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# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Calculate properties for electrons."""
import logging
import numpy
from .calculationmethod import Method
class Ele... | Schamnad/cclib | src/cclib/method/electrons.py | Python | bsd-3-clause | 1,269 | [
"cclib"
] | 0e0e7a99eb80412404f2e612e85c94144c7b061e6d2c06333c59aa99bab95612 |
# imports
import pandas as pd
import numpy as np
import time
import os
from tabulate import tabulate
import sys
from operator import add
from pyspark import SparkContext
from pyspark.sql import SparkSession
from pyspark.sql import SQLContext
from pyspark.sql import functions as F #https://stackoverflow.com/questions/3... | kcrandall/Kaggle_Mercedes_Manufacturing | spark/experiements/niki/experiment1.py | Python | mit | 13,526 | [
"Gaussian"
] | 134186991391b4e6bcb186c08d941642a13f9a1ab661e6f36bfc2c635ed7e35b |
"""
Support for cftime axis in matplotlib.
"""
import warnings
import cftime
import matplotlib.dates as mdates
import matplotlib.ticker as mticker
import matplotlib.transforms as mtransforms
import matplotlib.units as munits
import numpy as np
from ._version import version as __version__ # noqa: F401
_DEFAULT_RESO... | SciTools/nc-time-axis | nc_time_axis/__init__.py | Python | bsd-3-clause | 16,851 | [
"NetCDF"
] | 50591a061d00248a39fc48c3fe6da6c208374e4f536f5643b6f56a94dffa9654 |
#!/usr/bin/env python
"""
Reads a structure from a Gaussian Log file and other parameters from a
Gaussian Com file and creates a new Gaussian Com.
"""
import argparse
import sys
import os
# qt_scripts modules
from omg.gaussian.gaussian import GaussianLog
from omg.gaussian.gaussian import GaussianCom
from omg.misc im... | eduardoftoliveira/oniomMacGyver | scripts/gau_log2com.py | Python | gpl-3.0 | 2,333 | [
"Gaussian"
] | af3c45c6af400b52dadf3c510f9e02d9f86395a8d3432e8c663181de12ecb549 |
"""Script to combine ReferenceGenomes into a single one.
"""
import os
from Bio import SeqIO
from Bio.Alphabet.IUPAC import ambiguous_dna
from django.core.exceptions import ObjectDoesNotExist
from main.models import Dataset
from main.models import ReferenceGenome
from utils.import_util import add_dataset_to_entity
f... | woodymit/millstone_accidental_source | genome_designer/utils/combine_reference_genomes.py | Python | mit | 4,829 | [
"Biopython"
] | ae8405f3d11e4fd13e2a593a60bb97d74baa427908c07ad021da1017fc41b0cd |
from chemfiles import Trajectory
file = Trajectory("filename.xyz")
frame = file.read()
print("There are {} atoms in the frame".format(len(frame.atoms)))
positions = frame.positions
# Do awesome science here with the positions
if frame.has_velocities():
velocities = frame.velocities
# If the file contains in... | chemfiles/chemfiles.github.io | src/code/example.py | Python | bsd-3-clause | 383 | [
"Chemfiles"
] | d5dd0985ac7e6c2063942a6884bb7084275c904caf55ad797729cc7aff614cee |
# -*- coding: utf-8 -*-
""" *==LICENSE==*
CyanWorlds.com Engine - MMOG client, server and tools
Copyright (C) 2011 Cyan Worlds, Inc.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3... | zrax/moul-scripts | Python/Kadish.py | Python | gpl-3.0 | 3,388 | [
"VisIt"
] | a34e91586fc3b62881533cfe5de68d1c76a1faca05879b2c366821cb8af9d664 |
#!/usr/bin/env python2
"""RNAalignment - a module to work with RNA sequence alignments.
To see a full demo what you can do with this util, please take a look at the jupiter notebook (https://github.com/mmagnus/rna-pdb-tools/blob/master/rna_tools/tools/rna_alignment/rna_alignment.ipynb)
Load an alignment in the Stockh... | m4rx9/rna-pdb-tools | rna_tools/tools/rna_alignment/rna_alignment.py | Python | mit | 45,244 | [
"Biopython"
] | 28b7cbb9d31ed427759a6b5e1f435eb62da3fb2595483a1218f180e287d8aebf |
"""
Tests for xhr_handlers.py.
