text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""Classes for use with Yambo
Representation of a spectrum.
Main functionality is to read from Yambo output, o.qp files
and also netcdf databases.
"""
import re
import copy as cp
import numpy as np
import asetk.atomistic.fundamental as fu
import asetk.atomistic.constants as atc
from . import cube
class Dispersion:
... | cpignedoli/asetk | asetk/format/yambo.py | Python | mit | 9,512 | [
"NetCDF",
"Yambo"
] | 1a6a638233a1035fe63b28e358a452a93a8d71c1ab86e93464b147453b8f86cc |
import matplotlib.pyplot as plt
import math
from mpl_toolkits.mplot3d.axes3d import Axes3D
from matplotlib.pyplot import Rectangle # Used to make dummy legend
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("quadrant", type=int,
help="Options : 1, 2, 3, 4")
parser.add_argumen... | WillArmentrout/galSims | plotting/RegionsByQuadrant.py | Python | gpl-2.0 | 8,878 | [
"Galaxy"
] | e27dfff3a4960d2205e048f11633ec545ccd03d79f4734950a008dfd3cd6338f |
# Copyright (c) 2006, 2009-2010, 2012-2015 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2012, 2014 Google, Inc.
# Copyright (c) 2014-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelmc.ro>
# Copyri... | PyCQA/pylint | pylint/checkers/design_analysis.py | Python | gpl-2.0 | 23,270 | [
"VisIt"
] | 1fbaa0e45438034a2e27cb4e2347fc78448414dfe93283f9e1e5d946bf5ec20f |
import numpy as np
import numexpr
def lab2rgb(im):
l, a, b = np.dsplit(im, 3)
y = numexpr.evaluate('(l + 16) / 116.0')
x = numexpr.evaluate('a/500.0 + y')
z = numexpr.evaluate('y - b/200.0')
xyz = numexpr.evaluate(
'where(y**3>0.008856, y**3, (y - 16.0 / 116.0) / 7.787)*ref/100',
{
... | MathieuLeocmach/colloids | python/colloids/colors.py | Python | gpl-3.0 | 1,488 | [
"ParaView"
] | 066cbf6b48e547bb324e86237c833797520b5780dcf0e1d002db0b1f502596e3 |
# pylint: disable=C0111
# pylint: disable=W0621
import time
import os
from lettuce import world, step
from nose.tools import assert_true, assert_in # pylint: disable=no-name-in-module
from django.conf import settings
from student.roles import CourseRole, CourseStaffRole, CourseInstructorRole
from student.models impo... | hkawasaki/kawasaki-aio8-1 | cms/djangoapps/contentstore/features/common.py | Python | agpl-3.0 | 13,057 | [
"VisIt"
] | 716fcdd4c4735ba7cef20ae4f1e40dd0385c09bf07fa35d852ee5581f867c051 |
#!/usr/bin/env @PYTHON_EXECUTABLE@
"""
Description: Export a Siconos mechanics-IO HDF5 file in VTK format.
"""
from siconos.io.vview import VView, VExportOptions
from siconos.io.mechanics_hdf5 import MechanicsHdf5
if __name__=='__main__':
# Parse command-line
opts = VExportOptions()
opts.parse()
## O... | siconos/siconos | io/swig/io/siconos_vexport.py | Python | apache-2.0 | 515 | [
"VTK"
] | 74b302704d10cbe149ac800a7fc873a7e160bcfd608d318f514afa4be7990b7e |
# pylint: disable=C0111
"""All available endpoints of the chaospizza web project."""
from django.conf import settings
from django.conf.urls import include, re_path
from django.contrib import admin
from django.views import defaults as default_views
urlpatterns = [
re_path(r'^', include('chaospizza.orders.urls')),
... | chaosdorf/chaospizza | src/config/urls.py | Python | mit | 1,209 | [
"VisIt"
] | 7a11a9c7015c43af4c203f95a96d164f1f12224b00c1d34b462bd7f5c9205a4d |
from django.db.models import Q
from rest_framework import serializers
from rest_framework.exceptions import PermissionDenied
from users.models import Doctor, Patient
from timetable.models import WorkingHour
from .models import Visit
from users.serializers import DoctorSerializer, UserPatientSerializer
from timetable... | vechnoe/clinic | src/apps/reception_office/serializers.py | Python | mit | 1,826 | [
"VisIt"
