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"""
Generator that augments data in realtime
"""
import numpy as np
import skimage
import multiprocessing as mp
import time
import load_data
NUM_PROCESSES = 6
CHUNK_SIZE = 25000
IMAGE_WIDTH = 424
IMAGE_HEIGHT = 424
IMAGE_NUM_CHANNELS = 3
y_train = np.load("data/solutions_train.npy")
# split training data into ... | chrissly31415/amimanera | convnet_utils/realtime_augmentation.py | Python | lgpl-3.0 | 31,705 | [
"Gaussian"
] | ec6e90a0f95fac7c7295ea86e80332a82ace77ee0b6e0dc24f074bd01885ba97 |
#!usr/bin/env python
import scipy as np
from scipy import sparse
from scipy.sparse import csgraph
from scipy import stats
import sys
from time import time
import os
import gc
from struct import pack, unpack
from math import sqrt
import mimetypes
import gzip
import bz2 as bzip2
import bz2
#import numpy as np
from scipy... | Rinoahu/fastclust | bin/deprecate/mcl_sparse.py | Python | gpl-3.0 | 280,461 | [
"VisIt"
] | 99dbe6e2604a883c1c773e96e0902596ccc7868ee7de18465009cfec8219b097 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import json
from monty.json import MontyEncoder, MontyDecoder
from pymatgen.core.composition import Composition
from monty.json import MSONable
"""
This module implem... | Bismarrck/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 7,442 | [
"VASP",
"pymatgen"
] | cfb001e1056d2ff1706cfc7f2b609322e01d8faf9045187beee9457cfd762a8f |
# (c) 2016, Adrian Likins <alikins@redhat.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 License, or
# (at your option) any later vers... | Jorge-Rodriguez/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 21,794 | [
"Galaxy"
] | 76e49f501e6444c6fb0ed2d1c1f768bb6571c0e9c184195a80cc509acd733b6f |
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
# Name: zdde.py
# Purpose: Python based DDE link with ZEMAX server, similar to Matlab based
# MZDDE toolbox.
# Licence: MIT License
# This file is subject to the terms and co... | indranilsinharoy/PyZDDE | pyzdde/zdde.py | Python | mit | 493,037 | [
"Gaussian"
] | 141e88f10a40f7b693ec52b4ce9f41c181670d97a574433543c4bde9b6142493 |
#!/usr/bin/env python
"""
Copyright (C) 2007-2009 Vladimir Toncar
Contributors:
Redirect handling by Pavel "ShadoW" Dvorak
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 Fo... | lorensen/VTKExamples | src/Admin/sitemap_gen.py | Python | apache-2.0 | 11,018 | [
"VisIt"
] | 62a969f01fb77808df1a970b5dd598b8689d126d8f9b3c0c051d208291ebc742 |
# -*- 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.
"""Test the Electrons method in cclib"""
from __future__ import print_function
import sys
import os
import re
import log... | Schamnad/cclib | test/method/testelectrons.py | Python | bsd-3-clause | 1,475 | [
"Gaussian",
"cclib"
] | 6d4dfaa87e69b0d0fc1bb868fe27db56f79584cc3003906c7031e5c299048f93 |
# Copyright 2017 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... | allenlavoie/tensorflow | tensorflow/contrib/seq2seq/python/ops/attention_wrapper.py | Python | apache-2.0 | 59,873 | [
"DIRAC"
] | fb914f8d68610af3ffd3d5823b8f11c18d290da435de73681398159faf6845d8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#This program is distributed... | astyonax/mustached-bib | bibtexparser/tests/test_latexenc.py | Python | gpl-3.0 | 2,361 | [
"ASE"
] | e3c98820d2f76b3c287467cc3c2bddd76d27e152e6ca7092750bc7bcb2ebd575 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/tests/test_hdf5.py | Python | lgpl-2.1 | 10,397 | [
"MDTraj",
"OpenMM"
] | df95df704cb407175a3ce3f69a15f966196b92632623c4baf2942397a3276c86 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""This module defines a ``KPoint`` class and the derived ``GlobalKPoint``."""
import numpy as np
from gpaw.fd_operators import Gradient
from gpaw.utilities.blas import axpy
from gpaw import extra_parameters
class KPoint... | robwarm/gpaw-symm | gpaw/kpoint.py | Python | gpl-3.0 | 5,081 | [
"GPAW"
] | 29139ec5b18b50a236be4185e6c941952bb3e8bfa02d3fc98c5e9aa784acb2b0 |
# -*- coding: utf-8 -*-
# Spearmint
#
# Academic and Non-Commercial Research Use Software License and Terms
# of Use
#
# Spearmint is a software package to perform Bayesian optimization
# according to specific algorithms (the “Software”). The Software is
# designed to automatically run experiments (thus the code name
... | DavidMcDonald1993/ghsom | spearmint/spearmint/models/gp_classifier.py | Python | gpl-2.0 | 21,779 | [
"Gaussian"
] | d6b7b0690b686421d29e6d2e0722034a4248d6e379d7ea7ab3e378858e5e2c0f |
from __future__ import division
from spn.linked.layers import Layer
from spn.linked.layers import SumLayer
from spn.linked.layers import ProductLayer
from spn import AbstractSpn
from spn import LOG_ZERO
from collections import deque
import math
# from math import exp
try:
from time import perf_counter
except:... | leonardhussenot/spn | spn/linked/spn.py | Python | gpl-3.0 | 39,766 | [
"VisIt"
] | 43e14dfec2abf05ac64739e61fa61ec671bb61732d488ef1a8d73a68da7d7b2b |
from databroker.assets.sqlite import Registry
from databroker.headersource.sqlite import MDS
from databroker import Broker
import bluesky as bs
import bluesky.plans as bp
from pathlib import Path
import os
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.widgets i... | NSLS-II-XPD/ipython_ophyd | profile_collection_germ/startup/97-germ.py | Python | bsd-2-clause | 11,050 | [
