repo_name string | path string | copies string | size string | content string | license string |
|---|---|---|---|---|---|
GGiecold/Cluster_Ensembles | src/Cluster_Ensembles/Cluster_Ensembles.py | 1 | 48335 | #!/usr/bin/env python
# Cluster_Ensembles/src/Cluster_Ensembles/Cluster_Ensembles.py;
# Author: Gregory Giecold for the GC Yuan Lab
# Affiliation: Harvard University
# Contact: g.giecold@gmail.com, ggiecold@jimmy.harvard.edu
"""Cluster_Ensembles is a package for combining multiple partitions
into a consolidated c... | mit |
rs2/pandas | pandas/tests/scalar/period/test_period.py | 1 | 52954 | from datetime import date, datetime, timedelta
import numpy as np
import pytest
import pytz
from pandas._libs.tslibs import iNaT, period as libperiod
from pandas._libs.tslibs.ccalendar import DAYS, MONTHS
from pandas._libs.tslibs.parsing import DateParseError
from pandas._libs.tslibs.period import INVALID_FREQ_ERR_MS... | bsd-3-clause |
iotile/python_iotile_cloud | iotile_cloud/utils/mock_cloud.py | 1 | 48542 | """A simple mock iotile.cloud server for testing cloud interactions.
This class can be directly instantiated or used as a pytest fixture
with the name mock_cloud. It requires the following additional package:
- pytest_localserver
The point of this class is to allow spinning up an API-compatible
iotile.cloud server ... | mit |
pyrocko/kite | src/quadtree.py | 1 | 35440 | import numpy as num
import time
from hashlib import sha1
from pyrocko import guts
from pyrocko import orthodrome as od
from .util import Subject, property_cached, derampMatrix
class QuadNode(object):
""" A node (or *tile*) in held by :class:`~kite.Quadtree`. Each node in the
tree hold a back reference to the... | gpl-3.0 |
teolisitza/turtleart | ipython_histories/06102015.3rdgrade.py | 1 | 47954 | Last login: Tue Jun 9 22:22:23 on ttys010
MBPro ~> cd kids_sessions/
MBPro kids_sessions> ls
Screen Shot 2015-03-30 at 8.17.22 PM.png
Screen Shot 2015-03-31 at 2.09.39 PM.png
alessa.out
ava.eps
ava2.eps
ava3.eps
ava4.eps
ava_3_3_15.out
ava_advanced.png
ava_graph.eps
ava_graph.png
ava_graph2.out
avagraph.out
avagraph2.... | apache-2.0 |
danmoser/pyhdust | pyhdust/tabulate.py | 1 | 39690 | # -*- coding: utf-8 -*-
"""PyHdust auxiliary module: third-part pretty-print tabular data.
:license: MIT License
"""
from __future__ import print_function, unicode_literals
from collections import namedtuple
from platform import python_version_tuple
import re
if python_version_tuple()[0] < "3":
from itertools im... | gpl-3.0 |
marianotepper/dask | dask/bag/core.py | 1 | 30985 | from __future__ import absolute_import, division, print_function
import itertools
import math
import tempfile
import inspect
import gzip
import bz2
import os
try:
from urllib2 import urlopen
except ImportError:
from urllib.request import urlopen
from glob import glob
from collections import Iterable, Iterato... | bsd-3-clause |
uber/ludwig | ludwig/utils/visualization_utils.py | 1 | 40951 | #! /usr/bin/env python
# coding=utf-8
# Copyright (c) 2019 Uber Technologies, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unles... | apache-2.0 |
lfairchild/PmagPy | programs/thellier_gui.py | 1 | 399529 | #!/usr/bin/env pythonw
"""
Runs Thellier GUI PmagPy's main analysis GUI for thellier-type
paleointensity data. This can be used to obtain intensities for Thermal and
Microwave data. It allows export of figures and analysis results for upload
to the MagIC database and/or publication. For more information on how to
inter... | bsd-3-clause |
Tomasz-Kluczkowski/Weather-App | weather_app/weather_gui.py | 1 | 66718 | # Title: Weather App
# Author: Tomasz Kluczkowski
# email: tomaszk1@hotmail.co.uk
import platform
import os
import sys
import threading
import tkinter as tk
import tkinter.ttk as tkk
from PIL import Image, ImageTk
from weather_backend import Report
from controller import Controller
# Data file folders.
if getattr(sys... | mit |
boomsbloom/dtm-fmri | DTM/for_gensim/lib/python2.7/site-packages/matplotlib/widgets.py | 1 | 72785 | """
GUI Neutral widgets
===================
Widgets that are designed to work for any of the GUI backends.
