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#!/usr/bin/env python
"""Processed version of the documentation.
The documentation from the objects of raw_doc is further processed into
objects from the module proc_doc. These objects can then be processed
into structured documents such as HTML more easily.
"""
# TODO(holtgrew): Location traceability for entries an... | gkno/seqan | util/py_lib/seqan/dox/proc_doc.py | Python | bsd-3-clause | 46,842 | [
"VisIt"
] | 593dfdf4717b39a1628b9881eafb8f33a4f6528897cde7cd25eb52a5ebddfcc2 |
from ddapp import robotstate
import ddapp.vtkAll as vtk
from ddapp.transformUtils import poseFromTransform
from ddapp.fieldcontainer import FieldContainer
import numpy as np
import math
class ConstraintBase(FieldContainer):
__isfrozen = False
robotArg = 'r'
def __init__(self, **kwargs):
self._a... | gizatt/director | src/python/ddapp/ikconstraints.py | Python | bsd-3-clause | 24,993 | [
"VTK"
] | 5cfa3f82ca84e1eca7a329374bb14059b479d8d8dd4b6c3ea35aab5cf187704b |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Code to deal with various programs for sequencing and assembly.
This code deals with programs such as Phred, Phrap and Consed -- which provide
ut... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Sequencing/__init__.py | Python | gpl-2.0 | 412 | [
"Biopython"
] | d4f9a9e9ec9670d52993db0a9b7244d5b21b8fbfd279b620b14b74eefaef9512 |
import warnings
from collections import OrderedDict, defaultdict
import numpy as np
import pandas as pd
from .coding import strings, times, variables
from .coding.variables import SerializationWarning
from .core import duck_array_ops, indexing
from .core.common import contains_cftime_datetimes
from .core.pycompat imp... | shoyer/xray | xarray/conventions.py | Python | apache-2.0 | 25,750 | [
"NetCDF"
] | 33a6f7930849dcb93026b7687c357ad3de782f234e2e3497be008d3efee2efc4 |
#!/usr/bin/env python3
"""
Author: Kartamyshev A.I. (Darth Feiwante)
"""
def min_distance(database = None, calculation = ()):
"""
This function is used to find minimal distance in the lattice presented
as a part of the 'Calculation' object
INPUT:
- database (.gbdm3) - database dictionary; co... | dimonaks/siman | siman/analysis_functions.py | Python | gpl-2.0 | 26,024 | [
"VASP",
"pymatgen"
] | 9810a46ef7660b5527f1d3b2f7ea99a99351467dce4c9eee053db2f2339e389d |
'''
Utility module
This module contains a variety of convenience functions, including:
- get_dataset
- interp
- p_corrected_bonf
- p_critical_bonf
- smooth
'''
# Copyright (C) 2022 Todd Pataky
# updated (2022/02/06) todd
from math import sqrt,log
import numpy as np
from . stats._spm import plist2string as p2s
... | 0todd0000/spm1d | spm1d/util.py | Python | gpl-3.0 | 3,308 | [
"Gaussian"
] | 644e68d26d7280de95e22e7c408250e306963591be679af1d8d2dce43a96d1e7 |
#!/usr/bin/env python
# flake8: noqa
# pylint: disable=C0103,C0301,R0903
#
# A library that provides a Python interface to the Telegram Bot API
# Copyright (C) 2015 Leandro Toledo de Souza <leandrotoeldodesouza@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of t... | AndrewSamokhvalov/python-telegram-bot | telegram/emoji.py | Python | gpl-3.0 | 37,307 | [
"Octopus"
] | a9357b5e59ef864bec81a2d48b20ee338bb236208028ec64a708fe0983d15350 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# IPv4 dictionaries.
animal_adjectives = [
'agile',
'bashful',
'clever',
'clumsy',
'drowsy',
'fearful',
'graceful',
'hungry',
'lonely',
'morose',
'placid',
'ruthless',
'silent',
'thoughtful',
'vapid',
'weary'... | lord63/pyhipku | pyhipku/dictionary.py | Python | mit | 11,940 | [
"Elk",
"GULP"
] | 59ed045515064841228e1d43ef796693ea968c94c8887a7b8fdb8c0ca27fa978 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/lo/test/test_iao.py | Python | apache-2.0 | 1,541 | [
"PySCF"
] | 297867ea07ec6873b27b587c317aba031e39a9a7e2841528af651a821154c991 |
"""
Find an example demonstrating that floating point addition is not associative
Example output:
t1 = 0.11945064104636571
t2 = t1 / t1
t3 = 0.16278913131835504
t4 = 0.6323432862008465
assert associative_add(t4, t3, t2)
"""
from testmachine import TestMachine
from random import Random
# This is t... | rboulton/testmachine | testmachine/examples/floats.py | Python | bsd-2-clause | 1,860 | [
"exciting"
] | 73159f06dc3a249751d19036dad098ec0bd848ace1d79aa42243bb887ece3ccc |
import unittest
from hamcrest import *
from nose.tools import nottest
from test.features import BrowserTest
from test.features.support.splinter_matchers import has_text, has_class
class test_search(BrowserTest):
def test_search_page(self):
self.browser.visit("http://0.0.0.0:8000/search?keyword=gds")
... | imclab/transactions-explorer | test/features/test_search.py | Python | mit | 3,443 | [
"VisIt"
] | f1b6bb931f4448fce4d7becce299ccf81afe946a93ec4e98b9f28c5c3b7e10a3 |
# This Python file uses the following encoding: utf-8
retired_shows = [
{'art': 'http://twit.cachefly.net/coverart/abby/abby600.jpg',
'desc': 'Abby Laporte and her guests as they offer fresh perspectives on '
'difficult teen subjects.',
'feeds': {'MP3': 'http://feeds.twit.tv/abby.xml'},
'title': "... | divingmule/plugin.video.twit | resources/shows.py | Python | gpl-2.0 | 27,057 | [
"Brian"
] | 85479b2a93386c01dcc576abacc2f9884f0c119e608556affc7d5c4d5307e506 |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to truncate a data file to a QM system
Part of ComQum-ELBA
"""
import argparse
from collections import namedtuple
import numpy as np
from sgenlib import lammps
def _trunc_connectivity(conlist, atom_ids) :
newlist = []
for con in conlist:
... | SGenheden/Scripts | Lammps/lmp_truncate.py | Python | mit | 1,597 | [
"LAMMPS"
] | 2a1a9143d8093f1c2f18cf307813972cb9daff997bd8106be0673a7322b45c2e |
# -*- coding: utf-8 -*-
"""
Demonstrates use of PlotWidget class. This is little more than a
GraphicsView with a PlotItem placed in its center.
