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'''Pydons is a collection of manipulation add-ons for hierarchichal numerical data.
'''
__version__ = '0.2.5'
# import OrderedDict for Python < 2.7
# In Python 2.6 or Jython 2.5, ordereddict must be installed
for _collections in ('collections', 'ordereddict'):
try:
_collectionsModule = __import__(_collect... | coobas/pydons | pydons/__init__.py | Python | mit | 24,266 | [
"NetCDF"
] | 2562c415413ffb433189313b7486fd3f633802607144973083ba91272d587e98 |
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each input into a vector of dimension D = ... | pyemma/deeplearning | assignment2/cs231n/layers.py | Python | gpl-3.0 | 27,797 | [
"NEURON"
] | b1446c9fc5421048105a4b6cc6660542847a910d845dd37f83b13baa5c88581a |
#!/usr/bin/env python
#filename: mds.py
import os
import sys
import argparse
import mdtraj as md
import numpy as np
from sklearn.metrics import euclidean_distances
from sklearn.manifold import MDS
from lib.write_plot import write_plots, write_pcs, write_fig
from lib.traj_info import trajectory_info, get_internal_coordi... | RUBi-ZA/MODE-TASK | mds.py | Python | gpl-3.0 | 8,911 | [
"MDTraj"
] | ef20234ace9a1d22ea2c73ebaf97ea2c3996557f2c704fda994b4cd200dd0d35 |
import numpy as np
def parabola(xlim=(-5, 5), scale=1, offset=(0, 0), seed=None):
"""Sample from a parabolic distribution:
y = scale * (x - offset[0]) ** 2 + offset[1]
Parameters
----------
xlim : tuple, len=2
X-limits on which to sample the parabola.
scale : scalar, default=1
... | ejhumphrey/optimus | tests/sources.py | Python | isc | 3,460 | [
"Gaussian"
] | a1cb75c68096cf7fac789dc2f325133b906d6b7690503f6a2e4ba9f707fabd97 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function, \
absolute_import
import string
import random
import numpy as np
"""
function for calculating the convergence of an x, y data set
main api... | matk86/pymatgen | pymatgen/util/convergence.py | Python | mit | 14,863 | [
"pymatgen"
] | e4ba4af3478a1e4371ce9a37857911c7e62cda40703908455a075bcfb293be3a |
# Copyright 2016 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... | kevin-coder/tensorflow-fork | tensorflow/contrib/distributions/python/ops/mvn_diag_plus_low_rank.py | Python | apache-2.0 | 10,166 | [
"Gaussian"
] | cec4c23c0b35622a33a57ad0c69d72f89fd47a12af6628cd348f625983016ff0 |
# 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 the G... | espressopp/espressopp | src/interaction/OPLS.py | Python | gpl-3.0 | 3,616 | [
"ESPResSo"
] | 1439f3158327c6b63a8792726180d89bc45119c5f5b912add7cc2dc8c19e4c08 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'crystalProjUI.ui'
#
# Created by: PyQt4 UI code generator 4.12.1
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf8... | mompiou/crystal-proj | crystalProjUI.py | Python | gpl-2.0 | 14,716 | [
"CRYSTAL"
] | 123ba73fc0ec3c2062353cae5d0153deabc3f0170bfc6af973e36db2e535afc3 |
from setuptools import setup
setup(
name='ntsne',
author='Brian DeCost',
author_email='bdecost@andrew.cmu.edu',
version='0.1',
description='A simple numpy wrapper around bh_tsne.',
py_modules=['ntsne'],
install_requires=[
'numpy',
],
)
| bdecost/ntsne | setup.py | Python | mit | 283 | [
"Brian"
] | 2709ce3231115e616fba90565bdd8236316da0cc49b5adba5fff617da284d754 |
import numpy as np
import warnings
from scipy.stats import norm
def gaussian_acquisition_1D(X, model, y_opt=None, acq_func="LCB",
acq_func_kwargs=None):
"""
A wrapper around the acquisition function that is called by fmin_l_bfgs_b.
This is because lbfgs allows only 1-D input.... | ccauet/scikit-optimize | skopt/acquisition.py | Python | bsd-3-clause | 8,912 | [
"Gaussian"
] | 2cd34c6173ab4aeb323bc4b8db27e41c4a231968d9eb510069af3a8f4c915faf |
import pysam
import array
import numpy
def parse_bam_for_f_r(filename, input_dir):
num = 0
forward = {}
reverse = {}
infile =pysam.Samfile(input_dir+filename, 'rb')
for line in infile.fetch(until_eof = True):
num += 1
if num % 10000000 == 0 :
print ("{0:,} lines process... | shawnzhangyx/PePr | PePr/pre_processing/fileParser.py | Python | gpl-3.0 | 6,307 | [
"pysam"
] | c9817dca5710d1b5fc937b2a28423d5416e0b31755ae40c500df8c2d5f56eaee |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | wkeeling/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 13,346 | [
"Brian",
"Galaxy"
] | f7a360a5b6ff3637fc0a417ea62423cb5c21d45ddd5422997437691d5544d906 |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
import math
def main():
print ocl.revision()
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(-15, -8, 15)
myscreen.camera.SetFocalPoint(0,0, 0)
# axis arrows
camvtk.drawArrows(myscreen,center=(0,0,0))... | AlanZatarain/opencamlib | scripts/cutsim/cutsim_06.py | Python | gpl-3.0 | 3,565 | [
"VTK"
] | 200d4547cd84b009526fc23b6e21a06553e5679a89e2c549fb0d8d9ee4a89ef6 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | xyproto/turbine | djl/libs/SOAPpy/Client.py | Python | gpl-3.0 | 16,681 | [
"Brian"