All of these widgets require you to predefine an :class:`matplotlib.axes.Axes`
instance and pass that as the first arg. matplotlib doesn't try to
be too smart with respect to layout -- you will have to figure ou... | mit |
bgruening/EDeN | eden/graph.py | 1 | 43711 | #!/usr/bin/env python
import math
import numpy as np
from scipy import stats
from scipy.sparse import csr_matrix
from numpy.linalg import norm
from sklearn.linear_model import SGDClassifier
from sklearn.cluster import MiniBatchKMeans
from collections import defaultdict, deque
import itertools
import networkx as nx
imp... | gpl-3.0 |
vorwerkc/pymatgen | pymatgen/io/gaussian.py | 1 | 59625 | # coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements input and output processing from Gaussian.
"""
import re
import warnings
import numpy as np
import scipy.constants as cst
from monty.io import zopen
from pymatgen.core.composition ... | mit |
hrichstein/Stellar_mass_env_Density | Codes/Scripts/centrals_plotting.py | 1 | 51428 | # neigh_dict and nn_dict are the same thing.
# Need to combine/change variables at some point
# In[251]:
from __future__ import division, absolute_import
import astropy.stats
import glob
import math
import matplotlib.pyplot as plt
from matplotlib import ticker
from matplotlib.ticker import FormatStrFormatter
impor... | mit |
xji3/IGCexpansion | IGCexpansion/IndCodonGeneconv.py | 1 | 87306 | # This is Xiang's lazyness driven compromise.
# This differs from CodonGeneconv.py by that IGC in this file is assumed to be independent of sequence types aka context independent
# Uses Alex Griffing's JsonCTMCTree package for likelihood and gradient calculation
# Re-write of my previous CodonGeneconv class
# com... | gpl-3.0 |
davidhwyllie/findNeighbour2 | src/ewsnpstore.py | 1 | 37792 | # ew interface
# necessary libraries
import os
import unittest
import sqlalchemy
import uuid
import logging
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy import Table, Column, Integer, String, Float, DateTime, MetaData, select, func, or_, and_
from sqlalchemy import create_engine,... | lgpl-3.0 |
vortex-ape/scikit-learn | sklearn/utils/tests/test_validation.py | 2 | 30008 | """Tests for input validation functions"""
import warnings
import os
from tempfile import NamedTemporaryFile
from itertools import product
import pytest
from pytest import importorskip
import numpy as np
import scipy.sparse as sp
from scipy import __version__ as scipy_version
from sklearn.utils.testing import asser... | bsd-3-clause |
ceos-seo/data_cube_utilities | data_cube_utilities/wasard.py | 1 | 33773 | import datacube
import xarray as xr
import datetime
import warnings
import numpy as np
from datetime import datetime
from time import time
import matplotlib.pyplot as plt
from .dc_water_classifier import wofs_classify
import random
import itertools
from sklearn import svm
# from sklearn.externals import joblib
import... | apache-2.0 |
mistercrunch/panoramix | tests/db_engine_specs/presto_tests.py | 1 | 42322 | # 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 u... | apache-2.0 |
jmschrei/scikit-learn | sklearn/ensemble/forest.py | 1 | 64715 | """Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | bsd-3-clause |
ezralanglois/arachnid | arachnid/app/autopick.py | 1 | 36461 | ''' Automated particle selection (AutoPicker)
This script (`ara-autopick`) was designed locate particles on a micrograph using template matching
(like LFCPick), yet incorporates several post-processing algorithms to reduce the number of noise
windows and contaminants.
It will not remove all contaminants but experim... | gpl-2.0 |
vdrhtc/Measurement-automation | drivers/keysightM3202A.py | 1 | 34308 | """
product link:
https://www.keysight.com/en/pd-2747446-pn-M3202A/pxie-arbitrary-waveform-generator-1-gs-s-14-bit-400-mhz?cc=RU&lc=en
user's guide for Keysight SD1 version 2.x
https://literature.cdn.keysight.com/litweb/pdf/M3201-90001.pdf?id=2787170
user's guide for Keysight SD1 version 3.x
https://literature.cdn.ke... | gpl-3.0 |
tgquintela/pySpatialTools | pySpatialTools/tests/test_retriever.py | 1 | 66654 |
"""
test retrievers
---------------
test for retrievers precoded and framework of retrievers.