"""
import PyQt4.QtCore as q
import PyQt4.QtGui as qt
import numpy as np
import pyqtgraph as pg
import pyqtgraph.dockarea as dock
import zmq
import msgpack as msg
import m... | jkokorian/odm-live | lvclient_gui.py | Python | gpl-3.0 | 20,530 | [
"Gaussian"
] | 3305899b1dafb1839c497bb06e2ac083200f49aa455bba8f4d19d1d907d1fdd6 |
from django.conf.urls import patterns, include, url
from django.conf import settings
from catmaid.views import *
import catmaid
import vncbrowser
# Uncomment the next two lines to enable the admin:
from django.contrib import admin
from adminplus.sites import AdminSitePlus
admin.site = AdminSitePlus()
admin.autodisco... | AdaEne/CATMAID | django/projects/mysite/urls.py | Python | gpl-3.0 | 1,163 | [
"NEURON"
] | d91e3cef0335b999ebc94cfc49fb7bd46a23ba34a783824ec365baeb5af29273 |
#!/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... | h2oai/h2o-dev | h2o-py/tests/testdir_algos/stackedensemble/pyunit_stackedensemble_gaussian.py | Python | apache-2.0 | 6,514 | [
"Gaussian"
] | d0b45169dc074455da9438f0d7d623e059ef6f071a7db4b2970ea9c21d76f119 |
#!/usr/bin/env python
import sys
import os
def runfail(cmd):
print "Running : %s" % cmd
if not 0 == os.system(cmd):
sys.exit("Failed : %s " % cmd)
if not len(sys.argv) >= 2:
sys.exit("blast.py query.fa reference.fa")
if len(sys.argv) == 3:
query_file, ref_file = sys.argv[1:3]
no_ref = Fa... | RamsinghLab/nanocorr | nanocorr.py | Python | lgpl-3.0 | 2,495 | [
"BLAST"
] | 59ae6d2c7be025a8686cffb53ca88697f4c3eb6dafc22d037948dbe6785ba0d9 |
#!/usr/bin/python
#
# Copyright (c) 2011 Rime Project.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, m... | AI-comp/Orientation2015Problems | rime/core/taskgraph.py | Python | mit | 26,075 | [
"VisIt"
] | ae11c34a4288dd79b1a65b38c08ac5d4d7fe0689518b96f0346e4cc757ae6939 |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | eleftherioszisis/NeuroM | examples/neuron_iteration_analysis.py | Python | bsd-3-clause | 5,976 | [
"NEURON"
] | 14c625ff4076095da8772a7b327b2981a45ac9d695c97dcbd5b6c857097c2c82 |
#!/usr/local/bin/python -i
# Script: logplot.py
# Purpose: use GnuPlot to plot two columns from a LAMMPS log file
# Syntax: logplot.py log.lammps X Y
# log.lammps = LAMMPS log file
# X,Y = plot Y versus X where X,Y are thermo keywords
# once plot appears, you are in Python interpreter, typ... | val-github/lammps-dev | tools/python/logplot.py | Python | gpl-2.0 | 762 | [
"LAMMPS"
] | 228caf9fee6a74e0690b4e7d00181bffb675b8b4e34d1c33339c052c65b215dc |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/multiple_features/best_kNN_PCA/test11_cross_validate_categories_1200ms_scaled_method_v_force_motion.py | Python | mit | 5,088 | [
"Mayavi"
] | 474c5c5782508fe6a4a49408370409c5d6a172644982ea40a9d44f6e7a83e96c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | Forage/Gramps | gramps/plugins/tool/verify.py | Python | gpl-2.0 | 55,484 | [
"Brian"
