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#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/dft/libxc.py | Python | apache-2.0 | 98,072 | [
"DIRAC",
"Gaussian",
"Octopus",
"PySCF"
] | cb31d54ebb92db7f3539895ba0b9abb47f7d36aed16ecb7b9b74120e5a831a0d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
... | cmelange/ansible | lib/ansible/modules/files/acl.py | Python | gpl-3.0 | 11,638 | [
"Brian"
] | 35d271dc1ccea7e65230a2db957f276be020058e253edd4a587e8df982ff45b0 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/diversity/alpha/_ace.py | Python | bsd-3-clause | 4,650 | [
"scikit-bio"
] | 67c42b97398082dbb16cb624ee229b6f4e9299efac87be6b4d375df6794dd878 |
#!python
"""\
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ http://packages.python.org/distribute/easy_install.html
"""
import sys, os.p... | jokajak/itweb | data/env/lib/python2.6/site-packages/distribute-0.6.14-py2.6.egg/setuptools/command/easy_install.py | Python | gpl-3.0 | 69,824 | [
"VisIt"
] | 465069e79035401fbf894699002540f7cc2ed2251896bb4dc828b8b5cfb8235d |
import pysam
class fasta(object):
def __init__(self, fasta):
self.fasta = pysam.FastaFile(fasta)
self.lengths = dict([(x,y) for x,y in zip(
self.fasta.references, self.fasta.lengths)])
def extract(self, chrom, start, end, upper=False):
''' Function to extract seque... | adam-rabinowitz/ngs_analysis | fasta/pysam_extract.py | Python | gpl-2.0 | 3,734 | [
"pysam"
] | efcea8abe40633a162288d8bf413fdd60a9a0bebaae7e7b5b849ba48960b476a |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of source ... | trendelkampschroer/PyEMMA | pyemma/coordinates/tests/test_featurereader.py | Python | bsd-2-clause | 7,578 | [
"MDTraj"
] | b3e5711da2b7aed64a0a413d26ca69919f4cabb20019777d55a9653fe96ff849 |
#!/usr/bin/env python
"""
Generate plots for synthetic three-state force spectroscopy model.
"""
import bhmm
from bhmm.util.analysis import generate_latex_table
# dynamically import plotting tools
import os,sys,inspect
currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
parentdir =... | jchodera/bhmm-force-spectroscopy-manuscript | examples/p5ab-hairpin/generate-figure.py | Python | lgpl-3.0 | 2,862 | [
"NetCDF"
] | ab6db090cf2f041f4521663cdd67018ee0125797695da30edfb96587da9bd3c4 |
#!/bin/env python
#
#
# This file is part Protein Engineering Analysis Tool (PEAT)
# (C) Copyright Jens Erik Nielsen, University College Dublin 2003-
# All rights reserved
#
#
# Rewritten by D Farrell, Jan 2009
#
import cgi
import sys,os, string, types
os.environ['MPLCONFIGDIR']='/tmp'
from PEATDB.Base import PDatabas... | dmnfarrell/peat | PEATDB/web.py | Python | mit | 29,143 | [
"Jmol"
] | 6775e8fbc56050463fc6512f386685b6111e03e34407ac631131d8c7541cc9fe |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems 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.o... | dongjoon-hyun/neon | tests/test_branch_layer.py | Python | apache-2.0 | 5,174 | [
"Gaussian"
] | f931d5d1747c64abe5680c20841941d00c30d69efe70372fc66e4ff63c181750 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | uncertainty_baselines/models/resnet50_sngp.py | Python | apache-2.0 | 13,039 | [
"Gaussian"
] | 966dc5c35846a4e1504cc29598d2fce094648152b2d694231742a401b3791560 |
import numpy
def kurt2(*args):
''' Sample kurtosis (fourth moment divided by squared variance)
of a matrix. Kurtosis of a Gaussian distribution is 3.
MEAN (optional) and VAR (optional) make the computation faster. '''
if len(args) == 0:
print('Error: input matrix is required')
... | tochikuji/pyPyrTools | pyrtools/kurt2.py | Python | mit | 732 | [
"Gaussian"
] | ff241ed5851b6d3008a418f3d7ddf3354704858baf067acb2c0205d9d9b7134e |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2014 Paul Franklin
# Copyright (C) 2010-2015 Craig J. Anderson
#
# This program is free software; you can redistrib... | Fedik/gramps | gramps/plugins/drawreport/ancestortree.py | Python | gpl-2.0 | 42,346 | [
"Brian"
] | a3497c25def2d869a89b91c02b9a9406b76f86b4eb927279b33121163a76ef22 |
#!/usr/bin/env python
''' script for filtering insertions vs. the human reference GRCh37/hg19 '''
''' may be useful as a template for extension to other species '''
import pysam
import sys
import os
import logging
import argparse
import align
import numpy as np
import subprocess
from uuid import uuid4
ver... | adamewing/tebreak | scripts/misc/filter_hg19.py | Python | mit | 13,875 | [
"pysam"
] | 0934f09531139324a115fc11862583ebf0c5138a3a5be58e05d611926507d312 |
#!/usr/bin/python
# flake8: noqa
import unittest
from sznqalibs import hoover
import copy
import json
import unittest
class DictPathTest(unittest.TestCase):
def setUp(self):
super(DictPathTest, self).setUp()
class PathyDict(dict, hoover.DictPath):
pass
testDict = {
... | seznam/sznqalibs | tests/test_hoover.py | Python | mit | 27,441 | [
"VisIt"
] | 11d64da14a0820d78ca78b0270d9356d66edfda43b3e8a69e0015e59d8e5aea1 |
#!/usr/bin/env python
"""
Given a BLAST or DIAMOND JSON output files, the corresponding FASTA (or FASTQ)
sequence files, and filtering criteria, produce a summary of matched titles
and (optionally) an alignment panel.