] | ea7ba7dc4eaa530ee5b5e46ef372ca41ec16f675614c72fb9db61ad05d690051 |
# Copyright 2019-present Kensho Technologies, LLC.
from typing import Any, Dict, List, Union
from graphql import GraphQLSchema
from graphql.language.ast import (
DocumentNode,
FieldNode,
InterfaceTypeDefinitionNode,
NamedTypeNode,
ObjectTypeDefinitionNode,
OperationDefinitionNode,
Operation... | kensho-technologies/graphql-compiler | graphql_compiler/schema_transformation/rename_query.py | Python | apache-2.0 | 10,295 | [
"VisIt"
] | a733ea4b0dc3e630ac0108184e4b20e954a6cc8209536b713c39d0ec39034c87 |
# -*- coding: utf-8 -*-
from chempy.util.testing import requires
from chempy.units import units_library, default_units as u
from ..numbers import (
roman,
_float_str_w_uncert,
number_to_scientific_html,
number_to_scientific_latex,
number_to_scientific_unicode,
)
def test__float_str_w_uncert():
... | bjodah/aqchem | chempy/printing/tests/test_numbers.py | Python | bsd-2-clause | 2,198 | [
"ChemPy"
] | 1b97b315dbd43e4bf43341f6206d2b434129e7a4c1d09ed52c6b020d9267ccdf |
#
# Copyright (C) 2013,2014 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 l... | olenz/espresso | src/python/espressomd/highlander.py | Python | gpl-3.0 | 2,379 | [
"ESPResSo"
] | 0e80fbf96653baa36c22b2a8eade19e2dc6a404ae2175646f92c3fc8c94bff8f |
# -*- coding: utf-8 -*-
from __future__ import division, absolute_import, print_function
import os
import sys
from setuptools import find_packages, setup
from numpy.distutils.core import setup
from numpy.distutils.misc_util import Configuration
# Only way to get --noopt defaulted into the build environment
# since f2... | ocefpaf/seapy | setup.py | Python | mit | 2,001 | [
"Brian"
] | c86deb90d65c9bedc726d27e4a483fdf8946c5252357da1c3edc567665ff7221 |
# Copyright (C) 2019 - Raphael Valyi Akretion
# License LGPL-3.0 or later (https://www.gnu.org/licenses/lgpl-3.0.en.html).
import logging
import sys
import inspect
from odoo import api, models, SUPERUSER_ID
from .models.spec_models import SpecModel, StackedModel
_logger = logging.getLogger(__name__)
def post_init_h... | akretion/l10n-brazil | spec_driven_model/hooks.py | Python | agpl-3.0 | 5,170 | [
"VisIt"
] | 29a6ba4c66dc7aaf211f1a9ed403c008271aff19bd281dfb5b8f89a3a9d81e27 |
#!/usr/bin/env python3
# -*- Mode:python; c-file-style:"gnu"; indent-tabs-mode:nil -*- */
#
# Copyright (c) 2015, Colorado State University.
#
# This file is part of ndn-atmos.
#
# ndn-atmos is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as publish... | named-data/ndn-atmos | lib/ndn_cmmap_translators/atmos2ndn_translators/cmip5_translator.py | Python | gpl-3.0 | 5,996 | [
"NetCDF"
] | ed69326fd1e08f4c4912606d54532beafbc42a6735382f80d5d7bc9e9db0608f |
#!usr/bin/env python
"""nonmetric multidimensional scaling (nmds)
see, for example: Jan de Leeuw 2004 (monotone regression),
Rencher 2002: Methods of multivariate analysis, and the original work:
Kruskal 1964: Nonmetric multidimensional scaling
"""
from __future__ import division
from numpy import array, multiply, s... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/cogent/cluster/nmds.py | Python | mit | 18,594 | [
"Gaussian"
] | b24c9ec8f55ac2ad4b5f268287ac17151972761ccc4a5a443c87646edfdeb0ef |
"""This module sets up a random walk system then runs a simulation using
the given resampler. This profiles the performance of the resampler
using the data produced in the simulation.
The simulation data is saved using the WepyHDF5 reporter. To create a
WepyHDF5 reporter we create a dummy topology for the random walk
... | ADicksonLab/wepy | src/wepy_tools/sim_makers/toys/randomwalk.py | Python | mit | 15,458 | [
"MDTraj"
] | 790d409a1f5fc466b7fe73367f15293f058e8dc5aaac0e23838b835ae307233e |
import os, unittest, sqlalchemy
from sqlalchemy import create_engine
from igf_data.utils.dbutils import read_dbconf_json
from igf_data.igfdb.baseadaptor import BaseAdaptor
from igf_data.igfdb.fileadaptor import FileAdaptor
from igf_data.igfdb.collectionadaptor import CollectionAdaptor
from igf_data.igfdb.igfTables impo... | imperial-genomics-facility/data-management-python | test/utils/reference_genome_utils_test.py | Python | apache-2.0 | 4,879 | [
"BWA"
] | 5b5a83c0a794eb7558105aa79f8d26e23d5ed8e05b27237ad1a4ae65123934de |
# The command file for every external command not specifically for running
# the bot. Even more relevant commands like broadcast options and whitelists
# are treated as such.
#
# Every command in here should follow the basic structure of:
# elif cmd == 'commandHere':
# doYourThings(lots, of, variables)
# return... | awesomarcus/haaaaaaaah | commands.py | Python | mit | 23,961 | [
"BLAST"
] | 3977312e1e0040421f62ac06f80374e19ad90ed39df7eb989dfdc00504662324 |
#!/usr/bin/env python
import sys
import unittest
import vtk
from PyQt5 import QtCore, QtWidgets
from peacock.ExodusViewer.plugins.MeshPlugin import main
from peacock.utils import Testing
class TestMeshPlugin(Testing.PeacockImageTestCase):
"""
Testing for MeshControl widget.