] | 9a5a7255f3820a70858d5883e6079a27ffaaf83791aa91dae80d3a72eb4b33f4 |
# Copyright 2017 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.
import optparse
import threading
import py_utils
from devil.android import device_utils
from systrace import trace_result
from systrace import tracing_agen... | endlessm/chromium-browser | third_party/catapult/systrace/systrace/tracing_agents/walt_agent.py | Python | bsd-3-clause | 4,178 | [
"VisIt"
] | 0a5db0939fda812a023ce0ab76cfeb581d1c9e8acfe7a44cba7e0151761202cb |
import pdb
import sys, bisect, scipy.stats, gc, os
from string import maketrans
import getNew1000GSNPAnnotations, InBindingSite, GetCNVAnnotations, Mapping2
import binom
MAXREADLEN=75
#tmp_trans={"paternal":0, "maternal":1}
# This is unfortunate; Alex's map files used REF, PAT, MAT, but everywhere else we use patern... | gersteinlab/AlleleDB | alleledb_pipeline/GetSnpCounts.py | Python | cc0-1.0 | 9,440 | [
"Bowtie"
] | e828f4a3436d5d8c1a9f2366a30a1fa56759564bcfc0b81dc080d63d2ac6816b |
#!/usr/bin/env python
"""
An animated image
"""
from copy import copy
import netCDF4 as nc4
import numpy as np
import pysgrid
from datetime import timedelta
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FFMpegWriter
from matplotlib.widgets import Slider, Butto... | NOAA-ORR-ERD/pysgrid | demos/demo_matlabanim.py | Python | bsd-3-clause | 6,456 | [
"NetCDF"
] | 44b60a61c9d5a58666dda809870e371bf36c0845145056f72024cc07cc0a8242 |
#! /bin/env python
# -*- coding: utf-8 -*-
# Beief documentation:
# Pathperf client, estimate path BTC from vantage website to this client
# Written and tested under Fedora11 with Python 2.6
# parameter list:
# [-t1/--thread=1] [-i any/--interface=any] [-b/--bypassCDN] [-c/--crawl] [-q/---quota] [-v/--verbose] [-h/--he... | neoyk/search | pathperf_client.py | Python | apache-2.0 | 14,117 | [
"VisIt"
] | 8034b6f2b3df3986856eff54f45e5da04416be87454cf8aa5b9fded274c2426c |
#!/usr/bin/env python
import os
from collections import OrderedDict
import numpy as np
import matplotlib.pyplot as plt
from ase.io import read
from ase.units import Bohr
from pyDFTutils.ase_utils.ase_utils import symbol_number
from pyDFTutils.ase_utils.kpoints import ir_kpts
from .wannier import read_basis
from pyDFTu... | mailhexu/pyDFTutils | pyDFTutils/wannier90/wann_ham.py | Python | lgpl-3.0 | 10,371 | [
"ASE",
"VASP",
"Wannier90"
] | c6f4dc76a6900a009f6337ddabb58eb2e4667ef913c0a31c2316f898c077ab1c |
""" DIRAC FileCatalog Database """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.Directory... | vmendez/DIRAC | DataManagementSystem/DB/FileCatalogDB.py | Python | gpl-3.0 | 38,872 | [
"DIRAC"
] | 0050e5418f2dd14b6fbf07d0e73f71a5695fde956fe0d372673048157c281d09 |
''' Tests for netcdf '''
from __future__ import division, print_function, absolute_import
import os
from os.path import join as pjoin, dirname
import shutil
import tempfile
import warnings
from io import BytesIO
from glob import glob
from contextlib import contextmanager
import numpy as np
from numpy.testing import (... | apbard/scipy | scipy/io/tests/test_netcdf.py | Python | bsd-3-clause | 16,677 | [
"NetCDF"
] | 374cfdf27f2495e01d078b1ca8ff5cf0170644e57d7a9d4c9777f12d7225cc8d |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | mehdidc/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 41,636 | [
"Gaussian"
] | db75e7ebba216b1faa89154c957352889b2a070c599a493cc7b74a741520949f |
# Copyright 2019 Google 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/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | CloudVLab/professional-services | tools/slo-generator/slo_generator/backends/elasticsearch.py | Python | apache-2.0 | 4,740 | [
"Elk"
] | 855916e96d5dd1407f9196c445a959490d958b447fe72f50e22fecb130516f44 |
"""
DIRAC.StorageManagementSystem.Agent package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/StorageManagementSystem/Agent/__init__.py | Python | gpl-3.0 | 164 | [
"DIRAC"
] | f3b0e976c215154d28cf842ad97a7705f7967d230bd6b0b0a6d369f4466537a3 |
# -*- coding: utf-8 -*-
#
# DeBaCl documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 29 19:11:02 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | CoAxLab/DeBaCl | docs/conf.py | Python | bsd-3-clause | 8,305 | [
"Brian"
] | f71aad2fd000e7eed978c9d46351c35c3d3f9de24846175aad3f5150346d6015 |
from Bio import SeqIO
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
import sys
dna = set("ATGC-actg")
def validate(seq, alphabet=dna):
"Checks that a sequence only contains values from an alphabet"
leftover = set(seq.upper()) - alphabet
return not leftover
file = open('result.txt', 'w')
for... | gigascience/gigadb-website | protected/scripts/read_stat_script.py | Python | gpl-3.0 | 3,143 | [
"BLAST"
] | 9855a31670d5612bf14c1a10185de2282df5ec1742bf5c7474198f1810709ae2 |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# 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.
... | wulczer/ansible | v2/ansible/plugins/cache/redis.py | Python | gpl-3.0 | 3,394 | [
"Brian"
] | bd8c169d40f86eb03653a38a5eb018c9c8a4ba5b7ca9788077ece7be24439a6e |
#!/usr/bin/env python
"""
Test colormaps
@author alexander@gokliya.net
"""
from __future__ import print_function
from icqsol.shapes.icqShapeManager import ShapeManager
from icqsol import util
shape_mgr = ShapeManager()
s = shape_mgr.createShape('box', origin=(0., 0., 0.), lengths=[10., 1., 1.])