Run with --help for help.
"""
from __future__ import print_function
import os
import sys
import ar... | bamueh/dark-matter | bin/noninteractive-alignment-panel.py | Python | mit | 17,220 | [
"BLAST"
] | 6b0e7364188ee9bcf72648f986eb71efcfe26c0b19895f085a67f4d13e144c39 |
# 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):
# Adding field 'DataDomain.weight'
db.add_column('profiles_datadomain', 'weight', self.gf('django.db.model... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0032_auto__add_field_datadomain_weight.py | Python | mit | 14,381 | [
"MOE"
] | e2bc884ac1917cfc20b448a025125d56b48df0a599a314a66ec1db2339c04aaa |
"""
Create a profile from arbitrary ASCII text files
================================================
Script profile_from_txt
-----------------------
Use the TAMOC ambient module to create profiles for use by
TAMOC from data in text files. This file demonstrates working with data
digitized from plots of temperature ... | socolofs/tamoc | bin/ambient/np_profile_from_txt.py | Python | mit | 4,329 | [
"NetCDF"
] | 976934e2de094c5dd9c4455e92a89adcd5a81c7c41fbfa8145a62b9529b052a6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either v... | sam-m888/gramps | gramps/gen/plug/menu/_family.py | Python | gpl-2.0 | 1,787 | [
"Brian"
] | 9d27508fa3807ec3e3cc32fc980ed607baf0129229b5be6e2ef8da55b9044374 |
from __future__ import absolute_import
import copy
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, w... | madjar/cython | Cython/Compiler/ParseTreeTransforms.py | Python | apache-2.0 | 117,644 | [
"VisIt"
] | 1fc3ca7e05393fbebbcde66acd015e0ead9b4f3333b70d7d965619f82fdcaf02 |
#!/usr/bin/env python
"""Basic authentication example
This example demonstrates how to protect Flask endpoints with basic
authentication, using secure hashed passwords.
After running this example, visit http://localhost:5000 in your browser. To
gain access, you can use (username=john, password=hello) or
(username=sus... | miguelgrinberg/Flask-HTTPAuth | examples/basic_auth.py | Python | mit | 1,015 | [
"VisIt"
] | f31dcbdeb00c620f8bd5194cc626bf7833028b3124707af6c47ec2376563d3bc |
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches
def new_pulse_fig(figsize):
'''
Open a new figure and configure it to plot pulse schemes.
'''
fig, ax = plt.subplots(1, 1, figsize=figsize, frameon=False)
ax.axis('off')
fig.subplots_adjust(bottom=0, top=1, left=0, ri... | DiCarloLab-Delft/PycQED_py3 | pycqed/utilities/pulse_scheme.py | Python | mit | 5,469 | [
"DIRAC",
"Gaussian"
] | 30768906bf0a132408092db72f4e18a3effd0ae7175209483752f3731b7a8d55 |
######################################################################
# Alchemical Analysis: An open tool implementing some recommended practices for analyzing alchemical free energy calculations
# Copyright 2011-2015 UC Irvine and the Authors
#
# Authors: Pavel Klimovich, Michael Shirts and David Mobley
#
#This libra... | MobleyLab/alchemical-analysis | alchemical_analysis/parser_gromacs.py | Python | mit | 16,620 | [
"Gromacs"
] | aa24877eb82b2ca23ee3b755ff5d93379f415a031a54557a4451e9958df9360e |
"""
Acceptance tests for Studio.
"""
from bok_choy.web_app_test import WebAppTest
from ...pages.studio.asset_index import AssetIndexPage
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.course_info import CourseUpdatesPage
from ...pages.studio.edit_tabs import PagesPage
from ...pages.studio.imp... | shabab12/edx-platform | common/test/acceptance/tests/studio/test_studio_general.py | Python | agpl-3.0 | 5,572 | [
"VisIt"
] | 238b2f09d12da7a48c0cdae4e57839852188f8292df2d1d556f063a5e7b25be0 |
from collections import deque
import numpy as np
from scipy.spatial.distance import cdist
def precision_recall(swc1, swc2, dist1=4, dist2=4):
'''
Calculate the precision, recall and F1 score between swc1 and swc2 (ground truth)
It generates a new swc file with node types indicating the agreement between tw... | RivuletStudio/rivuletpy | rivuletpy/utils/metrics.py | Python | bsd-3-clause | 9,523 | [
"Gaussian",
"VisIt"
] | fee2bcbcbfe4f5fe290c7b43d44eab29b16a0a5a29b2a49041fb7c8b8dd8dcd3 |
import unittest
from pprint import pprint as pp
import diffier
text_1 = """
Using scent:
nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
test_config (tests.test_common.test_config.Test_Config) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.003s
... | zsong/diffy | diffy_lib/diffy_test.py | Python | mit | 1,225 | [
"ADF"