"Gaussian"
] | ed1e22f757d7ddd0d2b4eb1102136439c44a636ee90a32a907b28cbbdb336311 |
import py
import pytest
import tox
import os
import sys
from py.builtin import _isbytes, _istext, print_
from fnmatch import fnmatch
import time
from .config import parseconfig
from .venv import VirtualEnv
from .session import Action
from .result import ResultLog
def pytest_configure():
if 'TOXENV' in os.environ:... | cvegaj/ElectriCERT | venv3/lib/python3.6/site-packages/tox/_pytestplugin.py | Python | gpl-3.0 | 10,792 | [
"VisIt"
] | 913d57e78cb0af1b75c2f936ab1b2862453fb5d7fdf6504efbbe00bf4b264e27 |
"""
Learning kernel density estimation (KDE) for crime data
"""
import pandas as pd
import numpy as np
import overpass
import geopandas as gpd
import matplotlib.pyplot as plt
from ast import literal_eval as make_tuple
import psycopg2
import ipdb
import sys
import cost_models
from sklearn.neighbors.kde import KernelDen... | NahsiN/SafeWalk | kde_estimates.py | Python | mit | 3,173 | [
"Gaussian"
] | b18cae7fd7a75c59942efa24bfb21a4cd6c83cfbc33fdb7802786371b0ab1b2f |
import logging, os, re
from yaml import load, Loader
from abc import ABCMeta, abstractmethod, abstractproperty
# ----------------------------------------------------------------------
'''
Configuration for python logging
'''
class SingleLevelFilter(logging.Filter):
def __init__(self, passlevel, reject):
... | mirskytech/ansible-role-manager | arm/__init__.py | Python | apache-2.0 | 5,048 | [
"Galaxy"
] | 9c8d3c8a836cb12c1998c217a2e8dd0977db11d423946345f7fdde872461f85c |
#Code to find the best fit bayesian solution to the standard
#SSP fitting method, assuming a Calzetti dust model
###################################################################
#Import modules
import numpy as np
from scipy.io import readsav
from numpy import random
import emcee
import sys
import cPickle
from astro... | elizabethswann/RR_fitter | codes/bayesian_full_spectral_reconstruction.py | Python | mit | 8,301 | [
"Galaxy"
] | a615a9dbf44725ed6396d08890765e56a112789986ad631bd689c59a5e5a23c0 |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# 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 res... | f0rki/cb-multios | original-challenges/GreatView/poller/for-testing/machine.py | Python | mit | 5,678 | [
"Brian"
] | 1eb66d05a74df2d54ebb8f5c77978cd973a3a6e065fe34c66c63e51389ebcaa0 |
#
# QAPI command marshaller generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See ... | cherry-wb/qemu-dbaf | scripts/qapi-commands.py | Python | gpl-2.0 | 12,450 | [
"VisIt"
] | 9b0c1c809805f0a966371441888b047f1181bfeb741a66b6b7181b97714dce2e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# 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
ANSIBLE_METADATA = {'metadata_version': '1... | direvus/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 20,034 | [
"Brian"
] | dffaff4c9a6966c78e40d7e63c13744a5f090877c27db84e67ce7d2b981999d6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import itertools
from astroid import builder, InferenceError, NotFoundError
from astroid.nodes import (Module, Function, Class, CallFunc, Assign,
AssName, Name, Arguments, AssAttr)
from astroid.node_classes import Getattr
from as... | mickeynp/sona | sona/indexer.py | Python | gpl-3.0 | 6,966 | [
"VisIt"
] | 601a11239ffb36a3ab1edf7c73a1f35f9c033c184e0456e6393223a54ac38ef3 |
#!/usr/bin/env python
'''
Libraries for PDtrending algorithm. The major part of the libraries
consist of clustering routine.
'''
import sys
import math
from numpy import *
import rpy
from rpy import r
from misclib import *
sys.path.append('./')
def Pycluster_to_hcluster(tree):
'''
Transform tree structure of Py... | dwkim78/pdtrend | pdtrend/datasets/originals/clusterlib.py | Python | mit | 14,518 | [
"Gaussian"
] | 478fa4d3016294b2b3f56e97a0482fd941aaecef0c72d9d97e1c6af502eea9e6 |
"""\
This file contains functions used to deal with objects.
"""
from tp.netlib.objects import Structures
from tp.netlib.objects import parameters
from tp.netlib import objects
from tp.netlib import GenericRS
def getPositionList(obj):
"""
Get a list of the position references of a DynamicObject as tu... | thousandparsec/daneel-ai | extra/objectutils.py | Python | gpl-2.0 | 7,047 | [
"Galaxy"
] | 1936fca9abb00d2366391144928de0fffa7e7846d5cf7265c7d8a8ddf5010d4c |
from .utilsTest import (cp2k_available, remove_files)
from nac.common import is_data_in_hdf5
from nac.workflows.input_validation import process_input
from nac.workflows.workflow_single_points import workflow_single_points
from os.path import join
import pkg_resources as pkg
import pytest
import os
import sys
# Envir... | felipeZ/nonAdiabaticCoupling | test/test_worflow_single_points.py | Python | mit | 1,441 | [
"CP2K"
] | 356507d71299cdeff2bf272800217cedc3a2c228f309d2f9b297c68da276afdf |
#
# Copyright 2001 - 2011 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | Lukc/ospace-lukc | server/lib/ige/ospace/IAIPiratePlayer.py | Python | gpl-2.0 | 9,888 | [
"Galaxy"
] | 468579ba4222a93c85123bed6d48deba03c1424317b05172736bfa8058991936 |
""" File catalog class. This is a simple dispatcher for the file catalog plug-ins.
It ensures that all operations are performed on the desired catalogs.