"""
import numpy as np
from itertools import product
# Auxiliars
from pySpatialTools.utils.neighs_info import Neighs_Info
from pySpatialTools.SpatialRelations.relative_positioner import\
metric_distances, BaseRelativeP... | mit |
MSeifert04/astropy | astropy/visualization/wcsaxes/core.py | 1 | 30826 | # Licensed under a 3-clause BSD style license - see LICENSE.rst
from functools import partial
from collections import defaultdict
import numpy as np
from matplotlib import rcParams
from matplotlib.artist import Artist
from matplotlib.axes import Axes, subplot_class_factory
from matplotlib.transforms import Affine2D,... | bsd-3-clause |
cuemacro/chartpy | chartpy/style.py | 1 | 31010 | from __future__ import division
__author__ = 'saeedamen' # Saeed Amen
#
# Copyright 2016 Cuemacro
#
# 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
#
... | apache-2.0 |
pjryan126/solid-start-careers | store/api/zillow/venv/lib/python2.7/site-packages/pandas/io/tests/test_excel.py | 1 | 82123 | # pylint: disable=E1101
from pandas.compat import u, range, map, openpyxl_compat, BytesIO, iteritems
from datetime import datetime, date, time
import sys
import os
from distutils.version import LooseVersion
import warnings
import operator
import functools
import nose
from numpy import nan
import numpy as np
from num... | gpl-2.0 |
simongibbons/numpy | numpy/core/tests/test_multiarray.py | 1 | 315482 | import collections.abc
import tempfile
import sys
import shutil
import warnings
import operator
import io
import itertools
import functools
import ctypes
import os
import gc
import weakref
import pytest
from contextlib import contextmanager
from numpy.compat import pickle
import pathlib
import builtins
from decimal i... | bsd-3-clause |
lcpt/xc | python_modules/rough_calculations/masonryVault.py | 1 | 30527 | #-*- coding: utf-8 -*-
from __future__ import division
import scipy.interpolate
from matplotlib import pyplot as plt
import numpy
'''Based on the thesis: Capacité portante de ponts en arc en maçonnerie de pierre naturelle - Modèle d'évaluation intégrant le niveau d'endommagement. Alix Grandjean (2010). documenturl: ht... | gpl-3.0 |
MiraHead/mlmvn | src/gui/matplotlib_embed/backend_gtk3.py | 1 | 31701 | from __future__ import (absolute_import, division, print_function,
unicode_literals)
import os, sys
def fn_name(): return sys._getframe(1).f_code.co_name
try:
import gi
except ImportError:
raise ImportError("Gtk3 backend requires pygobject to be installed.")
try:
gi.require_versio... | gpl-2.0 |
polakowo/plnx-grabber | plnxgrabber/__init__.py | 1 | 32357 | # Grabber of trade history from Poloniex exchange
# https://github.com/polakowo/plnx-grabber
#
# Copyright (C) 2017 https://github.com/polakowo/plnx-grabber
# 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-3.0 |
yiqingj/airflow | airflow/www/views.py | 1 | 81375 | # -*- coding: utf-8 -*-
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
... | apache-2.0 |
colinbrislawn/scikit-bio | skbio/sequence/tests/test_sequence.py | 1 | 113531 | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | bsd-3-clause |
jbloom/mapmuts | src/main.py | 1 | 36335 | """Module for performing main script functions for `mapmuts` package.
This module contains higher-level functions that are designed to be
called fairly directly by scripts to perform complete operations in the
mapping of sequencing reads to genes.
List of functions
-------------------
`MakeAlignments` : Takes input ... | gpl-3.0 |
CompPhysics/ThesisProjects | doc/MSc/msc_students/former/vegard/kode/wlagui.py | 1 | 80203 | #pythonw wlagui.py
from Tkinter import *
import os, time, Pmw, tkFileDialog, tkMessageBox, tkSimpleDialog, master
import matplotlib.pyplot as mpl
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
class Gui:
def __init__(self, parent):
self.master = parent
#Set title of program
... | cc0-1.0 |
kevinnguyeneng/django-uwsgi-nginx | app/naf_autoticket/Modules/AggregateIncident.py | 1 | 33647 | # -*- coding: utf-8 -*-
__author__ = 'admin'
from naf_autoticket.models import AlertInfo, IssueLogDB, IncidentQueue, IncidentTicketProcess,IncidentQueueMapTicket
from naf_autoticket.Modules.jsonclient import getJsonClient
from naf_autoticket.Modules.Notifications import Notification_MFlow, Notification_ALERT_MSTEAM... | gpl-3.0 |
thunderhoser/GewitterGefahr | gewittergefahr/gg_utils/echo_top_tracking.py | 1 | 75000 | """Implements the echo-top-based storm-tracking algorithm.