] | 2a7dbb5c4ae72bcf8473c484305a9cb474188390616971a8f4e2e76423a66910 |
# Copyright 2013 Pawel Daniluk, Bartek Wilczynski
#
# This file is part of WeBIAS.
#
# WeBIAS 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 Foundation, either version 3 of
# the License, or (at your option) any l... | pawelld/webias | webias/application.py | Python | agpl-3.0 | 12,029 | [
"Biopython"
] | 27528e97ca839e934c20b906156061357b38d57c756f4871b736530137af91fb |
# Copyright 2018 Google LLC. 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 a... | PAIR-code/interpretability | text-dream/python/dream/token_search.py | Python | apache-2.0 | 5,144 | [
"NEURON"
] | 7febb4fcd81a4fdfd22351b2d876f50df1d4ea68ebbad183948fc53bc4b4616b |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | enriquesanchezb/practica_utad_2016 | venv/lib/python2.7/site-packages/setuptools/command/easy_install.py | Python | apache-2.0 | 85,913 | [
"VisIt"
] | febaa4b7489672d023327ed9db01184c808c9ed714695dbc88de9c7caae9436f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
from gi.repository import Gtk, Gio, GdkPixbuf, Gdk
class PhotoViewer(Gtk.Window):
"""
main class
"""
def __init__(self):
"""
initialization
"""
Gtk.Window.__init__(self)
self.set_title("PyGi Photo-Viewer")
height = 900
width = 500
self.set_de... | Chiheb-Nexus/PyGi-Photo-Viewer | photo_viewer.py | Python | gpl-3.0 | 18,040 | [
"VisIt"
] | 12affd589ccf71ad972b430f95ad9659c8bd662876d20a57299341217b614815 |
"""
Simulating a black body curve
"""
from scipy.optimize import curve_fit
import pylab as plt
import numpy as np
def blackbody_lam(lam, T):
""" Blackbody as a function of wavelength (um) and temperature (K).
returns units of erg/s/cm^2/cm/Steradian
"""
from scipy.constants import h,k,c
lam = 1e... | azariven/BioSig_SEAS | deprecated/black_body_example.py | Python | gpl-3.0 | 2,460 | [
"Gaussian"
] | 0ff7012ba5f7c962699b38f683c4a5c6c5d18173706df8404373202187e3599c |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_overlap_ni.py | Python | apache-2.0 | 1,536 | [
"PySCF"
] | 491f7760d61e1cf6e83c890d3ee26d76c3ed4d2f804910f5982b07179e0dd84e |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import functools
import io
import json
import random
import shutil
import tempfile
import ddt
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.core import mail
from django.core.fil... | miptliot/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 226,402 | [
"VisIt"
] | 18bdf840414aa14fcb35bbe6cacaa69291bdb6b721b32c7e2be166ed0da65058 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | jotes/ansible | v2/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 6,293 | [
"Brian"
] | 9704b68dc710041bf029b4fa3eae7bd01dea17f2db47b36a436156f86bcbde05 |
#!/usr/bin/env python
#
# Copyright (c) 2015, Simon Howard
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND TH... | fragglet/midisnd | midi.py | Python | isc | 4,962 | [
"CRYSTAL"
] | 8fd2530da40d3ca3c4a1bda59987eba2df192befecda36c188635c79afe5cac9 |
#! /usr/bin/env python
# ==========================================================================
# Display Instrument Response Function
#
# Copyright (C) 2017-2020 Juergen Knoedlseder
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pu... | ctools/ctools | examples/show_irf.py | Python | gpl-3.0 | 17,529 | [
"Gaussian"
] | 761775e6cd375e134acaf8f01fb303b7528e4c9eb7899d8adbe7ad7889ffcbe8 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 18 14:57:46 2013
Author: Josef Perktold
"""
import numpy as np
from statsmodels.genmod.generalized_estimating_equations import GEE, GEEMargins
from statsmodels.genmod.families import Gaussian
from statsmodels.genmod.tests import gee_gaussian_simulation_check as gees
... | bashtage/statsmodels | statsmodels/examples/try_gee.py | Python | bsd-3-clause | 2,149 | [
"Gaussian"
] | a5c03ed90f31c4a7628b3df3390fbf7c4697629cbe77fa4989a97bf07c70e04b |
from django import forms
from django.conf import settings
from django.contrib.formtools.wizard.views import SessionWizardView
from django.db import connection
from django.shortcuts import render_to_response
from catmaid.models import Class, ClassInstance, ClassInstanceClassInstance
from catmaid.models import Connector... | AdaEne/CATMAID | django/applications/catmaid/control/annotationadmin.py | Python | gpl-3.0 | 13,459 | [
"NEURON"
] | 6df95f9f337a4e5a1e05790ac50f9e2426f112c87793f339411144b079afa3a1 |
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program is distr... | zguangyu/rts2 | scripts/rts2saf/unittest/test_fitdisplay.py | Python | gpl-2.0 | 6,149 | [
"Gaussian",
"VisIt"
] | e68de1bf48ca63ce4908130605f27917cd984bcd09c6cc92c3feb4e84c58a6a1 |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/n/netcdf.py | Python | gpl-2.0 | 5,886 | [
"NetCDF"
