repo_name string | path string | copies string | size string | content string | license string |
|---|---|---|---|---|---|
enigmampc/catalyst | tests/pipeline/test_factor.py | 1 | 45558 | """
Tests for Factor terms.
"""
from functools import partial
from itertools import product
from nose_parameterized import parameterized
from unittest import TestCase
from toolz import compose
from numpy import (
apply_along_axis,
arange,
array,
datetime64,
empty,
eye,
log1p,
nan,
o... | apache-2.0 |
pme1123/pyroots | pyroots/batch_processing.py | 1 | 49762 | """
Batch processing functions:
- preprocessing_filter_loop
- preprocessing_actions_loop
- pyroots_batch_loop
- fishnet_loop
- tennant_batch
"""
import os
import numpy as np
from numpy import array, uint8
import pandas as pd
from pyroots import *
from skimage import io, color, filters, morphology, img_as_ubyte, img_a... | apache-2.0 |
LeeKamentsky/CellProfiler | cellprofiler/gui/cpartists.py | 1 | 47507 | """cpartists.py - Specialized matplotlib artists for CellProfiler
CellProfiler is distributed under the GNU General Public License.
See the accompanying file LICENSE for details.
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2014 Broad Institute
All rights reserved.
Please see the ... | gpl-2.0 |
gengliangwang/spark | python/pyspark/pandas/groupby.py | 1 | 109800 | #
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | apache-2.0 |
pybel/pybel | src/pybel/struct/graph.py | 1 | 51314 | # -*- coding: utf-8 -*-
"""Contains the main data structure for PyBEL."""
import logging
import warnings
from collections import Counter, defaultdict
from copy import deepcopy
from functools import partialmethod
from itertools import chain
from textwrap import dedent
from typing import Any, Dict, Hashable, Iterable, ... | mit |
cpcloud/dask | dask/bag/core.py | 1 | 56610 | from __future__ import absolute_import, division, print_function
from collections import Iterable, Iterator, defaultdict
from functools import wraps, partial
import itertools
import math
from operator import getitem
import os
import types
import uuid
from random import Random
from warnings import warn
from distutils.v... | bsd-3-clause |
bobbypaton/GoodVibes | goodvibes/GoodVibes.py | 1 | 103807 | #!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import
"""####################################################################
# GoodVibes.py #
# Evaluation of quasi-harmonic thermochemistry from Gaussian. #
# Par... | mit |
bsmurphy/PyKrige | pykrige/uk.py | 1 | 57722 | # coding: utf-8
"""
PyKrige
=======
Code by Benjamin S. Murphy and the PyKrige Developers
bscott.murphy@gmail.com
Summary
-------
Contains class UniversalKriging, provides greater control over 2D kriging by
utilizing drift terms.
References
----------
.. [1] P.K. Kitanidis, Introduction to Geostatistc... | bsd-3-clause |
hainm/mdtraj | mdtraj/core/topology.py | 1 | 44674 | ##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | lgpl-2.1 |
nal-epfl/line-sigcomm14 | scripts/plot-data.py | 1 | 36285 | #!/usr/bin/env python2
# Install dependencies:
# sudo apt-get install python-matplotlib dvipng
import colorsys
import getopt
import json
from nicePlot import nicePlot
import math
import numpy
import os
import pprint
import re
import subprocess
import sys
## Params
dataFile = 'data-plot1.txt'
latencyFile = 'latency.... | gpl-2.0 |
dotsdl/seaborn | seaborn/linearmodels.py | 1 | 66705 | """Plotting functions for linear models (broadly construed)."""
from __future__ import division
import copy
import itertools
import numpy as np
import pandas as pd
from scipy.spatial import distance
import matplotlib as mpl
import matplotlib.pyplot as plt
try:
import statsmodels.api as sm
import statsmodels.fo... | bsd-3-clause |
dbednarski/pyhdust | pyhdust/__init__.py | 1 | 50195 | # -*- coding:utf-8 -*-
"""
PyHdust main module: Hdust tools.