"""
qapp = QtWidgets.QAppli... | Chuban/moose | python/peacock/tests/exodus_tab/test_MeshPlugin.py | Python | lgpl-2.1 | 6,694 | [
"VTK"
] | 58f8fe07f308c0d87f6a75f18744e98debc93e7686671adf4ac8a1e102c20e37 |
#!/usr/bin/env python
# Copyright 2013 The Swarming Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0 that
# can be found in the LICENSE file.
import datetime
import hashlib
import json
import logging
import os
import StringIO
import subprocess
import sys
import ... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/tools/swarming_client/tests/swarming_test.py | Python | mit | 38,340 | [
"VisIt"
] | 9a7e3aea26cc4cb78dbf1ffc1a352b0e65dcc433b67ce53931fbb15421cda825 |
import os
from pywps.Process import WPSProcess
import logging
logger = logging.getLogger(__name__)
class FetchProcess(WPSProcess):
def __init__(self):
WPSProcess.__init__(self,
identifier="fetch",
title="Download Resources",
version = "0.1",
abstract="This ... | sradanov/flyingpigeon | flyingpigeon/processes/wps_fetch.py | Python | apache-2.0 | 1,657 | [
"NetCDF"
] | 13b8a26df7fd7841d55e27e89b0f9d735e944492748ee984167b1c0b38790590 |
import re
from collections import OrderedDict, defaultdict, Counter
from functools import reduce
from operator import add, or_
from typing import List
from sortedcontainers import SortedDict
from lhc.binf.genomic_coordinate import GenomicPosition as Position
from lhc.io.variant import VariantFile
class VariantMerger... | childsish/lhc-python | lhc/binf/variant/merger.py | Python | gpl-2.0 | 8,369 | [
"pysam"
] | e8e57997d2c771a37f85d90453fee76e260c475e5537eb97ac9a48a700c0f475 |
"""
Bonds options
-------------
Selecting "Draw bonds" will result in bonds being drawn between visible
atoms from this filter list. You must also select the bonds you want to
draw from the list (eg. "Pu-Pu" or "Pu-Ga").
The "Bond thickness" settings determine the size of the bonds when they are
rendered. "VTK" is ... | chrisdjscott/Atoman | atoman/gui/filterListOptions/bondsOptions.py | Python | mit | 8,436 | [
"VTK"
] | baab46e0160eb5a4888ed149c145ce914470cea8ad2eb3a69368637a04b9c5da |
"""
=====================================
Inference for Linear-Gaussian Systems
=====================================
This module implements the Kalman Filter, Kalman Smoother, and
EM Algorithm for Linear-Gaussian state space models
"""
import warnings
import numpy as np
from scipy import linalg
from .utils import a... | nils-werner/pykalman | pykalman/standard.py | Python | bsd-3-clause | 60,872 | [
"Gaussian"
] | 97bf2ba1acc153a66cd9bb0515b7f7bd3326fb9115fbacebb2d298daf5d08e76 |
import pyboof as pb
import numpy as np
original = pb.load_single_band('../../../data/applet/outdoors01.jpg',np.uint8)
gaussian = original.createSameShape() # useful function which creates a new image of the
mean = original.createSameShape() # same type and shape as the original
# Apply different types of blur to... | pacozaa/BoofCV | integration/pyboof/examples/example_blur_image.py | Python | apache-2.0 | 584 | [
"Gaussian"
] | 3d02c06b7b05f66f5f21e164d37f6c88a018ca4e0e65f43349b2c83a500c1317 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import functools
import io
import json
import random
import shutil
import tempfile
import ddt
from boto.exception import BotoServerError
from django.conf import settings
from django.contrib.auth.models import User
from django.core i... | Edraak/edraak-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 234,247 | [
"VisIt"
] | dea92d17832ce329345c6579e4b9f38c03bd9c92c3477fe2a5fd77b64fbc33e6 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/mpicc/kintermediates_rhf.py | Python | apache-2.0 | 70,221 | [
"PySCF"
] | 12e54126b1e5c3b10eb77bc7b5e6a50c32635e4446f8db59cc26041390997839 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/champ/assign.py | Python | gpl-2.0 | 9,105 | [
"ChemPy",
"PyMOL"
] | 9c785a6d2e0f25131ce22f1d3eae85f400ea3757df4d700b9b6c8685fdfdd4cd |
# -*- coding: utf-8 -*-
from django.db import models
from django.template.defaultfilters import slugify
from django.core.exceptions import ValidationError
from django.utils.safestring import mark_safe
from django.utils.encoding import smart_str, force_unicode
from django.utils.translation import ugettext_lazy as _
fro... | wtrevino/django-djobberbase | djobberbase/models.py | Python | mit | 12,504 | [
"VisIt"
] | 87ee5a5d8dc34db1d7f6d3c2a0473715ffa3271ee623351d0f6bb5c8196a3c64 |
#
#
# lmpsdata.py
#
# For reading, writing and manipulating lammps data files
# For calculation of certain properities using lammps data files
# For creating VMD input text files using lammps data files
# All x,y,z calculations assume the information includes image flags
class Lmpsdata:
def __init__(self,... | quang-ha/lammps | tools/polybond/lmpsdata.py | Python | gpl-2.0 | 83,856 | [
"LAMMPS",
"VMD"
] | dbcd315219adad38cd3d1debb74653b6568da93da4c6a06c38a416dd87e649d8 |
from alma.net_components import activation_function
from alma.util import vec_util
"""Package for neuro net net_components."""
class Layer:
def __init__(self, input_num, neuron_num,
activation_func=activation_function.simple):
self.neuron_num = neuron_num
self.weight_num = input_... | i-newton/AlmaNeuro | alma/net_components/layer.py | Python | apache-2.0 | 1,552 | [
"NEURON"
] | 83151c9eda34f3ebbc6152923b6cf5f77c6eaf217bfaf5927546d7002c3b2b41 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | francisco-dlp/hyperspy | hyperspy/models/model1d.py | Python | gpl-3.0 | 35,283 | [
"Gaussian"
] | d50c5bdde4bc766f639e6bc79ddc8e0585a620914423ebe1146e7c449505b048 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains an algorithm to solve the Linear Assignment Problem.