] | 9f258bd957a1823fe86aa2bebfad52dd753182a73ead6b3f46ecc08f0049dc12 |
# enc - A free utility for encrypting Python code bases.
# Copyright (C) 2017 M. Tyler Springer
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Licen... | MS-DDOS/enc | enc.py | Python | gpl-3.0 | 24,038 | [
"VisIt"
] | 329a078824496533c680596f0f5ba530e3a7d5c1a0785dfeb255b76fae5b95f7 |
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Caravel can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import hashlib
import lo... | giaosudau/caravel | caravel/viz.py | Python | apache-2.0 | 60,060 | [
"VisIt"
] | 2318b98a435f6bf953ad8d9518bf65dc35152ab9fe9c4ebffa3af0861a9e94ab |
def xoppy_calc_black_body(TITLE="Thermal source: Planck distribution",TEMPERATURE=1200000.0,E_MIN=10.0,E_MAX=1000.0,NPOINTS=500):
print("Inside xoppy_calc_black_body. ")
return(None)
def xoppy_calc_mlayer(MODE=0,SCAN=0,F12_FLAG=0,SUBSTRATE="Si",ODD_MATERIAL="Si",EVEN_MATERIAL="W",ENERGY=8050.0,THETA=0.0,S... | srio/Orange-XOPPY | devel/json/xoppy_calc_template.py | Python | bsd-2-clause | 7,142 | [
"CRYSTAL"
] | 84cbb755a404e21ebd8d5d8233d44b2f65426eb88e5ffc88a0db6a5ed5c3ec80 |
import os
import re
from setuptools import setup
f = open(os.path.join(os.path.dirname(__file__), 'README.md'))
readme = f.read()
f.close()
f = open(os.path.join(os.path.dirname(__file__), 'wandbox/__init__.py'))
for line in f:
if '__version__ = ' in line:
version_ = [x for x in re.split(r"[ ='... | srz-zumix/wandbox-api | setup.py | Python | mit | 5,316 | [
"CRYSTAL"
] | 621b7afdec82be4d91a6599951b25e2688b5763828e0cda9c8fd2184aeb7b5a6 |
#!/usr/bin/env python3
"""
Filter hetero. genotype based on sample AD(read depth) tags.
@Author: wavefancy@gmail.com
Usage:
VCFHetroADFilter.py -a minDP [-b|-p]
VCFHetroADFilter.py -h | --help | -v | --version | -f | --format
Notes:
1. Read vcf file from stdin, mask genotype... | wavefancy/BIDMC-PYTHON | Exome/VCFHetroADFilter/VCFHetroADFilter.py | Python | mit | 3,429 | [
"pysam"
] | 46e5dca8af3d1d2f8bb57d20e2e681cb66599622acc158f1e6e65336fef11de6 |
"""
This script extracts the time-variable from matching netCDF files and prints them to command line.
"""
import netCDF4
from glob import glob
from pathlib import Path
import matplotlib.pyplot as plt
NC_DIR = r"\\nve.no\fil\grid\metdata\prognosis\met_pp_nordic\forecast\archive\2021"
NC_FILES = "met_forecast_1_0km_No... | kmunve/APS | aps/util/get_nc_time.py | Python | mit | 643 | [
"NetCDF"
] | ab681a3299a7eee863d7fcf40639c3b0c730b847aac5a37668a7d79a370e7de0 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | TeamSPoon/logicmoo_workspace | packs_web/butterfly/lib/python3.7/site-packages/tornado/websocket.py | Python | mit | 61,476 | [
"VisIt"
] | 0e6f0749c04625274fba8d18627255e54b91bd156778580ed65d419f5c4bfadf |
import numpy as np
from scipy import linalg
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils.validation import check_array
from .utils import check_array_with_weights, weighted_mean
class WPCA(BaseEstimator, TransformerMixin):
"""Weighted Principal Component Analysis
This is a dir... | jakevdp/wpca | wpca/wpca.py | Python | bsd-3-clause | 8,371 | [
"Gaussian"
] | 050e56e8a18bff32ae85cde7ab925248df41056a932ac83d407abfcfefceb96c |
#!/usr/bin/env python3
import itertools
from warnings import warn
import networkx as nx
import numpy as np
from pgmpy.base import UndirectedGraph
from pgmpy.independencies import Independencies
class DAG(nx.DiGraph):
"""
Base class for all Directed Graphical Models.