:license: GNU GPL v3.0 (https://github.com/danmoser/pyhdust/blob/master/LICENSE)
"""
from __future__ import print_function
import os as _os
import time as _time
import datetime as _datetime
import math as _math
import numpy as _np
import re as _re
import st... | gpl-3.0 |
dsm054/pandas | pandas/tests/arithmetic/test_datetime64.py | 1 | 78003 | # -*- coding: utf-8 -*-
# Arithmetc tests for DataFrame/Series/Index/Array classes that should
# behave identically.
# Specifically for datetime64 and datetime64tz dtypes
import operator
from datetime import datetime, timedelta
import warnings
from itertools import product, starmap
import numpy as np
import pytest
imp... | bsd-3-clause |
andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Electrode_files/St_Jude6142_floating_profile.py | 1 | 31113 | # -*- coding: utf-8 -*-
###
### This file is generated automatically by SALOME v8.3.0 with dump python functionality
###### Run with DPS_lead_position_V9.py
import sys
import salome
salome.salome_init()
theStudy = salome.myStudy
import salome_notebook
notebook = salome_notebook.NoteBook(theStudy)
###
### GEOM comp... | gpl-3.0 |
dhomeier/astropy | astropy/table/table.py | 1 | 148382 | # Licensed under a 3-clause BSD style license - see LICENSE.rst
from .index import SlicedIndex, TableIndices, TableLoc, TableILoc, TableLocIndices
import sys
from collections import OrderedDict, defaultdict
from collections.abc import Mapping
import warnings
from copy import deepcopy
import types
import itertools
imp... | bsd-3-clause |
lennepkade/dzetsaka | scripts/mainfunction.py | 1 | 42030 | """!@brief Interface between qgisForm and function_historical_map.py
./***************************************************************************
HistoricalMap
A QGIS plugin
Mapping old landcover (specially forest) from historical maps
-----------------... | gpl-3.0 |
stephenliu1989/HK_DataMiner | hkdataminer/template_matching/two_stage_matching/matching_algorithm.py | 1 | 31727 | # Writed on July 16, 2018 by Wei Wang
# Modified on Aug 31, 2020 by Hanlin Gu
import numpy as np
from sklearn.metrics.pairwise import pairwise_distances
import mrcfile
import cv2
from skimage.exposure import rescale_intensity
from skimage import measure
import logging
import multiprocessing
import os
from sklearn.metr... | apache-2.0 |
ericpre/hyperspy | hyperspy/signal_tools.py | 1 | 81715 | # -*- coding: utf-8 -*-
# Copyright 2007-2021 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... | gpl-3.0 |
apevec/RMS | RMS/Formats/FrameInterface.py | 1 | 53957 | """ Module which provides a common functional interface for loading video frames/images from different
input data formats. """
from __future__ import print_function, division, absolute_import
import os
import sys
import copy
import time
import datetime
# tkinter import that works on both Python 2 and 3
try:
... | gpl-3.0 |
zohannn/motion_manager | scripts/old/task_2_reaching/var_1/training_task_2_var_1_20k.py | 1 | 299717 | #!/usr/bin/env python3
import sys
import pandas as pd
import sklearn
from sklearn import decomposition
from IPython import display
import seaborn as sns
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
# sklearn
from sklearn.cluster import KMeans
from sklearn import metrics
from sklearn impo... | mit |
isadoranun/FATS | FATS/FeatureFunctionLib.py | 1 | 37958 | import os
import sys
import time
import math
import bisect
import numpy as np
import pandas as pd
from scipy import stats
from scipy.optimize import minimize
from scipy.optimize import curve_fit
from statsmodels.tsa import stattools
from scipy.interpolate import interp1d
from Base import Base
import lomb
class Ampl... | mit |
kushalbhola/MyStuff | Practice/PythonApplication/env/Lib/site-packages/numpy/core/fromnumeric.py | 1 | 115626 | """Module containing non-deprecated functions borrowed from Numeric.
"""
from __future__ import division, absolute_import, print_function
import functools
import types
import warnings
import numpy as np
from .. import VisibleDeprecationWarning
from . import multiarray as mu
from . import overrides
from . import umat... | apache-2.0 |
rmcgibbo/numpy | numpy/lib/function_base.py | 1 | 126640 | from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | bsd-3-clause |
Kefeng91/EvoSeis | src/evolocGUI.py | 1 | 51467 | # -*- coding: utf-8 -*-
#==============================================================================
# evoloc_gui.py
#------------------------------------------------------------------------------
# evoloc_gui displays a graphical user interface for EvoLoc.
#
# Created by
# Keurfon Luu <keurfon.luu@mines-paris... | mit |
thunderhoser/GewitterGefahr | gewittergefahr/gg_utils/soundings.py | 1 | 61534 | """Atmospheric soundings.
--- NOTATION ---
The following letters will be used throughout this module.