] | 3ff030495b93cc581d6d6251bce2fb042410733151749856ec3ec7888b4091d5 |
#!/usr/bin/env python
# Created by: Lee Bergstrand
# Description: A simple python program that uses HMMER to search for 16S genes within a genome. Checks
# both the forward and reverse strand DNA strand of the genome.
#
# Requirements: - This program requires the Biopython module: http://biopython.org/wik... | LeeBergstrand/Phylogenetic-Tree-Building | HMMToFind16S/16SHMMER.py | Python | mit | 8,578 | [
"Biopython"
] | d26787cbf528f735eeb2d9f39b0161121a02797056c16b2d3fd88d06f144a8c2 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','license','co... | rubenfonseca/titanium-dropbox | build.py | Python | mit | 5,951 | [
"VisIt"
] | 82ea3ffd0ba47a45f473289ef31b4f477e6c85c68afd198fb8ee63a4963095ce |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | dermoth/gramps | gramps/gui/plug/_dialogs.py | Python | gpl-2.0 | 12,072 | [
"Brian"
] | 65c293de14e4625514ddf654097e869e1a494971f36ba6af61165262329a5295 |
import numpy as np
#print help(np.floor)
#print dir(np.zeros((1,1)))
#exit()
VERBOSE = True
#removes correaltions
class DistrInterface(object):
""" Measures and mimics correlation ininput data"""
def energy(self, state):
pass
def sample(self):
#sample freely, no input condisioned (clamped... | sohale/nn-it | boltz1.py | Python | gpl-3.0 | 15,347 | [
"Gaussian"
] | 9c4df2c970c2d1bf151a97c4a40555ae0c662f9b28769fc44168edbec60d1815 |
from queries import queries
#
# Main chart Monthly
#
class main_chart_queries(queries):
def __init__(self, cursor, output, refdate = 'now'):
super(main_chart_queries, self).__init__(cursor, output, refdate)
def generate_main_chart_all(self):
# Visit member
self.cursor.execute('''
... | niavok/elveos | stats/src/bloatitstats/queries/main_chart_queries.py | Python | agpl-3.0 | 12,399 | [
"VisIt"
] | 35633ea76c12d27206822d8b02b0328a052ff9d3a6f6aa11fe53b3f1b93a1947 |
from django.test import TestCase
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from django.contrib.auth import get_user_model
from django.contrib.auth.models import Group
from django.urls import reverse
from splinter import Browser
from estudios_socioeconomicos.models import Estudio
from per... | erikiado/jp2_online | base/test_views.py | Python | mit | 7,173 | [
"VisIt"
] | 64ceb590a99b9eae4b0c5994033fe3d6a6d0eec51ede7b081b85ed1e8875216a |
from ase import Atoms, Atom
from gpaw import GPAW
a = 4. # Size of unit cell (Angstrom)
c = a / 2
# Hydrogen atom:
atom = Atoms('H',
positions=[(c, c, c)],
magmoms=[1],
cell=(a, a, a))
# gpaw calculator:
calc = GPAW(h=0.18, nbands=1, xc='PBE', txt='H.out')
atom.set_calculator(c... | qsnake/gpaw | doc/tutorials/atomization/atomize.py | Python | gpl-3.0 | 857 | [
"ASE",
"GPAW"
] | fb5b44415202b083fd69ccf6aa683dbad50d82e324832795121c2d1a56965730 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | vinodpanicker/scancode-toolkit | tests/typecode/test_contenttype.py | Python | apache-2.0 | 48,662 | [
"VisIt"
] | 29803ff867a9729ddf18fbf407e0bf6a7cfcac10ac1983001df1eb476ec5e78c |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
import math
import os
import subprocess
import tempfile
import logging
import numpy as np
from monty.dev import requires
from monty.json import jsanitize
from monty.os import cd
from monty.os.path import which
from scipy.constants impo... | tallakahath/pymatgen | pymatgen/electronic_structure/boltztrap.py | Python | mit | 94,779 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | 2ae547e44f95beb9f2d5f95e66fc9b9c81fac71c90f9c3fcbfd35feddded2d01 |
import sys
from string import Template
from collections import namedtuple
from pycparser import c_parser, c_ast, parse_file
Func = namedtuple('Func', ('name', 'type', 'args'))
Arg = namedtuple('Arg', ('name', 'type'))
Type = namedtuple('Type', ('ptr', 'name', 'array'))
class FuncDeclVisitor(c_ast.NodeVisitor):
de... | helmi03/gogeos | geos/geoscapi.py | Python | mit | 4,354 | [
"VisIt"
] | 32dc88b1ef39e6a73f5b5fe269b61e4e006a91d0f212d4b194d626e4ed48886c |
#
# Copyright 2014-2015, 2020 Lars Pastewka (U. Freiburg)
# 2014 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 P... | libAtoms/matscipy | tests/test_hertz.py | Python | lgpl-2.1 | 3,746 | [
"Matscipy"
] | de087a97904d896a55d97104910151d15df69a3f91d4bda7789717eb450e9740 |
import pathlib
import platform
import numpy as np
import pytest
import vtk
import pyvista
from pyvista import PolyData, RectilinearGrid, UniformGrid, StructuredGrid, MultiBlock
from pyvista import examples as ex
skip_mac = pytest.mark.skipif(platform.system() == 'Darwin', reason="Flaky Mac tests")
@pytest.fixture()... | akaszynski/vtkInterface | tests/test_composite.py | Python | mit | 14,505 | [
"VTK"
] | 0fbe3a9a1efd85a8bafd5a118902b9f3cbcccff9c7bfcecb5906b3c654296a4c |
# Copyright(c) 2014, The LIMIX developers (Christoph Lippert, Paolo Francesco Casale, Oliver Stegle)
#
#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... | PMBio/limix | limix/deprecated/utils/preprocess.py | Python | apache-2.0 | 3,121 | [
"Gaussian"
] | 24c8f8b91c950876996189504dd0339083aa2d06f57e5aa5bd94940c2988a121 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/morphology/core/__init__.py | Python | bsd-2-clause | 4,204 | [
"NEURON"
] | 3d528feefcc65563ef50f3863b6a2af1a876b8866d68f745be79fb535c2536e0 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from bok_choy.page_object import XSS_INJECTION
from ...pages.lms.account_settings import AccountSettingsPage
from ...pages.lms.aut... | ampax/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 17,618 | [
"VisIt"
] | 01c1df48038ea9bcee359cfd4be958d1dc19ba5fd51bfdb029d0e905841d57d0 |
"""
Unit tests for various types of character variable.