Each node in the graph can represen... | pgmpy/pgmpy | pgmpy/base/DAG.py | Python | mit | 40,678 | [
"VisIt"
] | 8e45ed8ade410f05ec789824aab8676bd0cf627c36e10f07afa650717b08f585 |
import pylab as pyl
import cPickle as pickle
from scipy.stats import scoreatpercentile
galaxies = pickle.load(open('galaxies.pickle', 'rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I > 10., galaxies)
f1 = pyl.figure(1, figsize=(6,4))
f1s1 = f1.add_subplot(111)
# for the clipped points
arrow_right = [[0,0],[-1,1... | boada/ICD | sandbox/lowerSN/plot_icd_vs_ssfr.py | Python | mit | 1,929 | [
"Galaxy"
] | 286395f6134b26365d3d27458bebe4db33c44a8ddb0f0fe32866cfe6b91b165c |
# -*- coding: utf-8 -*-
''' The main script to run, enables profiling. '''
import numpy as np
import math
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from crystal import *
from plot_init_tools import *
def main(num_of_growths):
''' Main method to start simulation. Uncomment specific ... | roesel/growth | main.py | Python | cc0-1.0 | 1,837 | [
"CRYSTAL"
] | d7f11171da3d53f272e52a08a4872babd25459b478aaa5d44964f5a487901399 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/lb_streaming.py | Python | gpl-3.0 | 3,527 | [
"ESPResSo"
] | fca1d37c66866b4be307e75c924aa124b00edebf2b12058850506b33e4117f29 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# views.py
#
# Copyright 2014 Gary Dalton <gary@ggis.biz>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licen... | gary-dalton/Twenty47 | twenty47/forms.py | Python | mit | 2,898 | [
"Dalton"
] | 982378ad971ca133b644748af7018077646d7b0c55d05f59fd1181e42dc18d28 |
#!/usr/bin/env python
from __future__ import division, print_function
import numpy as np
import argparse
import re
import os, sys
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from mpl_toolkits.axes_grid1 import make_axes_locatable
from ase.data import ... | cpignedoli/asetk | scripts/cube-movie.py | Python | mit | 6,642 | [
"ASE",
"Gaussian"
] | 7f006f08ef134e2477acc4ad3e7f4902eb5a47113dca79817e7037ec8181dfaf |
## ################################################################# ##
## (C) SCRT - Information Security, 2007 - 2008 // author: ~SaD~ ##
## ################################################################# ##
## This program is free software: you can redistribute it and/or ##
## modify it under the terms... | wereallfeds/webshag | webshag/modules/module_spider.py | Python | gpl-3.0 | 27,016 | [
"VisIt"
] | 403f8c32732c6707746197071fc1ef8326faae15c28515e6a9e9b74db9ec3109 |
"""This directory is setup with configurations to run the main functional test.
It exercises a full analysis pipeline on a smaller subset of data.
"""
import os
import subprocess
import unittest
import shutil
import contextlib
import collections
import functools
from nose import SkipTest
from nose.plugins.attrib impo... | elkingtonmcb/bcbio-nextgen | tests/test_automated_analysis.py | Python | mit | 15,192 | [
"Galaxy"
] | c27a82be1ce9f07e71ee950a36518fd54968a3b5754d8fd272f36e09bbc8f7e0 |
from datetime import datetime
from urlparse import urlparse
from lettuce import before, step, world
from lettuce.django import django_url
from nose.tools import assert_equal
from splinter.exceptions import ElementDoesNotExist
from storybase_user.models import create_organization, create_project
@before.each_scenario
d... | denverfoundation/storybase | apps/storybase_story/features/story_admin-steps.py | Python | mit | 3,704 | [
"VisIt"
] | 8945f717f6178be6a9be3274311bea7512e54cab5abe68423a08d555cab9e224 |
""" Test TimeLeft utility
(Partially) tested here are SGE and LSF, PBS is TO-DO
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pytest
from importlib import reload
from DIRAC import S_OK, gLogger
from DIRAC.Resources.Computing.BatchSystems.T... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/test/Test_TimeLeft.py | Python | gpl-3.0 | 5,885 | [
"DIRAC"
] | b86f9ce9fc6a6d358f5d87c4fd9266d2b5664b0d0f476d3ec558b4d23406b7a0 |
from splinter import Browser
import time
#I used this because my chrome driver was throwing lots of issues.So,I thought switching the user agent would do the trick
fire_br = Browser(user_agent = "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2228.0 Safari/537.36")
fire_br.visit("https:... | gameFace22/Programs-and-Scripts. | whatsapp_spammer.py | Python | mit | 875 | [
"VisIt"
] | 4ec47158998aa012aec285c09687c47a0106de8320311b24df4ab5e0baa15cbb |
# from flask.ext.jwt import jwt_required
# from flask import Blueprint
import datetime
import requests
from werkzeug.security import gen_salt
from adsws.modules.oauth2server.models import OAuthClient, OAuthToken
from adsws.modules.oauth2server.provider import oauth2
from adsws.core import db, user_manipulator
from ... | ehenneken/adsws | adsws/accounts/views.py | Python | gpl-2.0 | 16,430 | [
"VisIt"
] | aea256821c594aa07cb8508f9e4e08e4880618fb3317ae3f18e76e4329fe1667 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from dropbox import client, rest, session
# Get your app key and secret from the Dropbox developer website
APP_KEY = ''