This algorithm is discussed in Section 3c of Homeyer et al. (2017). The main
advantage of this algorithm (in my experience) over segmotion (Lakshmanan and
Smith 2010) is that it provides more intuitive and longer storm tracks. The
main disadvantage of the ec... | mit |
r-owen/TUI | TUI/Scripts/Telescope/Pointing Data.py | 1 | 50125 | #!/usr/bin/env python
from __future__ import division, absolute_import
"""Collect data for the telescope pointing model
To make a quiver plot on a radial plot, simply compute the vectors in x-y
<http://stackoverflow.com/questions/13828800/how-to-make-a-quiver-plot-in-polar-coordinates>
radii = np.linspace(0.5,1,10)
th... | bsd-3-clause |
plotly/python-api | packages/python/plotly/plotly/graph_objs/_cone.py | 1 | 83525 | from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Cone(_BaseTraceType):
# class properties
# --------------------
_parent_path_str = ""
_path_str = "cone"
_valid_props = {
"anchor",
"autocolorscale",
"cauto",
"cmax",
... | mit |
Shaswat27/scipy | scipy/special/add_newdocs.py | 1 | 74473 | # Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | bsd-3-clause |
yavalvas/yav_com | build/matplotlib/lib/matplotlib/tests/test_mlab.py | 1 | 116853 | from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import tempfile
from numpy.testing import assert_allclose, assert_array_equal
import numpy as np
from nose.tools import (assert_equal, assert_almost_equal, assert_not_equal,
... | mit |
RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/doc/sphinxext/gen_rst.py | 2 | 38923 | """
Example generation for the scikit learn
Generate the rst files for the examples by iterating over the python
example files.
Files that generate images should start with 'plot'
"""
from __future__ import division, print_function
from time import time
import ast
import os
import re
import shutil
import traceback
i... | bsd-3-clause |
MTgeophysics/mtpy | legacy/occamtools.py | 1 | 287469 | # -*- coding: utf-8 -*-
"""
Created on Tue Aug 23 11:54:38 2011
@author: a1185872
"""
import fnmatch
import os
import shutil
import subprocess
import time
from operator import itemgetter
import matplotlib.colorbar as mcb
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as np
import... | gpl-3.0 |
MicrosoftGenomics/FaST-LMM | fastlmm/association/heritability_spatial_correction.py | 1 | 31016 | from fastlmm.util.runner import *
import logging
import fastlmm.pyplink.plink as plink
import pysnptools.util.pheno as pstpheno
import pysnptools.util as pstutil
import fastlmm.util.util as flutil
import numpy as np
import scipy.stats as stats
from pysnptools.snpreader import Bed
from pysnptools.standardizer import Dia... | apache-2.0 |
e-koch/pyspeckit | pyspeckit/spectrum/models/ammonia.py | 1 | 54193 | """
========================================
Ammonia inversion transition TROT fitter
========================================
Ammonia inversion transition TROT fitter translated from Erik Rosolowsky's
http://svn.ok.ubc.ca/svn/signals/nh3fit/
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
Module API
^^^... | mit |
apache/incubator-superset | tests/viz_tests.py | 1 | 53531 | # 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 u... | apache-2.0 |
phobson/statsmodels | statsmodels/tsa/vector_ar/var_model.py | 1 | 50532 | """
Vector Autoregression (VAR) processes
References
----------
Lutkepohl (2005) New Introduction to Multiple Time Series Analysis
"""
from __future__ import division, print_function
from statsmodels.compat.python import (range, lrange, string_types, StringIO, iteritems,
cStringIO)
fr... | bsd-3-clause |
evenmarbles/mlpy | mlpy/stats/_multivariate.py | 1 | 40793 | from __future__ import division, print_function, absolute_import
# noinspection PyUnresolvedReferences
from six.moves import range
import numpy as np
from scipy import linalg, special
from scipy.misc import doccer
__all__ = ["multivariate_normal", "multivariate_student", "invwishart", "normal_invwishart", "multigamma... | mit |
ctzhu/lifemodels | lifemodels/s_models.py | 1 | 32098 | import mortdist
import mortdist_cpsh
import util
import patsy
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import scipy.optimize as so
import scipy.integrate as si
import scipy.stats as ss
import itertools
#legacy import