T = number of lead times
n = number of storm objects
p = number of pressure levels, not including surface
P = number of pressure levels, including surface
F = number of sounding fields
N = number of soundings = T*n... | mit |
rcfduarte/nmsat | modules/parameters.py | 1 | 48086 | """
========================================================================================================================
Parameters Module
========================================================================================================================
(incomplete documentation)
Module for dealing with mode... | gpl-2.0 |
jasonfleming/asgs | output/kalpana.py | 1 | 44597 | #!/usr/bin/env python
## Importing all the necessary Python Modules ##
import matplotlib
## matplotlib.use('Agg') is used to specify a matplotlib backend ##
## which if not specified creates an error while running in cluster##
matplotlib.use('Agg')
import pylab as pl
import matplotlib.pyplot as pplot
from shapel... | gpl-3.0 |
neherlab/treetime | treetime/treetime.py | 1 | 42796 | from __future__ import print_function, division, absolute_import
import numpy as np
from scipy import optimize as sciopt
from Bio import Phylo
from . import config as ttconf
from . import MissingDataError,UnknownMethodError,NotReadyError
from .utils import tree_layout
from .clock_tree import ClockTree
rerooting_mechan... | mit |
fraricci/pymatgen | pymatgen/analysis/phase_diagram.py | 1 | 84602 | # coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines tools to generate and analyze phase diagrams.
"""
import re
import collections
import itertools
import math
import logging
from monty.json import MSONable, MontyDecoder
from functools ... | mit |
jkitzes/macroeco | macroeco/empirical/_empirical.py | 1 | 43354 | from __future__ import division
import os
import re
import copy
from configparser import ConfigParser
import itertools
from copy import deepcopy
import logging
import numpy as np
import pandas as pd
import scipy.spatial.distance as dist
try:
import shapely.geometry as geo
except:
pass
# TODO: Make shapely impo... | bsd-2-clause |
mgrp/humanencoding | humanencoding/wordlist_v1.py | 1 | 838013 | words = ('aardvark', 'aardvarks', 'aarti', 'aartis', 'aback', 'abacks',
'abacus', 'abalone', 'abandon', 'abandons', 'abash', 'abashed',
'abashest', 'abashing', 'abashless', 'abashment', 'abashments',
'abate', 'abated', 'abates', 'abating', 'abba', 'abbas', 'abbaser',
'abbasers', 'abb... | lgpl-3.0 |
yl565/statsmodels | statsmodels/tsa/statespace/tests/test_smoothing.py | 1 | 41176 | """
Tests for smoothing and estimation of unobserved states and disturbances
- Predicted states: :math:`E(\alpha_t | Y_{t-1})`
- Filtered states: :math:`E(\alpha_t | Y_t)`
- Smoothed states: :math:`E(\alpha_t | Y_n)`
- Smoothed disturbances :math:`E(\varepsilon_t | Y_n), E(\eta_t | Y_n)`
Tested against R (FKF, Kalman... | bsd-3-clause |
MaestroGraph/sparse-hyper | experiments/attention.py | 1 | 38757 | from _context import sparse
from sparse import util
from util import Lambda, Debug
from util import od, prod, logit
import time, os, math, sys, PIL
import torch, random
from torch.autograd import Variable
from torch import nn, optim
import torch.nn.functional as F
from torch.nn import Parameter
from tqdm import tran... | mit |
geophysics/mtpy | mtpy/imaging/plotpt.py | 1 | 35027 | # -*- coding: utf-8 -*-
"""
Created on Thu May 30 17:07:50 2013
@author: jpeacock-pr
"""
#==============================================================================
import matplotlib.pyplot as plt
import numpy as np
import os
from matplotlib.ticker import MultipleLocator
import matplotlib.colors as colors
import... | gpl-3.0 |
stuarteberg/lazyflow | lazyflow/operators/opDetectMissingData.py | 1 | 40118 | ###############################################################################
# lazyflow: data flow based lazy parallel computation framework
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/o... | lgpl-3.0 |
quantrocket-llc/quantrocket-client | quantrocket/master.py | 1 | 46380 | # Copyright 2020 QuantRocket - All Rights Reserved
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | apache-2.0 |
zfrenchee/pandas | pandas/tests/test_resample.py | 1 | 138388 | # pylint: disable=E1101
from warnings import catch_warnings
from datetime import datetime, timedelta
from functools import partial
from textwrap import dedent
from operator import methodcaller
import pytz
import pytest
import dateutil
import numpy as np
import pandas as pd
import pandas.tseries.offsets as offsets
im... | bsd-3-clause |
alephu5/Soundbyte | environment/lib/python3.3/site-packages/matplotlib/font_manager.py | 1 | 45096 | """
A module for finding, managing, and using fonts across platforms.