"""
import json
import os
import re
import StringIO
from django.contrib.auth import authenticate
from django.contrib.auth.models import User
from django.core.files.uploadedfile import UploadedFile
from django.core.urlresolvers import reverse
from django.http.request import HttpRequest
f... | woodymit/millstone | genome_designer/main/tests/test_xhr_handlers.py | Python | mit | 25,193 | [
"BWA"
] | 4aeddfc313aedaea480c7e70e1a0a466fd373c2ff0dfaba934000c133a642ab1 |
# ===========================================================
# RV PLOTS
# ===========================================================
# ===========================================================
# Plot RV timeseries
# ===========================================================
def plot_rv_t... | oscaribv/pyaneti | src/plot_rv.py | Python | gpl-3.0 | 12,995 | [
"Gaussian"
] | 85828293cd558555016990163bd244f52203cdb498555b5d85af5ca5024e5c9e |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/state_network_size_response.py | Python | apache-2.0 | 12,891 | [
"VisIt"
] | c0637598387358186445136a44bd8e8dd996c9343394f9d13728e0957d50e57b |
import mmap
from bup import _helpers
from bup.helpers import *
MIDX_VERSION = 4
extract_bits = _helpers.extract_bits
_total_searches = 0
_total_steps = 0
class PackMidx:
"""Wrapper which contains data from multiple index files.
Multiple index (.midx) files constitute a wrapper around index (.idx) files
... | fengyuanjs/catawampus | tr/vendor/bup/lib/bup/midx.py | Python | apache-2.0 | 3,935 | [
"exciting"
] | 3956a10e63f3fe08a09ff74ea5465b63343db0ac09b562c19f4fcc46f5442e2e |
from os import path, makedirs
import itertools
from netCDF4 import Dataset
import sys
import time
from gusto.diagnostics import Diagnostics, Perturbation, SteadyStateError
from firedrake import (FiniteElement, TensorProductElement, HDiv, DirichletBC,
FunctionSpace, MixedFunctionSpace, VectorFunct... | firedrakeproject/dcore | gusto/state.py | Python | mit | 26,831 | [
"NetCDF"
] | 531202d9194fc7899c42259819ec2fe953b001a816a02f302b4aacb26b8507b7 |
# proxy module
from __future__ import absolute_import
from mayavi.filters.mask_points import *
| enthought/etsproxy | enthought/mayavi/filters/mask_points.py | Python | bsd-3-clause | 95 | [
"Mayavi"
] | 158fe3c4f9cd1c64fdb2c2c327ea8ec5fa1303b4121ece6d1409b2b1e2e28b2e |
#!/usr/bin/env python
# By Jason Ladner
from __future__ import division
import sys, optparse, os, pysam, itertools
#Identifies individual reads covering 2 positions of interest and records the combined genotypes
#In version 2.0, starting saving read name info in order to handle R1 and R2 in a smarter way, but this ... | jtladner/Scripts | intraread_phasing/intraread_phasing_2.0.py | Python | gpl-3.0 | 6,122 | [
"pysam"
] | 20022008ed90a953001a6099c27e984f74c7997a91e7a23c22b3293844695f16 |
from pprint import pprint
# import pytest
from trackma.extras import AnimeInfoExtractor
DEFAULTS = {
'resolution': '',
'hash': '',
'subberTag': '',
'videoType': [],
'audioType': [],
'releaseSource': [],
'extension': '',
'episodeStart': None,
'episodeEnd': None,
'volumeStart': ... | z411/trackma | tests/test_anime_info_extractor.py | Python | gpl-3.0 | 7,402 | [
"Galaxy"
] | 2ebb4461ab375ebbfaf261e25ac60d2a9e5bea39746550ba2c55e2c04c604536 |
''' Tests for pyleoclim.core.ui.MultipleSeries
Naming rules:
1. class: Test{filename}{Class}{method} with appropriate camel case
2. function: test_{method}_t{test_id}
Notes on how to test:
0. Make sure [pytest](https://docs.pytest.org) has been installed: `pip install pytest`
1. execute `pytest {directory_path}` in t... | LinkedEarth/Pyleoclim_util | pyleoclim/tests/test_ui_MultipleSeries.py | Python | gpl-3.0 | 13,572 | [
"Gaussian"
] | 80bd15cf1e383013a47dc0ea662dd536436588e7a5cc8ddd87ea8b63acf24d27 |
"""
test_frost_number_bmi.py
tests of the frost_number component of permamodel using bmi API
"""
import datetime
import os
import numpy as np
import pytest
from dateutil.relativedelta import relativedelta
from pytest import approx
from permamodel.components import bmi_frost_number_Geo, frost_number_Geo, perma_base
... | permamodel/permamodel | permamodel/tests/test_frost_number_Geo_bmi.py | Python | mit | 11,868 | [
"NetCDF"