s2 = shape_mgr.refine... | gregvonkuster/icqsol | tests/testColormaps.py | Python | mit | 1,160 | [
"VTK"
] | 89daaa82548068c29a50b09ffe450a4a6bc3617ab3f8b4985b3a05d8c7435272 |
import os
import time
from page_objects import *
def go_to_web_pro(context):
context.browser.visit(context.base_url+ '/login/')
time.sleep(1)
def hide_tool_bar(context):
time.sleep(1)
context.browser.find_by_id('djHideToolBarButton').click()
def go_to_login_page(context):
time.sleep(1)
return... | rapidpro/ureport-web-participation | features/steps/page_actions.py | Python | agpl-3.0 | 2,079 | [
"VisIt"
] | 9ede17d2bb51fa6d402187cdfad9d3eefb742d9da8aa91a32c5c35d5db48811f |
import numpy as np
from .interp_dens_map import interp_dens_map
from .xyz_coords import xyz_coords
from .best_fit_angles import get_angles
from .method1 import m1_ccc_map
from .method2 import m2_fix_plane_perp_dist
from .method3 import m3_min_perp_distance
def draw_rand_dep_dist(d_g, e_d_g):
'''
Take each 3D... | Gabriel-p/mcs_rot_angles | modules/mc_errors.py | Python | gpl-3.0 | 4,014 | [
"Galaxy"
] | 84edfe20cd8292fa6a275ca2471f0eeb560be5a07d4df1f2c16cf69415fb5027 |
# -*- coding: utf-8 -*-
"""
Authors: Gonzalo E. Espinoza-Dávalos
IHE Delft 2017
Contact: g.espinoza@un-ihe.org
Repository: https://github.com/gespinoza/waterpix
Module: waterpix
"""
from __future__ import division
import os
import tempfile
from .davgis import (Spatial_Reference, Buffer, Feature_to_Raster, Res... | wateraccounting/wa | Models/waterpix/wp_gdal/create_input_nc.py | Python | apache-2.0 | 12,191 | [
"NetCDF"
] | 2e8e62c4b8e1746092508b852846f44362fc0b6f825687cac305d9b4a511cef3 |
#!/usr/bin/python2
# tf_train.py
#
# Collection of ML algorithms to fingerprint radio devices using Tensorflow.
# A high level overview of the functionality provided by this code is given in
# the paper entitled "Physical-Layer Fingerprinting of LoRa devices using
# Supervised and Zero-Shot Learning", which was present... | rpp0/lora-phy-fingerprinting | tf_train.py | Python | bsd-3-clause | 73,515 | [
"Gaussian",
"NEURON"
] | a35d1a98e46dfe2615afcd9af475197d49a2fdb7893cc009609f215783193139 |
import numpy as np
from alis import almsgs
from alis import alfunc_base
msgs=almsgs.msgs()
class ThAr(alfunc_base.Base) :
"""
Returns a 1-dimensional gaussian of form:
p[0] = amplitude
p[1] = centroid of the gaussian
p[2] = FWHM
"""
def __init__(self, prgname="", getinst=False, atomic=None,... | rcooke-ast/ALIS | alis/alfunc_thar.py | Python | gpl-3.0 | 5,501 | [
"Gaussian"
] | 612f293ef3c9786fcf1f53cb9d9d0a803bfed9342601e7f53ec21c5ca5e3e966 |
#
# @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 file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/constants/physconst.py | Python | lgpl-3.0 | 3,542 | [
"Psi4"
] | 3e822fa9d868e89b4ff3accc1eed2ff8cbebd93db900c84b48843e8a8e7040b4 |
#!/usr/bin/env python
# Copyright 2016 Daniel Nunes
#
# 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... | GandaG/fomod-designer | src/exceptions.py | Python | apache-2.0 | 4,178 | [
"VisIt"
] | af254bde8e9030b8fc8859de335e5378576c9bad91ff3c8c9836ac3a2bf6bedf |
import cPickle as pickle
from sympy.matrices import Matrix
from sympy import sympify
import sys
from ...utils.misc import extract_model
from ...utils.misc import get_filename_from_caller
from ...modeltools import make_path, get_file_path
from ...latextools import LatexExpr
from .symca_toolbox import SymcaToolBox as SM... | exe0cdc/PyscesToolbox | psctb/analyse/_symca/_symca.py | Python | bsd-3-clause | 14,914 | [
"PySCeS"
] | dc37f7a6bc958199546177f3c63228366ca09dc194d15a82aed7ca81a9523282 |
#!/usr/bin/env python
# encoding: utf-8
#
# @Author: Brian Cherinka, José Sánchez-Gallego, Brett Andrews
# @Date: Oct 25, 2017
# @Filename: base.py
# @License: BSD 3-Clause
# @Copyright: Brian Cherinka, José Sánchez-Gallego, Brett Andrews
from __future__ import absolute_import, division, print_function
from astropy ... | sdss/marvin | python/marvin/utils/datamodel/drp/MPL.py | Python | bsd-3-clause | 6,763 | [
"Brian"
] | fa54529610dd0c06be506a4ee4eed4ad45a336406be0ed0a259cee1e86d7c563 |
#!/usr/bin/env python
#MIT License
#Copyright (c) 2017 Massimiliano Patacchiola
#
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#t... | mpatacchiola/dissecting-reinforcement-learning | src/6/drone-landing/qlearning_drone_landing.py | Python | mit | 9,824 | [
"VisIt"
] | 77aaddf01498cb19c8a1272442471645077493994d4f7e41457e5af2a353d128 |
from sklearn.utils import shuffle
import numpy as np
import cv2
import csv
def get_data_path(data_folders, minimum_speed=10.0, angle_correction=0.25, target_avg_factor = 1.0, num_bins=40):
'''
This function gets the path to the training samples, adjust the angles for left/right images and discard those samples... | camigord/Self-Driving-Car-Nanodegree | P3-Behavioral-Cloning/utils/utils.py | Python | mit | 6,328 | [
"Gaussian"
] | a59067e491f86df029e5672f92cf7c11252eb625bcdf37f9875f19db08e24386 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | liuwenf/moose | python/MooseDocs/commands/build.py | Python | lgpl-2.1 | 9,630 | [
"MOOSE"
] | 689fc33f80d528ca554c5b21ed4ae25eaffdcd9c2b560794e0a787ec01f92e19 |
# opts.py - module to parse command line options and output what parameters will be used for this run
import os
import os.path
import json
import sys
import yaml
from argparse import ArgumentParser
# fs-drift module dependencies
from common import OK, NOTOK, FsDriftException, FileAccessDistr, USEC_PER_SEC
from commo... | bengland2/fsstress | opts.py | Python | apache-2.0 | 22,098 | [
"Gaussian"
] | 481aab4c3513c1f4f430b34b361bf7413b9f90b6235106d286957d138c027108 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | DailyActie/Surrogate-Model | 01-codes/tensorflow-master/tensorflow/python/ops/control_flow_grad.py | Python | mit | 8,308 | [
"VisIt"
] | f62953b8aa171e9cfd82990bf135ed4b7b9eed10bd43dc130a5da503ec17a84c |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import time
import os
import subprocess
from os.path import join, abspath
from zeroinstall.injector import model, qdom
from repo import incoming, build, catalog, cmd
DAY = 60 * 60 * 24
TIME_TO_GRADUATE = 14 * DAY... | 0install/0repo | repo/cmd/update.py | Python | lgpl-2.1 | 3,147 | [
"VisIt"
] | 5fb0773792f068c1c0e4bd77a1d2399840652552e87cf554dbe574f3869dafd1 |
""" This is a test of the chain
ReportsClient -> ReportsGeneratorHandler -> AccountingDB
It supposes that the DB is present, and that the service is running.