"""
import os
import tempfile
import unittest
import cdlparser
import numpy as np
import netCDF4 as nc4
#---------------------------------------------------------------------------------------------------
class TestCharVars(unittest.TestCase) :
#-----------------... | ocehugo/cdlparser | test/test_charvars.py | Python | bsd-3-clause | 3,532 | [
"NetCDF"
] | 79ce99ba03bda1f0fd12b310c3dc20b0fa0aa492131f942fe31bd17f8b039daa |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/vecutil.py | Python | gpl-2.0 | 11,265 | [
"Psi4"
] | 27c54433e34b555e7250bcc2b30afe3fb88ef0f0c0423a766d3a6b9d6912d1b9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# rmvgridres - remove vgrid resource
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | heromod/migrid | mig/shared/functionality/rmvgridres.py | Python | gpl-2.0 | 5,374 | [
"Brian"
] | b60dcdecd5b6bac35c236c07b9c260b2f97bf87cb9fa46523f3edfb0ed85461c |
# coding: utf-8
import constance
from django.conf import settings
from hub.models import ConfigurationFile, PerUserSetting
from hub.utils.i18n import I18nUtils
def external_service_tokens(request):
out = {}
if settings.GOOGLE_ANALYTICS_TOKEN:
out['google_analytics_token'] = settings.GOOGLE_ANALYTICS_... | onaio/kpi | kpi/context_processors.py | Python | agpl-3.0 | 2,327 | [
"VisIt"
] | 220034a87fe870f55179f628294e277de39b547be55f9561453b679968b97b13 |
""" Based on
https://greentreesnakes.readthedocs.io
"""
import ast
class AstTransformer(ast.NodeTransformer):
pass
def apply_transformers(tree):
tree = AstTransformer().visit(tree)
# Add lineno & col_offset to possibly modified nodes
ast.fix_missing_locations(tree)
return tree
| avanov/solo | solo/import_hooks/hooks.py | Python | mit | 302 | [
"VisIt"
] | 0c26aa058dbfb8323a7d318ea71cdf4fce063f02353c12f67a6e9bc3ceae9f23 |
import numpy as np
from scipy.ndimage.filters import gaussian_filter, gaussian_laplace
import itertools as itt
import math
from math import sqrt, hypot, log
from numpy import arccos
from ..util import img_as_float
from .peak import peak_local_max
from ._hessian_det_appx import _hessian_matrix_det
from ..transform impo... | bennlich/scikit-image | skimage/feature/blob.py | Python | bsd-3-clause | 16,627 | [
"Gaussian"
] | 8cdee2a64ac99a47a54d25c8628f29c2afd0d716d90112c2552e7f81817a7859 |
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2016 - 2017, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/or modify
# it und... | marionleborgne/nupic.research | projects/l2_pooling/noise_tolerance_l2.py | Python | agpl-3.0 | 19,191 | [
"Gaussian"
] | bb63a60ae88babdceb829a1c8e24ef8978e9a973ab8fa01edc5385132da35cd5 |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag config_path) the path of a json file that dictates the file... | pyokagan/gyp | pylib/gyp/generator/analyzer.py | Python | bsd-3-clause | 21,402 | [
"VisIt"
] | 6c41bfac26a1d3189e94c4d8476d2fd49d99ca3a73b09c2b124799cda54278ea |
#!/usr/bin/python3
from Bio import SearchIO
import os
# fetch files in current working directory
files = [f for f in os.listdir('.') if os.path.isfile(f)]
#print(files)
def convert_to_tab():
for f in files:
if f.endswith('.xml'):
# print(f)
# print(f.replace('.xml', '.xml.tab')
print("converting ", f, " to... | manasb/genomics | 469/FASTA/RESULTS/23_NOV_2015/TESTING/xml-to-tab.py | Python | gpl-3.0 | 649 | [
"BLAST"
] | c266f6a9250de28b1d9e96c3eaae2dff8d3bd051ea489b48dc225679a40ef404 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
from pymatgen.command_line.aconvasp_caller import get_num_division_kpoints, \
get_minkowski_red, get_vasp_kpoint_file_sym
from pymatgen.core.composi... | matk86/pymatgen | pymatgen/command_line/tests/test_aconvasp_caller.py | Python | mit | 1,881 | [
"pymatgen"
] | d78697b9c7ce740516d34c883b51cb9440707794a60dfc372efb57978782d4e1 |
#!/usr/bin/env python
import pysam
import argparse, sys
import math, time, re
from collections import Counter
from argparse import RawTextHelpFormatter
__author__ = "Colby Chiang (cc2qe@virginia.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2015-09-28 11:31 $"
# --------------------------------------
#... | abelhj/svtools | svtools/bin/svtyper/scripts/vcf_modify_header.py | Python | mit | 14,777 | [
"pysam"
] | cd4d7f0290e1fb6d023fc6dc0e8f7c964f3a276fee26916f9bfc93028dfbf1ae |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the unique domains visited analysis plugin."""