] | 57004a227c157d335e2348750812093ece6243b77a132dfaaf46150ab946e6bd |
################################################################################
# Copyright (C) 2015 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for `gamma` module.
"""
import warnings
warnings.simpl... | SalemAmeen/bayespy | bayespy/inference/vmp/nodes/tests/test_gamma.py | Python | mit | 5,650 | [
"Gaussian"
] | 8e94e6c621b8426985ec58163fb31313abc22e8411d42e2ca70e994544c088e1 |
import lie_group_diffeo as lgd
import odl
import numpy as np
action_type = 'geometric'
transform_type = 'affine'
space = odl.uniform_discr([-1, -1], [1, 1], [101, 101], interp='linear')
coord_space = odl.uniform_discr([-1, -1], [1, 1], [101, 101], interp='linear').tangent_bundle
# Select deformation type of the targ... | adler-j/lie_grp_diffeo | examples/diffemorphism_2d_tomo.py | Python | gpl-3.0 | 3,986 | [
"Gaussian"
] | 5baf5021c962c8751613066480a109218e407a8116cbb36850150d06e1b49b2b |
import numpy as np
from scipy.linalg import eig
from mjhmc.samplers.algebraic_hmc import AlgebraicDiscrete, AlgebraicContinuous
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from exceptions import RuntimeError
def get_eigs(sampler, order, steps=1000, energies=None):
"""Runs the sampler, r... | rueberger/MJHMC | mjhmc/misc/mixing.py | Python | gpl-2.0 | 4,915 | [
"Gaussian"
] | e2e80831cebd7e468b5d1a2d89fb12c4d6e90825fb918682cf93363311fd22b6 |
#! /usr/bin/env python3
from vasppy import procar
from vasppy.outcar import reciprocal_lattice_from_outcar
import argparse
def minimum_length( nmin ):
class MinimumLength( argparse.Action ):
def __call__( self, parser, args, values, option_string=None ):
if not nmin <= len( values ):
... | bjmorgan/vasppy | vasppy/scripts/effective_mass.py | Python | mit | 2,107 | [
"VASP"
] | a2d1642484be2d92a7b98698a2cddcaac376e622ef1cabe14e905a54d405c95b |
"""
test views
"""
import datetime
import json
import re
import pytz
import ddt
import unittest
from mock import patch, MagicMock
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.field_overrides import OverrideFieldData # pylint: disable=import-... | shubhdev/openedx | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 32,224 | [
"VisIt"
] | 2cd7083c518978d463912224dc01bd7663fcc7f74a7e097252e2b49639055647 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Ansible module to configure .deb packages.
(c) 2014, Brian Coca <briancoca+ansible@gmail.com>
This file is part of Ansible
Ansible is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Softwa... | ag-wood/ansible-modules-extras | system/debconf.py | Python | gpl-3.0 | 5,267 | [
"Brian"
] | e9f43d90f5ad3626969d05f2d3a0ec6a986c3d3630bc873a51813a7784c27c68 |
# ==========================================================================
#
# Copyright NumFOCUS
#
# 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/... | thewtex/ITK | Modules/Filtering/GPUImageFilterBase/wrapping/test/itkGPUNeighborhoodOperatorImageFilterTest.py | Python | apache-2.0 | 3,108 | [
"Gaussian"
] | e33dd4cb36fd98174285df041c82a8929e7ff91615f3b7b85108df60670881cd |
"""
The module contains classes and functions to generate different types of
simulated movements.
Author: Sivakumar Balasubramanian
Date: March 13, 2014
"""
import numpy as np
def data_span(data):
"""
Returns the ampltide span of the given list or array.
Parameters
----------
data : np.arr... | siva82kb/SPARC | scripts/movements.py | Python | isc | 8,753 | [
"Gaussian"
] | fdb430e8303789e374351a94dae9a5c4e8eb6bafdee1824ff8dedbe7df9b2391 |
"""
===========================
PPV Grouping and Clustering
===========================
Functions and routines to perform clustering analysis on the BGPS HCO+/N2H+
molecular line survey.
"""
from __future__ import division
import numpy as np
import pandas as pd
import cPickle as pickle
from collections import deque
... | autocorr/besl | besl/ppv_group.py | Python | gpl-3.0 | 31,445 | [
"Gaussian"
] | d60204082456c97c20e2b108a8f6aea7b6f241c45350c830103b91c31fecbee5 |
def writeClassical(mdpclean,outdir,mdpf,nondimer,rcoulomb,ew_rtol,pme):
"""
Gromacs MDP file for the classical replica.