It has the same functionality as linear_assignment.pyx, but is much slower
as it is vectorized in numpy rather than cython
"""
__a... | gVallverdu/pymatgen | pymatgen/optimization/linear_assignment_numpy.py | Python | mit | 8,203 | [
"pymatgen"
] | 0ce6be818019e5b1e21d88992994a02ab777815dbc6965aec82c495d3e537907 |
# 7.1.2015
# Builtins
import os, sys
# from armchair biology blog (now implemented in biopython)
from KGML_parser import read
from KGML_vis import KGMLCanvas
from KGML_scrape import retrieve_kgml_to_file, retrieve_KEGG_pathway
import argparse
import pandas as pd
############################
psr = argparse.ArgumentPars... | bluegenes/MakeMyTranscriptome | scripts/util/color_pathways2.py | Python | bsd-3-clause | 3,579 | [
"Biopython"
] | cd2cdbe060d36b9a606817acd55ae0def0f2fff8e3c4f3a5c6c18e4124e5bd45 |
from mpi4py import MPI
import numpy
import pycf90
import pygaussian
from floatpy.parallel import t3dmod
from floatpy.utilities import data_reshaper
class Filter(object):
"""
Class to perform parallel filter operations
"""
def __init__(self, grid_partition, filter_type, dimension=3, periodic_dimension... | FPAL-Stanford-University/FloATPy | floatpy/filters/filter.py | Python | lgpl-3.0 | 17,424 | [
"Gaussian"
] | 1af0c78d47d35e9c2d8a9302ed613ce52f1782007990efc9da18dee91f319899 |
import numpy as np
from math import floor, sqrt
import bayesflare as bf
from ..stats.general import logminus
class Model():
"""
A class with methods for a generic model.
Parameters
----------
mtype : string
The model type, currently this can be 'flare', 'transit', 'expdecay', 'impulse', 'g... | BayesFlare/bayesflare | bayesflare/models/model.py | Python | gpl-2.0 | 33,417 | [
"Gaussian"
] | eb3a4343eaf960ec389a433c712b7da961819a1efeb0fae60f44a9c12d23d848 |
# -*- coding: utf-8 -*-
# This work is licensed under the MIT License.
# To view a copy of this license, visit https://opensource.org/licenses/MIT
# Written by Abdullah Diab (mpcabd)
# Email: mpcabd@gmail.com
# Website: http://mpcabd.xyz
# Ported and tweaked from Java to Python, from Better Arabic Reshaper
# [https:... | imiolek-ireneusz/eduActiv8 | classes/rtl/arabic_reshaper/arabic_reshaper.py | Python | gpl-3.0 | 5,799 | [
"VisIt"
] | ebe73a572bf9dc43cd61c7ca04996cda3abb03e42ac53b7ffd0f33985a306f35 |
#!/usr/bin/env python
"""
A simple utility to redo the failed/errored tests.
You need to specify the session directory in order for this script to locate the
tests which need to be re-run.
See also dotest.py, the test driver running the test suite.
Type:
./dotest.py -h
for help.
"""
from __future__ import print_... | endlessm/chromium-browser | third_party/llvm/lldb/packages/Python/lldbsuite/test/redo.py | Python | bsd-3-clause | 6,713 | [
"VisIt"
] | 038514ba9d904be595d8c623b6a4e69d93fea6f2f947208c38bd4fde53e27367 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from torch.distributions import constraints
from torch.nn import Parameter
import pyro
import pyro.distributions as dist
from pyro.contrib.gp.models.model import GPModel
from pyro.contrib.gp.util import conditional
fr... | uber/pyro | pyro/contrib/gp/models/vgp.py | Python | apache-2.0 | 6,563 | [
"Gaussian"
] | 1d6837f65d6661f92728ec0e61c25d9f8ed0111e1ab19fe4749845331505990c |
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License Version
# 1.1 (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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/db/exceptions.py | Python | gpl-2.0 | 1,872 | [
"Brian"
] | 8c11ef51d1d894d55f3635779746c65bf9e53fb79689a384a4ba89f4a14820b5 |
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module provides code to work with the prosite.doc file from
Prosite.
