee1e587e9553718079976b7c33afb776c51c06090381789e |
""" Python test discovery, setup and run of test functions. """
import enum
import fnmatch
import inspect
import itertools
import os
import sys
import typing
import warnings
from collections import Counter
from collections import defaultdict
from collections.abc import Sequence
from functools import partial
from typing... | alfredodeza/pytest | src/_pytest/python.py | Python | mit | 58,223 | [
"VisIt"
] | c7faf15a568c66b1240dbcb7c27891b4b842ceeb978d4cbe1d84d892b6462028 |
"""A quick DOM implementation.
Python's xml.dom is very slow. The xml.sax module is also slow (as it imports urllib2).
This is our light-weight version.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from xml.parsers import expat
class Element(object):
"""... | timdiels/0install | zeroinstall/injector/qdom.py | Python | lgpl-2.1 | 3,773 | [
"VisIt"
] | 1714883cfab613e7907c6365d11b22b219c826115da978ea82fe40ef2c136cd0 |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | d7415/merlin | Arthur/views/home.py | Python | gpl-2.0 | 5,398 | [
"Galaxy"
] | 9e39357e12c8fdce65d7d4e0d8259bda798476da09640eeae03b411c97c265bc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import os
import json
import collections
import itertools
from abc import ABCMeta, abstractmethod
import random
import warnings
from fnmatch import... | nisse3000/pymatgen | pymatgen/core/structure.py | Python | mit | 140,131 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"exciting",
"pymatgen"
] | 813b028daa79cc00a88a9007dba59f180bda8550f7acc61b26e6b97c99cf916d |
"""Internal helper files for user output."""
__author__ = ("Luc Anselin luc.anselin@asu.edu, "
"David C. Folch david.folch@asu.edu, "
"Levi John Wolf levi.john.wolf@gmail.com, "
"Jing Yao jingyao@asu.edu")
import numpy as np
import copy as COPY
from . import diagnostics
from .... | lixun910/pysal | pysal/model/spreg/user_output.py | Python | bsd-3-clause | 18,352 | [
"COLUMBUS"
] | 150b747e7469b942a7f89dab493c94afdce4cecad043e8e4ab10b0f8616e43fb |
# ***************************************************************************
# *
# * Copyright (C) 2013-2016 University of Dundee
# * All rights reserved.
# *
# * This file is part of SAMoS (Soft Active Matter on Surfaces) program.
# *
# * SAMoS is free software; you can redistribute it and/or modify
# * it unde... | sknepneklab/SAMoS | utils/Writer.py | Python | gpl-3.0 | 8,769 | [
"VTK"
] | 378a5322ef4615ee907fceada7291fb94df00bafbc7159f173f2412bb87f76b9 |
from kinko.nodes import Symbol, Tuple, String, Number, Keyword, Dict, List
from kinko.nodes import Placeholder, NodeVisitor
from kinko.errors import Errors
from kinko.parser import parser, parse as _parse, ParseError, DICT_ERROR
from kinko.parser import IMPLICIT_TUPLE_ERROR, EXPLICIT_TUPLE_ERROR
from .base import NODE... | vmagamedov/kinko | tests/test_parser.py | Python | bsd-3-clause | 8,627 | [
"VisIt"
] | f3c079755b0deb5a95e314c3be802a2a3bec1fbdc720309eb153f90f6e0a6277 |
########################################################################
#
# File: cmdline.py
# Author: Alex Samuel
# Date: 2001-03-16
#
# Contents:
# QMTest command processing
#
# Copyright (c) 2001, 2002, 2003 by CodeSourcery, LLC. All rights reserved.
#
# For license terms see the file COPYING.
#
###########... | MentorEmbedded/qmtest | qm/test/cmdline.py | Python | gpl-2.0 | 68,308 | [
"VisIt"
] | 1f24ab87349536922d2bc408adb2b46e14297300a9d5074549be3c44905bbb9b |
""" StorageManagementDB is a front end to the Stager Database.
There are five tables in the StorageManagementDB: Tasks, CacheReplicas, TaskReplicas, StageRequests.
The Tasks table is the place holder for the tasks that have requested files to be staged.
These can be from different systems and have differen... | sposs/DIRAC | StorageManagementSystem/DB/StorageManagementDB.py | Python | gpl-3.0 | 62,782 | [
"DIRAC"
] | 752de7ca12b454687c8e584eef4f05a03f4f35a3bc2a17ba10583cbabdc75458 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | mol_dqn/chemgraph/dqn/deep_q_networks.py | Python | apache-2.0 | 30,250 | [
"RDKit"
] | 40f92a411fb3dce4396ba020579b1429f5227e0f4c35ee581a1e20cb2b04c3b1 |
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