The classical replica has its own settings that differ from
those of the other delocalized replicas. A Dimer simulation with
a classical replica will thus have two .mdp files, one... | marckn/dimerizer | dimerizer/mdp/mdp_writer.py | Python | gpl-3.0 | 3,535 | [
"Gromacs"
] | 77614ac618de99363174463f6d9f2dc41c9f0714811de29c4a4d6c6fb7943043 |
# -*- coding: utf-8 -*-
u"""
Created on 2015-7-23
@author: cheng.li
"""
import unittest
import math
import copy
import tempfile
import pickle
import os
from PyFin.Math.Distributions import InverseCumulativeNormal
from PyFin.Math.Distributions import NormalDistribution
from PyFin.Math.Distributions import CumulativeNo... | wegamekinglc/Finance-Python | PyFin/tests/Math/Distributions/testDistribution.py | Python | mit | 5,716 | [
"Gaussian"
] | f63095c357e463e55a0ea5de8e8a938caec1bc8cb7c9897be3bef66a3ffc81ae |
import numpy as np
from Methods import *
class NaiveBayes(Predictor):
def __init__(self):
self.class_probabilities = {}
self.probs = {}
@staticmethod
def moment_1(instances, i):
summation = 0
instance_count = 0
for instance in instances:
instance_count ... | thewickedaxe/Artificial-Intelligence---600.435 | HW-4/NaiveBayes.py | Python | gpl-3.0 | 2,886 | [
"Gaussian"
] | d074673560543b6bd1d8af710b6c2f35155a458ebf629b3c29a665f3715ef96a |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/diffusionmap.py | Python | gpl-2.0 | 15,865 | [
"MDAnalysis"
] | 1a00701eacad60588cfaa7c3d856247d20f73d4e4c44b76e568410a0120db88e |
##############################################################################
#
# Copyright (C) 2018 Compassion CH (http://www.compassion.ch)
# @author: Emanuel Cino <ecino@compassion.ch>
#
# The licence is in the file __manifest__.py
#
#########################################################################... | CompassionCH/compassion-switzerland | website_event_compassion/forms/group_visit_payment.py | Python | agpl-3.0 | 3,372 | [
"VisIt"
] | b1c1c74525a628a052a0910419427c0a85becc69ebcdef8909322edb76bf9121 |
"""
Test helper functions and base classes.
"""
import functools
import inspect
import json
import operator
import os
import pprint
import unittest
import urlparse
from contextlib import contextmanager
from datetime import datetime
from unittest import TestCase
import requests
from bok_choy.javascript import js_defin... | fintech-circle/edx-platform | common/test/acceptance/tests/helpers.py | Python | agpl-3.0 | 34,563 | [
"VisIt"
] | 0fcf8ec22a354bc85e972d0ceabb65875ebd14f862fceef5caed273df86a3da0 |
#
# Copyright (C) 2002 greg Landrum and Rational Discovery LLC
#
""" generates license files for our primitive license handler
"""
from rdkit.utils import Licensing
import sha,base64,time,StringIO
import sys
_salt = Licensing._salt
def DataFromTextDate(dText,mods=None):
""" expected format: day-month-year
"""
... | rdkit/rdkit-orig | rdkit/utils/GenLicense.py | Python | bsd-3-clause | 1,289 | [
"RDKit"
] | bf53f06c3e85c758230bdd9a8c41cf1a3a956d62a9326bd9ff1f56668cc6f1ac |
""" Example smearing script
This script:
* Reads in mc spectra from hdf5
* Smears spectra, default is to use weighted Gaussian method, but can
also use specify random Gaussian method via command line
* Smeared spectrum is saved to the same directory with ``_smeared``
added to the file name
Examples:
T... | EdLeming/echidna | echidna/scripts/dump_smeared.py | Python | mit | 1,992 | [
"Gaussian"
] | 0a3706c48cf6119ffdf903f4e41370fe4fe6d4e0151a94477d165eaa2b1370a7 |
import os
from django.test import TestCase
from django.test.client import Client
from hq.models import ExtUser, Domain
from buildmanager.models import Project, ProjectBuild, BuildDownload
from buildmanager.tests.util import setup_build_objects
from datetime import datetime