http://www.expas... | bryback/quickseq | genescript/Bio/ExPASy/Prodoc.py | Python | mit | 4,787 | [
"Biopython"
] | b4ca7c36c7d35b5807faaf40ab8b1d8d1d3bc7acb86e7f7986f4eddb1cb6ef60 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-22 22:43:15
# @Last modified by: Brian Cherinka
# @Last modified time: 2018-11-12 17:06:25
from __future__ import absolute_import, division, print_function
import copy as copy_mod
... | sdss/marvin | python/marvin/utils/datamodel/query/base.py | Python | bsd-3-clause | 31,361 | [
"Brian"
] | 26065588a08ffdaadd46addfab26043608487242fab5ece8d88a9a420c09871b |
# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License : BSD 3-clause
from copy import deepcopy
import numpy as np
from ..fixes import _import_fft
from ..io.pick import _pick_data_channels, pick_info
from ..utils import verbose, warn, fill_do... | rkmaddox/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 9,692 | [
"Gaussian"
] | f6a4d2c54144d571503f254cc3fcd889b043d8cae4293742ed54d6c20908bc1d |
#
# Copyright (C) 2017-2018 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... | mkuron/espresso | testsuite/python/auto_exclusions.py | Python | gpl-3.0 | 2,326 | [
"ESPResSo"
] | 84e4a332925ebec7cc505a7c9f87cde17c62a27198ec40f26acc3195e4564721 |
import numpy
import sys
from mmdlab.readers.backup_data_reader import BackupDataReader
from mmdlab.readers import transport
from mmdlab.filters import RegionFilter
from mmdlab.utils import init_mlab_scene
from mmdlab.utils import showable
from mmdlab.utils import saveimg
from mmdlab.utils import offscreen
from maya... | detorto/mdvis | src/simple_backup.py | Python | mit | 1,136 | [
"Mayavi"
] | 695809ffe4d12db0012cbe3fc668e19cb29072922bf441058d19386ce83f0ed2 |
# ############################# #
# #
# STEM Moire GPA Software #
# #
# ############################# #
#
# #####################################################################################
#
# Python script calculating the 2D relative strain maps fr... | slimpotatoes/STEM_Moire_GPA | src/main.py | Python | bsd-3-clause | 4,692 | [
"CRYSTAL"
] | aa6d6bb2b35599052acdeeef4387012cd037f742bf547646056657fa5fa2b5ba |
"""
experiment_src_separation_clean.py: generate the phase transition plot with real LOFAR layout (CLEAN)
Copyright (C) 2017 Hanjie Pan
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... | hanjiepan/LEAP | experiment_src_separation_clean.py | Python | gpl-3.0 | 24,782 | [
"DIRAC"
] | 02d05adfbc9a9b502a0f2751e572340ca1ff24b4118d555378aa54ec00711690 |
"""
=========================================================
Gaussian Processes regression: basic introductory example
=========================================================
A simple one-dimensional regression example computed in two different ways:
1. A noise-free case
2. A noisy case with known noise-level per ... | manhhomienbienthuy/scikit-learn | examples/gaussian_process/plot_gpr_noisy_targets.py | Python | bsd-3-clause | 5,306 | [
"Gaussian"
] | 73ffce89dee214fe4bdd9207e290494122ac43536a4b1d2434d4b949144b4ede |
########################################################################
# $Id$
# File : InProcessComputingElement.py
# Author : Stuart Paterson
########################################################################
""" The simplest Computing Element instance that submits jobs locally.
"""
__RCSID__ = "$Id$"
imp... | vmendez/DIRAC | Resources/Computing/InProcessComputingElement.py | Python | gpl-3.0 | 4,537 | [
"DIRAC"
] | d3d9af35ea2ed78f5e8675f6021a10758891964dc3977816adf64d0db7bc6606 |
# 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 | doc/tutorials/07-electrokinetics/scripts/eof_electrokinetics.py | Python | gpl-3.0 | 4,087 | [
"ESPResSo"
] | cbeb9f0f653dd25c2f5205f4fb961465eaf3f80d2e8d7560e94e7a4506f83b04 |
"""
This class controls the textbox GUI for any shop state.
A Gui object is created and updated by the shop state.
"""
import sys
import pickle
import pygame as pg
from . import setup, observer
from . components import textbox
from . import constants as c
#Python 2/3 compatibility.
if sys.version_info[0] == 2:
im... | justinmeister/The-Stolen-Crown-RPG | data/shopgui.py | Python | mit | 24,008 | [
"BLAST"
] | 9035f206c34b92c231bff8e77c6c0f8317d7990da6cb2557496107648f060240 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Thom Sturgill
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008-2011 Rob G. Healey <robhealey1@gmail.com>
# Copyright (C) 2008 Jason Simanek
# Copyright (C) 2010 Jakim Friant
... | Forage/Gramps | gramps/plugins/webreport/webcal.py | Python | gpl-2.0 | 68,358 | [
"Brian"
] | fe63d218553dccf70abe2d50cf0f6299086bd90dc96a35bfb6d17822f09da662 |
# -*- coding: utf-8 -*-
import math
import warnings
import pydash as _
from .fixtures import parametrize
@parametrize('case,expected', [
((), []),
(([],), []),
(([1, 2, 3],), [1, 2, 3]),
(([1, 2, 3], [4, 5, 6]), [1, 2, 3, 4, 5, 6]),
(([1, 2, 3], [4, 5, 6], [7]), [1, 2, 3, 4, 5, 6, 7]),
((1, ... | jacobbridges/pydash | tests/test_arrays.py | Python | mit | 16,552 | [
"MOE"
] | b5cfd41ae0423187111b47d09b300157cdf412bae7a6256a4266209d2fdf2d3b |
#!/usr/bin/env python
import os
# import time
# import ephem
import aipy as a
import numpy as np
from scipy.optimize import curve_fit
from scipy.interpolate import UnivariateSpline
from scipy.linalg import eigh, inv
import h5py
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
# data_dir = '/h... | zuoshifan/dishary | scripts/uv_matrix.py | Python | gpl-2.0 | 17,760 | [
"Gaussian"
] | 645d042372e61be8dd66e48fd9cd2792523504ba351a4b25a287659348c9047d |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/tinker/keyword.py | Python | gpl-2.0 | 1,896 | [
"ChemPy",
"PyMOL"
] | 47c9c9ab0e9deca6e6201bfdbb7f2e8bf5ee5d40b1e8e5babd9c3c07b8b32601 |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
from six.moves import xrange, zip, zip_longest
from collections import Sized
import functools
import itertools
import math
import warnings
import numpy as np
from numpy import ma
import matplotlib... | jonyroda97/redbot-amigosprovaveis | lib/matplotlib/axes/_axes.py | Python | gpl-3.0 | 286,184 | [
"Gaussian"
] | ea1987f9fda9f05b31e0d4c43b4bd5e96f3dbca3270b004f8e2e743b9a33d24f |
"""
Module provides symbolical calculation of the anisotropic Structure Factor
of a Crystal of given Space Group and Asymmetric Unit up to
dipole-quadrupole (DQ) approximation.
