text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import calendar
import ccdproc
import collections
import datetime
import glob
import logging
import math
import numpy as np
import os
import pandas
import random
import re
import scipy
import subprocess
import ... | soar-telescope/goodman | goodman_pipeline/core/core.py | Python | bsd-3-clause | 177,808 | [
"Gaussian"
] | bde14b46eed66c342b7e95ae03b0070b57f5d03fbad909d05f290e474ae1846b |
#! /usr/bin/env python
#Parser for blast -m 8 or blast+ -m 6 and 7 output file with description inserted
import sys
##Query id,Subject id,Description, % identity, alignment length,mismatches,gap openings,q. start,q. end,s. start,s. end,e-value,bit score
dict1={}
for line in open(sys.argv[1]):
data = line.split('\t'... | chnops/code | blast_parser_b_multi.py | Python | mit | 1,213 | [
"BLAST"
] | 44a533fd878a85560c193ca6e9531c9cb743b066c21ed0ab45235acca1a0d247 |
from sys import exit, stderr, argv
from math import log10, pi
import re
import json
try :
#import cairo
import cairocffi as cairo
except ImportError :
pass
# height, width, font size, tree width
# or just box width and everything derives from that
def dendropy2internal(tnode) :
if tnode.is_leaf() :
... | ajm/seance | seance/heatmap.py | Python | gpl-3.0 | 17,157 | [
"BLAST"
] | 65b710b830418bdc88cbec4f6ee95105445ad8a4a66c14272edb993813c7b313 |
#! /usr/bin/env python
import sys
sys.path.insert(0, '../')
from config import config as cc
cc.loadConfig('../local/config.yml')
import db.db as db
import pandas as pd
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import MACCSkeys
from sets import Set
LELIMIT = 10000
... | PMitura/smiles-neural-network | computing/rdkit_db.py | Python | bsd-3-clause | 4,216 | [
"RDKit"
] | 59808f8622ce02a69b4fdd3ae93875bbbf54e3d35fd6f299132744fad9c81b81 |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs 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, ... | JoseBlanca/ngs_crumbs | crumbs/mapping.py | Python | gpl-3.0 | 13,532 | [
"BWA",
"Bowtie"
] | aa0393406d58a2492a4d7cf1352774201029cde633d9decd65bcb0776a6600f3 |
"""Class for fitting and plotting 3 parameter Gaussian distributions."""
__author__ = "Ganesh N. Sivalingam <g.n.sivalingam@gmail.com>"
import matplotlib.pyplot as plt
import numpy as np
from scipy import optimize
class Gaussian():
def __init__(self):
self.centre = 0.0
self.fwhm = 0.0
s... | gnsiva/Amphitrite | msClasses/Gaussian.py | Python | gpl-2.0 | 3,630 | [
"Gaussian"
] | 55c2e44437d00fd97df816c3212b56eb1c9ef125c2fbd3dbc4d046c5f0c17109 |
# coding: utf-8
# wcm spint. script to log into public wifi with a script
# In[1]:
import splinter
# In[2]:
spb = splinter.Browser()
# In[3]:
spb.visit('http://10.4.0.11/upload/custom/TE%20TAKERE/Te%20Takere%20Disclaimer.html')
# In[ ]:
but = spb.find_by_name('Login')
# In[ ]:
but.click()
# In[ ]:
| wcmckee/wcmckee | wcmspint.py | Python | mit | 320 | [
"VisIt"
] | 3df458185f11ac21fb056450fc1705eb269abff330df579d652c7dabd00144a1 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import (
UniqueCourseTest,
EventsTestMixin,
load_data_str,
generate_... | AkA84/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 45,451 | [
"VisIt"
] | 0881bd171ec84904c7d9460bd3b8d2181b567036a459d2e7ea553848013129ca |
from mayavi import mlab
import numpy as np
import geoprobe
import scipy.ndimage
hor = geoprobe.horizon('data/seismic/Horizons/channels.hzn')
vol = geoprobe.volume('data/seismic/Volumes/example.vol')
data = vol.load()
# Because we're not working in inline/crossline, convert to "pixel" coords.
z = hor.grid
z = vol.mode... | joferkington/scipy2015-3d_printing | slice_3d_example.py | Python | mit | 1,014 | [
"Mayavi"
] | 3b8f58b1ed6107b80135f84c781893b5dbc0d00644f92c32034aa99e73fe9dbf |
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
#(0) Set parameters:
np.random.seed(123456789)
nResponsesA = 5
nResponsesB = 5
nNodes = 101
FWHM = 10.0
nIterations = 5000
### derived parameters:
nA,nB = nResponsesA, nResponsesB
nTotal = nA + nB
df = nA + nB ... | 0todd0000/spm1d | spm1d/rft1d/examples/val_max_2_twosample_t_1d.py | Python | gpl-3.0 | 1,413 | [
"Gaussian"
] | 4469ba78711342a44d903f34c0dcfeca95fa145f655b53c1375fb6c207d17050 |
## To Do:
## More descriptive description and use to correct terminology
# Author: Daryl Harrison
# Enthought library imports.
from enthought.traits.api import Instance, List, String, Int, Bool
from enthought.traits.ui.api import View, Group, Item
from enthought.tvtk.api import tvtk
from math import *
from numpy imp... | rjferrier/fluidity | mayavi/mayavi_amcg/filters/tensor_eigenvectors_eigenvalues.py | Python | lgpl-2.1 | 6,931 | [
"Mayavi"
] | 7f9fb466701f936e04b7e9a402d73d9604015ab5271fbd96f769c2e440cd4fcd |
"""
Jennifer's scientific computing cheatsheet - fancy formatting for plots.