from __future__ import unicode_literals
import unittest
from plaso.analysis import unique_domains_visited
from plaso.lib import definitions
from tests.analysis import test_lib
class UniqueDomainsPluginTest(t... | rgayon/plaso | tests/analysis/unique_domains_visited.py | Python | apache-2.0 | 2,121 | [
"VisIt"
] | 23f5ec5c875e59c6efaa3b17de6d0aea48dcdda7ece8e81bf2710559b6813397 |
import re
import subprocess
from thefuck.utils import replace_command
def match(command, script):
return command.script.startswith('gulp')\
and 'is not in your gulpfile' in command.stdout
def get_gulp_tasks():
proc = subprocess.Popen(['gulp', '--tasks-simple'],
stdout=sub... | NguyenHoaiNam/thefuck | thefuck/rules/gulp_not_task.py | Python | mit | 643 | [
"GULP"
] | 4adda2de60ae73e5f96e93eecf20bc826ccd5008d232547eab2bae07490d9b76 |
# 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 | src/python/espressomd/shapes.py | Python | gpl-3.0 | 8,473 | [
"ESPResSo"
] | 22232286522c213d6e525e5f9e4213b7f689e96410b3e66d2e6f0eaecd0ed5a6 |
#!/usr/bin/env python
""" task_setup.py - Version 1.0 2013-12-20
Set up a number of waypoints and a charging station for use with simulated tasks using
SMACH and teer.
Created for the Pi Robot Project: http://www.pirobot.org
Copyright (c) 2013 Patrick Goebel. All rights reserved.
This program i... | peterheim1/robbie_ros | robbie_ai/src/robbie_ai/task_setup.py | Python | bsd-3-clause | 7,076 | [
"VisIt"
] | ee1c765db3bdaab4171f2c30b02614a719dbddf5374ae28f1895c37b70032ca3 |
""" simple hello world job
"""
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.DataManagementSystem.Utilities.DMSHelpers import DMSHelpers
j = Job()
j.setName("helloWorld-test")
j.setExecutable("exe-script.py", "", "Executable.log")
# <-- user settings
j.setCPUTime(... | DIRACGrid/DIRAC | src/DIRAC/tests/Workflow/Regression/helloWorld.py | Python | gpl-3.0 | 509 | [
"DIRAC"
] | ebd782805b95498a3e98adc38f6770d5cea0f3ab05e4592c2827fc5766865683 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import datetime
import errno
import json
from sqlalchemy import orm
from DIRAC.DataManagementSystem.Client.FTS3Job import FTS3Job
from DIRAC.DataManagementSystem.private import FTS3Utilities
from DIRAC.DataMana... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Client/FTS3Operation.py | Python | gpl-3.0 | 22,972 | [
"DIRAC"
] | 31e922724414d797594691adad16c9e1a497e2194f9fba7596faefa732c4f7d3 |
from numpy import array, matrix, diag, exp, inner, nan_to_num
from numpy.core.umath_tests import inner1d
from numpy import argmin, array
class GKS:
"""Gaussian kernel smoother to transform any clustering method into regression. setN is the list containing numpy arrays which are the weights of clustering centors.
... | sbxzy/pygks | pygks/ae_backup.py | Python | bsd-3-clause | 4,229 | [
"Gaussian"
] | d7f7969fb72b7a605999662a089bf37fb8e2fad6f9f9b49a3d6aaf1a4061e2dc |
#!/usr/bin/env python
"""
The dependencies module determines which descriptions depend on which other
descriptions.
"""
from ctypesgencore.descriptions import *
from ctypesgencore.ctypedescs import *
from ctypesgencore.messages import *
def find_dependencies(data, opts):
"""Visit each description in `data` and f... | AsherBond/MondocosmOS | grass_trunk/lib/python/ctypes/ctypesgencore/processor/dependencies.py | Python | agpl-3.0 | 5,207 | [
"VisIt"
] | 5764544431e2770a75098e885675fbc6965e5847a6386b3bef7d9fa43758a107 |
# #############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors: Robert T. McGibbon
#
# MDTraj is fre... | mattwthompson/mdtraj | mdtraj/core/selection.py | Python | lgpl-2.1 | 15,049 | [
"MDTraj",
"VisIt"
] | bf9f2b4185a194808ea20bd34c23dcc142f225e53641965f9390238f67b6e0d8 |
# Copyright 2016 Battelle Energy Alliance, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | idaholab/civet | ci/views.py | Python | apache-2.0 | 44,683 | [
"MOOSE"
] | 1f613bcae8505a20eafbc90885c6bafc0a08a0a2bc1db853b60bf651870287cb |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# fakecgi - fake a cgi request
# Copyright (C) 2003-2013 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | heromod/migrid | mig/cgi-bin/fakecgi.py | Python | gpl-2.0 | 3,111 | [
"Brian"
] | e2d3975c7bb6c148c4d4e9c7b1bfa8f1757b5511fd10de3d4659c527e15e5d22 |
# -*- coding: utf-8 -*-
"""methods_utils.py:
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ ... | dilawar/moose-core | python/moose/methods_utils.py | Python | gpl-3.0 | 1,096 | [
"MOOSE"
] | c5cf1d662fe78060f1c735f97aaeb8748cfacdfc63ceb7c5888aad6ed7898e88 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.contrib.auth import views as auth_views
urlpa... | edanweis/overdewey | config/urls.py | Python | bsd-3-clause | 1,488 | [
"VisIt"
] | ed9dbf261e5cdb24d7e6c31197879bd551b9dd1590e0e91a3be5b1c1b7c4e052 |
import copy
import json
import multiprocessing
import os.path
import random
import shutil
import string
import tempfile
from contextlib import contextmanager
from os import chdir, getcwd, mkdir
from os.path import exists
from subprocess import CalledProcessError, check_call, check_output
import pkgpanda.build.constant... | BenWhitehead/dcos | pkgpanda/build/__init__.py | Python | apache-2.0 | 50,458 | [
"VisIt"
] | f741cb3f92e6a2ec70e695e10b6971d6175b731ffdfebd6bc795e1d007e09871 |
# -*- coding: utf-8 -*-
import os
import tempfile
from datetime import datetime
import numpy as np
import pytest
from numpy.testing import assert_array_almost_equal
from pysteps.io import import_netcdf_pysteps
from pysteps.io.exporters import _get_geotiff_filename
from pysteps.io.exporters import close_forecast_file... | pySTEPS/pysteps | pysteps/tests/test_exporters.py | Python | bsd-3-clause | 2,913 | [
"NetCDF"
] | d2f128e951c6f222495563cce0f8da2196fd28a9fb8fd8256864581d5e6361d9 |
# $Id$
"""
Introduction
============
``fortune`` is a stripped-down implementation of the classic BSD Unix
``fortune`` command. It combines the capabilities of the ``strfile`` command
(which produces the fortune index file) and the ``fortune`` command (which
displays a random fortune). It reads the traditional ``fort... | spasticVerbalizer/fortune | fortune/__init__.py | Python | bsd-3-clause | 9,974 | [
"Brian"
] | fc951cb3a2682bde57784ae695b1aca1aa4698f39dbaef377d11922cf867ba44 |
# shrunk - Rutgers University URL Shortener
"""Database-level interactions for shrunk. """
import datetime
import random
import string
import pymongo
class DuplicateIdException(Exception):
"""Raised when trying to add a duplicate key to the database."""