Written by Carsten Richter (carsten.richter@desy.de)
http://www.desy.de/~crichter
"""
from __future__ import print_functio... | carichte/pyasf | pyasf/pyasf.py | Python | gpl-3.0 | 106,997 | [
"Avogadro",
"CRYSTAL",
"FEFF",
"Gaussian"
] | c6e10d79c184826b9b0b1a4b8904b868bb643f69fd357d1bf910ff2df85588fb |
r"""
=====================================================================
The Johnson-Lindenstrauss bound for embedding with random projections
=====================================================================
The `Johnson-Lindenstrauss lemma`_ states that any high dimensional
dataset can be randomly projected i... | chrsrds/scikit-learn | examples/plot_johnson_lindenstrauss_bound.py | Python | bsd-3-clause | 7,753 | [
"Gaussian"
] | 366c16c37b18d647e835d43e2e18908b84166f6b7a6d6a82ad48f7a16ea05ff5 |
import pkg_resources
# can't find it in the frozen library.zip...
# pkg_resources.require("pysam>=0.8.1")
import pysam
NEEDED_VERSION = "0.8.1"
assert pkg_resources.parse_version(pysam.version.__version__) >= pkg_resources.parse_version(NEEDED_VERSION), "PySam version at least %s required"%(NEEDED_VERSION,)
| HorvathLab/NGS | attic/readCounts/src/pysamimport.py | Python | mit | 309 | [
"pysam"
] | 67a3f6459cb0174a612461bc441a125f9b0765b069d515a9452afd52252045c7 |
# Copyright (c) 2012 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | lastweek/gem5 | configs/spec2k6_classic/se.py | Python | bsd-3-clause | 8,419 | [
"GAMESS",
"Gromacs",
"NAMD"
] | ece4e775fb3ecb8594d76c26db77857882d5851197889f19b9a6bd43cf074639 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# 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.
#
""" unit testing code... | adalke/rdkit | rdkit/Chem/UnitTestSurf.py | Python | bsd-3-clause | 4,095 | [
"RDKit"
] | 331ba0fa676feb18a23b445a288e178fa6b2cce6c9d472e3c185882701c98518 |
#!/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 | python/peacock/tests/execute_tab/JobRunner/test_JobRunner.py | Python | lgpl-2.1 | 3,317 | [
"MOOSE"
] | 82584abc7ed88703626f610585f0dd6568656cf93c3b5271d5655fc20578a272 |
# Time: O(n), is the length of cpdomains (assuming the length of cpdomains[i] is fixed)
# Space: O(n)
# A website domain like "discuss.leetcode.com" consists of various subdomains.
# At the top level, we have "com", at the next level, we have "leetcode.com",
# and at the lowest level, "discuss.leetcode.com".
# When w... | kamyu104/LeetCode | Python/subdomain-visit-count.py | Python | mit | 2,846 | [
"VisIt"
] | d6c468a4b460af25f19a6bc01f413b348d929b25aa23089a11e8117ac36420c3 |
# convcmd - convert extension commands definition
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from common import NoRepo, MissingTool, SKIPREV, mapfile
from cvs import conv... | iaddict/mercurial.rb | vendor/mercurial/hgext/convert/convcmd.py | Python | mit | 17,238 | [
"VisIt"
] | 0162782a86c2e16b60586be364c415acc1dd9e6e8be6d5c1abba9efe532943c0 |
"""
Skymap draws the axes, radio source positions, current and target position crosshairs.
Author: Ronnie Frith
Contact: frith.ronnie@gmail.com
"""
import random,math,time
from PyQt4 import QtGui, QtCore
from srt import CoordinateSystem,Status,Mode
from radiosource import RadioSource, GalacticPlane
from astropy.time ... | transientlunatic/acreroad_1420 | acreroad_1420/skymap.py | Python | bsd-3-clause | 15,998 | [
"Galaxy"
] | c4f7ec47774aba1d9d375f2234aa5959d32be2e1bf2fa17389df526f545c58d7 |
#!/usr/bin/env python
# Copyright 2014-2020 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... | sunqm/pyscf | pyscf/fci/test/test_selected_ci.py | Python | apache-2.0 | 29,861 | [
"PySCF"
] | 90a41c8894df5b5ebeab9f65a4d191fcc0adc5abdf540564a8a85ae28e780ad6 |
from Sire.IO import *
from Sire.Mol import *
from Sire.CAS import *
from Sire.System import *
from Sire.Move import *
from Sire.MM import *
from Sire.FF import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Maths import *
from Sire.Base import *
from Sire.Qt import *
import Sire.Stream
import os,re,sys
... | michellab/SireUnitTests | unittests/SireIO/test_amber2.py | Python | gpl-3.0 | 11,708 | [
"Amber"
] | 5cfed10b265c4a056a838ae81dcc7ed9e52c7511410c8c5de5a710ebadc36cec |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
#import hrl_lib.mayavi2_util as mu
import h... | tapomayukh/projects_in_python | rapid_categorization/variable_length_training_data/hmm_force_motion_two_objects.py | Python | mit | 31,731 | [
"Gaussian",
"Mayavi"
] | ce55358746cdfd05a162346fbcf4e45b7f6bc1d2540949bcc5ec2da72c02fa4f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# symbiflow-arch-defs documentation build configuration file, created by
# sphinx-quickstart on Thu Oct 18 14:29:14 2018.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present ... | SymbiFlow/symbiflow-arch-defs | docs/source/conf.py | Python | isc | 6,574 | [
"Amber"
] | 7384bc54ca9d49828b4885bdeab40cb2f3513ca27ebb5049fe93011578b10d86 |
#! /usr/bin/env python
"""
Implementation of the STIM map from [PAI18]
.. [PAI18]
| Paret et al, 1018
| **STIM map: detection map for exoplanets imaging beyond asymptotic Gaussian residual speckle noise**