"""
import types, re
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.... | rajanandakumar/DIRAC | Resources/Catalog/FileCatalog.py | Python | gpl-3.0 | 11,021 | [
"DIRAC"
] | b5300effd0a9bcf99912acfe3da8a14fa72ab7b15ffec46a02b178278023959f |
import importlib
from typing import List, Type # noqa
from pandas.util._decorators import Appender
from pandas.core.dtypes.common import is_integer, is_list_like
from pandas.core.dtypes.generic import ABCDataFrame, ABCSeries
import pandas
from pandas.core.base import PandasObject
from pandas.core.generic import _sh... | cbertinato/pandas | pandas/plotting/_core.py | Python | bsd-3-clause | 61,981 | [
"Gaussian"
] | 0ce9d25f367add2b3f3260e61058a7692089ac7a143af0a509103ae290c5fe86 |
import simtk.unit as units
from intermol.decorators import accepts_compatible_units
from intermol.forces.abstract_bond_type import AbstractBondType
class NonlinearBondType(AbstractBondType):
__slots__ = ['epsilon', 'r0', 'lamda', 'order', 'c']
@accepts_compatible_units(None, None,
... | ctk3b/InterMol | intermol/forces/nonlinear_bond_type.py | Python | mit | 1,553 | [
"LAMMPS"
] | 19040322feb22b2f69c1e0336a32463b5f07050982dcdff9f49fa4291fdef6cc |
import numpy as np
class MultiArmedBandit(object):
"""
A multi-armed bandit aka たぬき
"""
def __init__(self, k_arms):
self.k_arms = k_arms
self.actions_values = np.zeros(k_arms)
self.optimal = 0
def reset(self):
self.actions = np.zeros(self.k_arms)
self.optim... | yngtodd/tanuki | tanuki/bandit.py | Python | mit | 1,052 | [
"Gaussian"
] | f249cca62f5dcc1e9c3fe795b854d1ac73b81ff137aa1cf19e1550fac2739e6a |
# ihm format writer
# A simple support for generating genome structure models in mmCIF firmat
from __future__ import division, print_function
KEY = 'KEY'
TEXT = 'TEXT'
import struct
import json
import os
datafile = os.path.join(os.path.dirname( os.path.abspath(__file__) ),
"config/ihm_template.j... | alberlab/alabtools | alabtools/ihm.py | Python | gpl-3.0 | 6,757 | [
"CHARMM",
"NAMD"
] | b721eb807af198832c2d709f8827a7317e07e3a3b93b81d7ad2c2cf5fc5368d9 |
########################################################################
# This example demonstrates a relaxation oscillator emerging from
# cross-compartment traffic. See US Bhalla, Biophysical Journal 2011
# for the theory.
# Key learning points here:
# * Use of chemDistrib for multi-compartment reaction sy... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex6_chem_osc_different_vols.py | Python | gpl-2.0 | 1,632 | [
"MOOSE"
] | 2868e0450ce69a5c02540cec7b95eaa39f39cc408b682a93886829fd1d623557 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from preggy import expect
from octopus import Octopus
from octopus.limiter.redis.per_domain import Limiter as PerDomainRedisLimiter
from octopus.limiter.in_memory.per_domain import Limiter as PerDomainInMemoryLimiter
from tests import TestCase
class TestThreadedOctopusA... | heynemann/octopus | tests/test_octopus_limited.py | Python | mit | 2,369 | [
"Octopus"
] | f5327feef46e6126fdd6e5e353b7fb9a32543713b74c86b1f78927954eec4501 |
# Copyright 2017 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... | codrut3/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_full_covariance.py | Python | apache-2.0 | 7,499 | [
"Gaussian"
] | d1629d6585f4117f3fb5d697c28106a2c9216165a1574ff4b205c4cf2d8913d5 |
# Copyright 2019 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 applicabl... | tensorflow/tensorboard | tensorboard/notebook.py | Python | apache-2.0 | 14,704 | [
"VisIt"
] | d7a9d80c24663b5af94579ed89ea34964c84171597879fc26e097b17e97c475a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
It produces a report with the summary of the fusion genes found. Also
FASTQ and FASTA files containing the supporting reads corresponding to each
fusion gene is generated.
Author: Daniel Nicorici, Daniel.Nicorici@gmail.com
Copyright (c) 2009-2021 Daniel Nicorici
Th... | ndaniel/fusioncatcher | bin/build_report_fusions_map.py | Python | gpl-3.0 | 39,176 | [
"ASE",
"BLAST",
"Bowtie"
] | 3ebd2326e52e33ca0c48df49acf409d79f453291cbb9ef1413a2c05685c28ad1 |
"""
gts v0.01
genetic test sequencer
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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
... | Pascal66/ga-bitbot | gts.py | Python | gpl-3.0 | 20,392 | [
"Brian"
] | 7f8596796badac9b7c928b14202f4897107a5450c611f051397de71f8e8ce06a |
from coyote_framework.testing.coyote_test import CoyoteTest
from example.example_app.config.example_config import ExampleConfig
from coyote_framework.drivers.coyote_driverfactory import driver_context
from example.example_app.page_objects.example_follow_page import ExampleFollowPage
from example.example_app.page_object... | Shapeways/coyote_framework | example/example_tests/TestFollowLink_YouFollowedItGood.py | Python | mit | 1,568 | [
"VisIt"
] | 52db6125a5c9a8a0216e199b114e0d7008a77d9ded8cd614315c248239686e63 |
"""
==========================================================
Compute point-spread functions (PSFs) for MNE/dSPM/sLORETA
==========================================================
PSFs are computed for four labels in the MNE sample data set
for linear inverse operators (MNE, dSPM, sLORETA).