import DeDayMLEcore as core
#_x = np.linspace(-10, 10, 10)
#_y = np.l... | mit |
sho-87/cognitive-battery | tasks/mrt.py | 1 | 38850 | import os
import time
import pandas as pd
import numpy as np
import pygame
from pygame.locals import *
from sys import exit
class MRT(object):
def __init__(self, screen, background):
# Get the pygame display window
self.screen = screen
self.background = background
# sets font and... | mit |
plotly/python-api | packages/python/plotly/plotly/graph_objs/layout/ternary/_aaxis.py | 1 | 66366 | from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Aaxis(_BaseLayoutHierarchyType):
# class properties
# --------------------
_parent_path_str = "layout.ternary"
_path_str = "layout.ternary.aaxis"
_valid_props = {
"color",
... | mit |
dennisss/sympy | sympy/utilities/runtests.py | 1 | 78688 | """
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | bsd-3-clause |
yl565/statsmodels | statsmodels/regression/linear_model.py | 1 | 98603 | # TODO: Determine which tests are valid for GLSAR, and under what conditions
# TODO: Fix issue with constant and GLS
# TODO: GLS: add options Iterative GLS, for iterative fgls if sigma is None
# TODO: GLS: default if sigma is none should be two-step GLS
# TODO: Check nesting when performing model based tests, lr, wald,... | bsd-3-clause |
mitdbg/aurum-datadiscovery | ontomatch/matcher_lib.py | 1 | 71844 | from enum import Enum
import time
from collections import defaultdict
from nltk.corpus import stopwords
from dataanalysis import nlp_utils as nlp
from ontomatch import glove_api
from ontomatch import ss_utils as SS
from datasketch import MinHash, MinHashLSH
from knowledgerepr.networkbuilder import LSHRandomProjectionsI... | mit |
MSeifert04/astropy | astropy/time/formats.py | 1 | 60242 | # -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import fnmatch
import time
import re
import datetime
import warnings
from decimal import Decimal
from collections import OrderedDict, defaultdict
import numpy as np
from astropy.utils.decorators import lazyproperty
from astropy.ut... | bsd-3-clause |
jewettaij/sabl_mpl | sabl_mpl/sabl.py | 1 | 136170 | #!/usr/bin/env python
# sabl.py: "spline analysis of bumps and lumps..."
#
# As of v1.3.1, matplotlib is currently too unstable and feature-poor for me
# me to recommend using it for an interactive program much fancier than this.
# If you need a more sophisticated graphical user interface (with text-entry
# fields, or... | mit |
mrshu/scikit-learn | sklearn/linear_model/ridge.py | 1 | 31987 | """
Ridge regression
"""
# Author: Mathieu Blondel <mathieu@mblondel.org>
# Reuben Fletcher-Costin <reuben.fletchercostin@gmail.com>
# Fabian Pedregosa <fabian@fseoane.net>
# License: Simplified BSD
from abc import ABCMeta, abstractmethod
import warnings
import numpy as np
from scipy import linalg
f... | bsd-3-clause |
belkinsky/SFXbot | src/pyAudioAnalysis/audioFeatureExtraction.py | 1 | 32091 | import sys
import time
import os
import glob
import numpy
import pickle
import aifc
import math
from numpy import NaN, Inf, arange, isscalar, array
from scipy.fftpack import rfft
from scipy.fftpack import fft
from scipy.fftpack.realtransforms import dct
from scipy.signal import fftconvolve
from matplotlib.mlab import f... | mit |
loli/sklearn-ensembletrees | sklearn/hmm.py | 2 | 48577 | # Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | bsd-3-clause |
skymanaditya1/numpy | numpy/core/tests/test_multiarray.py | 1 | 221200 | from __future__ import division, absolute_import, print_function
import collections
import tempfile
import sys
import shutil
import warnings
import operator
import io
import itertools
if sys.version_info[0] >= 3:
import builtins
else:
import __builtin__ as builtins
from decimal import Decimal
import numpy as... | bsd-3-clause |
chrisfilo/NeuroVault | neurovault/apps/statmaps/views.py | 1 | 71339 | import csv
import functools
import gzip
import json
import nibabel as nib
import shutil
import numpy as np
import os
import re
import shutil
import tarfile
import tempfile
import traceback
import urllib
import zipfile
import zipstream
from collections import OrderedDict
from django.contrib import messages
from django.c... | mit |
thomasvangurp/epiGBS | Arabidopsis analysis/DMP_comparison_Arabidopsis_thaliana.py | 1 | 31771 | __author__ = 'thomasvangurp'