APP_SECRET = ''
# ACCESS_TYPE should be 'dropbox' or 'app_folder' as configured for your app
ACCESS_TYPE = 'app_folder'
sess = session.DropboxSession(APP_... | tripplet/dropbox_cli | registerUser.py | Python | agpl-3.0 | 957 | [
"VisIt"
] | 2af7e31353a94b2e61009d4a2a78c38c2cce11490275d957531f235604f3fee5 |
""" Test for WMS clients
"""
# pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
import os
import unittest
import importlib
import StringIO
from mock import MagicMock
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
from DIRAC import S_OK
from DIRAC.WorkloadManagement... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Client/test/Test_Client_WorkloadManagementSystem.py | Python | gpl-3.0 | 6,818 | [
"DIRAC"
] | 7958c50c12694ecbff0c157de1e4f35714ad5ee48c4b70b9c9f9b282561ddee8 |
from Sire.IO import *
from Sire.Mol import *
from Sire.MM import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Maths import *
from Sire.Qt import *
from nose.tools import assert_almost_equal
coul_cutoff = 15 * angstrom
lj_cutoff = 10 * angstrom
compare_energies = False
if compare_energies:
(water... | michellab/SireUnitTests | unittests/SireMM/test_newinter.py | Python | gpl-3.0 | 7,391 | [
"Amber"
] | 9473b7e608b792ecbdd9f89500d3a2545a574b5075f69d75d00018ef61953048 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 3: Deep Learning and Neural Networks
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2015 by Jeff Heaton
Licensed under the Apache License, V... | JPMoresmau/aifh | vol3/vol3-python-examples/examples/example_boltzmann.py | Python | apache-2.0 | 4,751 | [
"VisIt"
] | dcbd9cdb85869b10081d6febe637ee99e5b40e5182e45b101eafbb2d3d6a6180 |
"""This is a collection of miscellaneous helper functions, which cover such
tasks as grabbing data batches, providing activation functions, etc
"""
import numpy as np
import theano
import theano.tensor as T
Tfloat = theano.config.floatX
Tsh = theano.shared
MAX_CHANNELS = 20
def gen_weights(rng, w_shape, mean, st... | dereklarson/nnGen | nnGen/NNlib.py | Python | mit | 4,098 | [
"Gaussian"
] | 18f4c8cb1a960f350925426f0e6f35617151bef81b700518fab18612ebdc023d |
import os.path
import shutil
import tarfile
import json
from django.conf import settings
from django.http import HttpResponse
from django.db.models import Count
from catmaid.control.authentication import requires_user_role
from catmaid.control.common import get_relation_to_id_map, id_generator
from catmaid.control.cr... | AdaEne/CATMAID | django/applications/catmaid/control/treenodeexport.py | Python | gpl-3.0 | 21,850 | [
"NEURON"
] | 128624e4879435f6698df12a1a66811aeceb7637bdce0205b6027706f569cfe3 |
"""
LineBOT
LineBOT is an advanced bot, demonstrating the fusion of a
general (connected) topology leader election algorithm (see
Wavebot) and a pattern formation scheme (see Abot),
hardcoded to produce a line starting from the leader.
LineBOT does the following:
* choose an identity at random
* shout out to n... | ajhalme/kbsim | Bots/LineBOT.py | Python | gpl-3.0 | 18,346 | [
"VisIt"
] | 094bbdd2770079648ae21be47c3a85db5ee94e6fbc7f2a2d44819625831a2673 |
# 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
# distributed under t... | stackforge/python-openstacksdk | openstack/tests/unit/test_proxy.py | Python | apache-2.0 | 22,980 | [
"Brian"
] | a59dca7690b294fd21c7bbeeaaa58811817d4c901d3fed17f770cfb0065d0c03 |
# -*- coding: utf-8 -*-
import pygame
import random
import os
import classes.board
import classes.extras as ex
import classes.game_driver as gd
import classes.level_controller as lc
import classes.drw.img
class Board(gd.BoardGame):
def __init__(self, mainloop, speaker, config, screen_w, screen_h):
self.... | imiolek-ireneusz/eduActiv8 | game_boards/game089.py | Python | gpl-3.0 | 19,986 | [
"Jaguar",
"MOOSE"
] | e428ce7724b780d28e51cca817f2a2eac036f342337e6a909438ad26402dc66c |
"""
========================
Random Number Generation
========================
==================== =========================================================
Utility functions
==============================================================================
random_sample Uniformly distributed floats over ``[0, 1)`... | LumPenPacK/NetworkExtractionFromImages | win_build/nefi2_win_amd64_msvc_2015/site-packages/numpy/random/info.py | Python | bsd-2-clause | 5,199 | [
"Gaussian"
] | 1c1a0e73631888cd8e6938a4c269c35116737c1b2097968edd22882f0cb82f2a |
import functools
from wadl2rst.nodes.parameters import ParametersNode
def wrap_param_elements(tree):
""" Find all the <param> nodes and make sure they are wrapped by <params>
nodes. """
# grab all the param nodes
param_nodes = []
param_vistor = functools.partial(get_param_nodes, param_nodes)
... | annegentle/wadl2rst | wadl2rst/transformations/wrap_param_elements.py | Python | apache-2.0 | 1,145 | [
"VisIt"
] | 9d8e92918c82426fd2b4f116e725c88d56fe4e087d5b75e10502bfae84fe4c16 |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""testing code inspi... | rdkit/rdkit-orig | rdkit/Chem/UnitTestOldBugs.py | Python | bsd-3-clause | 3,266 | [
"RDKit"