PSFs describe the spread o... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/examples/inverse/plot_mne_point_spread_function.py | Python | bsd-3-clause | 3,204 | [
"Mayavi"
] | ba7b2809c2713c80a99ca9267f3d50f8ed4ea4ad5b6b663a05791727dc8186ee |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2016 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | crisely09/horton | horton/meanfield/builtin.py | Python | gpl-3.0 | 5,729 | [
"DIRAC"
] | 4a2db71ce3083299a10c35eb5d14259231c35c3ae2ffcc3370e16a59217a9d55 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=1) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=1) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list of fil... | 2ndy/RaspIM | usr/lib/python2.6/mimetypes.py | Python | gpl-2.0 | 18,822 | [
"NetCDF"
] | 4e95dfbe95baca411a0c6c5b7cd807abf5a49cca0d830ea255dfaac71b43496d |
#!python
#############################################################################
# cubit2specfem3d.py #
# this file is part of GEOCUBIT #
# #... | geodynamics/specfem3d | CUBIT_GEOCUBIT/geocubitlib/cubit2specfem3d.py | Python | gpl-3.0 | 67,397 | [
"NetCDF"
] | d5e80178ed06ac3dbe3a5bf42c70c19846d4bbffd580a6d0ad731052c8a9459c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function)
import argparse
import pysam
import sys
usage = '''
Filter classes of small RNAs from library.
Classes are defined by read sequence length
'''
def getArgs():
"""Pars... | imbforge/NGSpipe2go | tools/smallRNA/filterSmallRNAclasses.py | Python | gpl-3.0 | 3,764 | [
"pysam"
] | 6fdc07c2347ad525dbf04fbc97c392c3fd3dda0116d9bd84689831bcf30827e5 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/jobfolder/ordered_dict.py | Python | gpl-3.0 | 4,581 | [
"CRYSTAL",
"VASP"
] | 8109240a6cf1c1736f70baa629ba2e6044624d0c41d4cd08c150a13f1bbcccc9 |
import ast
import sys
import traceback
from ..java import opcodes as JavaOpcodes
from .modules import Module
from .methods import MainFunction, InitMethod, to_java
from .structures import (
IF, ELSE, END_IF,
TRY, CATCH, FINALLY, END_TRY,
START_LOOP, END_LOOP,
ArgType,
jump, OpcodePosition,
AddT... | cflee/voc | voc/python/ast.py | Python | bsd-3-clause | 76,466 | [
"VisIt"
] | f46224bab0d7a7c75aea0dff3fe3bcc8cde7650050fb5bd32702fd5f2e410922 |
import numpy as np
import matplotlib.pyplot as plt
import scipy.constants as const
from pint import UnitRegistry
from scipy.optimize import curve_fit
import scipy.integrate as integrate
from uncertainties import ufloat
import uncertainties.unumpy as unp
import data
u = UnitRegistry()
Q_ = u.Quantity
##################... | smjhnits/Praktikum_TU_D_16-17 | Fortgeschrittenenpraktikum/Protokolle/V47_Molwärme/Python/auswertung.py | Python | mit | 7,654 | [
"Dalton"
] | 86c5ac4ba23bd99c320cdfd6c3f5afe5d5ef692f863fd8eadf329e1910f7e79e |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subresultants,
resu... | Davidjohnwilson/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 106,519 | [
"Gaussian"
] | 3cd781c077cc1749dd3e8a63e7add2e7987c5a84894464c3d558c5e05510f540 |
from datetime import date
from ..core import WesternCalendar, MON, TUE, WED, THU, FRI, SAT
from ..astronomy import solar_term
from ..registry_tools import iso_register
# https://www.feriados.cl
# http://www.feriadoschilenos.cl
@iso_register('CL')
class Chile(WesternCalendar):
"Chile"
FIXED_HOLIDAYS = Wester... | novafloss/workalendar | workalendar/america/chile.py | Python | mit | 3,736 | [
"COLUMBUS"
] | c813d099b7de3ec09e2c3ce04cd52300bb1fc425cdec4f01956f508091db077a |
from flow_workflow import future_operation
from flow_workflow import factory
from flow.petri_net import color
from flow.petri_net.net import Net
from flow_workflow.parallel_by import actions
from flow_workflow.parallel_id import ParallelIdentifier
from test_helpers import fakeredistest
import mock
import unittest
cl... | genome/flow-workflow | unit_tests/parallel_by/test_actions.py | Python | agpl-3.0 | 11,597 | [
"exciting"
] | 6281b26fe77cbc6e34c854ea107729ff0203a3b0dab6e0f7f5c21192e1ed3b95 |
import numpy as np
from scipy.special import expit as sigmoid
from simplenet.core import BackpropLayer
def sigmoid_derivative(x):
return sigmoid(x) * (1-sigmoid(x))
class SigmoidLayer(BackpropLayer):
def __init__(self, num_inputs, num_neurons, apply_bias=True):
super(SigmoidLayer, self).__init__(num_i... | rileymcdowell/simplennet | simplenet/layers/sigmoid_layer.py | Python | mit | 1,351 | [
"NEURON"
] | 80eeb0a99dac562477848d3e5ec0424ad975a62c133a38ea10f4d79741c8f001 |
# Author: Alexis Mignon <alexis.mignon@probayes.com>
from .cygmm import cy_gmm
import numpy as np
def gmm(x, n_clusters=10, max_num_iterations=100, covariance_bound=None,
init_mode='rand', init_priors=None, init_means=None, init_covars=None,
n_repetitions=1, verbose=False):
"""Fit a Gaussian mixtu... | menpo/cyvlfeat | cyvlfeat/gmm/gmm.py | Python | bsd-2-clause | 5,190 | [
"Gaussian"
] | 0b5c22a501c1a53f82b6bfb0cf6c66f3422490e113ed814fc80e97b770bbc1b9 |
""" Python test discovery, setup and run of test functions. """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import collections
import fnmatch
import inspect
import os
import sys
import warnings
from functools import partial
from textwrap import dedent
i... | hackebrot/pytest | src/_pytest/python.py | Python | mit | 54,016 | [
"VisIt"
] | 160f340d571e5aff23eec1ae0a2b3e701694deb0d56226f1f86056e97ab5c688 |
"""Execute notebooks as tests, reporting an error if cell throws an exception.