Also the service DataStore has to be up and running.
this is pytest!
"""
from __future__ import absolute_import
from __future__ import division
... | ic-hep/DIRAC | tests/Integration/AccountingSystem/Test_ReportsClient.py | Python | gpl-3.0 | 2,505 | [
"DIRAC"
] | 59c7e86c2b235237938e7fb19e9f1409dffc0f82c5fe1801ca545c1a7434d4ba |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
import pickle
import os
from numpy.testing import (assert_equal, assert_array_equal,
assert_almost_equal, assert_array_almost_equal,
... | lhilt/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 148,441 | [
"Gaussian"
] | ba842f6c0967d69947fe9aef48a6b75b60558f90891bffbf051fbbb5f1ac0a39 |
#!/usr/bin/env python
##!/Users/pamram/anaconda/bin/python
#import math
#math.pi
import scipy
import scipy.constants as const
import time
import datetime
import sys
"""
THIS PROGRAM COMPUTE A SCANNING SEQUENCE FOR PF/SAM/SOAR
Philippe Amram
previous update: 2015, March, 19
last update: 2016, Sep... | b1quint/samfp | scripts/FP_sami6.4.py | Python | bsd-3-clause | 26,474 | [
"Galaxy"
] | a922111efd6f599d48d1b756d0c291690d03741c69787c5ecd3c6548553fefa9 |
from optparse import OptionParser
import logging
from collada import *
import vtk
def main():
logging.basicConfig(level=logging.DEBUG)
logging.debug('This is a debug message')
logging.warning('This is a warning message')
logging.error('This is an error message')
logging.critical('This is a critic... | KonstantinosKr/delta | setup/setup.py | Python | mit | 2,550 | [
"VTK"
] | 112bdde586ab147477a2ba3abf91a58628226be807b31876f3c7140b4915ceea |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import neuroseries as nts
import sys
import scipy.ndimage.filters as filters
from sklearn.mixture import Gauss... | gviejo/ThalamusPhysio | python/main_make_autocorr_glm.py | Python | gpl-3.0 | 6,229 | [
"Gaussian"
] | 83abc12d9a41460542e98801240b0ee66c10494b9c2c6acbf3a9737ca1392670 |
# Copyright (C) 2014 Sereina Riniker
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Torsion Fingerprints (Deviation) (TFD)
According to a paper from Schulz-Gasch et a... | strets123/rdkit | rdkit/Chem/TorsionFingerprints.py | Python | bsd-3-clause | 23,314 | [
"RDKit"
] | a28da2190439dec02bbfbf1544534d0931ce024d1154763c54834cac99b59cf3 |
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 23 15:54:36 2014
This file is part of pyNLO.
pyNLO 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 optio... | ycasg/PyNLO | src/validation/Old and Partial Tests/ppln_generate_random_design.py | Python | gpl-3.0 | 2,357 | [
"CRYSTAL"
] | 4d9275c9b8967cf313dafaae5758aa1bc2b9d9c44a285e40fadc9e24eb3f6576 |
# -*- coding: utf-8 -*-
import os
import time
import shutil
import bisect
import tempfile
from math import sqrt
import numpy as np
import netCDF4 as nc4
from pyaxiom.netcdf import EnhancedDataset, EnhancedMFDataset
from pysgrid import load_grid
from pysgrid.read_netcdf import NetCDFDataset as SGrid
from pysgrid.proces... | sci-wms/sci-wms | wms/models/datasets/sgrid.py | Python | gpl-3.0 | 23,182 | [
"NetCDF"
] | b5d6a76550c8d44d0a15aa1761728ca1b1099c9e1e047ff4f71906a3521578d7 |
# Copyright 2016 Autodesk 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/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | tkzeng/molecular-design-toolkit | moldesign/interfaces/openbabel.py | Python | apache-2.0 | 12,337 | [
"Pybel"
] | 8596c5421b7982641790aeb73ae5a3a24d753f789ccd388dff8220a9b701c751 |
# $Id$
#
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors as rdMD, Descriptors
from rdkit.Chem import AllChem
from rdkit import DataStructs
from rdkit import RDConfig
from rdkit.Geometry import rdGeometry as rdG
import unittest
def feq(v1, v2, tol=1.e-4) :
return a... | adalke/rdkit | Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py | Python | bsd-3-clause | 17,455 | [
"RDKit"