Contents:
- Formatting examples
- Styles
This cheatsheet is all about making plots pretty. For the basics of
how to create different types of plots, see science_plots.py
Each section of this cheatsheet can be copy/pasted into ipython (usin... | jenfly/python-cheatsheets | science_prettyplots.py | Python | mit | 4,992 | [
"NetCDF"
] | 08c576942d2f30be8044c2874521dd44ca0d579edd8c231dc38bfbe6be443cc8 |
#!/usr/bin/python
#
# Copyright (C) 2013-2017 Free Software Foundation, Inc.
#
# This script 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, or (at your option)
# any later version.
# This s... | mickael-guene/gcc | contrib/update-copyright.py | Python | gpl-2.0 | 26,824 | [
"Brian"
] | c4152f36f3bd30cbb8bab80ef6b011d79fd15d531e3ab23e79af53758b26fcf3 |
import caching.base as caching
import jingo
import jinja2
from tower import ugettext_lazy as _
import amo
from addons.models import Addon
from api.views import addon_filter
from bandwagon.models import Collection, MonthlyPick as MP
from versions.compare import version_int
# The global registry for promo modules. Ma... | anaran/olympia | apps/discovery/modules.py | Python | bsd-3-clause | 10,747 | [
"VisIt"
] | 3f62cf713687456aa074aa52a6a59fd16a66aba38ef04c28730f901a85885260 |
#!/bin/python
import pandas as pd
import numpy as np
import os
import matplotlib
matplotlib.style.use('ggplot')
import matplotlib.pyplot as plt
from bokeh.plotting import figure, show
from bokeh.io import output_notebook, hplot
from bokeh.palettes import Spectral9, brewer
from scipy import constants
from scipy import ... | laserkelvin/IPython-Notebook-Tools | FittingRoutines.py | Python | gpl-3.0 | 44,482 | [
"Gaussian"
] | fb9dc220d680204110895239d284fc8d17a602a138cf5215bc28db8d52d1112e |
"""Weight initializer."""
from __future__ import absolute_import, print_function
import re
import logging
import warnings
import json
import numpy as np
from .base import string_types
from .ndarray import NDArray, load
from . import random
from . import registry
# inherit str for backward compatibility
class InitDesc... | likelyzhao/mxnet | python/mxnet/initializer.py | Python | apache-2.0 | 22,210 | [
"Gaussian"
] | 7cf70429b54975799bdba780e8aa65ea6a8e96bcc5fc21c3c8804346255890ff |
#!/usr/bin/env python2.7
from bioblend.galaxy import GalaxyInstance
import requests
import datetime
import argparse
requests.packages.urllib3.disable_warnings()
def parse_args():
args = argparse.ArgumentParser(description="Rename history items using a tabular file." +"\n" +
"Ex... | ARTbio/tools-artbio | scripts/helper_scripts/rename_history_items/rename_hist_items.py | Python | mit | 2,334 | [
"Galaxy"
] | 4a228368f25a05743b6144ccc64672ac33a848129607abdcaf870ac30231f4f8 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | marscher/PyEMMA | pyemma/coordinates/tests/test_random_access_stride.py | Python | lgpl-3.0 | 21,529 | [
"MDTraj",
"NetCDF"
] | 5f98a40351fe18dc05ec1dce8b1944517c0aa0c51877b231abc51a817929dbe9 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 25 11:20:57 2019
@author: butenko
"""
import os
import fileinput
def paste_to_hoc_python3(axonnodes,paranodes1,paranodes2,axoninter,axontotal,v_init,fiberD,paralength1,paralength2,nodelength,nodeD,axonD,paraD1,paraD2,deltax,nl,steps_per_ms):
#e... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Axon_files/Parameter_insertion_python3.py | Python | gpl-3.0 | 4,068 | [
"NEURON"
] | 46b78d71db4310e3fcf0f19b3c193902e90c8f7229b0addd9d8b0c1e7e52c356 |
from distutils.spawn import find_executable
from os.path import join
import h5py
import fnmatch
import shutil
import os
def remove_files():
""" Remove tmp files in cwd """
for path in fnmatch.filter(os.listdir('.'), "plams_workdir*"):
shutil.rmtree(path)
for ext in ("hdf5", "db", "lock"):
... | felipeZ/nonAdiabaticCoupling | test/utilsTest.py | Python | mit | 1,153 | [
"CP2K"
] | fda12f2cb17511de8a46a6735ba82a4d08a064e0a4f715f1c2dc791589cfeaed |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright 2011 Carlos Abalde <carlos.abalde@gmail.com>
#
# This file is part of duplicity.
#
# Duplicity 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 Foundat... | CloudBrewery/duplicity-swiftkeys | duplicity/backends/gdocsbackend.py | Python | gpl-2.0 | 8,820 | [
"VisIt"
] | f5cdfee1276cd76f02b8c5f1bc8fa7ff737e9c5d982915a10b7019bc6fc803ed |
# coding: utf-8
import os
import glob2
from flask.ext.script import Manager
from flask.ext.migrate import Migrate, MigrateCommand
from application import create_app
from application.models import db
# Used by app debug & livereload
PORT = 5000
app = create_app()
manager = Manager(app)
# db migrate commands
migrate =... | hustlzp/Flask-Boost | flask_boost/project/manage.py | Python | mit | 1,046 | [
"GULP"
] | ee69b729fc3474e6afef68a43074ca96c45dd631274f6f4938f2541ae95e45a5 |
"""
Plugin: jonni.userTracker
Tracks users in a MySQL database defined in the core.TS3db config.
Later there are some more tracked things like last visit, amount of time being on the server, ...