Adapted from MDTraj https://github.com/mdtraj/mdtraj/pull/1130 which adapted
from https://gist.github.com/minrk/2620876.
"""
import glob
import os
from jupyter_client import KernelManager
import nbformat
import pytest
EXAMPLE_NOTEBOOKS ... | sallai/mbuild | mbuild/examples/test_examples.py | Python | mit | 1,445 | [
"MDTraj"
] | 79bec6de0bf6c91ab340aeb7288d40120222d99214e24bf52bfc42340ebb8741 |
# -*- coding: utf-8 -*-
# python-holidays
# ---------------
# A fast, efficient Python library for generating country, province and state
# specific sets of holidays on the fly. It aims to make determining whether a
# specific date is a holiday as fast and flexible as possible.
#
# Authors: dr-prodigy <maurizio.... | dr-prodigy/python-holidays | holidays/countries/chile.py | Python | mit | 6,728 | [
"COLUMBUS"
] | 4d1176095269867ef4f72b0b08ed837683749eb18d02573853f4d8e65f6240aa |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | tutorials/darcy_thermo_mech/step07_adaptivity/problems/step7abc.py | Python | lgpl-2.1 | 3,210 | [
"MOOSE",
"VTK"
] | 0b8c5a873a579dbf2671cf9f71b6ece4f3350624c299072e3dfc94122e2c66e5 |
import numpy as np
from ..core import indexing
from ..core.pycompat import integer_types
from ..core.utils import Frozen, FrozenDict, is_dict_like
from ..core.variable import Variable
from .common import AbstractDataStore, BackendArray, robust_getitem
class PydapArrayWrapper(BackendArray):
def __init__(self, arr... | shoyer/xarray | xarray/backends/pydap_.py | Python | apache-2.0 | 2,938 | [
"NetCDF"
] | d1218e7eaac227bcbbc6a70a4641f637b701dc5a29c87e975664ffea085a9281 |
from property import *
# Neuron common parameters
iaf_neuronparams = {'E_L': -70.,
'V_th': -50.,
'V_reset': -67.,
'C_m': 2.,
't_ref': 2.,
'V_m': -60.,
'tau_syn_ex': 1.,
'tau_syn_i... | research-team/robot-dream | direct_translation/scripts/step_1 (columns)/parameters.py | Python | mit | 1,871 | [
"NEURON"
] | 602bd8a3553875782d766be99cb38873aaf2c4e1125ecfb7526aa1a2861b2ee7 |
#
# Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
# 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 code must retain the above copyri... | ptosco/rdkit | Contrib/RxnRoleAssignment/identifyReactants.py | Python | bsd-3-clause | 20,607 | [
"RDKit"
] | 8cb3966a246228edf52523daec66e8209c0c6e9f7df68ec3bdd65f1ceedc421c |
import os
from setuptools import setup
import sys
os.chdir(os.path.abspath(os.path.dirname(__file__)))
packages = []
for rootdir, dirs, files in os.walk('vistrails'):
if '__init__.py' in files:
packages.append(rootdir.replace('\\', '.').replace('/', '.'))
requirements = [
# 'PyQt<5.0',
'numpy'... | VisTrails/VisTrails | setup.py | Python | bsd-3-clause | 2,807 | [
"VTK"
] | e0e1fb25cf5f33c9b112493191d7d6946bcafb4b8be1515d65f391780e5ffe76 |
import numpy as np
import csv
import timeit
import os
import pickle as pkl
import matplotlib as mpl
mpl.use('PS')
import matplotlib.pyplot as plt
import chippr
from chippr import defaults as d
from chippr import utils as u
from chippr import sim_utils as su
from chippr import gauss
from chippr import discrete
from ch... | aimalz/chippr | chippr/catalog.py | Python | mit | 19,513 | [
"Galaxy",
"Gaussian"
] | 964edc4ef44dbb571ec7bcec603d181578cb9de2f38e2e9140edde3ec73f41d4 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/LennardJonesEnergyCapped.py | Python | gpl-3.0 | 9,485 | [
"ESPResSo"
] | 605ea94086f6c846c757fdb246a04818a2a7d921e14adde2666c43d4d7160b7f |
#!/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/lib/tblis_einsum.py | Python | apache-2.0 | 4,698 | [
"PySCF"
] | ab387585987544e32b8da23795674a686a6a5569c7511e65d4f698a336f4b5f2 |
#! /usr/bin/python
from subprocess import call, Popen, PIPE
import re
import sys
import argparse
#xyz2cub - This program takes as input a Turbomole xyz file (with grid
# point coordinates followed by property values) and converts
# it to a cub format file. This xyz file is NOT the
# ... | magee256/TurbomoleScripts | OutputParsing/Production/xyz2cub/xyz2cub.py | Python | mit | 11,059 | [
"TURBOMOLE"
] | 1b0fd1b4a1e51965c2b33fad8ba5cc3fed1d2fbbd42688c9c64045f2a9f729da |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-15 10:06:03 by Brian McFee <brian.mcfee@nyu.edu>
'''Helpful tools for deprecation'''
import warnings
from decorator import decorator
from functools import wraps
import six
__all__ = ['moved', 'deprecated', 'optional_jit']
def moved(moved_from, version... | stefan-balke/librosa | librosa/util/decorators.py | Python | isc | 2,726 | [
"Brian"
] | 1c0ee12941850b838697cd33772ed50fcade2df02fa2c9e6c035eeca7d1e5c78 |
import numpy as np
import dask.array as da
from dask import delayed
from sklearn.base import BaseEstimator
from sklearn import naive_bayes as _naive_bayes
from dask_ml.base import _BigPartialFitMixin, _copy_partial_doc
class GaussianNB(BaseEstimator):
"""
Fit a naive bayes model with a Gaussian likelihood
... | daniel-severo/dask-ml | dask_ml/naive_bayes.py | Python | bsd-3-clause | 4,985 | [
"Gaussian"
] | 632c8f0e28e6c213972ba400a4147af7d39456961b81df6092dc2bb1833c215a |
# READ THE DOCUMENTATION FOR ENUMLIB
#from io import StringIO, BytesIO, FileIO
import argparse
import io
from numpy import array
import os
from random import uniform
import subprocess as sp
import yaml
from multiprocessing import cpu_count, Process, Manager, Queue