pass
class ForbiddenNameException(Exception):
""... | ksuarz/shrunk | shrunk/client.py | Python | mit | 21,781 | [
"VisIt"
] | 61289d1e4f9714fbe1db98ad032f33249d04ef3233f4101c4b1936ac505252d0 |
#!/usr/bin/env python3
import os
import sys
import random
import time
from random import seed, randint
import argparse
import platform
from datetime import datetime
import imp
from time import sleep
# from run_parameter import *
parser = argparse.ArgumentParser(
description="This is a python3 script to\
automa... | luwei0917/awsemmd_script | restart.py | Python | mit | 4,735 | [
"LAMMPS"
] | ea76a21132b309f33c911010e8caa5dfd7833727de19b7f553a0edf23910bed2 |
#!/usr/bin/env python
import sys
import os
# Locate MOOSE directory
MOOSE_DIR = os.getenv('MOOSE_DIR', os.path.join(os.getcwd(), 'moose'))
if not os.path.exists(MOOSE_DIR):
MOOSE_DIR = os.path.join(os.getenv('HOME'), 'projects', 'moose')
if not os.path.exists(MOOSE_DIR):
raise Exception('Failed to locate MOOSE... | katyhuff/moose | docs/moosedocs.py | Python | lgpl-2.1 | 642 | [
"MOOSE"
] | b53f4e3cd720fad917adf1ba2340c3bd5de54bf2f3e97602b6d62ec7147dc1f3 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/bookmarks.py | Python | gpl-3.0 | 9,803 | [
"ORCA"
] | 946f59ba062c4a4a38d582862008fba42d7a71039637c52dd8d828d95c51921b |
#!/usr/bin/env python
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib import ticker, gridspec
import QM_parser.util.util as u
eV2wn = u.energy_conversion['wn'] / u.energy_conversion['eV']
#
# Spectral Prefactors for UV and CD
#
uv_cnst = 108.8983364615
cd_cnst = 4.35184... | dpadula85/ExSPy | stable/Spec.py | Python | gpl-3.0 | 9,436 | [
"Gaussian"
] | b8b0456d7eabe2bab42172f8f6412994cecf52a8e0028e9986007253a2e813bd |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/cc/eom_kccsd_rhf_ea.py | Python | apache-2.0 | 2,448 | [
"PySCF"
] | 6650ccc2a32f924de2bf53e85c61854da8afc4ddcf06bcedd358ca3d6e3966f8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Stephane Charette
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the ter... | ennoborg/gramps | gramps/plugins/tool/removeunused.py | Python | gpl-2.0 | 19,797 | [
"Brian"
] | 40958d17aa600ea353e24b6fa90d2bde67716c00a31f3f3b79f5d9840cd58f9e |
../../../../../../../share/pyshared/orca/scripts/apps/nautilus/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/nautilus/__init__.py | Python | gpl-3.0 | 74 | [
"ORCA"
] | adba3660b69fc723279964fe6962a9eebce28be069e94b7dd1b1df0d6983d918 |
"""
This contains the TRPO class. Following John's code, this will contain the bulk
of the Tensorflow construction and related code. Call this from the `main.py`
script.
(c) April 2017 by Daniel Seita, based upon `starter code` by John Schulman, who
used a Theano version.