This module provides a single :class:`FontManager` instance that can
be shared across backends and platforms. The :func:`findfont`
function returns the best TrueType (TTF) font file in the local or
system font path that matches the specified :class... | gpl-3.0 |
kevin-intel/scikit-learn | sklearn/ensemble/_hist_gradient_boosting/tests/test_gradient_boosting.py | 2 | 40152 | import numpy as np
import pytest
from numpy.testing import assert_allclose, assert_array_equal
from sklearn.datasets import make_classification, make_regression
from sklearn.datasets import make_low_rank_matrix
from sklearn.preprocessing import KBinsDiscretizer, MinMaxScaler, OneHotEncoder
from sklearn.model_selection ... | bsd-3-clause |
ViennaRNA/forgi | examples/coaxial_stacking.py | 1 | 50045 | # coding: utf-8
from __future__ import print_function, absolute_import, division, unicode_literals
from builtins import str
from builtins import zip
from builtins import next
from builtins import input
from builtins import map
from builtins import range
from builtins import object
from builtins import (ascii, bytes, ch... | gpl-3.0 |
mattvonrocketstein/smash | smashlib/ipy3x/html/notebookapp.py | 1 | 42350 | # coding: utf-8
"""A tornado based IPython notebook server."""
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
from __future__ import print_function
import base64
import datetime
import errno
import io
import json
import logging
import os
import random
import re
i... | mit |
datapythonista/pandas | pandas/tests/series/methods/test_interpolate.py | 2 | 31676 | import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
Index,
MultiIndex,
Series,
date_range,
isna,
)
import pandas._testing as tm
@pytest.fixture(
params=[
"linear",
"index",
"values",
"nearest",
... | bsd-3-clause |
kevin-intel/scikit-learn | sklearn/decomposition/_nmf.py | 2 | 50260 | """ Non-negative matrix factorization.
"""
# Author: Vlad Niculae
# Lars Buitinck
# Mathieu Blondel <mathieu@mblondel.org>
# Tom Dupre la Tour
# License: BSD 3 clause
import numbers
import numpy as np
import scipy.sparse as sp
import time
import warnings
from math import sqrt
from ._cdnmf_fast... | bsd-3-clause |
vossman/ctfeval | appionlib/apCtf/ctfdisplay.py | 1 | 43159 | #!/usr/bin/env python
import os
import sys
import math
import numpy
import time
import random
from pyami import imagefun
from pyami import ellipse
from pyami import mrc
from appionlib import apDisplay
#from appionlib import lowess
from appionlib.apImage import imagefile
from appionlib.apImage import imagefilter
from a... | apache-2.0 |
huggingface/pytorch-transformers | examples/pytorch/question-answering/run_qa_beam_search_no_trainer.py | 1 | 37543 | #!/usr/bin/env python
# coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. 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/LI... | apache-2.0 |
herilalaina/scikit-learn | sklearn/linear_model/least_angle.py | 1 | 58351 | """
Least Angle Regression algorithm. See the documentation on the
Generalized Linear Model for a complete discussion.
"""
from __future__ import print_function
# Author: Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux
#
# License: BSD 3 ... | bsd-3-clause |
effigies/mne-python | mne/time_frequency/tfr.py | 1 | 45989 | """A module which implements the time frequency estimation.
Authors : Alexandre Gramfort, alexandre.gramfort@telecom-paristech.fr
Hari Bharadwaj <hari@nmr.mgh.harvard.edu>
License : BSD 3-clause
Morlet code inspired by Matlab code from Sheraz Khan & Brainstorm & SPM
"""
import warnings
from math import sq... | bsd-3-clause |
meren/anvio | anvio/drivers/MODELLER.py | 1 | 39607 | # coding: utf-8
"""
Interface to MODELLER (https://salilab.org/modeller/).