from ase import Atoms
from ase.db import connect
from... | msg-byu/enumlib | aux_src/Enumerate.py | Python | mit | 16,743 | [
"ASE",
"CRYSTAL",
"VASP"
] | 3dfd0c5c6fcda1fd090b17dd324fb8a7caebde6d6a0c13bd3305172e8ac0afe7 |
##############################################################################
# Copyright (c) 2013-2017, 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... | wscullin/spack | var/spack/repos/builtin/packages/r-a4core/package.py | Python | lgpl-2.1 | 1,650 | [
"Bioconductor"
] | 4ab9545933a195d19159648d958a4f4e9a6424d74d6b43b3680e53414904b927 |
""" Author: Ning Guo <ceguo@connect.ust.hk>
run `mv retainingSmooth.yade.gz 0.yade.gz`
to generate initial RVE packing
How to run this script:
sudo apt install python-escript
cd examples/FEMxDEM
export PYTHONPATH="/usr/lib/python-escript:../../py/FEMxDEM"
export LD_LIBRARY_PATH=/usr/lib/python-... | yade/trunk | examples/FEMxDEM/retainingSmooth.py | Python | gpl-2.0 | 3,940 | [
"VTK"
] | d1472177c413cb0b1577c15acf177f94773a7bbc4d25193f1c70f5be01ea5fac |
# Copyright 2016 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 unittest
from form_classification_test import FormClassificationTest
"""Unittest class for testing signin forms.
The test methods were generated by ... | axinging/chromium-crosswalk | components/test/data/password_manager/form_classification_tests/signin_forms_test.py | Python | bsd-3-clause | 24,192 | [
"ADF"
] | 3c0e7b4d59dd027951bbd71110aa6af5a1081c00991a59fb860597d4da229e57 |
"""
Tools for the instructor dashboard
"""
import dateutil
import json
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from django.utils.timezone import utc
from django.utils.translation import ugettext as _
from courseware.models import StudentFieldOverride
from courseware.... | louyihua/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 7,771 | [
"VisIt"
] | 6790f605fc5b8e233b5730a7712b273e51c5878ef3c34ad43036f38f9c7c66a0 |
from firefly.qt import QMessageBox
from firefly.version import FIREFLY_VERSION
ABOUT_TEXT = """
<b>Firefly - Nebula broadcast automation system client application</b>
<br><br>
Named after American space Western drama television series which ran from 2002–2003,
created by writer and director Joss Whedon
<br><br>
Firefl... | immstudios/firefly | firefly/dialogs/about.py | Python | gpl-3.0 | 796 | [
"Firefly",
"VisIt"
] | dd25c25b1693b003dbc87ec1aea25b76c5c47c4b90c186a91afa4213de5b5b09 |
##########################################################################
# This file is part of ssm.
#
# ssm 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
# ... | ntncmch/ssm | src/Cmodel.py | Python | gpl-3.0 | 17,172 | [
"DIRAC"
] | 7f07c51958fa484a44c5cde8ace9fa039eec1c3e59b17dce88747577b15c3427 |
# -*- coding: utf-8 -*-
import sys
import textwrap
import pytest
from _pytest import fixtures
from _pytest.fixtures import FixtureLookupError
from _pytest.fixtures import FixtureRequest
from _pytest.pathlib import Path
from _pytest.pytester import get_public_names
from _pytest.warnings import SHOW_PYTEST_WARNINGS_ARG
... | hackebrot/pytest | testing/python/fixture.py | Python | mit | 118,502 | [
"VisIt"
] | 9b041e2b6f661a566e1048d87ed30d77995499c12d875d8a8ad3c93e4dd52e01 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/qcdb/libmintsgshell.py | Python | lgpl-3.0 | 12,927 | [
"GAMESS",
"Psi4"
] | 1268f8b63af3094e84c07b99a0bf53863f9a1ce773a8f4c7035bb5be6c70c8f6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pathlib import Path
import json
import gzip
import numpy as np
import warnings
from shutil import copyfile, copyfileobj
from monty.tempfile import ScratchDir
import xml.etree.c... | montoyjh/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 65,534 | [
"VASP",
"pymatgen"
] | 63b0a20add906d1ac4cde564259d479bbb25ae255dc025a1619416caef127ddb |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/data/gen_coulomb_2d_ref_data.py | Python | gpl-3.0 | 1,710 | [
"ESPResSo"
] | d05d7fe49c15c2bb9e7e5817cce2ca372484e9c4dad879e83447b1f32e85b3d6 |
# -*- coding: utf-8 -*-
# Copyright (c) 2007, 2008, Benoît Chesneau
# Copyright (c) 2007 Simon Willison, original work on django-openid
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | fitoria/askbot-devel | askbot/deps/django_authopenid/views.py | Python | gpl-3.0 | 54,174 | [
"VisIt"
] | 78068216b3801280f42709d10b51ab9254c0b8d894f480a40ff1bb9cfa59cc55 |
""" Chisq based on sine-gaussian tiles """
import numpy
import logging
from pycbc.waveform.utils import apply_fseries_time_shift
from pycbc.filter import sigma
from pycbc.waveform import sinegauss
from pycbc.vetoes.chisq import SingleDetPowerChisq
from pycbc.events import newsnr
class SingleDetSGChisq(SingleDetPower... | tjma12/pycbc | pycbc/vetoes/sgchisq.py | Python | gpl-3.0 | 7,236 | [
"Gaussian"
] | 4a2df6820c33a800082b43de5cbb368cb8aca8b37e7766cc6bb4fbb0dada70fa |
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2018 ssolanki <sushobhitsolanki@gmail.com>
# Copyright (c) 2018 Sushobhit <31987769+sushobhit27@users.noreply.github.com>
# Copyright (c) 2018 Nick Drozd <nicholasdrozd@gmail.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-l... | kczapla/pylint | pylint/reporters/ureports/nodes.py | Python | gpl-2.0 | 5,196 | [
"VisIt"
] | 4498fe1df0c0c8683b4dba6558c38e0eca8cf7aabfa5cd0f7c2c76bf83d9de7a |
"""
Test course discovery.