] | 116167dfe5918ad071142cbfc0b4f310109b21db6e48eed0e386a9cf75e8daee |
#!/usr/bin/env python3
########################################################################
# Solves problem 17 from projectEuler.net.
# Finds how many characters are needed to write all numbers from one
# to one thousand in English.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free soft... | sanSS/programming-contests | project-euler/problem017.py | Python | gpl-3.0 | 3,149 | [
"VisIt"
] | ba7c2b9d71a42fee8ffa795dff5996b2aeb9981b59a02af799eb8b74a52bc173 |
"""
Some functions to make radmeth callable from python
"""
from sklearn.metrics import roc_curve, auc
import itertools as it
import numpy as np
import os
import pandas as pd
import toolshed as ts
from collections import defaultdict
import tempfile
import atexit
import shutil
def rad_format(fmethylated, fcounts, fout)... | brentp/crystal | crystal/radmeth.py | Python | mit | 2,630 | [
"CRYSTAL"
] | 5f4fc23703d98a227831b3ee614749c96417e222d01063402a6bb3f728bc2b6f |
#!/usr/bin/env python3
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, e... | espressopp/espressopp | testsuite/lattice_boltzmann/test_extForce.py | Python | gpl-3.0 | 4,098 | [
"ESPResSo"
] | 48efca5b071821f1a793212d634c965cdb78371cb8b03229c5b700f0be5472f7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Most features of this module has been moved to monty. Please refer to
monty.json and monty.serialization documentation.
"""
import functools
import json
import pickle
from pymatgen.core.periodic_table import Element
de... | vorwerkc/pymatgen | pymatgen/util/serialization.py | Python | mit | 3,689 | [
"pymatgen"
] | 08a30c874a79d6d8a59625bd976c8fe1e19c1fa579505fd8a589dd5ec4dab698 |
import pytest
from time import sleep
from capybara.tests.app import AppError
from capybara.tests.helpers import extract_results
class TestRefresh:
def test_reloads_the_page(self, session):
session.visit("/form")
assert session.has_select("form_locale", selected="English")
session.select("... | elliterate/capybara.py | capybara/tests/session/test_refresh.py | Python | mit | 1,141 | [
"VisIt"
] | ed81f4da4b448a2e2e53348bf8b58557c35af604c7341ebf4ed29c0afc82363e |
"""API for traversing the AST nodes. Implemented by the compiler and
meta introspection.
"""
from .nodes import Node
class NodeVisitor:
"""Walks the abstract syntax tree and call visitor functions for every
node found. The visitor functions may return values which will be
forwarded by the `visit` method.... | pallets/jinja2 | src/jinja2/visitor.py | Python | bsd-3-clause | 3,184 | [
"VisIt"
] | d0301427059200cdaf65dca2402fd450dfd45a4f8b3cb7e1e5cf794dcf7f4dab |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 Foundation, either version 3 of th... | clreinki/GalaxyHarvester | udSchematicImage.py | Python | agpl-3.0 | 5,210 | [
"Galaxy"
] | b55b9e3c6251a9fad0fc61a76d36b7cc668bd979a645fb75ae05b823fe6728d3 |
import pylab as pyl
import cPickle as pickle
from mpl_toolkits.axes_grid1 import AxesGrid
from colsort import colsort
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ICD_IH is not None, galaxies)
f1 = pyl.figure(1, figsize=(5,5))
f1s1 = f1.add_subplot(111)
low_mass = []
l... | boada/ICD | sandbox/legacy_plot_code/plot_color_vs_mass.py | Python | mit | 1,971 | [
"Galaxy"
] | 3906577b05b3cdf12dc0fbcd06380a0cfff0a1697c1f4cd3f573358f938279ef |
from pprint import pprint
from datetime import datetime
import pytest
from bs4 import BeautifulSoup
from django.utils import timezone
from ..tasks import parse_mw_deck, parse_tournament
def test_parse_tournament():
"""Asserts that bs4 tags for a given tournament are correctly parsed.