] | 5d90b7f06dc18d7dc02d422ff47df436197ad3df4d10d7df59995de8389a37d3 |
#!/usr/bin/env python
import sys
# WE RELY ON THESE BEING SET !!!
# set default verbose level
# verbose = os.environ.get('RADICAL_PILOT_VERBOSE', 'REPORT')
# os.environ['RADICAL_PILOT_VERBOSE'] = verbose
# set default URL to IMP Mongo DB
# path_to_db = os.environ.get(
# 'RADICAL_PILOT_DBURL', "mongodb://ensembl... | jrossyra/adaptivemd | examples/tutorial/test_adaptive.py | Python | lgpl-2.1 | 3,628 | [
"OpenMM"
] | 53016ecc975e6604658bfe2bd6993ae66cedab1b802a63a40ebaa126c458e393 |
"""
Logger class
"""
import fcntl
import os
from collections import OrderedDict as od
def _create_path(system, style='folder'):
"""
Create a path from the system.
Parameters
----------
system : lammps System
The system to create path from
style : {'folder', 'hash'}
Style to use. Folder crea... | pabloalcain/lammps-python | pylammps/Logger.py | Python | gpl-3.0 | 3,430 | [
"LAMMPS"
] | 721ebed5f7ce02c620ed543da4e4dfde003b44bc235ad1231778a973aff9a574 |
# (C) British Crown Copyright 2013 - 2014, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | scollis/iris | lib/iris/tests/unit/fileformats/netcdf/test_Saver.py | Python | gpl-3.0 | 11,072 | [
"NetCDF"
] | 3cabfa0996c8c88d6ab144c543cc5bf9f08b3dab30a4e21b0794b54a259513df |
#!/usr/bin/env python
"""Automatically install required tools and data to run bcbio-nextgen pipelines.
This automates the steps required for installation and setup to make it
easier to get started with bcbio-nextgen. The defaults provide data files
for human variant calling.
Requires: git, wget, bgzip2, Python 3.x, P... | a113n/bcbio-nextgen | scripts/bcbio_nextgen_install.py | Python | mit | 14,511 | [
"BWA",
"Bioconda",
"Bowtie",
"Galaxy"
] | 3420dca6e5c89eb3f18581c4e877644bb55b45116274d77a37399774a5da41f7 |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
repex
=====
Replica-exchange simulation algorithms and specific variants.
D... | jchodera/yank | Yank/repex.py | Python | lgpl-3.0 | 121,075 | [
"MDTraj",
"NetCDF",
"OpenMM"
] | f851482ac12c620059cf86fbd403d13b9ff3ea9495f13f857793c998c33ffa1d |
import os
import sys
import time
import pkg_resources
from django.template import Context, Template
from selenium.webdriver.support.ui import WebDriverWait
from workbench import scenarios
from workbench.test.selenium_test import SeleniumTest
from .resources import ResourceLoader
class SeleniumBaseTest(SeleniumTe... | hosamshahin/xblock-utils-old | xblockutils/base_test.py | Python | agpl-3.0 | 3,410 | [
"VisIt"
] | c959bced51e6b9afb0d11b2b17cb45f07a52102d7f4d74b01bbebfa5197b5040 |
import copy
import datetime
import json
import os
from email.utils import formataddr
from django.conf import settings
from django.core import mail
from django.urls import reverse
from unittest import mock
import pytest
from waffle.testutils import override_switch
from olympia import amo
from olympia.access.models ... | mozilla/addons-server | src/olympia/activity/tests/test_utils.py | Python | bsd-3-clause | 29,093 | [
"VisIt"
] | 257343f945b54ae582ce8ff4fea4c205a09e7d587d5dae2f7dd368c04e5215c8 |
from __future__ import print_function, division
import os, sys, pwd, json
import pkg_resources
from cosmos.api import Cosmos, Dependency, default_get_submit_args
from yaps2.utils import to_json, merge_params, natural_key, ensure_directory
class Config(object):
def __init__(self, job_db,
input_jso... | indraniel/yaps2 | yaps2/pipelines/b38.py | Python | bsd-2-clause | 5,222 | [
"BWA"
] | 1823ba7e195259ff1f47b47db33a57d095e2b237ea4479a879f53536cec9e5d9 |
# -*- coding: utf-8 -*-
# coding: utf-8
from __future__ import print_function, division, unicode_literals, absolute_import
from builtins import open, str
import warnings
from ....pipeline import engine as pe
from ....interfaces import utility as niu
from ....interfaces import fsl as fsl
def create_dmri_preprocessin... | carolFrohlich/nipype | nipype/workflows/dmri/fsl/epi.py | Python | bsd-3-clause | 35,131 | [
"Gaussian"
] | e9d2306d39069411e2b3e998143a58f2d01a342e8289c74f43378602b3ab2cbb |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import sys
from GPy.models.sparse_gp_regression import SparseGPRegression
class SparseGPLVM(SparseGPRegression):
"""
Sparse Gaussian Process Latent Variable Model
:param Y:... | gusmaogabriels/GPy | GPy/models/sparse_gplvm.py | Python | bsd-3-clause | 1,818 | [
"Gaussian"
] | c1f88bea0b6a03c5df2155f55622f91014d858c0129043fe6ba962fe90fbe130 |
# Copyright 2015 Kevin B Jacobs
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | bioinformed/vgraph | vgraph/dbmatch.py | Python | apache-2.0 | 11,556 | [
"pysam"
] | fc10c01547111b8178e1a7696529c27108cecd6ca204ff4ebc907551fc17f491 |
#!/usr/bin/env python
__author__ = 'Benjamin Bolduc'
import sys
import os
import optparse
import math
import csv
import datetime
from collections import OrderedDict
from pprint import pprint