"""
import datetime
from flaky import flaky
import json
import os
from bok_choy.web_app_test import WebAppTest
from ...pages.common.logout import LogoutPage
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.discovery import CourseDiscoveryPage
from ...fixtures.course impor... | rhndg/openedx | common/test/acceptance/tests/lms/test_lms_course_discovery.py | Python | agpl-3.0 | 2,495 | [
"VisIt"
] | a134dbab53df5cc113d83ec5480a4ec2845918b27bb79eedfcf2a481997d5f97 |
"""
Convenience functions for the construction of spatial weights based on
contiguity and distance criteria.
"""
__author__ = "Sergio J. Rey <srey@asu.edu> "
import pysal
from Contiguity import buildContiguity
from Distance import knnW, Kernel, DistanceBand
from util import get_ids, get_points_array_from_shapefile, m... | badjr/pysal | pysal/weights/user.py | Python | bsd-3-clause | 34,151 | [
"COLUMBUS",
"Gaussian"
] | 435c25ea86af21810bdbaa29e19db2fbcfd7b446f361e92c136e5e8e7c281b51 |
from django.db import models
from utils import enums
import utils.models as utils
class AutomatedMessageQuerySet(utils.BaseQuerySet):
"""
Used to map a single description to an AutomatedMessage.
"""
def from_description(self, description, exact=False):
"""
Return AutomatedMessage for... | tperrier/mwachx | backend/models.py | Python | apache-2.0 | 6,883 | [
"VisIt"
] | e4039700afbab739ba88acb46126dba10da0c7e4a78b8771eb448bbaec5cb761 |
"""
.py v 1.0.0
Auteur: Bruno DELATTRE
Date : //2017
"""
# !/usr/bin/env python
# -*- coding: utf-8 -*-
from lib.driver.oled.demo_opts import device
from lib.driver.oled.virtual import viewport
from lib.driver.oled.render import canvas
from PIL import Image
import os, time
import datetime
dayofweek = ['Lundi', 'Mar... | delattreb/TemperatureHumidityServer | src/viewporttest.py | Python | gpl-3.0 | 2,217 | [
"Galaxy"
] | 69221985ec0aeeff029be354c4080f593fc00aa9c2660c6a1ec525282f24275d |
"""Tools for analyzing a Python codebase as a whole. Analysis happens
before indexing in order to compute data that requires knowledge of the
entire codebase.
"""
import ast
import os
from collections import defaultdict
from warnings import warn
from dxr.build import unicode_contents
from dxr.plugins.python.utils imp... | jbradberry/dxr | dxr/plugins/python/analysis.py | Python | mit | 10,299 | [
"VisIt"
] | 7732193bef928e551941b2ad857b40cb0a05fedcf1886359c6b50d8e46f0a46e |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa core (__init__.py)
#
# Run me as follows:
# cd tests/
# nosetests -v --with-coverage --cover-package=librosa
#
from __future__ import print_function
# Disable cache
import os
try:
os.environ.pop(... | Cortexelus/librosa | tests/test_core.py | Python | isc | 33,211 | [
"Brian"
] | b6aa9063b7d5a8faf0da2777adbbda3802377a92168e9ff4147ea12b72e48295 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/LBInit.py | Python | gpl-3.0 | 3,568 | [
"ESPResSo"
] | bb8d252ec8771231048573c8f68c7921296067fadd13a02a1f9d1f2bb2b04f30 |
"""
=============================================
Integration and ODEs (:mod:`scipy.integrate`)
=============================================
.. currentmodule:: scipy.integrate
Integrating functions, given function object
============================================
.. autosummary::
:toctree: generated/
quad ... | anntzer/scipy | scipy/integrate/__init__.py | Python | bsd-3-clause | 4,057 | [
"Gaussian"
] | 775a5aa234b6439c243bdc2f4431d1bc932ae102facc6a60a79dfb3b18f5b5a5 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Mathematical models."""