class ViewsTestCase(TestCase):
de... | commtrack/commtrack-old-to-del | apps/buildmanager/tests/views.py | Python | bsd-3-clause | 3,463 | [
"Brian"
] | ae0038c99b684da58286bcda479565646f9867d2ce9c3634d6a9d6b17dd364f8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines the FeffInputSet abstract base class and a concrete
implementation for the Materials Project. The basic concept behind an input
set is... | xhqu1981/pymatgen | pymatgen/io/feff/sets.py | Python | mit | 16,295 | [
"FEFF",
"pymatgen"
] | 60444c8f0510e8d52219c60a9e37e75a6ef8fa6ac3ec6f4dc99f275334ccc593 |
#!/usr/bin/python
####
# 02/2006 Will Holcomb <wholcomb@gmail.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 (at your option) any later v... | Miners/MinusAPI | nautilus-minus/minus_utils/multipart.py | Python | apache-2.0 | 5,044 | [
"Brian"
] | c4ac4c7cf13b7049afabc1610edea491b6ee344f0be5e2d272341443ecd25f28 |
"""SOM utils"""
# Adapted from:
# Vahid Moosavi 2015 05 12 09:04 pm
# sevamoo@gmail.com
# Chair For Computer Aided Architectural Design, ETH Zurich
# Future Cities Lab
# www.vahidmoosavi.com
import numpy as np
from matplotlib import pyplot as plt
import matplotlib.gridspec as gridspec
import numexpr as ne
from time i... | thorwhalen/ut | ml/decomp/sompy.py | Python | mit | 45,652 | [
"Gaussian"
] | 963a2ba132738ca49a05ba5a0c0d5995ec609f0a83bbd60d60f00f4ec47496cc |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 1000
n = 2000
testMehrotra = True
testIPF... | birm/Elemental | examples/interface/LPDirectDense.py | Python | bsd-3-clause | 3,253 | [
"Gaussian"
] | 0b8e6ce58f5fb01e6a034bcae926f03d335cd984b2b04ec8674e8bd388bb1279 |
# Copyright 2015 Adriana Supady
#
# This file is part of fafoom.
#
# Fafoom is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | FHIBioGroup/fafoom-dev | fafoom/utilities.py | Python | gpl-3.0 | 14,972 | [
"RDKit"
] | c4774ba30ae30db6a93c2afa7863ebfffd85b2706a855965f8e85a64b3477578 |
from .mle import saccade_model_mle
from .utils import *
def saccade_model_em(pointlist):
'''
Estimates the reaction time and duration of the saccade by
fitting a saccade model to the data.
The model consists of three phases:
1) source phase, gaze is fixated onto a point
2) saccade phase, g... | infant-cognition-tampere/saccademodel-py | saccademodel/em.py | Python | mit | 4,165 | [
"VisIt"
] | 547036834d52f558369daddd45e538aaef936e6d0fcb39c0716a791bb2559bc5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/topology/tpr/utils.py | Python | gpl-2.0 | 34,782 | [
"Gromacs",
"MDAnalysis"
] | 255350b1035b6f6474f4faf014b7653d088bd979f85ca44dc322a7af9f03a784 |
'''OpenAnything: a kind and thoughtful library for HTTP web services
This program is part of 'Dive Into Python', a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
'''
__author__ = 'Mark Pilgrim (mark@diveintopython.org)'
__version__ = '$Revision: 1.6 $'[11:-2]
_... | mdraeger/gmapcatcher | gmapcatcher/openanything.py | Python | gpl-2.0 | 6,305 | [
"VisIt"
] | dd55efce23f2df5c1918ee51af50b2af7b2f540f9060fe06149f30187af586b8 |
# -*- coding: utf-8 -*-
#############################################################################
# #
# FLEQ (Free LibreSoft Educational Quizbowl) #
# A synchronous on-line competition software to improve and... | cristilav/FLEQ | quizbowl/views_tournaments.py | Python | agpl-3.0 | 13,518 | [
"VisIt"
] | 7024a6ea7e20af41a622bbd3173b2ed4588da46397db9859f7cc97f77ccda2c6 |
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | LoHChina/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 58,703 | [
"exciting"
] | 6772bd03b3a08ea166f2d7dc8581114c81fb6fccc41ff8ef970f7a31bd3c13ec |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('get_jobs')
@click.option(
"--state",
help="Job states to filter on."