"""Filter methylation bed file with coverage criterion on both strands"""
from Bio import SeqIO
import os
import subprocess
from scipy import stats
def split_sample(header,dir,type):
"""Split watson and crick bam file into sample specific reads groups"""
for name in header[4:]:
... | mit |
miic-sw/miic | miic.core/src/miic/core/stretch_mod_pre.py | 1 | 41439 | """
@author:
Eraldo Pomponi
@copyright:
The MIIC Development Team (eraldo.pomponi@uni-leipzig.de)
@license:
GNU Lesser General Public License, Version 3
(http://www.gnu.org/copyleft/lesser.html)
Created on Aug 19, 2011
"""
# Main imports
import numpy as np
import scipy.ndimage
from scipy.interpolate import Univaria... | gpl-3.0 |
ChyLau/weviation | weviation/old/notebook.py | 1 | 51341 | import wx
import methods
import parse as p
import numpy as np
import matplotlib
from matplotlib.figure import Figure
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
from matplotlib import cm
class TabTorenbeek(wx.ScrolledWindow):
def __init__(self, parent):
""""""
wx... | gpl-2.0 |
datapythonista/pandas | pandas/tests/frame/test_reductions.py | 1 | 60840 | from datetime import timedelta
from decimal import Decimal
from dateutil.tz import tzlocal
import numpy as np
import pytest
from pandas.compat import is_platform_windows
import pandas.util._test_decorators as td
from pandas.core.dtypes.common import is_categorical_dtype
import pandas as pd
from pandas import (
... | bsd-3-clause |
nickhand/pyRSD | pyRSD/rsdfit/results/emcee_results.py | 1 | 33251 | from ... import numpy as np
from .. import logging
import scipy.stats
from collections import OrderedDict
import warnings
logger = logging.getLogger('rsdfit.emcee_results')
logger.addHandler(logging.NullHandler())
class EmceeParameter(object):
"""
Class to hold the parameter fitting result
"""
def __i... | gpl-3.0 |
mbrner/funfolding | funfolding/model/_model.py | 1 | 48690 | import warnings
import numpy as np
from scipy import linalg
from scipy import stats
from numpy.linalg import svd
class Model(object):
name = 'Model'
status_need_for_eval = 0
""" Base class for a model. Actual models should inherit from this class.
In this class the functions that should be implemente... | mit |
OpenDrift/opendrift | tests/models/test_run.py | 1 | 43525 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of OpenDrift.
#
# OpenDrift 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, version 2
#
# OpenDrift is distributed in the hope that it will b... | gpl-2.0 |
wilmarcardonac/fisher-mcmc | class_montanari-lensing/plot_comparison_cls.py | 1 | 33358 | import matplotlib as mpl
mpl.use('Agg')
import numpy as np
import matplotlib.pyplot as py
#import pylab as py
# Loading data files into arrays
# Fiducial model without anisotropic stress
Clfid = np.loadtxt('../data/Cl_fiducial_lensing_cl.dat',unpack=True)
Clfidnl = np.loadtxt('../data/Cl_fiducial_no_lensing_cl.dat... | gpl-2.0 |
kedz/cuttsum | trec2015/cuttsum/pipeline/_features.py | 1 | 32241 | from cuttsum.resources import MultiProcessWorker
from cuttsum.pipeline import DedupedArticlesResource
from cuttsum.misc import english_stopwords, event2lm_name
import cuttsum.srilm
import gzip
import corenlp as cnlp
import os
import re
from itertools import izip
import numpy as np
from nltk.corpus import wordnet as wn
... | apache-2.0 |
davidbrown3/reinforcement-learning | lib/RL_Library.py | 1 | 48315 | import itertools
import os
import sys
import gym
import numpy as np
import click
import time
import plotly.offline as py
import plotly.graph_objs as go
import pickle
import math
import tflearn
import tensorflow as tf
from collections import deque
from operator import itemgetter
from timeit import default_timer as tim... | mit |
darcamo/pyphysim | pyphysim/channels/pathloss.py | 1 | 53936 | #!/usr/bin/env python
"""
Implement classes for several Path loss models.
The :class:`PathLossBase` class implements the common code to every path loss model and
only two methods need to be implemented in subclasses: the
:meth:`PathLossBase.which_distance_dB` and the
:meth:`PathLossBase._calc_deterministic_path_loss_d... | gpl-2.0 |
aashish24/seaborn | seaborn/distributions.py | 1 | 80369 | """Plotting functions for visualizing distributions."""