from collections import OrderedDict
import numpy as np
from astropy import units as u
from astropy.units import Quantity, UnitsError
from .core import (Fittable1DModel, Fittable2DModel,
ModelDefinitionErro... | bsipocz/astropy | astropy/modeling/functional_models.py | Python | bsd-3-clause | 77,586 | [
"DIRAC",
"Gaussian"
] | fed17cf090c04c8ef6f7ac9ac2e1be2f654db26f3c93217f635790f684a64c66 |
import imp
import json
import logging
import time
from slackclient import SlackClient
from .brain import Brain
from .listener import Listener
from .listener import ListenerType
from .message import Message
from .repl import EspressoConsole
from .user import User
from .plugin_api import PluginAPI
class Espresso(Plug... | ratchetrobotics/espresso | espresso/bot.py | Python | bsd-3-clause | 4,370 | [
"ESPResSo"
] | 9349d527360487ccf6b9b8b7d2ffce3f2c4d2680faa7afdf9aeac8af9ebcf639 |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
# added -fpermissive to CMAKE_CXX_FLAGS to workaround g++ 4.3 compile
# problem on the included CPT code. We were getting "changes meaning
# of" errors as documented in
# http://stupefydeveloper.blogspot.com/2008/11/c-name-... | nagyistoce/devide.johannes | install_packages/ip_vtktud.py | Python | bsd-3-clause | 4,013 | [
"VTK"
] | 8aa6b97028e096af86d53c8ea01e02c3e55eb2f4452b45e9ce4dacb27dccdef1 |
"""Tools for generating E3FP fingerprints.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
from __future__ import division, print_function
import os
import logging
import numpy as np
from rdkit import Chem
import mmh3
from python_utilities.io_tools import touch_dir
from python_utilities.scripting import setup_loggi... | keiserlab/e3fp | e3fp/fingerprint/fprinter.py | Python | lgpl-3.0 | 37,842 | [
"RDKit"
] | 103f13cc6cb058c203bbcad71302bafb8a4c266e54117b9c8b82557702b75a18 |
import re, os, shutil
from arm import Role
from . import Route, RouteException
import requests
from yaml import load, Loader
from arm.util import fetch_git_repository
GALAXY_SERVER_DEFAULT = 'galaxy.ansible.com'
class GalaxyRoute(Route):
owner__name = r'(?P<owner>[a-zA-Z][\w_.-]+)\.(?P<name>[a-zA-Z][\w_.-]+... | mirskytech/ansible-role-manager | arm/routes/galaxy.py | Python | apache-2.0 | 2,618 | [
"Galaxy"
] | 03df6d6f03eb3d19734aff7724f3eb0bb698d5d8d6f1a6144d008c1b871cda43 |
import pysam, sys, os, collections, vcf, datetime
from jobTree.src.bioio import fastaRead, system, fastaWrite, logger
import numpy as np
from margin.utils import *
import math
from cPecan.cPecanEm import Hmm
from itertools import product
try:
import cPickle
except ImportError:
import pickle as cPickle
BAS... | isovic/marginAlign | src/margin/marginCallerLib.py | Python | mit | 11,440 | [
"pysam"
] | 17fc0084719ed780d045ce2d384a9087b88a5b6942bb89f4003efb06848dc35d |
#!/usr/bin/env python
#-----------------------------------------------------------------------------
# update_backscatter.py, Angeline G. Burrell (AGB), UoL
#
# Comments: Update the beam's groundscatter flag, calculate the virtual height
# and propagation path, determine the origin field-of-view, update
# ... | Shirling-VT/davitpy_sam | davitpy/pydarn/proc/fov/update_backscatter.py | Python | gpl-3.0 | 135,866 | [
"Gaussian"
] | 6c04fc82946e8e6fa5999c628f9e265264b49055f565256ff062d7ac32b9e6f8 |
"""
Classes for hydrodynamic inputs (Hydro) and D-WAQ setup
(Scenario) for using Delft Water Quality.
"""
from __future__ import print_function
import os
import re
import textwrap
import glob
import sys
import subprocess
import shutil
import datetime
import numpy as np
import numpy.lib.recfunctions as rfn
from scipy... | rustychris/stompy | stompy/model/delft/waq_scenario.py | Python | mit | 468,952 | [
"ADF",
"NetCDF"
] | 8b05acdafcfafb70c378f485c94dbe73c748268e0c0304e895354f8d81e1fe00 |
# proxy module
from __future__ import absolute_import
from mayavi.filters.image_change_information import *
| enthought/etsproxy | enthought/mayavi/filters/image_change_information.py | Python | bsd-3-clause | 108 | [
"Mayavi"
] | e2685cc19d96665ebae103ae844d43b47c0dd90cb48ac014775763fdbccdf5c0 |
# Predicted Mean Vote Comfort Calculator
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify
# it u... | samuto/ladybug | src/Ladybug_PMV Comfort Calculator.py | Python | gpl-3.0 | 39,930 | [
"EPW"
] | ecdd6a0e2a36f1e3431ed1927059a9cd2b1b548b8e4a9dcf4f3cdce0d72142cc |
# -*- coding: utf-8 -*-
################################
# Interactive filtering test
################################
import pylab as pl
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider
import numpy.ma as ma
import cv2
def update(val):
# Get parameter
vmin = ... | peter-kiechle/tactile-sensors | python/filtering_spatial/denoising_interactive.py | Python | gpl-3.0 | 6,785 | [
"Gaussian"
] | d53e7ae2a3c0c8ed36f0cce8573fab9d1de2b59b6c97aac88281c6a8528bbf6e |
import logging
from hercules import Token, Stream
from treebie import Node
from visitors import Visitor
class Parser(object):
'''Chains lexer, Node, and arbitrary visitors together.
'''
def __init__(self, *classes, **options):
self.classes = classes
self.options = options
def __call_... | twneale/tater | tater/parser.py | Python | bsd-3-clause | 714 | [
"VisIt"
] | 6778b76e3be6c825a2ab68c61cafbb22bcae8f18dfa6f982595b947455f9b28a |
from .. import ast
from string import Template
import sys
import os
def iscallable(obj):
return hasattr(obj, "__call__")
class Environment(dict):
"""A class to facilitate instantiating string templates.
"""
def update(self, *args, **kwargs):
super().update(*args, **kwargs)
return ... | ldionne/nstl-lang | nstl/passes/codegen.py | Python | bsd-3-clause | 17,023 | [
"VisIt"
] | 7c46f93ee39d53aae104f00a847d125390a63fd6267332f70704db739ba61ba7 |
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