)
@click.option(
"--history_id",
help="Encoded history ID to filter on.",
type=str
)
@click.... | galaxy-iuc/parsec | parsec/commands/jobs/get_jobs.py | Python | apache-2.0 | 2,961 | [
"Galaxy"
] | eac8205a389d353144edf2b717c38260801e11b737d3c5f0769e62dc2f813c98 |
# File: AthenaCommon/share/SystemOfUnits.py
# Author: Wim Lavrijsen (LBNL, WLavrijsen@lbl.gov)
# Created: 01/21/04
# Last: 01/21/04
# This script is a direct adaptation of CLHEP/Units/SystemOfUnits.h
# and the following is the originial CLHEP comment:
#
# -----
# HEP coherent system of Units
#
# This file h... | vvolkl/DD4hep | DDCore/python/SystemOfUnits.py | Python | gpl-3.0 | 6,279 | [
"Brian"
] | 3fe1a8110be65899a50c0ba4be68542abf7787cea1cd212f1ea7918cf7e5e037 |
# 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 ... | hmenke/espresso | testsuite/python/scafacos_dipoles_1d_2d.py | Python | gpl-3.0 | 5,774 | [
"ESPResSo"
] | 7d7ab21a46897177f1c5cf5f98b0800f77b7199baa426fe7feab0b6ad092bc23 |
import astropy.io.fits as fits
import numpy as np
def lumwtd(filename='colira.fits'):
s = fits.getdata(filename)
keep = (s['INTERF'] != 2)# & (s['GALNAME']=='ngc3034')
W10 = np.nansum(s['CO10'][keep])
W21 = np.nansum(s['CO21'][keep])
W32 = np.nansum(s['CO32'][keep])
W10_err = (np.nansum((s['CO1... | low-sky/colira | bayes/lumwtd.py | Python | gpl-2.0 | 1,761 | [
"Galaxy"
] | 67861f3eceb2356c459f22fa3712c12ff4de63922d9933a8de84d5f243a9b9fb |
# Copyright 2013 by Kai Blin.
# 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.
import unittest
from os import path
from Bio import GenBank
from Bio import SeqIO
class GenBankTests(unittest.TestCase... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_GenBank_unittest.py | Python | gpl-2.0 | 1,343 | [
"Biopython"
] | 619a8876a77314328b4321787dca25eafe5caf6f60680b6c0d53b9168c927056 |
from datetime import datetime
import json
import logging
from . import configuration
from . import dispersiongrid as dg
from . import dispersion_file_utils as dfu
from . import dispersionimages
from . import smokedispersionkml
from . import fires
def main(options):
if options.verbose:
logging.basicConfig... | pnwairfire/blueskykml | blueskykml/makedispersionkml.py | Python | gpl-3.0 | 3,293 | [
"NetCDF"
] | bfa7afa27966dfb4e6b5b22223c906b0c91702a265c92f8bd308481b88fac35b |
from buildbot.plugins import steps
from buildbot.steps.shell import ShellCommand
from buildbot.locks import SlaveLock
from buildbot.process.properties import Interpolate
class Steps:
def __init__(self,Environ):
# Max number of running builds
build_lock = SlaveLock('build',
maxCount = 2,
m... | QEF/q-e_schrodinger | test-suite/buildbot/Cineca_farm/slave.py | Python | gpl-2.0 | 17,087 | [
"EPW",
"Wannier90"
] | 744e443491e1782f40bf1bd86a0da6be1b319a413744b723a11b98a984ca4f0d |
# Copyright (C) 2004-2008 Paul Cochrane
#
# 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 distribut... | paultcochrane/pyvisi | examples/simpleLinePlot.py | Python | gpl-2.0 | 2,124 | [
"VTK"
] | cb6a8d176985723bab26ab1164be3c0ca193d4e8a92ae0955d5649c449225731 |
from collections import OrderedDict
from chempy import Reaction
from chempy.kinetics.rates import MassAction, RadiolyticBase
from chempy.units import to_unitless, default_units as u
def jl_dict(od):
return "Dict([%s])" % ", ".join(["(:%s, %.4g)" % (k, v) for k, v in od.items()])
def _r(r, p, substmap, parmap, *... | bjodah/aqchem | chempy/util/_julia.py | Python | bsd-2-clause | 5,909 | [
"ChemPy"
] | 0af518908e2dfc1e012401cecc10bdf6e57c6ae12be3e834d5bd6eeeddba428d |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@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 ... | ashemedai/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 31,861 | [
"Galaxy"
] | 15aae5c88c28d2e75ffeae8ace88ec4fe225498e9561486f718540f118cb11b2 |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os.path
import re
import sh... | alxgu/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 34,060 | [
"Galaxy"
] | 159d18e7132b41a9dc30fd4ed588b3e1f25c54e5f52edf58312f725a5ae50d24 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | models.py | Python | apache-2.0 | 12,570 | [
"Brian"
] | 0ab2cf0f25cb4e09a3decab0918b2d96a3c1535d308e8a7897aaa22f14f89fa0 |
#!/usr/bin/env python
import askap.analysis.evaluation
import numpy as np
import matplotlib
matplotlib.use('Agg')
import pylab as plt
import math
import scipy.special
from askap.analysis.evaluation.readData import *
import askap.analysis.evaluation.modelcomponents as models
from askap.analysis.evaluation.sourceSelect... | ATNF/askapsdp | Code/Components/Analysis/evaluation/current/scripts/imageEval.py | Python | gpl-2.0 | 12,197 | [
"Gaussian"
] | 7c1892579a08d810bf80e9cef461cc6b158f929c5aedd302da885ab6cb44ca55 |
"""Test Payment for Family Camp Bookings.