"""
import time
""" Changelog
-------------
2. kandru
- fixed UPDATE statements. Should now only update one user, not all
-... | Kandru/TS3eventscripts | plugins/jonni/jonni_userTracker.py | Python | gpl-3.0 | 4,236 | [
"VisIt"
] | 7ca5f5257780ab8970ce742c58fdf6422c78df740a2685b3c46cab9b5c1db16d |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | snippets/gssaRDspiny.py | Python | gpl-2.0 | 10,860 | [
"MOOSE",
"NEURON"
] | 712f3628660e9d497e29cd0a8e310a18760e08b9d73f4e3537bc496d3f289108 |
import threading
import math
import GPy
from atom.enum import Enum
from scipy.misc import logsumexp
from sklearn.cluster import MiniBatchKMeans, KMeans
from GPy.util.linalg import mdot
import numpy as np
from scipy.linalg import cho_solve, solve_triangular
from GPy.core import Model
from util import mdiag_dot, jitchol... | adezfouli/savigp | GP/savigp.py | Python | apache-2.0 | 48,556 | [
"Gaussian"
] | 535d8383723d6e87c00fb010d7e99ecf261419081993329654be341c1893c383 |
def agts(queue):
queue.add('N2Cu_relax.agts.py',
creates=['N2Cu-N2.csv', 'N2Cu-surf.csv'])
if __name__ == "__main__":
from ase.optimize.test.N2Cu_relax import *
| qsnake/gpaw | doc/devel/ase_optimize/N2Cu_relax.agts.py | Python | gpl-3.0 | 184 | [
"ASE"
] | a600d0de810c5c99a07f56704d1ff79af4d97fb2c8a7a834708c6dcc451121d4 |
"""
Geographically weighted regression
"""
import numpy as np
from .gwr.base.gwr import GWR as PySAL_GWR
from .gwr.base.sel_bw import Sel_BW
import json
from crankshaft.analysis_data_provider import AnalysisDataProvider
import plpy
class GWR:
def __init__(self, data_provider=None):
if data_provider:
... | CartoDB/crankshaft | src/py/crankshaft/crankshaft/regression/gwr_cs.py | Python | bsd-3-clause | 7,537 | [
"Gaussian"
] | ba4fac7f1314315c07726f0e64b813b9c4a71934193cfee89dd024324098d034 |
# -*- coding: utf-8 -*-
# Copyright 2018 The Conversation-AI.github.io Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... | conversationai/wikidetox | research/context/analysis/art.py | Python | apache-2.0 | 10,648 | [
"Gaussian"
] | 586e9ec6a64109e981705772065978d626ede6bb6020d84a72d7563ef9243f78 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | sandeepdsouza93/TensorFlow-15712 | tensorflow/models/image/cifar10_new/cifar10.py | Python | apache-2.0 | 14,488 | [
"Gaussian"
] | 03b80e1d4d9d979d5f48d14995e5940136c55ef77e5031e5e676b1eb6f28d1cd |
from rdkit import Geometry
from rdkit.Chem import AllChem, rdMolTransforms
class TreeNode:
"""
Class containing a node of the SyGMa tree
:key mol:
RDKit Molecule
:key parents:
Dictonary {inchikey_of_parent: rulename_transforming_parent_to_self}
:key children:
List of inchi... | 3D-e-Chem/sygma | sygma/treenode.py | Python | gpl-3.0 | 2,336 | [
"RDKit"
] | 5d23a1003a3ba321033d4ce73e2dfd372399ea6e939a268c119e19fa82abc99a |
import os
import re
import datetime
import numpy as np
from scipy.io.netcdf import NetCDFFile
COMPONENT_SEP = '.'
def read_exodb(filename):
db = DatabaseFileReader(filename)
return db.df
def read_npzdb(filename):
from pandas import DataFrame
f = np.load(filename, allow_pickle=True)
return DataFra... | matmodlab/matmodlab2 | matmodlab2/core/database.py | Python | bsd-3-clause | 15,442 | [
"NetCDF"
] | eebbbe1fcf085cf3151814e0bde053c0e4b7a4d26e37dfcff9ebf9b6dbec7c0b |
from __future__ import absolute_import
import os.path as op
import numpy as nm
from sfepy import data_dir
from sfepy.base.testing import TestCommon
import six
def init_vec(variables):
return nm.random.rand(variables.di.ptr[-1])
def check_vec(self, vec, ii, ok, conds, variables):
from sfepy.discrete.common.... | vlukes/sfepy | tests/test_conditions.py | Python | bsd-3-clause | 9,724 | [
"VTK"
] | 66ed5a8a4a8af9e5f92b9a793788b921a3c5ad149e56c605dd854a6d593ef4e3 |
import shutil
import os
def main():
# Backup current qview settings
try:
shutil.rmtree(os.path.expandvars('$HOME/.Isis/qview.squishbackup'))
except Exception:
pass
try:
os.rename(os.path.expandvars('$HOME/.Isis/qview'), os.path.expandvars('$HOME/.Isis/qview.squishbackup'))
... | corburn/ISIS | isis/src/qisis/tsts/SquishTests/suites/suite_qview/tst_Nomenclature tool/test.py | Python | gpl-3.0 | 6,705 | [
"VisIt"
] | 2f71da70785d6da1266829cfd42de88e494932b550d219b6fa7ca2654eaa465c |
import sys
from services.spawn import MobileTemplate
from services.spawn import WeaponTemplate
from resources.datatables import WeaponType
from resources.datatables import Difficulty
from resources.datatables import Options
from java.util import Vector
def addTemplate(core):
mobileTemplate = MobileTemplate... | ProjectSWGCore/NGECore2 | scripts/mobiles/yavin4/giant_crystal_snake.py | Python | lgpl-3.0 | 1,654 | [
"CRYSTAL"
] | e0ea13c4775faad55d110284111fea98055db340107504de0aa0b07e9ade9cfe |
__author__ = 'LIU Song <liusong299@gmail.com>'
__contributors__ = "Lizhe ZHU, Tiago Lobato Gimenes, Xuhui HUANG"
__version__ = "0.91"
# Copyright (c) 2016, Hong Kong University of Science and Technology (HKUST)
# All rights reserved.
# ===============================================================================
# GL... | stephenliu1989/HK_DataMiner | hkdataminer/cluster/aplod_.py | Python | apache-2.0 | 17,907 | [
"Gaussian"
] | d07f40187075016f16d7cdfd56952a84839282291817ec70151dd2975e02b6af |
from octopus.modules.es import dao
class SpreadsheetJobDAO(dao.ESDAO):
__type__ = 'spreadsheet'
@classmethod
def list_by_status(cls, status):
q = SpreadsheetStatusQuery(status)
return cls.object_query(q.query())
@classmethod
def query_by_filename(cls, filename):
return cls... | CottageLabs/oacwellcome | service/dao.py | Python | apache-2.0 | 8,316 | [
"Octopus"
] | df55692c42eff68632a27bbd641bf8d5b5db1d88999de0b44310a53d0cf3e96b |
# -*- coding: utf-8 -*-
"""print_utils.py: A library with some print functions. Very useful during
development.