| *submitted in Monthly Notices of the Royal Astronomical Society*
"""
import numpy as np
f... | carlgogo/vip_exoplanets | vip_hci/metrics/stim.py | Python | bsd-3-clause | 1,664 | [
"Gaussian"
] | ea2de6663d21254199884aafcf0c8d9733ee5181a80ab0150f61d2ffe9e244e0 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import datetime
import math
import random
import os
# this might be useful:
# http://code.activestate.com/recipes/409413-a-python-based-descriptive-statistical-analysis-to/
def drawLine(myscreen, p1, p2):
myscreen.addActor(ovdvtk.Line(p1=(p1.x, p1.y,... | aewallin/openvoronoi | python_examples/poisson/poisson_stat_1.py | Python | lgpl-2.1 | 3,341 | [
"VTK"
] | e67e86fde66979589f30a1d8b43bb34f88fbe9f1bb2b072c827f108ddd5a74df |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
import os
from conte... | 15Dkatz/pants | tests/python/pants_test/backend/python/test_python_chroot.py | Python | apache-2.0 | 10,644 | [
"VisIt"
] | 6be150d0c627034f231dc3770d3808620aa2d0b2a0d3d40ac4735f44420696d7 |
# test_nws_tools.py - Testing module for `nws_tools.py`, run with `pytest --tb=short -v` or `pytest --pdb`
#
# Author: Stefan Fuertinger [stefan.fuertinger@esi-frankfurt.de]
# Created: October 5 2017
# Last modified: <2017-11-23 17:51:15>
from __future__ import division
import pytest
import os
import sys
import pdb
... | pantaray/Analytic-Tools | tests/test_nws_tools.py | Python | gpl-3.0 | 79,797 | [
"Mayavi"
] | d7f4a44e2af2b5643096ba992b0ce795da221d2c2fb1fe023a672550adbf418e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default_views
urlpatterns = [
# Django Admin, use {% url 'admi... | elsantodel90/RAAGo | config/urls.py | Python | gpl-3.0 | 1,494 | [
"VisIt"
] | 09f9af0d0796771d962bd3c1be86e68f1edf020958895a82ce74e68452aa2c9b |
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
import os, sys, time
import numpy as np
from pdb import set_trace
import montage_wrapper as montage
import shutil
import gal_data
import config
import glob
from scipy.ndimage.interpolation import zoom
#_TOP_DIR = '/data/tycho/0/leroy.42/allsky/'
#_INDEX_DIR... | arlewis/arl_galbase | single_cutout_test_newmethod.py | Python | mit | 18,179 | [
"Galaxy"
] | 8b25dbe830c187cfcfe9e85b84dbe99bc9bafffbbd493f3785048422fd41ba7c |
# 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 following conditions are ... | BlueBrain/NeuroM | neurom/core/__init__.py | Python | bsd-3-clause | 1,946 | [
"NEURON"
] | ea2bdf3cf671f42405d327f4e8bb67377f357346634b3766a26e3f1b022dadbc |
"""
Manage pools of connections so that we can limit the number of requests per site and reuse
connections.
@since: 1.6
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys
if sys.version_info[0] > 2:
from urllib import parse as urlparse # Python 3
els... | linuxmidhun/0install | zeroinstall/injector/scheduler.py | Python | lgpl-2.1 | 5,473 | [
"VisIt"
] | d5caee827a7c0920269f2292898351139fc4f02f66b78284e2523b54cd77c427 |
# Owrang - web based ERP (http://owrang.yellowen.com)
# Copyright (C) 2012 Web Notes Technologies Pvt Ltd
#
# 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
#... | Yellowen/Owrang | home/__init__.py | Python | agpl-3.0 | 3,502 | [
"VisIt"
] | 54e6eaf2152c24baae11789096b653fa6c7403c653a952ce9ba457dd47a5b924 |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your... | pvagner/orca | src/orca/object_properties.py | Python | lgpl-2.1 | 8,245 | [
"ORCA"
] | 7ad4134de1686969a32c4d88a81923165942bb7e6b7b63c3de6977cc3c8081c9 |
import os
import pytest
from selenium.webdriver.chrome.options import Options
import capybara
from capybara.session import Session
from capybara.selenium.driver import Driver
from capybara.tests.app import app
from capybara.tests.suite import DriverSuite
from tests.selenium_session_test_case import SeleniumSessionTest... | elliterate/capybara.py | tests/_test_selenium_chrome.py | Python | mit | 2,176 | [
"VisIt"
] | 50ef8ecfbbd61f7fbf8f08d17807a8496cadab364ac9517b2a46f6af18a33a90 |
#!/usr/bin/env python
#
# Author: Oliver J. Backhouse <olbackhouse@gmail.com>
# George H. Booth <george.booth@kcl.ac.uk>
#
'''
A simple example of unrestricted AGF2.
Default AGF2 corresponds to the AGF2(1,0) method outlined in the papers:
- O. J. Backhouse, M. Nusspickel and G. H. Booth, J. Chem. Theory Com... | sunqm/pyscf | examples/agf2/01-simple_uagf2.py | Python | apache-2.0 | 803 | [
"PySCF"
] | 2fabc5dd4013d75ea1e1737dc720d9940853a66468fae3af4fb61a1f9a32354f |
import json
from dateutil import parser
from django.test import TransactionTestCase, Client
from django.contrib.auth.models import Group
from hs_core.hydroshare import create_resource, create_account, \
create_empty_resource, create_new_version_resource, \
update_science_metadata, copy_resource
from hs_core... | ResearchSoftwareInstitute/MyHPOM | hs_collection_resource/tests/test_collection.py | Python | bsd-3-clause | 49,313 | [
"NetCDF"
] | dee9df7c5ebe04b6ffe7c8d9062dfb34cbe2a936d3793ec409c20c5ab29adb00 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Adds EC annotation to each gene ID that passes the specified thresholds
(max. e-value, min. bitscore, min. identity) in the BLAST results file.