p = optparse.OptionParser(description="""A simple script that creates a graph (*.graphml format) from a BLAST file and
applies ... | chrisLanderson/rumen_virome | scripts/BLAST2Network.py | Python | mit | 27,771 | [
"BLAST"
] | 90b10c6ccb270ce4f11b71643d3169e0be203d3b0770a9199bce4cceafca1b50 |
import shutil
import os
modules = ["trimgalore", "fastqc", "kallisto", "star", "star-fusion", "picard", "picard_IS", "htseq-gene", "htseq-exon", "varscan", "gatk", 'jsplice']
module_names = {"trimgalore":"",
"fastqc":"",
"kallisto":"",
"star":"",
"star-fu... | HudsonAlpha/aRNAPipe | lib/html_lib.py | Python | mit | 33,948 | [
"HTSeq"
] | 9863c2916bfcd15a14b2f7412706a21d6a02d5a0bec962561d6656763061447b |
# Copyright 2004-2012 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modi... | MSEMJEJME/tkot | renpy/screenlang.py | Python | gpl-2.0 | 33,978 | [
"VisIt"
] | d8d3b0ca076e0d4bbe019be9d887b04f45ec523b56d5a8cadd5588a209e3a8cf |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/chombo/package.py | Python | lgpl-2.1 | 5,904 | [
"Brian"
] | fd089c24bc41d7200c15e77e9a8882d517c8edaa75ab7d64d3f305174f65f3d2 |
# coding=utf-8
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | S-YOU/grumpy | compiler/expr_visitor.py | Python | apache-2.0 | 16,850 | [
"VisIt"
] | 59a65b6dbfe1e112c8dbaf10d4c66202803a8ae5b9ccf7f32ae1865cd471975e |
#!/usr/bin/env python
#author: Peter Thorpe September 2016. The James Hutton Insitute,Dundee,UK.
#Title:
#script perform stats on the coverage files already generated"
#imports
import os
import sys
import numpy
from sys import stdin,argv
import sys
import datetime
from optparse import OptionParser
#################... | widdowquinn/THAPBI | ITS_region_genomic_coverage/python_pipeline_draft/supporting_scripts/Summary_stats.py | Python | mit | 5,169 | [
"BLAST"
] | b709e82ce99a4de28bdacb88aa28daebaeddbe8d3a8f9ad143179a3997d32479 |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 5.0
d = 1.0
x = d / 3**0.5
atoms = Atoms([Atom('C', (0.0, 0.0, 0.0)),
Atom('H', (x, x, x)),
Atom('H', (-x, -x, x)),
Atom('H', (x, -x, -x)),
Atom('H', (-x... | robwarm/gpaw-symm | gpaw/test/degeneracy.py | Python | gpl-3.0 | 1,168 | [
"ASE",
"GPAW"
] | 322614c08888d2d40f1fd2f1e33fb6d2da8cbb201e6d62ba5ced07e66c2610d7 |
"""Command-line utility for training"""
import argparse
from model import train
import numpy as np
import pickle
def main():
parser = argparse.ArgumentParser()
parser.add_argument('path', help='Path to the data')
parser.add_argument('--runs', type=int, default=10, help='Number of independent runs of the a... | michael135/count-vector-paper-experiments | train.py | Python | bsd-2-clause | 2,287 | [
"NEURON"
] | e0abd0b94cb913ace939a7a77ac0c6732826b8b09efc4fbd42a1339cac350e71 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/duplicatesongremovalform.py | Python | gpl-2.0 | 17,812 | [
"Brian"
] | 0eb173feba1e1aaa7725cdf51bad34c4dc48ae575990298ba8db6c92f64beaf9 |
import os
import numpy as np
from numpy.linalg import inv
from datetime import datetime
import models.sxrd_new1 as model
from models.utils import UserVars
import batchfile.locate_path as batch_path
import dump_files.locate_path as output_path
import models.domain_creator as domain_creator
import supportive_functions.cr... | jackey-qiu/genx_pc_qiu | scripts/Manual to use RAXS CTR for muscovite polymer system_debug.py | Python | gpl-3.0 | 13,908 | [
"Gaussian"
] | 4ea496856cbb426adb6e90981eeef86c5d7f5dd37e33ed90230c61b3e99999d8 |
# Copyright 2019 Google 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/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | CloudVLab/professional-services | tools/hive-bigquery/hive_to_bigquery/resource_validator.py | Python | apache-2.0 | 6,856 | [
"VisIt"
] | 1fe35446e85d7d63aa8f3feb115b75ace83325152e07aa82a2c8cc24d2177847 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-allelicimbalance/package.py | Python | lgpl-2.1 | 2,759 | [
"Bioconductor"
] | 7b50ef05b7b8581c151fe39421aec998cbebf3e75dff62268401a3d2bdf2e4fe |
#!/usr/bin/env python
# This code is a direct translation of the Tcl code in
# ImagePlaneWidget.tcl. It could easily be written using a nice class
# to do the job but the present code should definitely make for an
# illustrative example.
# This example demonstrates how to use the vtkImagePlaneWidget
# to probe a 3D ... | ashray/VTK-EVM | Examples/GUI/Python/ImagePlaneWidget.py | Python | bsd-3-clause | 10,228 | [
"VTK"
] | e8b7771e2f83f98668493854261c008052350c53cdd29c9974d951ab9eeeb0dc |
## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py
## class ChainSeperator:
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it unde... | ostrokach/biskit | Biskit/ChainSeparator.py | Python | gpl-3.0 | 19,938 | [
"BLAST"
] | ada8b4708462069ea433cf94840512c48d2e7ae65430b8304f2d50789cd384e9 |
###import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
total_proc=2
#Render={}
#Disp={}
#get active source.