"""
import os
import sys
import anvio
import shutil
import argparse
import subprocess
import pandas as pd
import anvio.utils as utils
import anvio.fastalib as u
import anvio.terminal as terminal
import anvio.constants as constants
import anvio... | gpl-3.0 |
BiaDarkia/scikit-learn | sklearn/linear_model/tests/test_coordinate_descent.py | 5 | 30882 | # Authors: Olivier Grisel <olivier.grisel@ensta.org>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
# License: BSD 3 clause
import numpy as np
import pytest
from scipy import interpolate, sparse
from copy import deepcopy
from sklearn.datasets import load_boston
from sklearn.exceptions import ConvergenceW... | bsd-3-clause |
cython-testbed/pandas | pandas/tests/reshape/test_concat.py | 1 | 99958 | from warnings import catch_warnings, simplefilter
from itertools import combinations
from collections import deque
import datetime as dt
import dateutil
import numpy as np
from numpy.random import randn
from datetime import datetime
from pandas.compat import StringIO, iteritems, PY2
import pandas as pd
from pandas im... | bsd-3-clause |
DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/metrics/tests/test_classification.py | 1 | 54364 | from __future__ import division, print_function
import warnings
from functools import partial
from itertools import product
import numpy as np
from scipy import linalg
from scipy.spatial.distance import hamming as sp_hamming
from sklearn import datasets
from sklearn import svm
from sklearn.datasets import make_multil... | mit |
waditu/tushare | tushare/stock/trading.py | 1 | 52594 | # -*- coding:utf-8 -*-
"""
交易数据接口
Created on 2014/07/31
@author: Jimmy Liu
@group : waditu
@contact: jimmysoa@sina.cn
"""
from __future__ import division
import time
import json
import lxml.html
from lxml import etree
import pandas as pd
import numpy as np
import datetime
from tushare.stock import c... | bsd-3-clause |
e-koch/FilFinder | fil_finder/filfind_class.py | 1 | 72225 | # Licensed under an MIT open source license - see LICENSE
import numpy as np
import matplotlib.pyplot as p
import scipy.ndimage as nd
from scipy.stats import lognorm
from scipy.ndimage import distance_transform_edt
from skimage.morphology import remove_small_objects, medial_axis
from scipy.stats import scoreatpercenti... | mit |
gengliangwang/spark | python/pyspark/pandas/tests/test_groupby.py | 1 | 117764 | #
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | apache-2.0 |
pulsatrixwx/PulsatrixWx | base/MapPlotter.py | 1 | 53521 | from datetime import datetime, timedelta
import calendar
from copy import copy
from math import sqrt, ceil
import numpy as np
import matplotlib
from matplotlib.transforms import Bbox
matplotlib.use('agg')
import pylab
from mpl_toolkits.basemap import Basemap
import pyproj
from util.config import Config
import util.... | mit |
influxdata/influxdb-python | influxdb/tests/dataframe_client_test.py | 1 | 52326 | # -*- coding: utf-8 -*-
"""Unit tests for misc module."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from datetime import timedelta
import json
import unittest
import warnings
import requests_mock
from nose.too... | mit |
xiyuw123/Tax-Calculator | taxcalc/functions.py | 1 | 44187 | import pandas as pd
from pandas import DataFrame
import math
import numpy as np
from .decorators import *
@iterate_jit(nopython=True)
def FilingStatus(MARS):
if MARS == 3 or MARS == 6:
_sep = 2
else: _sep = 1
return _sep
@iterate_jit(parameters=["ALD_StudentLoan_HC", "ALD_SelfEmploymentTax_HC", ... | mit |
itoledoc/gWTO2 | wtoAlgorithm.py | 1 | 40183 | from datetime import datetime
from datetime import timedelta
import numpy as np
import pandas as pd
import ephem
from lxml import objectify
from wtoDatabase import WtoDatabase
import ruvTest as rUV
from scipy.stats import rayleigh
"""
wtoAlgorithm.py: the gWTO selector and scorer library.
===========================... | gpl-2.0 |
dssg/wikienergy | disaggregator/build/pandas/pandas/tests/test_strings.py | 1 | 45418 | # -*- coding: utf-8 -*-
# pylint: disable-msg=E1101,W0612
from datetime import datetime, timedelta, date
import os
import operator
import re
import warnings
import nose
from numpy import nan as NA
import numpy as np
from numpy.testing import assert_array_equal
from numpy.random import randint
from pandas.compat imp... | mit |
sargas/scipy | scipy/cluster/hierarchy.py | 1 | 94403 | """
========================================================
Hierarchical clustering (:mod:`scipy.cluster.hierarchy`)
========================================================
.. currentmodule:: scipy.cluster.hierarchy
These functions cut hierarchical clusterings into flat clusterings
or find the roots of the forest f... | bsd-3-clause |
jyhmiinlin/cineFSE | CsTransform/pynufft.py | 1 | 94502 | '''
package docstring
author: Jyh-Miin Lin Cambridge University
address: jyhmiinlin at gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it under the terms of the... | gpl-3.0 |
leeping/mdtraj | mdtraj/core/topology.py | 1 | 57619 | ##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | lgpl-2.1 |
tobias-gill/STM_database | flatfile_data_extract.py | 1 | 35071 | #!/usr/bin/env python
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Omicron .Flat File Analysis Functions %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
"""
import Tkinter as Tkinter
from Tkinter import Tk
from tkFileDialog import askopenfilename
from tkFileDialog import askdirectory
import num... | gpl-3.0 |
plaes/numpy | numpy/core/code_generators/ufunc_docstrings.py | 1 | 83597 | # Docstrings for generated ufuncs
docdict = {}
def get(name):
return docdict.get(name)
def add_newdoc(place, name, doc):
docdict['.'.join((place, name))] = doc
add_newdoc('numpy.core.umath', 'absolute',
"""
Calculate the absolute value element-wise.