"""
bs4_tag = """<... | thomasperrot/MTGTrader | mtg/tournaments/tests/test_crawl_tournaments.py | Python | mit | 8,184 | [
"BLAST"
] | 2e956eb4852250fa9cefaf1cdc0339531082e040f002692d3208681d5aa443f1 |
# Copyright (C) 2015-2021 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU General Public License version 3, or any later version
# See top-level LICENSE file for more information
import datetime
from typing import Tuple
import attr
from swh.mode... | SoftwareHeritage/swh-storage | swh/storage/tests/storage_data.py | Python | gpl-3.0 | 23,995 | [
"VisIt"
] | 3349c85c51fb43c751c8d5da2c27bd9e89937b8b5d3e7758b7895ef671e5a0c8 |
# Copyright 2013 by Zheng Ruan (zruan1991@gmail.com).
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code for dealing with Codon Alignment.
"""
from __future__ import print... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/codonalign/__init__.py | Python | apache-2.0 | 33,163 | [
"Biopython"
] | 3a837149609db4e8797785c9625aa4812eca67a8e41345372c82d9250c9d2f62 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/p4util/testing.py | Python | lgpl-3.0 | 12,754 | [
"Psi4"
] | 8d2abc86bf6b21c0a4586ed5f5b99e0c52280bb91f4d038acd26688a7f35363a |
# The MIT License (MIT)
#
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# ... | wrocket/Tulip-Chess | tests/basic-tests/test_result.py | Python | mit | 5,509 | [
"Brian"
] | 15151e3b8c668597302aa3c55007791fab478d6ceb168c33bc9f5f9dc438a21d |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag config_path) the path of a json file that dictates the file... | li-xiao-nan/gyp_tools | pylib/gyp/generator/analyzer.py | Python | bsd-3-clause | 16,504 | [
"VisIt"
] | 06a329c2d54215c20cde5ca9810dfe0d6bff4beb31a76a9dcf4ad6ee4e190f97 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | samples/minimal-polymer.py | Python | gpl-3.0 | 2,871 | [
"ESPResSo"
] | c263e1cadae2eabe2758e4de2241b5d8e46b0cdab441eaf27e752479b3fd0d64 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Demonstration of DNest4 in Python using the "StraightLine" example
"""
import dnest4
import numpy as np
import numpy.random as rng
from numba import jitclass, int32
# Load the data
data = np.loadtxt("../../../code/Examples/StraightLine/road.txt")
@jitclass([('dummy',... | eggplantbren/DNest4 | python/examples/straightline/straightline.py | Python | mit | 2,908 | [
"Gaussian"
] | eed60828c3b12365ae3d3dffb8eab2e401a2b9aedc1209590d14ba0dab11bd92 |
# coding: utf-8
# # This notebook shows how to performa heteroscedastic lengthscale, variance, and noise solve
# In[1]:
from ionotomo import *
import numpy as np
import pylab as plt
plt.style.use('ggplot')
import astropy.units as au
import os
import gpflow as gp
from doubly_stochastic_dgp.dgp import DGP
from scipy... | Joshuaalbert/IonoTomo | src/ionotomo/data/heteroscedastic_model.py | Python | apache-2.0 | 52,858 | [
"Gaussian"
] | 530d52fbc387b166e70fe23574175dfd9b7ad7668b3aaedb53a50ff4425cdcd4 |
"""
This module provides functions to get the dimensionality of a structure.