Last modified: Sat Jan 18, 2014 05:01PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license... | dharmasam9/moose-core | python/moose/print_utils.py | Python | gpl-3.0 | 3,229 | [
"MOOSE"
] | 5d3a3e7d6feb677dfe4b53779a25e1c07575792001040ad68a6b371f35148c0a |
# VMware vSphere Python SDK
# Copyright (c) 2008-2016 VMware, Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | tianhao64/pyvmomi | pyVmomi/VmomiSupport.py | Python | apache-2.0 | 61,110 | [
"VisIt"
] | 2ed15b2fbe5e34a203b846c4df41d3d4b81669566a26f703063e03ee54607de2 |
#!flask/bin/python
# -*- coding: utf-8 -*-
import code
from enum import Enum
from random import shuffle
class CardValues(Enum):
ACE = 'A'
TWO = '2'
THREE = '3'
FOUR = '4'
FIVE = '5'
SIX = '6'
SEVEN = '7'
EIGHT = '8'
NINE = '9'
TEN = '10'
JACK = 'J'
QUEEN = 'Q'
KING =... | luchasei/Blackjack | blackjack.py | Python | mit | 10,251 | [
"CASINO"
] | 824c11a87c10666792ed952d389c9ef0a2ef168eda4d9bde6bbb17a2247441d7 |
# -*- coding: utf-8 -*-
"""Functions to plot evoked M/EEG data (besides topographies)."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# C... | mne-tools/mne-python | mne/viz/evoked.py | Python | bsd-3-clause | 111,067 | [
"Gaussian"
] | 63c6e2fd9e8a98bcd6c79c306d9046fedde028fbda0d79a4c1b17aad2250b9d0 |
import scanner
import unittest
class ScannerTestCase(unittest.TestCase):
def testProvides(self):
source = """
goog.provide('goog.dom');
goog.provide('goog.style');
goog.require('goog.array');
goog.require('goog.string');
"""
provides = list(scanner.YieldProvides(source))
requires = list(scanner.YieldRe... | Prachigarg1/Prachi | scanner_test.py | Python | apache-2.0 | 2,901 | [
"MOOSE"
] | ff1ecde15e6339c1b3bfa0eff5f39fd6e07acadc6a0513ab6d996bbe764f404a |
#! /usr/bin/python
import os
from setuptools import setup
def read(filename):
return open(os.path.join(os.path.dirname(__file__), filename)).read()
#
# Begin the program yo
#
setup(
name = "Blast for Basis",
version = "0.0.1",
author = "Adam Presley",
author_email = "adam@adampresley.com",
description = "A se... | adampresley/Blast-for-Basis | setup.py | Python | bsd-2-clause | 1,506 | [
"BLAST"
] | da53901648e054ae3f6a71686e5beee5b6dec3c87f91d2fd0c3c2a3ab64a36dd |
import logging
import time
import traceback
import warnings
from collections.abc import Mapping
import numpy as np
from ..conventions import cf_encoder
from ..core import indexing
from ..core.pycompat import dask_array_type
from ..core.utils import FrozenDict, NdimSizeLenMixin
# Create a logger object, but don't add... | shoyer/xarray | xarray/backends/common.py | Python | apache-2.0 | 11,880 | [
"NetCDF"
] | 626bbf871005eaca4b1219d95bc009a9894fc23c0adf7a830cd9aa54c5fcecd8 |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/trends_places_to_sheets_via_query_dag.py | Python | apache-2.0 | 4,999 | [
"VisIt"
] | 227839ea0a48abbe9c077697c4fb784f9d5b7245f69f37f6c8735048b31a80be |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Calculation of residue depth using command line tool MSMS.
This module uses Michel San... | zjuchenyuan/BioWeb | Lib/Bio/PDB/ResidueDepth.py | Python | mit | 5,010 | [
"Biopython"
] | 91b5c9eaed700dc0343e74e068949750601803b9b1f02acaa122cef504575ad1 |
# ast.py
# Copyright (C) 2006, 2007, 2008, 2009, 2010 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""utilities for analyzing expressions and blocks of Python
code, as well as generating Python from A... | CeltonMcGrath/TACTIC | src/mako/ast.py | Python | epl-1.0 | 5,646 | [
"VisIt"
] | 79ffa0fa1f3d1424bb01addc38a02aab5bce94abcb76f1705d9b083492929db4 |
"""
Package install information
"""
import ast
import os
import re
from setuptools import find_packages, setup
# Cannot use "from cloudbridge import get_version" because that would try to
# import the six package which may not be installed yet.
reg = re.compile(r'__version__\s*=\s*(.+)')
with open(os.path.join('clou... | ms-azure-cloudbroker/cloudbridge | setup.py | Python | mit | 2,864 | [
"Galaxy"
] | b45a81bbf79de91c5c02cac57987c32d8146de0d0a19c7bfcec924ea49ad2128 |
# -*- coding: utf-8 -*-
"""
Class for reading data from Neuralynx files.
This IO supports NCS, NEV and NSE file formats.