Usage: annotateEC.py <file> <max log e-value> <min bitscore> <min identity>
"""
from config import *
import sys
import itertools
... | pseudonymcp/keggmapping | annotateEC.py | Python | gpl-3.0 | 4,458 | [
"BLAST"
] | 448f0de1b61ef1d3d6afc5c538739adb2736638f8c7a0c3320965d91cc69cb31 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Simple example script how to make plots with the nc2map module
This script is part of the nc2map Python module, version 0.0b.
The nc2map.Maps class is the basic class which can be used for a plot.
This script shows you an easy example how to open it and how to save a pd... | Chilipp/nc2map | demo/update_demo.py | Python | gpl-2.0 | 2,365 | [
"NetCDF"
] | 4b5888aa371b144c6d8afcc4752ae354a07356b633106349596c948dcb81674e |
debugging = 1
import os
from neuron import h
if debugging:
from neuron import gui
else:
h.load_file('noload.hoc')
from mpi4py import MPI
from matplotlib import pyplot
from neuronpy.graphics import spikeplot
import helper_functions as hf
import Ia_network as Ia_net
os.chdir('E:\\Google Drive\\Github\\Spinal-C... | penguinscontrol/Spinal-Cord-Modeling | Python/run_main.py | Python | gpl-2.0 | 1,581 | [
"NEURON"
] | cd3861315ccaf45f84da9b66827cfd16c43a48c5e0de5463aec54e5546ed0558 |
""".. _nsdf-label:
NSDF
====
NSDF (Neuroscience Simulation Data Format) is a file format built on
top of `HDF5 <http://www.hdfgroup.org/>`_.
Although the design and development started with the aim of storing
data generated from simulations in computational neuroscience, this
format is generic enough that any time s... | nsdf/nsdf | nsdf/__init__.py | Python | gpl-3.0 | 7,353 | [
"NEURON"
] | f7be8d9300ea118e113647fcac54c2e66867865ff944b111a25e86dd963f9732 |
import shutil
import os
import tarfile
import tempfile
import mdtraj
import itertools
import pandas as pd
min_num_gen = 50
source_dir = "/cbio/jclab/projects/fah/fah-data/PROJ8900/"
destination_dir = "./Trajectories/"
provenance_file = file("./provenance.csv", 'a')
traj = mdtraj.load("./system.pdb")
top, bonds = tr... | choderalab/MSMs | attic/src/code/fahprocessing/old/concat_xtc.py | Python | gpl-2.0 | 1,453 | [
"MDTraj"
] | 47736e88a2baf15248708b9b41d1c61794aabdc0651dd06449fee344d30c0cf7 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkSelectPolyData(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkSelectPolyData.py | Python | bsd-3-clause | 518 | [
"VTK"
] | 5ac7eb7bc0610e399863c47c97dc48cb1d7f54ca976fc6d1ba9e487308f27c17 |
import os
import sys
from rope.base import pyobjects, exceptions, stdmods
from rope.refactor import occurrences
from rope.refactor.importutils import importinfo
class ImportInfoVisitor(object):
def dispatch(self, import_):
try:
method_name = 'visit' + import_.import_info.__class__.__name__
... | Bryan792/dotfiles | vim/vim.symlink/eclim/autoload/eclim/python/rope/refactor/importutils/actions.py | Python | mit | 13,998 | [
"VisIt"
] | bff31ac69babd5641486b2950355a4b98191ba7b77579d608712108a38c19c2f |
from __future__ import unicode_literals
import re
from django import forms
from django.utils.encoding import force_text
from django.utils.translation import ugettext_lazy as _
from account.models import Team
from milkyway.models import Challenge
class FlagForm(forms.Form):
flag = forms.CharField(label=_("Flag")... | galaxy-ctf/milky-way | milkyway/forms.py | Python | agpl-3.0 | 1,881 | [
"Galaxy"
] | 83c7047b32166c5083d5111efaafbcf1925cc8519a75d5d530dc9cfb325f8563 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# co... | jwallen/ChemPy | chempy/kinetics.py | Python | mit | 18,770 | [
"ChemPy"
] | fc85d83092cc2ee219f1e6ba6d8b9194894316a5617bb949a6040025cbae755c |
# -*- coding: utf-8 -*-
"""
Plot different solutions to rate equations problems and lattices
Created on Thu Dec 1 11:46:29 2016
@author: Pedro
"""
from typing import List, Union, Tuple, Type
import numpy as np
import scipy.interpolate as interpolate
import matplotlib.pyplot as plt
import matplotlib as mpl
from si... | pedvide/simetuc | simetuc/plotter.py | Python | mit | 13,366 | [
"Gaussian"
] | 75d1f68229f24adf774dd3f9c1b47002c76a61df81fc6e65dd96cff59f6a902b |
import matplotlib.pyplot as plt
from pysal.lib.weights.contiguity import Queen
import pysal.lib as lp
from pysal.lib import examples
import geopandas as gpd
import numpy as np
import unittest
from pysal.explore.esda.moran import (Moran_Local, Moran, Moran_BV,
Moran_Local_BV, Moran_BV_matrix)
... | lixun910/pysal | pysal/viz/splot/tests/test_viz_esda_mpl.py | Python | bsd-3-clause | 7,587 | [
"COLUMBUS"
] | b3846e16ec4b85aa966eb0795ce381a5a2fccb5d1a70ca6066a95c410dff9914 |
""" DISET request handler base class for the TransformationDB.
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.TransformationSystem.DB.TransformationDB import Tr... | calancha/DIRAC | TransformationSystem/Service/TransformationManagerHandler.py | Python | gpl-3.0 | 31,857 | [
"DIRAC"
] | 39845cf9e3869d52f8d3300b6a0abaed71f9103f9f507ef4d5aff9140981a2b0 |
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