Usage:
test_pay_for_camp.py <email> <adults> <children> <infants>
Options:
-d,--debug Turn on debug output.
-h,--help Show this screen.
--version Show version.
"""
from splinter import Browser
from time import sleep
from docopt import docopt
URL = "... | hippysurfer/family-camp | family_camp/test/test_pay_for_camp.py | Python | mit | 1,811 | [
"VisIt"
] | 959e6ff67d5999c2d039ed6f2788f9b26624e78d984af1e04f558628706ed35d |
import os, sys, shutil
from pymatgen.io.vasp import Poscar, Kpoints, Potcar, VaspInput
from pymatgen import Structure
from pymatgen.apps.borg.hive import SimpleVaspToComputedEntryDrone
from pymatgen.apps.borg.queen import BorgQueen
from ctypes import *
from mpi4py import MPI
from timeit import default_timer as timer
im... | skasamatsu/py_mc | py_mc/applications/latgas_abinitio_interface/run_vasp_mpi.py | Python | gpl-3.0 | 8,265 | [
"VASP",
"pymatgen"
] | 8a7cba9c6880f22db1fb612260b78f6e085d19ce30b4bfab005881dfc08d4b00 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Zsolt Foldvari
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2013 Vassilii Khachaturov
#
# 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 F... | beernarrd/gramps | gramps/plugins/docgen/cairodoc.py | Python | gpl-2.0 | 11,747 | [
"Brian"
] | a7010fb1020215914a728457b7c03d8d98f3ec082cb0119eec6d1cdba2527155 |
#!/usr/bin/python
#Icefilms.info v1.1.0 - Eldorado
#All code Copyleft (GNU GPL v2) Eldorado and icefilms-xbmc team
############### Imports ############################
#standard module imports
import sys,os
import time,re
import urllib,urllib2,base64
import random
import copy
import threading
import string
import tr... | azumimuo/family-xbmc-addon | plugin.video.icefilms/default.py | Python | gpl-2.0 | 145,284 | [
"VisIt"
] | 90651877ccec4b49ddf18b2ed24d48397dff05e6bf53632ae2a7e718ecda5a41 |
from django.test import TestCase
from splinter import Browser
class TestBaseViews(TestCase):
def setUp(self):
self.browser = Browser('chrome')
def tearDown(self):
self.browser.quit()
def test_home(self):
self.browser.visit('http://localhost:8000')
test_string = 'Hello, w... | tosp/ProjectStud | base/test_views.py | Python | mit | 773 | [
"VisIt"
] | af0ac93b9e58006becd1e9ebe52aeafa70a3fe339ac5ef4975d1d82eb347cf39 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import Specie
from pymatgen.analysis.bond_valence im... | tschaume/pymatgen | pymatgen/analysis/tests/test_bond_valence.py | Python | mit | 2,988 | [
"pymatgen"
] | abb1fbe52f48451ec7b2ed25d8f395ab6d141d75c69b1d6cd2262948ae2e214d |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def offset_gaussian():
# Connect to a pre-existing cluster
insurance = h2o.import_file(pyunit_utils.locate("smalldata/glm_test/insurance.csv"))
insurance["offset"] = ... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_offset_gaussian_gbm.py | Python | apache-2.0 | 1,986 | [
"Gaussian"
] | 52cff547ae27fd4069344dee2d560e5beeb73ca9d08d66d6c3e8de76bb347ad3 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import sys
import numpy as np
from ...core.parameterization.parameterized import Parameterized
from kernel_slice_operations import KernCallsViaSlicerMeta
from ...util.caching import Cache_this
from GPy.core... | strongh/GPy | GPy/kern/_src/kern.py | Python | bsd-3-clause | 11,880 | [
"VisIt"
] | 0b311f5a7532795c41378d4563913bb06f5a95ca7abeed08a789c8a72b785b35 |
__author__ = "mfreer"
__date__ = "2011-09-15 17:09"
__version__ = "1.6"
__all__ = ["FileCore", "get_file_list"]
import glob
import logging
class FileCore(object):
"""
Abstract class which holds basic file access methods and attributes.