Depends on: numpy
Supported: Read
Author: Julia Sprenger, Carlos Canova
Adapted from the exampleIO of python-neo
"""
# needed for python 3 compatibility
from __future__ import absolute_import, di... | mgr0dzicki/python-neo | neo/io/neuralynxio.py | Python | bsd-3-clause | 106,780 | [
"NEURON"
] | 2e2751f453e501500fe3018470f7970ac4d29d94e97a3a84ca009dcd83d9e0b1 |
# coding: utf8
from __future__ import unicode_literals
BASE_EXCEPTIONS = [
"0-day",
"0-days",
"1000Base-T",
"100Base-T",
"100Base-T4",
"100Base-TX",
"10BASE-F",
"10Base-T",
"1,1-diméthylhydrazine",
"11-septembre",
"11-Septembre",
"120-cellules",
"1,2,3-tris-nitrooxy-propane",
"1,2-diazine",
"1,2-dichloropropane",
"1... | Gregory-Howard/spaCy | spacy/fr/_tokenizer_exceptions_list.py | Python | mit | 513,595 | [
"FLEUR",
"Jaguar"
] | 87a12c495645a371d3c7b6d3d0f204f44ed2b2ce425a418d1ab84bfd2d583579 |
# -*- coding: utf-8 -*-
from csirtg_indicator.format.zjson import Json, get_lines
import pytest
from csirtg_indicator import Indicator
@pytest.fixture
def indicator():
i = {
'indicator': "example.com",
'itype': 'fqdn',
'provider': "me.com",
'tlp': "amber",
... | csirtgadgets/csirtg-indicator-py | test/format/test_json.py | Python | mpl-2.0 | 893 | [
"Amber"
] | 65933cd3832d0057980516e93a6201f677b31ff0a1daf89ace6ef31c5bdb3519 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/diversity/beta/_base.py | Python | bsd-3-clause | 3,415 | [
"scikit-bio"
] | 2e93b30696dcd26f3d74833a3620cae9ba0b8e4bc25c49642e140a5feb59b92a |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide... | gleicher27/Tardigrade | moose/gui/vtk/ExodusRenderWidget.py | Python | lgpl-2.1 | 5,124 | [
"VTK"
] | 7b6445da43c98aa549084eb16f7894a591c25a9d40c5d4a57301149dbc34a9fd |
'''OpenAnything: a kind and thoughtful library for HTTP web services
This program is part of 'Dive Into Python', a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
'''
__author__ = 'Mark Pilgrim (mark@diveintopython.org)'
__version__ = '$Revision: 1.6 $'[11:-2]
_... | CLPeters/DeFFNetIzer | openanything.py | Python | apache-2.0 | 4,000 | [
"VisIt"
] | eb5169a634296ec781b07b821f18c0c688d73faf96db6d1be0dbf53c54b3d7dc |
#!/bin/env python3
import re
import sys
from VASP import execCmd, CmdRrror
if len(sys.argv) == 1:
print("")
print("Usage: %s -a (for all frequencies)" % sys.argv[0].split('/')[-1])
print("Usage: %s -i (for all image frequencies)" % sys.argv[0].split('/')[-1])
print("Please try again!")
print("")
... | Mabinogiysk/VASP-script | exfreq.py | Python | gpl-2.0 | 1,825 | [
"VASP"
] | 9cd6a9b3349af15d3a9bab3ca67b80e505afec41cb89d52ac490d20d8e5f6b8d |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 2000
n = 4000
testMehrotra = True
testIPF... | mcopik/Elemental | examples/interface/LPDirect.py | Python | bsd-3-clause | 3,555 | [
"Gaussian"
] | adf6fc260f1429e709ea61e0da48112bb85b2c78623d29405de57a473290e77d |
"""Convert to and from Roman numerals
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Steve Lamm, Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage9/roman9.py | Python | mit | 2,614 | [
"VisIt"
] | 7070394b44a1d3cfcaf1a1717514d4cfef254b2d7fe27b7b7babf1e06ec248fa |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | mcr/ietfdb | django/conf/global_settings.py | Python | bsd-3-clause | 19,255 | [
"VisIt"
] | 24ad799c74da89414e3ba7fa849a092937d19417840c55e243f2ccb9aa2ba7cc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# restartallexes - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the ter... | heromod/migrid | mig/cgi-bin/restartallexes.py | Python | gpl-2.0 | 1,132 | [
"Brian"
] | c321409635f206a49f492abd157604e8846da7e85dd9bf3b3c3b24db15944c3b |
# -*- coding: utf-8 -*-
"""
This is a python implementation of the fast algorithm developed by
Vincent Mazet and Nicolas Chopin.
(see http://miv.u-strasbg.fr/mazet/rtnorm/rtnorm-en.htm)
The version this code is based on is the Matlab implementation from 2012.
It's about three times faster than the scipy implementatio... | irap-omp/deconv3d | lib/rtnorm.py | Python | mit | 202,484 | [
"Gaussian"
] | 8ebc31d74229bf7be11d2c4bc427d0d77d3eb14e3cea53c2c250aedc69c701fd |
# -*- coding: utf-8 -*-
#
# brunel_siegert_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 Lic... | lekshmideepu/nest-simulator | pynest/examples/brunel_siegert_nest.py | Python | gpl-2.0 | 8,342 | [
"NEURON"
] | 68893f4d52afcd7c2b84acf4463aa8bb8294c033d4520d133cb55c28b76ebdf7 |
from math import ceil
from logic.smbool import SMBool
from logic.helpers import Helpers, Bosses
from logic.cache import Cache
from rom.rom_patches import RomPatches
from graph.graph_utils import getAccessPoint
from utils.parameters import Settings
class HelpersGraph(Helpers):
def __init__(self, smbm):
sel... | theonlydude/RandomMetroidSolver | graph/vanilla/graph_helpers.py | Python | mit | 37,071 | [
"CRYSTAL"
] | c8366b37704f16221e0375db20ee43ed0bf5b6a2dfb89abd353faa2df69e5bf2 |
from eWUDAPT_analysis.utils import *
from pylab import *
from netCDF4 import Dataset, num2date
import datetime
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
class analysis_multiple:
def __init__(self, args, json):
self.outputdir = args.outputdir
self.usecase = args.usecase
self.stage ... | eWUDAPT/eWUDAPT-analysis | eWUDAPT_analysis/analysis_multiple.py | Python | apache-2.0 | 8,892 | [
"NetCDF"
] | 7ea832706427ba96ce67ebc2044bba9cd3bbe71ae087bce89967b6aa3c56d918 |
"""Sensor that can display the current Home Assistant versions."""