from __future__ import division
from textwrap import dedent
import colorsys
import numpy as np
from scipy import stats
import pandas as pd
from pandas.core.series import remove_na
import matplotlib as mpl
import matplotlib.pyplot as plt
import warnings
try:
i... | bsd-3-clause |
aaronprunty/starfish | vezda/plotWiggles.py | 1 | 31532 | # Copyright 2017-2018 Aaron C. Prunty
#
# 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 agree... | apache-2.0 |
jluscher/SCANIT | scanit_v034.py | 1 | 90959 | #! /usr/bin/env python3
#
# SCANIT - Control A spectrometer and collect data
#
# LICENSE:
# This work is licensed under the Creative Commons Zero License
# Creative Commons CC0.
# To view a copy of this license, visit
# http://directory.fsf.org/wiki/License:CC0
# or send a letter to:
# Creative Commons, PO Box 1866, M... | cc0-1.0 |
aclerc/PCWG | Analysis.py | 1 | 66316 | import pandas as pd
import numpy as np
import scipy as sp
import hashlib
import os
import datetime
import math
import configuration
import dataset
from dataset import DeviationMatrix
import binning
import turbine
import rews
import reporting
def chckMake(path):
"""Make a folder if it doesn't exist"""
if not... | mit |
meteoswiss-mdr/precipattractor | pymodules/stat_tools_attractor.py | 1 | 59730 | #!/usr/bin/env python
'''
Module to perform various statistics on the data
(anisotropy estimation, spectral slope computation, WAR statistics, etc).
Documentation convention from https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
26.09.2016
Loris Foresti
'''
from __future__ import divisio... | gpl-3.0 |
ndingwall/scikit-learn | sklearn/cluster/_kmeans.py | 1 | 78633 | """K-means clustering."""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.pretten... | bsd-3-clause |
jni/skan | skan/csr.py | 1 | 38144 | import numpy as np
import pandas as pd
from scipy import sparse, ndimage as ndi
from scipy.sparse import csgraph
from scipy import spatial
import numba
from .nputil import raveled_steps_to_neighbors
## NBGraph and Numba-based implementation
csr_spec = [
('indptr', numba.int32[:]),
('indices', numba.int32[:]... | bsd-3-clause |
kushalbhola/MyStuff | Practice/PythonApplication/env/Lib/site-packages/pandas/tests/indexes/interval/test_interval.py | 1 | 42578 | from itertools import permutations
import re
import numpy as np
import pytest
import pandas as pd
from pandas import (
Index,
Interval,
IntervalIndex,
Timedelta,
Timestamp,
date_range,
interval_range,
isna,
notna,
timedelta_range,
)
import pandas.core.common as com
from pandas.... | apache-2.0 |
dparks1134/STAMP | stamp/STAMP.py | 1 | 86724 | #=======================================================================
# Author: Donovan Parks
#
# Copyright 2011 Donovan Parks
#
# This file is part of STAMP.
#
# STAMP 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 F... | gpl-3.0 |
andrew-lundgren/gwpy | gwpy/plotter/core.py | 1 | 34460 | # -*- coding: utf-8 -*-
# Copyright (C) Duncan Macleod (2013)
#
# This file is part of GWpy.
#
# GWpy 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 ... | gpl-3.0 |
fjorba/invenio | modules/webstat/lib/webstat_engine.py | 1 | 93984 | ## This file is part of Invenio.
## Copyright (C) 2007, 2008, 2010, 2011 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later ... | gpl-2.0 |
kbase/coexpression | lib/biokbase/CoExpression/CoExpressionImpl.py | 2 | 38468 | #BEGIN_HEADER
import os
import sys
import traceback
import argparse
import json
import logging
import time
from pprint import pprint
import string
import subprocess
from os import environ
from ConfigParser import ConfigParser
import re
from collections import OrderedDict
import uuid
from string import Template
# 3rd ... | mit |
Danie1Johnson/research | polyhedra.py | 1 | 42880 | import numpy as np
import scipy as sp
import os
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.cm as cm
#give coordinates of polyhedra centered at origin with unit edges and face cent... | mit |
ARM-software/trappy | trappy/ftrace.py | 1 | 36891 | # Copyright 2015-2017 ARM Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in w... | apache-2.0 |
jaeilepp/eggie | mne/preprocessing/ica.py | 1 | 100890 | # Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Juergen Dammers <j.dammers@fz-juelich.de>
#
# License: BSD (3-clause)
import warnings
from copy import deepcopy
from inspect import getargspec, isfunction
from collections import ... | bsd-2-clause |
GEMScienceTools/gmpe-smtk | smtk/trellis/configure.py | 1 | 36003 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# Copyright (C) 2014-2017 GEM Foundation and G. Weatherill
#
# OpenQuake is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License as published
# by the Free Software F... | agpl-3.0 |
dmargala/blupe | python/correction.py | 1 | 30609 | #!/usr/bin/env python
import argparse
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
# import warnings
# warnings.filterwarnings('error', category=FutureWarning)
# np.seterr(all='raise')
import matplotlib.pyplot as plt
import scipy.interpolate
import bossdata
import specsim
from astropy.table import ... | mit |
SiLab-Bonn/pyBAR | pybar/analysis/analyze_raw_data.py | 1 | 88134 | ''' Script to convert the raw data and to plot all histograms'''
from __future__ import division
import logging
import warnings
import os
import multiprocessing as mp
from functools import partial
from matplotlib.backends.backend_pdf import PdfPages
import tables as tb
from tables import dtype_from_descr, Col
import ... | bsd-3-clause |
kecnry/autofig | autofig/call.py | 1 | 115058 | import numpy as np
import astropy.units as u
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.collections import LineCollection, PolyCollection
from mpl_toolkits.mplot3d.art3d import Line3DCollection, Poly3DCollection
from . import common
from . import callbacks
def _map_none(v... | gpl-3.0 |
Alex-Ian-Hamilton/sunpy | sunpy/cm/color_tables.py | 1 | 78490 | """
Nothing here but dictionaries for generating LinearSegmentedColormaps,
and a dictionary of these dictionaries.