Parameters
----------
x : array_like... | bsd-3-clause |
yugangzhang/chxanalys | chxanalys/XPCS_SAXS.py | 1 | 87083 | """
Dec 10, 2015 Developed by Y.G.@CHX
yuzhang@bnl.gov
This module is for the SAXS XPCS analysis
"""
from chxanalys.chx_libs import ( colors, colors_copy, markers, markers_copy,
colors_, markers_, )
from chxanalys.chx_libs import ( Figure, RUN_GUI )
from chxanalys.chx_generic_fu... | bsd-3-clause |
fabioz/PyDev.Debugger | tests_python/test_debugger.py | 1 | 169337 | # coding: utf-8
'''
The idea is that we record the commands sent to the debugger and reproduce them from this script
(so, this works as the client, which spawns the debugger as a separate process and communicates
to it as if it was run from the outside)
Note that it's a python script but it'll spawn a ... | epl-1.0 |
pizzathief/scipy | scipy/stats/_distn_infrastructure.py | 2 | 129146 | #
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from scipy._lib._util import getfullargspec_no_self as _getfullargspec
import sys
import keyword
import re
import types
import warnings
import inspect
from itertools import zip_longest
from scipy._lib import doccer... | bsd-3-clause |
towle-lab/electrode-registration-app | app/app.py | 1 | 64694 | # description: GUI application to interactively segment and register
# ECoG electrodes with post-implant CT and pre-implant MRI
#
# Copyright (C) 2014 Zhongtian Dai
#
# 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... | gpl-2.0 |
m4rx9/rna-pdb-tools | rna_tools/tools/PyMOL4RNA/PyMOL4RNA.py | 1 | 33955 | #!/usr/bin/env python
"""
Quick reference:
- clarna: show contacts classification of the selected fragment based on ClaRNA
- ss: show secondary structure of the selection based on py3dna.py (3DNA (Lu, Olson 2003))
- ss_all: the same as ss() but for all objects
- pdbsrc: show PDB content (source) of selection.
- seq: s... | mit |
gpetretto/pymatgen | pymatgen/analysis/graphs.py | 1 | 42429 | # coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import warnings
import subprocess
import numpy as np
import os.path
from pymatgen.analysis.local_env import LocalStructOrderParams
from pymatgen.core import S... | mit |
jcmgray/xarray | xarray/core/common.py | 1 | 36053 | from __future__ import absolute_import, division, print_function
import warnings
from distutils.version import LooseVersion
import numpy as np
import pandas as pd
from . import duck_array_ops, dtypes, formatting, ops
from .arithmetic import SupportsArithmetic
from .pycompat import OrderedDict, basestring, dask_array... | apache-2.0 |
iagapov/ocelot | gui/accelerator.py | 1 | 34511 | '''
user interface for viewing/editing electron optics layouts
'''
import sys, os, csv
import matplotlib
from matplotlib.figure import Figure
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.collections import PatchCollection
import matplotlib.patches as mpatches
import matplotlib.path as mpath
i... | gpl-3.0 |
zfrenchee/pandas | pandas/tests/frame/test_query_eval.py | 1 | 40922 | # -*- coding: utf-8 -*-
from __future__ import print_function
import operator
import pytest
from pandas.compat import (zip, range, lrange, StringIO)
from pandas import DataFrame, Series, Index, MultiIndex, date_range
import pandas as pd
import numpy as np
from numpy.random import randn
from pandas.util.testing imp... | bsd-3-clause |
brodeau/barakuda | python/modules/barakuda_plot.py | 1 | 75026 | # -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
#
########################################################################
#
# B a r a K u d a
#
# Ploting functions and utilities
#
## Authors:
# --------
# 2010-2015: Laurent Brodeau (original primitive code)
# 2016: Saeed Falahat ... | gpl-2.0 |
goldmedal/spark | python/pyspark/sql/dataframe.py | 1 | 91020 | #
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | apache-2.0 |
theislab/scanpy | scanpy/plotting/_dotplot.py | 1 | 38043 | from typing import Optional, Union, Mapping # Special
from typing import Sequence # ABCs
from typing import Tuple # Classes
import numpy as np
import pandas as pd
from anndata import AnnData
from matplotlib.axes import Axes
from matplotlib import pyplot as pl
from matplotlib.colors import Normalize
from .. import ... | bsd-3-clause |
Astroua/SCIMES | scimes/scimes.py | 1 | 35124 | """