"""
import gym
import numpy as np
import tens... | DanielTakeshi/rl_algorithms | trpo/trpo.py | Python | mit | 19,601 | [
"Gaussian"
] | fbed2942241a61bce44c9b54e7e5f64a246cb4b18d398ef2ac5c68a16701707f |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLPUnstructuredGridWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkXMLPUnstructuredGridWriter.py | Python | bsd-3-clause | 532 | [
"VTK"
] | 54539aab21583a529baa6a399642896d35fb252a3b8856b6222b5f55c9142ef0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | jralls/gramps | gramps/gen/filters/rules/source/__init__.py | Python | gpl-2.0 | 2,039 | [
"Brian"
] | 92a8901c7c98ff47974cecf66656adb99451a2820810de01738e8f60320b1e3b |
# Imports
import os
import vcf
import math
import h5py
import pysam
import vqsr_cnn
import numpy as np
from Bio import Seq, SeqIO
from collections import Counter
# Keras Imports
import keras.backend as K
def run():
args = vqsr_cnn.parse_args()
if 'write_reference_and_annotation_tensors' == args.mode:
... | broadinstitute/hellbender | src/main/resources/org/broadinstitute/hellbender/tools/walkers/vqsr/training.py | Python | bsd-3-clause | 46,409 | [
"pysam"
] | 3d60c3aa3fe88dc7f81c68960a006bedef8d402980a721bd212a97e81f0e9360 |
import time
import unittest
import os
import numpy as np
from phonopy.interface.vasp import read_vasp
from phonopy.structure.cells import _get_smallest_vectors, get_primitive
from upho.harmonic.dynamical_matrix import (
get_smallest_vectors as get_smallest_vectors_upho)
POSCAR_DIR = os.path.join(os.path.dirname(__... | yuzie007/ph_unfolder | tests/test_get_smallest_vectors.py | Python | mit | 1,720 | [
"VASP",
"phonopy"
] | c39a3f73ad4765f08c420bdae47623f84441cb08dc67a0eba3f5cfe20e400544 |
from __future__ import division
from builtins import input
from builtins import range
import numpy as np
from matplotlib import pyplot as plt
plt.interactive(True)
from pybasicbayes import models, distributions
GENERATE_DATA = True
###########################
# generate or load data #
###########################
... | mattjj/pybasicbayes | examples/meanfield_steps.py | Python | mit | 1,265 | [
"Gaussian"
] | 6c462556b23bb3df8ac06358f88e8fb4087de3ed914f180f99f8e952e2b421ba |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Licen... | camradal/ansible | lib/ansible/modules/system/runit.py | Python | gpl-3.0 | 9,034 | [
"Brian"
] | feb3170cdd69c293a40289cfb0d8fe4969a9163f3f38956db32eff5fcf45a09e |
# CubETL
# Copyright (c) 2013-2019 Jose Juan Montes
# This is a CubETL example
# See: https://github.com/jjmontesl/cubetl
from cubetl import flow, fs, script, olap, table, geoip
from cubetl.cubes import cubes10
from cubetl.http import useragent
from cubetl.olap import sqlschema, query
from cubetl.olap.sql import Tab... | jjmontesl/cubetl | examples/loganalyzer/loganalyzer.py | Python | mit | 8,564 | [
"VisIt"
] | bab0929098d0426a2a3cdafac1388e8cec5d24e1e6e2ac43fa3085ffffc5fe1d |
# $Id$
from itcc.molecule import relalist
from itcc.tinker import molparam
__revision__ = '$Rev$'
def gettortype(mol, tor):
assert len(tor) == 4
return tuple([mol.atoms[idx].type for idx in tor])
def gettorsbytype(mol, types):
types = [molparam.torsion_uni(type_) for type_ in types]
result = {}
... | lidaobing/itcc | itcc/tinker/analyze.py | Python | gpl-3.0 | 608 | [
"TINKER"
] | d59f50fd9ca2369cee8ae5223bc72d90b3a46acec87e66d0cfd1ba2295ce2ff4 |
'''
Created on Feb 5, 2014
@author: mborodin
'''
import tempfile
import xml.dom.minidom
import zipfile
import requests
import xlrd
def open_tempfile_from_url(url,tempfile_suffix):
filename = tempfile.mkstemp(suffix=tempfile_suffix)[1]
response = requests.get(url)
response_status_code = respo... | kiae-grid/panda-bigmon-core | core/xls_parser.py | Python | apache-2.0 | 5,533 | [
"FEFF"
] | efb6c97d6f6658d4cb013b71ad85969f7c66a5e22acdfd6b6dd4bcfc85a95f3d |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/jax | examples/gaussian_process_regression.py | Python | apache-2.0 | 4,604 | [
"Gaussian"
] | c0946ecd4cf126d4da62a1d3b04c712871afcd12cf467171ff4329f244ecf6aa |
#Input file for test problem for pyaneti
#Created by Barragan O.
#This file contains the basic parameters to change for simple pyaneti run
#There are more flags which can control the input/output of the code
#They can be found inside src/default.py, all the flags inside this file
#can be changed inside the input file.
... | oscaribv/pyaneti | inpy/test/input_fit.py | Python | gpl-3.0 | 3,970 | [
"Gaussian"
] | 4504cf3f891cf64ed75b8df5fb498f5fff5be60e20f166ca282b186f251968ca |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# Configuration, please edit
# Data about this site
BLOG_AUTHOR = "Matías Lang"
BLOG_TITLE = "Nodo Las Pircas"
# This is the main URL for your site. It will be used
# in a prominent link
SITE_URL = "http://laspircas.lan/"
# This is the URL w... | sh4r3m4n/Nikola-BuenosAiresLibre | conf.py | Python | gpl-3.0 | 20,401 | [
"VisIt"
] | 01f3e958795f1e8cf90e2501ceaa45d720bbc91953a1036c8c09ff1542a99fc4 |
# coding=utf-8
import base64
import datetime
import json
import time
import mock
from nose.tools import eq_, ok_
from nose.plugins.attrib import attr
from pyquery import PyQuery as pq
from urlparse import urlparse
from django.conf import settings
from django.contrib.auth.models import User
from django.contrib.sites.... | scrollback/kuma | kuma/wiki/tests/test_views.py | Python | mpl-2.0 | 162,884 | [
"VisIt"
] | d1271beb086391aa34b1d706266555adb98847cf68eaca6943ca5ba4a2e4ea04 |
"""
pyNEAT
Copyright (C) 2007-2008 Brian Greer
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in ... | liquidkarma/pyneat | pyNEAT/Synapse.py | Python | gpl-2.0 | 1,244 | [
"Brian"
] | f0ac54197c62025c1c83a8ccac68b1377b0b2fc757fe45832b76bf7a7e95970b |
"""
local path implementation.