"""
from __future__ import absolute_import, division, print_function
import numpy as np
import matplotlib.colors as colors
from sunpy.extern.six.moves import range, zip
__all__ = ['aia_color_table', 'las... | bsd-2-clause |
boland1992/seissuite_iran | seissuite/ant/pscrosscorr.py | 2 | 152285 | #!/usr/bin/env python
"""
Module that contains classes holding cross-correlations and related
processing, such as frequency-time analysis (FTAN) to measure
dispersion curves.
"""
from seissuite.ant import pserrors, psutils, pstomo
import obspy.signal
try:
import obspy.io.xseed
except:
import obspy.xseed
... | gpl-3.0 |
CoucheLimite/LifetimeSpectroscopy | IDLSanalyzer_process.py | 1 | 38747 | import numpy as np
import sys
import os
import time as tm
import openpyxl as xls
from PyQt5.QtWidgets import QApplication, QMainWindow, QFileDialog, QListWidgetItem, QLineEdit, QLabel, QRadioButton, QGridLayout, QPushButton, QAction, QActionGroup, QMenu, QInputDialog
from PyQt5 import QtGui, QtWidgets
from PyQt5... | mit |
plotly/plotly.py | packages/python/plotly/plotly/graph_objs/layout/ternary/_aaxis.py | 1 | 67629 | from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Aaxis(_BaseLayoutHierarchyType):
# class properties
# --------------------
_parent_path_str = "layout.ternary"
_path_str = "layout.ternary.aaxis"
_valid_props = {
"color",
... | mit |
vtsuperdarn/davitpy | davitpy/utils/plotUtils.py | 1 | 38386 | # -*- coding: utf-8 -*-
# Copyright (C) 2012 VT SuperDARN Lab
# Full license can be found in LICENSE.txt
"""plotUtils module
Plotting utilities (maps, colormaps, ...)
Functions
--------------------------------------------------------------
genCmap generate a custom colormap
drawCB draw a colorbar
cu... | gpl-3.0 |
mulhod/bob_dylan_lyrics | bob_dylan_lyrics/__init__.py | 1 | 30754 | """
Collection of variables, methods, and functions that support the
functionality of the `htmlify` module. Code contained here ranges from
defining types for commonly-used data structures, organizing data
related to albums/songs into classes, providing functions for reading
in album/song metadata, and generally pre-/p... | mit |
bdh1011/wau | venv/lib/python2.7/site-packages/pandas/tseries/tdi.py | 1 | 30928 | """ implement the TimedeltaIndex """
from datetime import timedelta
import numpy as np
from pandas.core.common import (ABCSeries, _TD_DTYPE, _INT64_DTYPE,
is_timedelta64_dtype, _maybe_box,
_values_from_object, isnull, is_integer, is_float)
from pandas.cor... | mit |
phobson/bokeh | bokeh/charts/glyphs.py | 1 | 36921 | from __future__ import absolute_import, division
from collections import defaultdict
import numpy as np
import pandas as pd
from bokeh.charts import DEFAULT_PALETTE
from bokeh.core.enums import DashPattern
from bokeh.models.glyphs import Rect, Segment, Line, Patches, Arc
from bokeh.models.renderers import GlyphRende... | bsd-3-clause |
dmitriz/zipline | tests/test_algorithm.py | 1 | 68007 | #
# Copyright 2014 Quantopian, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | apache-2.0 |
dp7-PU/QCLAS_public | src/hapi.py | 1 | 751958 | # -*- coding: utf-8 -*-
'''
This module provides an access to the HITRAN data.
Data is downloaded and cached.
This module serves as a simple database manager frontend.
API is aimed to be RESTful, which means that interaction
between local API and remote data-server will be held
via sending RESTful queries (API->rem... | mit |
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