from datetime import timedelta
from pyhaversion import (
DockerVersion,
HaIoVersion,
HassioVersion,
LocalVersion,
PyPiVersion,
)
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA
from homeassistan... | tboyce021/home-assistant | homeassistant/components/version/sensor.py | Python | apache-2.0 | 3,820 | [
"TINKER"
] | 5df7af40c7d5fd032590739b4108a348fc8777c08641a523377de5df6b15f05a |
#
# 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... | markflyhigh/incubator-beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py | Python | apache-2.0 | 19,825 | [
"VisIt"
] | f23cdc0177cbebec411f22a5fed8b184a3504e378f34d818a14d99bc0bae71bc |
# -*- coding: utf-8 -*-
import csv
import operator
import re
import StringIO
import unittest
from probe import extract, PRIORITY_PROPERTIES
TESTS = (
##("Positioning", (
("po", ("position", "")),
("pos", ("position", "static")),
("poa", ("position", "absolute")),
("por", ("position", "relative")),
... | hayaku/tests | hayaku_test_to_fix.py | Python | mit | 37,798 | [
"VASP"
] | fc65b17264265b8ea2de9ee5a5696addc03147433b1071fd0165c7eed3b32dd7 |
"""SCons.Tool.javac
Tool-specific initialization for javac.
There normally shouldn't be any need to import this module directly.
It will usually be imported through the generic SCons.Tool.Tool()
selection method.
"""
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# Per... | BenLand100/rat-pac | python/SCons/Tool/javac.py | Python | bsd-3-clause | 8,677 | [
"VisIt"
] | bc9b12377a1989820ce1fe96e126d3b90d549783905c7804454f194f419dd575 |
import unittest
from ctree.c.nodes import *
from ctree.transformations import PyBasicConversions
import ast
class TestUnaryOps(unittest.TestCase):
def setUp(self):
self.foo = SymbolRef("foo")
def _check(self, op_cls, expected_string):
node = op_cls(self.foo)
self.assertEqual(str(node... | ucb-sejits/ctree | test/test_unops.py | Python | bsd-2-clause | 1,958 | [
"VisIt"
] | d1ce22d3de0637fe1b81a716e66a358c45b8c43293b8ae61c33b7a5819516701 |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | comocheng/RMG-Py | rmgpy/molecule/molecule.py | Python | mit | 82,645 | [
"RDKit",
"cclib"
] | 6c0b656f2ae7043b8b5d62d7ff117ae1b903b6971c313683098a13735dac4c5b |
#!/usr/bin/python2.4
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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/L... | MatthewWilkes/mw4068-packaging | thirdparty/google_appengine/lib/ipaddr/ipaddr/ipaddr_test.py | Python | apache-2.0 | 26,824 | [
"FEFF"
] | e4d1746733b3099776ff15f8fadf0d73c9706259c339203dbfefcc0eee24c6e6 |
"""Test generation helpers
Intended to functionalize common tasks when working with the pytest_generate_tests hook.
When running a test, it is quite often the case that multiple parameters need to be passed
to a single test. An example of this would be the need to run a Provider Add test against
multiple providers. W... | nachandr/cfme_tests | cfme/utils/testgen.py | Python | gpl-2.0 | 13,421 | [
"VisIt"
] | ecbb13af9a12d050fb80ee838f30e83a55c3aec3c6d981a031fcc029245861e4 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/General/Testing/Python/clipTet.py | Python | gpl-3.0 | 5,185 | [
"VTK"
] | 3d165541865e921a6b1a0c073a2c66f83a3ac20918cf1bb333da22d9acca677a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
from os import path
import threading
import numpy as np
import subprocess
import locale
import os
import traceback
import time
import base64
from glob import glob
import pkgutil
import ZIBMolPy.plots
from ZIBMolPy.pool import Pool
import pango # Pango is a libr... | CMD-at-ZIB/ZIBMolPy | tools/zgf_browser.py | Python | lgpl-3.0 | 134,496 | [
"VMD"
] | e07d6c2c07733b37a09d218a064142be90974c063164891a10f900aded9a57c7 |
"""
It used used to create different plots.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import errno
from io import BytesIO
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.Graphs import barGraph, lineGraph, pieGraph, qualityGraph, textGrap... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Plotting/Plots.py | Python | gpl-3.0 | 5,405 | [
"DIRAC"
] | d85b165244985a8c2097fef2df73ebc26fe329c50beba84b557754240d1d051e |
# examples/api/01_fci.py
"""Example of a FCI computation on singlet lithium dimer using RHF orbitals"""
import psi4
import forte
psi4.geometry("""
0 1
Li 0.0 0.0 0.0
Li 0.0 0.0 3.0
units bohr
""")
psi4.set_options(
{
'basis': 'sto-3g', # <-- set the basis set
'scf_type': 'pk', # <-- request con... | evangelistalab/forte | examples/api/01_fci.py | Python | lgpl-3.0 | 529 | [
"Psi4"
] | 7b4d942ff181be1ee620b6d81d999fe702611313b5a16a772ae44305c263dc2e |
"""
Interactive kinetics app with sliders.