#ActiveReader= GetActiveSource()
# get active view
#renderView1 = GetActiveViewOrCreate('Rende... | zhixuanc/Volcano_Plume_SPH | bin/post_show_Vz.py | Python | gpl-3.0 | 1,106 | [
"ParaView"
] | 6d44b2f13988e4b70ed14c550787bc4d5535f4ff83b4d7db5ed62eb67df8979b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package provides the packages and modules to perform IO from various
input file formats and pymatgen objects.
"""
| sonium0/pymatgen | pymatgen/io/__init__.py | Python | mit | 233 | [
"pymatgen"
] | b4e9057404e4852f60b9f9e3e6de19e084226959db1612eba5313f8803b970ba |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=1>
# Save Tower CSV data as NetCDF
# <markdowncell>
# ### Set local variables
# <codecell>
url='http://geoport.whoi.edu/thredds/fileServer/usgs/data2/notebook/data/CR3000_SN3557_Table1_MainTowerCR3000_ground_V6.CR3.txt'
input_data="data.txt"
... | rsignell-usgs/notebook | People/Julia/tower_to_netcdf.py | Python | mit | 2,275 | [
"NetCDF"
] | 523491774c3e0e673df9c190ef1870233dd0986c8d25932740c9833c5bfaf2cc |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_region_health_check_services.py | Python | apache-2.0 | 97,275 | [
"Octopus"
] | bd0f998c65e84d1b9a52d1b05f4b2e7e5d8c4535ce2b13fd98605f7566080157 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | davidzchen/tensorflow | tensorflow/python/ops/nn_ops.py | Python | apache-2.0 | 236,626 | [
"Gaussian"
] | 68930cfc5c92b62bceab08631712d9fe425cb5681722e832e31090cf41b6263d |
# -*- coding: utf-8 -*-
"""
equip.analysis.flow
~~~~~~~~~~~~~~~~~~~
Extract the control flow graphs from the bytecode.
:copyright: (c) 2014 by Romain Gaucher (@rgaucher)
:license: Apache 2, see LICENSE for more details.
"""
import opcode
from operator import itemgetter, attrgetter
from itertools import tee,... | sukwon0709/equip | equip/analysis/flow.py | Python | apache-2.0 | 13,747 | [
"VisIt"
] | 9beb44e0a67dfb9a54fa5c1bea9e83cd8ccc4938fbdfb815d2514a06c4a565f1 |
import multiprocessing
bind = "127.0.0.1:8000"
workers = multiprocessing.cpu_count() * 2 + 1
worker_connections = 3000
keepalive = 1
daemon = True
loglevel = 'info'
pidfile = '/var/run/moe.pid'
errorlog = '/var/log/gunicorn.error.log'
accesslog = '/var/log/gunicorn.access.log'
| bung87/moto-moe | conf/gunicorn_conf.py | Python | mit | 279 | [
"MOE"
] | 3a551317b87f05ff156db82494a8532dd3fec37054c0ad6c449c5dbdb46a8586 |
from setuptools import setup, find_packages
from os import path
# io.open is needed for projects that support Python 2.7
# It ensures open() defaults to text mode with universal newlines,
# and accepts an argument to specify the text encoding
# Python 3 only projects can skip this import
from io import open
here = pat... | ekzhu/SetSimilaritySearch | setup.py | Python | apache-2.0 | 8,192 | [
"VisIt"
] | 81c419cfb7926a99fa5efb82faa9ce5bdad2a8cfe9f62fea21af7d51347eba99 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/sequence/tests/test_nucleotide_sequences.py | Python | bsd-3-clause | 21,247 | [
"scikit-bio"
] | 750fb6580903ec9b8792c8420948e6f6cefa003d3ed2cf4da674a239972c25c5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements the pickler objects used in abinitio.
"""
from __future__ import unicode_literals, division, print_function
import pickle
from pymatgen.core.periodic_table import Element
class Pmg... | aykol/pymatgen | pymatgen/serializers/pickle_coders.py | Python | mit | 2,874 | [
"pymatgen"
] | cbb483b6b3c3e8e1458af4922341a3e07f141767bd86f73ff14c11e2ce45d1a1 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides a class used to describe the elastic tensor,
including methods used to fit the elastic tensor from linear response
stress-strain data
"""
import itertools
import warnings
from collections import Orde... | vorwerkc/pymatgen | pymatgen/analysis/elasticity/elastic.py | Python | mit | 40,737 | [
"VASP",
"pymatgen"
] | 890e97b64c452c6a7f6ee79bd6533b2f8769b071b739b8a443a3913ccf54b025 |
# 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 | keypose/utils.py | Python | apache-2.0 | 36,285 | [
"Gaussian"
] | d1906c16e041b12462d8d15ace96fbfbfa4b0197d116ed104434a3e6c192bba9 |
# #
# Copyright 2009-2019 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (... | gppezzi/easybuild-framework | easybuild/tools/filetools.py | Python | gpl-2.0 | 74,118 | [
"NetCDF"
] | d288bb3cdc25a21d24499c6d7a272104a05b2fe5f40709031aba0d66f0a785b2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing VASP input files. All major VASP input
files.
"""
import os
import re
import itertools
import warnings
import logging
import math
import json
import glob
import sub... | fraricci/pymatgen | pymatgen/io/vasp/inputs.py | Python | mit | 80,938 | [
"VASP",
"pymatgen"
] | 79393a95102f1057f0e58e62e7514eadc9edcc141ecd996a786041787b93e50b |
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