The SCIMES core package
"""
import numpy as np
import random
from itertools import combinations, cycle
from matplotlib import pyplot as plt
from astropy.io import fits
from astropy.table import Column
from sklearn.metrics import silhouette_score
from sklearn.manifold import spectral_embedding
from sklearn.cluster.k... | gpl-2.0 |
imochaz/epilepsy-system | seizure detection code/Stacked Autoencoders for Seizure Detection/pylearn2ext/epilepsiae.py | 1 | 36904 | import datetime
import math
import numpy as np
import os
import pickle
import pandas as pd
from scipy.io import loadmat
from pylearn2.format.target_format import OneHotFormatter
from scipy.signal import butter, filtfilt
from sklearn import preprocessing
from pylearn2.datasets.dense_design_matrix import DenseDesignMatri... | bsd-3-clause |
quantopian/odo | odo/backends/sql.py | 1 | 34206 | from __future__ import absolute_import, division, print_function
import numbers
import os
import re
import subprocess
import sys
import decimal
import warnings
from functools import partial
from operator import attrgetter
from itertools import chain
from collections import Iterator
from datetime import datetime, date... | bsd-3-clause |
eljost/pysisyphus | deprecated/plot.py | 1 | 30386 | #!/usr/bin/env python3
import argparse
import os
from pathlib import Path
import sys
import h5py
import matplotlib
from matplotlib.animation import FuncAnimation
from matplotlib.patches import Rectangle
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import s... | gpl-3.0 |
nithyanandan/PRISim | prisim/examples/codes/BispectrumPhase/multiday_closure_PS_analysis.py | 1 | 159173 | import copy, glob
import progressbar as PGB
import numpy as NP
import numpy.ma as MA
from scipy import interpolate
import matplotlib.pyplot as PLT
import matplotlib.colors as PLTC
import matplotlib.ticker as PLTick
import yaml, argparse, warnings
from astropy.io import ascii
import astropy.units as U
import astropy.con... | mit |
mdtraj/mdtraj | mdtraj/core/topology.py | 1 | 60630 | ##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | lgpl-2.1 |
sonium0/pymatgen | pymatgen/io/abinitio/flows.py | 1 | 57707 | # coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A Flow is a container for Works, and works consist of tasks.
Flows are the final objects that can be dumped directly to a pickle file on disk
Flows are executed using abirun (abipy).
"""
from __future__ impo... | mit |
fmfn/UnbalancedDataset | imblearn/tests/test_pipeline.py | 2 | 43608 | """
Test the pipeline module.
"""
# Authors: Guillaume Lemaitre <g.lemaitre58@gmail.com>
# Christos Aridas
# License: MIT
import itertools
import re
import shutil
import time
from tempfile import mkdtemp
import numpy as np
import pytest
from pytest import raises
from joblib import Memory
from sklearn.utils... | mit |
wateraccounting/wa | Models/waterpix/main.py | 1 | 33397 | # -*- coding: utf-8 -*-
"""
Authors: Gonzalo E. Espinoza-Dávalos
IHE Delft 2017
Contact: g.espinoza@un-ihe.org
Repository: https://github.com/gespinoza/waterpix
Module: waterpix
"""
from __future__ import division
import datetime as dt
from warnings import filterwarnings
import pandas as pd
import netCDF4
fro... | apache-2.0 |
vlas-sokolov/pyspeckit | pyspeckit/spectrum/plotters.py | 1 | 33224 | """
=======
Plotter
=======
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
from __future__ import print_function
import matplotlib
import matplotlib.figure
import numpy as np
import astropy.units as u
import copy
import inspect
from astropy import log
try:
from matplotlib.cbook import BoundMethod... | mit |
dsm054/pandas | pandas/core/panel.py | 1 | 55149 | """
Contains data structures designed for manipulating panel (3-dimensional) data
"""
# pylint: disable=E1103,W0231,W0212,W0621
from __future__ import division
import numpy as np
import warnings
from pandas.core.dtypes.cast import (
infer_dtype_from_scalar,
cast_scalar_to_array,
maybe_cast_item)
from panda... | bsd-3-clause |
races1986/SafeLanguage | CEM/catimages.py | 1 | 208101 | #!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Image by content categorization derived from 'checkimages.py'.
Script to check uncategorized files. This script checks if a file
has some content that allows to assign it to a category.