Designed to be subclassed by NetCDF, NASA Ames and basic text file
... | eufarn7sp/egads-eufar | egads/input/input_core.py | Python | bsd-3-clause | 3,537 | [
"NetCDF"
] | d12c47d7219bcc5dc0bf122b64b8b7ff5ff5183e2cf66cea3c950021e43260fd |
'''This file contains code for the unit:Number Theory. '''
import numpy as np
import matplotlib.pyplot as plt
from scipy.special import ndtri
import pylab
'''Method that returns returns value of the gaussian given an input array and mean and standard deviation'''
def Normal(x, mu,sigma):
return np.exp(- (x-mu)**2/... | cloudmesh/book | examples/physics/number-theory/higgs_classIII.py | Python | apache-2.0 | 19,448 | [
"Gaussian"
] | 760f92d21df1dda7f7691926be10d7f979e7712ae0ed9cce89f1ff31d95f1828 |
#!/usr/bin/python
########################################################################## RAD4SNPs:##############################################################################
# A set of Python scripts to select and validate independent SNPs markers from a list of read files #
#################################... | glassalle/Rad4Snps | RAD4SNPs_Main.py | Python | gpl-3.0 | 12,997 | [
"BWA"
] | 0fd724303503e8f90d650d5a2f4ecc3b37ddba1d6cbfd52562b19041b1c5a5a4 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2019, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test single point logfiles in cclib."""
import datetime
import os
import unittest
import numpy
import p... | langner/cclib | test/data/testSP.py | Python | bsd-3-clause | 26,270 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"MOLCAS",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"TURBOMOLE",
"cclib"
] | cf9d3b49a84091552e51784824bb312ad756e16cd636f6201d97e597aab2c3b4 |
# uncompyle6 version 2.9.10
# Python bytecode 2.7 (62211)
# Decompiled from: Python 3.6.0b2 (default, Oct 11 2016, 05:27:10)
# [GCC 6.2.0 20161005]
# Embedded file name: ast.py
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract ... | DarthMaulware/EquationGroupLeaks | Leak #5 - Lost In Translation/windows/Resources/Python/Core/Lib/ast.py | Python | unlicense | 11,832 | [
"VisIt"
] | 3df8e80240260e71c78fe66876ac026f8704ff9b0319c99bf57b8e9c6fa76b6a |
# -*- coding: utf-8 -*-
"""Suite of methods common operation on res.partner."""
import base64
import logging
import pprint
import random
from openerp import api, models, fields
_logger = logging.getLogger(__name__)
class ResPartnerGetStudios(models.Model):
"""Overcharge the definition of a partner with methods ... | cgstudiomap/cgstudiomap | main/local_modules/frontend_studio/models/res_partner.py | Python | agpl-3.0 | 10,035 | [
"VisIt"
] | 2aaacfeb6a8e54de183b88b3acfddd3700533deea6660e50dd433ee1784089ad |
#
# 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... | Forage/Gramps | gramps/plugins/textreport/summary.py | Python | gpl-2.0 | 11,013 | [
"Brian"
] | e154a9faed0b8e4fe59de95bcd463fe12f020330f4e1ca0309f6493f3f9cb58f |
"""
Utilties for loading static pipe_analysis PNGs into holoviews DynamicMaps
See 'qa-image-browser.ipynb' demo notebook for examples of usage.
"""
from __future__ import print_function, division
import re, os, glob
from itertools import product
from functools import partial
import numpy as np
import holoviews as h... | timothydmorton/qa_explorer | explorer/static.py | Python | mit | 5,381 | [
"VisIt"
] | c6ded926eea19819b71e462c01f485d2faeee21646c63a0981cb623075af023f |
#!/usr/bin/python
"""
Last edited by: Siddhanathan Shanmugam <siddhanathan@gmail.com>
Copyright (C) 2014 Siddhanathan Shanmugam
LICENSE: LGPL v2.1, or (at your opinion) any later version.
-------------------------------------------------------------------------------
SimpleOSC:
Copyright (c) Daniel Holth & Clinton ... | siddhanathan/raga | OSC.py | Python | gpl-3.0 | 84,732 | [
"VisIt"
] | 5928ab965a996ccfc473e336a9c497f7b3496087eb1998afc25f1408050d4fb8 |
# proxy module
from __future__ import absolute_import
from mayavi.plugins.envisage_engine import *
| enthought/etsproxy | enthought/mayavi/plugins/envisage_engine.py | Python | bsd-3-clause | 99 | [
"Mayavi"
] | 19362411c761ec23be6bd67844ec12dfcaf968b0ae1d8928e32058dfa54f3812 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Base types for nodes in a GRIT resource tree.
'''
import ast
import os
import types
from xml.sax import saxutils
from grit imp... | hujiajie/chromium-crosswalk | tools/grit/grit/node/base.py | Python | bsd-3-clause | 22,026 | [
"xTB"
] | 7d551037f96b7515e474602a9d119859aa8c88a3ad426e91acdd5c9e75e36216 |
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