Start by runing:
$ bokeh serve interactive.py
Add --show argument or navigate to:
http://localhost:5006/interactive
"""
from collections import defaultdict
import sys
from chempy import Reaction, ReactionSystem
from chempy.kinetics.rates import MassAction
from chempy.... | bjodah/aqchem | examples/bokeh_interactive_robertson.py | Python | bsd-2-clause | 1,366 | [
"ChemPy"
] | 47a7697e4376ce7c4fee2bcedcc771b3c7e78e00eb305c1e3e96e40407589b4e |
#!/usr/bin/env python2.7
import os, sys
from numpy import *
##################
### For gREM ###
##################
#
# Take walker enthalpies/energies from multiple, identical
# length trajectories, concatenate, and follow exchanges
# to get replica enthalpies/energies. Start and stop are
# file handles for each re... | dstelter92/gREM | examples/lj-fullexample-temper/analysis/get-hist-enthalpies.py | Python | gpl-2.0 | 3,016 | [
"LAMMPS"
] | 53e6630247385adfe5b844272ec06d8e706302f948642d6cee40dc7383654d1f |
import matplotlib.pyplot as plt
import numpy as np
import scipy.ndimage as ndimage
import scipy.signal as signal
def showImage(image, label, vmin=0.0, vmax=1.0):
plt.figure().suptitle(label)
plt.imshow(image, cmap="gray", vmin=vmin, vmax=vmax)
def showOrientations(image, orientations, label, w=32, vmin=0.0, v... | tommythorsen/fingerprints | utils.py | Python | unlicense | 13,595 | [
"Gaussian"
] | 2a4b7fc367e52d0918fe81b14837fec9fe60c3ff7ab44f6785cdf092a1a8010d |
"""
The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts a thread for execution of the job
and a Watchdog Agent that can monitor its progress.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN JobWrapper
:end-before: ##END
:caption: JobW... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 71,003 | [
"DIRAC"
] | 1de221660b0294cc560f9c6e01f170c5c2731cb67091f3b0c19f05878598b0fa |
import theano
import theano.tensor as T
from theano.tensor import nnet
from theano.tensor.nnet import conv
from hmmlearn import hmm
import np as np
class ConvPoolLayer(object):
def __init__(self, rng, input, filter_shape, image_shape, poolsize=(1, 1)):
"""
Allocate a LeNetConvPoolLayer with share... | dssg/wikienergy | proto/pylearn2/cnn_with_data.py | Python | mit | 6,121 | [
"NEURON"
] | 781e50c55680609a308e86a9827f3f8e13a5c858d8e15d8bebf70f97f6498f10 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageEuclideanToPolar(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkImageEuclideanToPolar.py | Python | bsd-3-clause | 505 | [
"VTK"
] | 67c7bdf4f397880bc768992767427bce6ab08305a43df830f4740d8ff65e32b8 |
"""
.. _tut_compute_covariance:
Computing a covariance matrix
=============================
Many methods in MNE, including source estimation and some classification
algorithms, require covariance estimations from the recordings.
In this tutorial we cover the basics of sensor covariance computations and
construct a no... | olafhauk/mne-python | tutorials/source-modeling/plot_compute_covariance.py | Python | bsd-3-clause | 8,997 | [
"Gaussian"
] | 4a958332220a143ca833d481e589c4f80c13bb2170a245f235046dd6fd1f8c88 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
序列
序列类型支持关系操作符in，大小计算函数len()，分片[]，并且是可迭代的。
Python 内置5种序列类型：bytearray, bytes, list, str 与 tuple。
"""
def tuple_test():
"""
1. 什么是元组
有序的序列，包含n个对象引用，支持分片和步距，固定的
2. 如何创建元组
函数调用tuple() —— 不指定参数返回空元组，使用tuple作参数返回其浅拷贝，其他参数将尝试将其转换为元组
不使用函数调用 —— 空元组使用... | xuehao/stickpython | Programming_in_Python/chapter_03/3.1/a_sequence_tuple.py | Python | mit | 2,020 | [
"Amber"
] | 7d692415770561ae2980ac97eee4e65237647538f686a1aa7d37ae2757feef47 |
"""
Instructor Dashboard Views
"""
from django.views.decorators.http import require_POST
from django.contrib.auth.decorators import login_required
import logging
import datetime
import pytz
from django.utils.translation import ugettext as _
from django_future.csrf import ensure_csrf_cookie
from django.views.decorators... | nicky-ji/edx-nicky | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 18,940 | [
"VisIt"
] | 0ecda29667f8eab8f9810ea79270449b5046ef4428bda597eaaa4866a109e6da |
from datetime import datetime, timedelta
from django.test import TestCase
from django.urls import reverse
from django.test.utils import override_settings
from django.shortcuts import get_object_or_404
from zds.member.factories import ProfileFactory
from zds.member.models import Profile
from django.conf import setting... | ChantyTaguan/zds-site | zds/middlewares/tests/tests_setlastvisitmiddleware.py | Python | gpl-3.0 | 1,569 | [
"VisIt"
] | f0d2dea6a1caa6a0354b1a40185b1653f31a74e20b4977d6f19e9f534d5885e1 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
className
A QGIS plugin
description
-------------------
begin : 2016-12-03
copyright : (C) 2016 by Nico
... | lennepkade/dzetsaka | processing/train.py | Python | gpl-3.0 | 9,197 | [
"Gaussian"
] | b22942f4e9b4c6973d8b0c0c9b2a1ce6282f65b144f39faa3d25c0b7b9115785 |
import json
import numpy as np
import pytest
import pprint
import os
from distutils import dir_util
import psi4
pytestmark = [pytest.mark.quick, pytest.mark.smoke]
# Generating
# * equivalent to test_psi4. copy over the job, then run below to generate atomicinput
# atin = psi4.driver.p4util.state_to_atomicinput(d... | jturney/psi4 | tests/pytests/test_psi4_qcschema.py | Python | lgpl-3.0 | 6,578 | [
"Psi4"
] | 33412b4a304b878f09d49ba208af7143977d83c2a0e1fc40466a2cf53cc7327c |
OUTFOLDER = ROOTFOLDER + 'out/'
CLIPTRIMOUT = OUTFOLDER + 'cliptrim1/'
ALIGNOUT = OUTFOLDER + 'align2/'
TMP = OUTFOLDER + 'tmp/'
STATSOUT = OUTFOLDER + 'stats4/'
FEATURECOUNTSOUT = OUTFOLDER + 'featurecounts3/'
'''
Collecting file names
'''
PAIREDFASTQFILES = [file.replace(FASTQFOLDER, '').replace('.fastq.gz','')for ... | cbg-ethz/NGS-pipe | snake/rna/rna_snake.py | Python | apache-2.0 | 17,333 | [
"HTSeq"
] | 50f60c365ef3ac3e20d9a85d76d45e9e513f438c68c5f4e003c1f53bb2c448f6 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/cleaveland4/package.py | Python | lgpl-2.1 | 1,995 | [
"Bowtie"
] | bd1ad018268c4bb38d5230642f6802e21c610c44a6a37f21023c597d43a6063f |
#!/usr/bin/env python
import ast
import os
import sys
class MetadataFinder(ast.NodeVisitor):
def __init__(self):
self.version = None
self.summary = None
self.author = None
self.email = None
self.uri = None
self.licence = None
def visit_Assign(self, node):
... | photocrowd/dj-stripe | setup.py | Python | bsd-3-clause | 2,748 | [
"VisIt"
] | df6d53b436814504e40b2a65b03c0750fa3885f86143b106bed2024facc29192 |
from p03_ParseSam import get_name
def annotateBlast(blastFile,anno_type):
"""
This function annotates the results got by running all sorts of
blast algorithm. It adds the names of reference genomes
* blastFiles: str. blast file name
* anno_type: str. 'nucleotide' or 'protein'
out... | shl198/Pipeline | Modules/p04_ParseBlast.py | Python | mit | 7,337 | [
"BLAST"
] | 7a512984d69f8073256b684f1d5114943f550006f34910459466a6ca0d0044d0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
See __doc__ for setup_com_from_mae.