This script runs on commons only. It needs also external libraries
(see imports and co... | epl-1.0 |
noelcjr/EntropyMaxima | em/in_development/KNN_HMM.py | 1 | 48695 | #!/usr/bin/python
"""
Created on Fri Jun 10 20:25:03 2016
@author: noel
"""
import pandas as pd
import numpy as np
from collections import Counter
from random import randint
file_path = '/home/noel/Projects/Job_Interviews/2ndGenome/scop2_processed_data.csv'
df_pdb = pd.read_csv(file_path)
df_pdb = df_pdb.set_index([... | gpl-3.0 |
volodymyrss/3ML | threeML/utils/time_series/event_list.py | 1 | 31101 | __author__='grburgess'
import collections
import copy
import os
import numpy as np
import pandas as pd
from pandas import HDFStore
from threeML.config.config import threeML_config
from threeML.exceptions.custom_exceptions import custom_warnings
from threeML.io.file_utils import sanitize_filename
from threeML.io.prog... | bsd-3-clause |
ndingwall/scikit-learn | sklearn/linear_model/_stochastic_gradient.py | 2 | 65504 | # Authors: Peter Prettenhofer <peter.prettenhofer@gmail.com> (main author)
# Mathieu Blondel (partial_fit support)
#
# License: BSD 3 clause
"""Classification and regression using Stochastic Gradient Descent (SGD)."""
import numpy as np
import warnings
from abc import ABCMeta, abstractmethod
from joblib imp... | bsd-3-clause |
iancrossfield/aries_reduce | tools.py | 1 | 148551 | """A collection of tools, tips, and tricks.
2009-07-20 22:36 IJC: Created
2010-10-28 11:53 IJMC: Updated documentation for Sphinx.
2011-06-15 09:34 IJMC: More functions have been added; cleaned documentation.
"""
import pdb
import numpy as np
def getfigs():
"""Return a list of all open matplotlib figures.
... | mit |
TomAugspurger/pandas | pandas/tests/arithmetic/test_datetime64.py | 1 | 90010 | # Arithmetic tests for DataFrame/Series/Index/Array classes that should
# behave identically.
# Specifically for datetime64 and datetime64tz dtypes
from datetime import datetime, time, timedelta
from itertools import product, starmap
import operator
import warnings
import numpy as np
import pytest
import pytz
from pa... | bsd-3-clause |
ratnania/caid | caid-gui/geometryActions.py | 1 | 38849 | # -*- coding: UTF-8 -*-
import wx
import os
from geometry import geometry
from caid.cad_geometry import cad_geometry
from viewer import Viewer
from numpy import pi, linspace
import numpy as np
from classActions import *
from objectActions import *
class GeometryActions(ClassActions):
def __init__(self, parent, par... | mit |
Odingod/mne-python | mne/viz/raw.py | 2 | 30957 | """Functions to plot raw M/EEG data
"""
from __future__ import print_function
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
import copy
from functools import partial
import numpy as np
from ..externals.six import string_types
from ..io.pick import pick_types
from ..io.proj import setu... | bsd-3-clause |
jakevdp/altair | altair/vegalite/v3/api.py | 1 | 74944 | # -*- coding: utf-8 -*-
import warnings
import hashlib
import json
import jsonschema
import six
import pandas as pd
from .schema import core, channels, mixins, Undefined, SCHEMA_URL
from .data import data_transformers, pipe
from ... import utils, expr
from .display import renderers, VEGALITE_VERSION, VEGAEMBED_VERS... | bsd-3-clause |
keflavich/pvextractor | ah_bootstrap.py | 1 | 37360 | """
This bootstrap module contains code for ensuring that the astropy_helpers
package will be importable by the time the setup.py script runs. It also
includes some workarounds to ensure that a recent-enough version of setuptools
is being used for the installation.
This module should be the first thing imported in th... | bsd-3-clause |
plotly/python-api | packages/python/plotly/plotly/figure_factory/_county_choropleth.py | 1 | 33743 | import io
import numpy as np
import os
import pandas as pd
import warnings
from math import log, floor
from numbers import Number
from plotly import optional_imports
import plotly.colors as clrs
from plotly.figure_factory import utils
from plotly.exceptions import PlotlyError
import plotly.graph_objs as go
pd.option... | mit |
mne-tools/mne-python | mne/utils/docs.py | 1 | 115901 | # -*- coding: utf-8 -*-
"""The documentation functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
from copy import deepcopy
import inspect
import os
import os.path as op
import sys
import warnings
import webbrowser
from ..defaults import HEAD_SIZE_DEFAULT
from ..externals.doccer ... | bsd-3-clause |
hadim/spindle_tracker | spindle_tracker/tracking/cen2_tracker.py | 1 | 38982 | import logging
import os
import itertools
import numpy as np
import pandas as pd
import scipy.spatial.distance as dist
import scipy.cluster.hierarchy as hier
from ..tracker.solver import ByFrameSolver
from ..utils.progress import progress_apply
from ..trajectories import Trajectories
from ..io.trackmate import track... | bsd-3-clause |
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