"""
from __future__ import with_statement
from contextlib import contextmanager
import sys, os, re, atexit, io
import py
from py._path import common
from stat import S_ISLNK, S_ISDIR, S_ISREG
from os.path import abspath, normpath, isabs, exists, isdir, isfile, islink
iswin32 = sys.plat... | Spanarchie/pyRest | pyRest/lib/python2.7/site-packages/py/_path/local.py | Python | unlicense | 31,893 | [
"VisIt"
] | 9d15b75a0fb865a13cdfa0100d4cb75ac8f9e5e2b7b62b5bb0a734af4ce510e8 |
"""Mayavi/traits GUI for setting MRI fiducials"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..externals.six.moves import map
# allow import without traits
try:
from mayavi.core.ui.mayavi_scene import MayaviScene
from mayavi.tools.mlab_scene_model imp... | jniediek/mne-python | mne/gui/_fiducials_gui.py | Python | bsd-3-clause | 16,783 | [
"Mayavi"
] | cae3cb8689c8fd4c7c690a0980733148616e3e56c984574cbad3b309c874d248 |
"""Get useful information from live Python objects.
This module encapsulates the interface provided by the internal special
attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion.
It also provides some help for examining source code and class layout.
Here are some of the useful functions provided by this module:... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.5.0/Lib/inspect.py | Python | mit | 113,311 | [
"VisIt"
] | 5d6cf4394b41ac526c7c142ffc53ade3ba55165a6512c47c95707eb2c2a213a2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -*- Python -*-
# coding: shift_jis
"""
DoCoMoChatSrv.py
The project is hosted on GitHub where your could fork the project or report
issues. Visit https://github.com/roboworks/
:copyright: (c) 2015 by Hiroyuki Okada, All rights reserved.
:license: MI... | okadahiroyuki/trcp | trcp_chat/nodes/DoCoMoChatSrv.py | Python | mit | 3,049 | [
"VisIt"
] | 2aa81efe9c5029e8207a65f16aad0450cace9f1d2c077227fb947c7f08500e04 |
#-*- coding: utf-8 -*-
import datetime
sms = local_import('sms')
m = sms.sms.Sms()
with open("/home/kam/web2py_test", "a") as f:
notifications = db(db.powiadomienia).select()
for notification in notifications:
now = datetime.datetime.now().hour * 100 + datetime.datetime.now().minute
then = in... | alatar-/iwm-project | cron/notifications.py | Python | mit | 1,241 | [
"VisIt"
] | a0e021f0f71307ef0ea37f7a6598595f1d74e63953d0d2bae8a44b53cda5f872 |
'''
Created on 02.03.2014
@author: bluesbreaker
'''
from CSUStAn.astng.astng import ASTNGHandler
from CSUStAn.astng.control_flow import UCFRLinker
from CSUStAn.cross.duck_typing import DuckTypeHandler
from CSUStAn.exceptions import CSUStAnException
from lxml import etree
class UCFRBuilder(ASTNGHandler,DuckTypeHand... | exbluesbreaker/csu-code-analysis | logilab-astng XML Generator/src/CSUStAn/ucfr/builder.py | Python | gpl-2.0 | 5,752 | [
"VisIt"
] | d33eeb57232f08944b289d7d00f101c069b35527294b4fec2699dc505cbda203 |
#!/usr/bin/env python
# Greg Von Kuster
"""
Subtract an entire query from another query
usage: %prog in_file_1 in_file_2 begin_col end_col output
"""
import sys, sets, re
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
assert sys.version_info[... | dbcls/dbcls-galaxy | tools/new_operations/subtract_query.py | Python | mit | 3,034 | [
"Galaxy"
] | 55b89b6f5ceb4cf09f7c6203727339f83bbfe68917992a6197b14b9b82960191 |
"""
Test Logger Wrapper
"""
__RCSID__ = "$Id$"
#pylint: disable=invalid-name
import unittest
import logging
import sys
from StringIO import StringIO
from DIRAC.FrameworkSystem.private.logging.Logger import Logger
from DIRAC.FrameworkSystem.private.standardLogging.LoggingRoot import LoggingRoot
from DIRAC.FrameworkS... | arrabito/DIRAC | FrameworkSystem/test/testLogging/Test_Logging.py | Python | gpl-3.0 | 2,659 | [
"DIRAC"
] | 8e60cf52cfde050c49c23528e6a73af35aed40dff8cf9ac3c3bce9c7901dccbe |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/opencv/package.py | Python | lgpl-2.1 | 14,992 | [
"VTK"
] | 6da26f62164b7342ee06e63b7e61dffdee1fb3d7335f717f57467d8e7b06facf |
""" Using FFT image registration to find larger offsets between the platepar and the image. """
from __future__ import print_function, division, absolute_import
try:
import imreg_dft
IMREG_INSTALLED = True
except ImportError:
IMREG_INSTALLED = False
import os
import sys
import copy
import shutil
import... | CroatianMeteorNetwork/RMS | RMS/Astrometry/FFTalign.py | Python | gpl-3.0 | 14,794 | [
"Gaussian"
] | fdd152b23c8ec8349debf868ee784e5454be2930a8584187463cf4d74434cae6 |
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