Job Types
---------
cs - Conformational search
Appends "_cs".
mini - Minimization
Appends "_mini".
re - Redundant conformer elimination
Appends "_re".
"""
import argparse
import os
import sys
from itertools ... | Q2MM/q2mm | screen/setup_com_from_mae_many.py | Python | mit | 3,240 | [
"MacroModel"
] | bff5a0eb4bb37b2c5a4945fc8128024bc3b8b046942d239ccfd9baa223fa2800 |
#!/usr/bin/env python
from __future__ import print_function, absolute_import, division
from mdtraj.utils.six.moves import xrange
import sys, os
import warnings
import numpy as np
import mdtraj as md
from mdtraj import io
from msmbuilder import arglib
from msmbuilder import clustering
from msmbuilder import Project
from... | msmbuilder/msmbuilder-legacy | scripts/Cluster.py | Python | gpl-2.0 | 13,125 | [
"MDTraj"
] | ddeee5963b15727ad8d4621bbf9e8ab63398710e89d4bd0fa19a3594634aa1a4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 Licens... | hryamzik/ansible | lib/ansible/modules/network/cnos/cnos_vlan.py | Python | gpl-3.0 | 9,820 | [
"VisIt"
] | 6ba2239ea066efca91739863952b89db9d7b593b0c9a530d2837eb12783543fb |
#-------------------------------------------------------------------------------
#
# Define classes for (uni/multi)-variate kernel density estimation.
#
# Currently, only Gaussian kernels are implemented.
#
# Written by: Robert Kern
#
# Date: 2004-08-09
#
# Modified: 2005-02-10 by Robert Kern.
# Contr... | mingwpy/scipy | scipy/stats/kde.py | Python | bsd-3-clause | 17,303 | [
"Gaussian"
] | 1843318dbe866bb31809248fb77a1b2fef03bbead44f8f96e65c1785f28054f9 |
import json
from os import path
from numpy import floor
from sympy import Symbol
from IPython.display import display
import ipywidgets as widgets
from pysces import ModelMap
from d3networkx_psctb import ForceDirectedGraph
from d3networkx_psctb import EventfulGraph
from ... import modeltools
from ..misc import split_c... | exe0cdc/PyscesToolbox | psctb/utils/model_graph/_model_graph.py | Python | bsd-3-clause | 18,844 | [
"PySCeS"
] | 431753d9654e962499a6effc8458993dadfde627224242b63f0347d5dcd40765 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from bok_choy.web_app_test import WebAppTest
from ..helpers import (
UniqueCourseTest,
Even... | vismartltd/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 39,843 | [
"VisIt"
] | e6621dfae22b50d65ee6bf503e3bd644d91f023e5e26e0eaa61b78b534e733c2 |
# $HeadURL$
""" TopErrorMessagesReporter produces a list with the most common errors
injected in the SystemLoggingDB and sends a notification to a mailing
list and specific users.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentMo... | Sbalbp/DIRAC | FrameworkSystem/Agent/TopErrorMessagesReporter.py | Python | gpl-3.0 | 5,388 | [
"DIRAC"
] | 2cbb827536511ca8956b61c3047f7203b0ece2817f0aacff9c30ad7453c133c9 |
##############################################################
# Basic ElasticSearch connectivity settings
##############################################################
# index information to use in live
ELASTIC_SEARCH_HOST = "http://localhost:9200"
ELASTIC_SEARCH_INDEX = "db"
ELASTIC_SEARCH_VERSION = "0.90.13"
# i... | JiscPER/magnificent-octopus | octopus/modules/es/settings.py | Python | apache-2.0 | 8,551 | [
"Octopus"
] | ab9ddaf0c028136f49f2084f6fd2e70f7862f834bbde9bd4494d125fa475e694 |
# Natural Language Toolkit: Conditional Random Fields
#
# Copyright (C) 2001-2012 NLTK Project
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
"""
An interface to Mallet <http://mallet.cs.umass.edu/>'s Linear Chain
Conditional Random Fiel... | cortext/crawtextV2 | ~/venvs/crawler/lib/python2.7/site-packages/nltk/tag/crf.py | Python | mit | 31,236 | [
"Gaussian"
] | d8a76834cc8defba0666977c8f9c833283e526bb587ee97fd43de75613bb5010 |
# Main GWR classes
__author__ = "Taylor Oshan Tayoshan@gmail.com"
import copy
import numpy as np
import numpy.linalg as la
from scipy.stats import t
from scipy.special import factorial
from itertools import combinations as combo
from pysal.model.spglm.family import Gaussian, Binomial, Poisson
from pysal.model.spglm.g... | lixun910/pysal | pysal/model/mgwr/gwr.py | Python | bsd-3-clause | 66,873 | [
"Gaussian"
] | 28369b1dfe50a6dbf974eea02c565dc7365408fa0cbe22b69a2b06856a76bfd3 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.