A number of different algorithms are implemented. These are based on the
following publications:
get_dimensionality_larsen:
- P. M. Larsen, M. Pandey, M. Strange, K. W. Jacobsen. Definition of a
scoring parameter to identify low-dimens... | gmatteo/pymatgen | pymatgen/analysis/dimensionality.py | Python | mit | 22,027 | [
"CRYSTAL",
"Jmol",
"VisIt",
"pymatgen"
] | 46ecf82f6271bf65f36f3c345282d5b574c1ddbf286e4c3837f556088f9234ef |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | CodeMonkeyJan/hyperspy | hyperspy/components1d.py | Python | gpl-3.0 | 3,496 | [
"Gaussian"
] | 3c386b1e81fb9d4ce6d2bb655bf33b21a0324f2317bb87b4ee580c681426c6c5 |
""" Functions necessary for smoothing 2D terrain """
import sys, pickle, os.path, itertools, collections, errno
import numpy
try:
import scipy.ndimage
except ImportError, e:
pass
filters = {
'smooth': 'smooth',
'gauss': 'gsmooth',
}
def ftrim(a, cut):
"""
Takes a 2D DFT... | hetmankp/mcmerge | filter.py | Python | isc | 3,210 | [
"Gaussian"
] | aba9cea05501c6702a9647f072ae84eda29e96aca01ab630b9e998a3266b4991 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2012 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | tiagocardosos/stoq | stoqlib/__init__.py | Python | gpl-2.0 | 874 | [
"VisIt"
] | 555f8c1b379b1093e8ff893e0903b2aa162732b9a9568248de294c7ca7a6f39a |
from deepplantphenomics import loaders, layers, SemanticSegmentationModel
import tensorflow.compat.v1 as tf
import numpy as np
import os
import warnings
import numbers
import itertools
import shutil
from tqdm import tqdm, trange
from PIL import Image
import cv2
import copy
class HeatmapObjectCountingModel(SemanticSeg... | p2irc/deepplantphenomics | deepplantphenomics/heatmap_object_counting_model.py | Python | gpl-2.0 | 22,127 | [
"Gaussian"
] | 7d12cdc11a0c889e251e4085d64b118b44f6e94259123cf00cafd895fb187da5 |
#!/usr/bin/env python
# Standard packages
import os
import sys
import argparse
# Third-party packages
from toil.job import Job
# Package methods
from ddb import configuration
from ddb_ngsflow import gatk
from ddb_ngsflow import annotation
from ddb_ngsflow import pipeline
from ddb_ngsflow.align import bwa
from ddb_ng... | GastonLab/ddb-scripts | workflow-somatic_amplicon_filtered.py | Python | mit | 19,425 | [
"BWA"
] | f6403bd5d4b458000af850e5c45bd4568130d1d67a30abf38b57dba25ab63fdb |
# -*- coding: utf-8 -*-
"""Various text used throughout the website, e.g. status messages, errors, etc.
"""
# Status Messages
#################
# NOTE: in status messages, newlines are not preserved, so triple-quotes strings
# are ok
# Status message shown at settings page on first login
# (upon clicking primary em... | asanfilippo7/osf.io | website/language.py | Python | apache-2.0 | 8,397 | [
"VisIt"
] | b97f64bc4de163927bf45a78c0b029d911cb3c21b85ad54a74b3480f8ca43f1e |
#
# This file is part of Bakefile (http://bakefile.org)
#
# Copyright (C) 2008-2013 Vaclav Slavik
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without... | vslavik/bakefile | src/bkl/interpreter/analyze.py | Python | mit | 6,577 | [
"VisIt"
] | fa6f21c18251d32fcd2d6ef55fe6c420ef21b7f6cb46b87cadfdc43fa933a97d |
"""
This is the window manager part of pySSN
pySSN is available under the GNU licence providing you cite the developpers names:
Ch. Morisset (Instituto de Astronomia, Universidad Nacional Autonoma de Mexico)
D. Pequignot (Meudon Observatory, France)
Inspired by a demo code by:
Eli Bendersky (eliben@gmail.c... | Morisset/pySSN | pyssn/qt/pyssn_qt.py | Python | gpl-3.0 | 220,441 | [
"Gaussian"
] | 2ea37b9c924313cf7b2509f74cbfd21df103b585c307af898c13a0c89c2a3983 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import json
import warnings
import numpy as np
import tempfile
from pymatgen import Structure
from pymatgen.io.lobster import Cohpcar, Icohplist, Doscar, Charge, Lobsterout, Fatband, L... | blondegeek/pymatgen | pymatgen/io/tests/test_lobster.py | Python | mit | 86,415 | [
"Gaussian",
"VASP",
"pymatgen"
] | 4a2b4856cbde2c52a7cdbc8faf7f1133b80a95ccca83e928012fbb0121529454 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2015-2020 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
# Copyright 2015-2018 lamarpavel
#
# This file is part of qutebrowser.
#
# qutebrowser is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Lic... | t-wissmann/qutebrowser | tests/unit/browser/webkit/test_cache.py | Python | gpl-3.0 | 6,370 | [
"VisIt"
] | 883074a32ca4610afebfb6ff1e5152af4f00257572186da4b00d6ddb2ab804ce |
import subprocess
import numpy as np
import Bio.PDB as PDB
import networkx as nx
import cylinder_fitting
from . import geometry
def make_dssp_dict(pdb_path, dssp_path):
'''Make a dictionary that stores the DSSP information of a
protein. The keys are (chain_id, res_id).
Return values:
- a DSSP information... | Kortemme-Lab/protein_feature_analysis | ProteinFeatureAnalyzer/features/secondary_structures.py | Python | mit | 18,229 | [
"Gaussian"
] | 577ee23e6475f1c7de0359be062476086a55ed24596b25167219c1757767fa1c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#******************************************************************************
#*
#* Copyright (C) 2015 Kiran Karra <kiran.karra@gmail.com>
#*
#* This program is free software: you can redistribute it and/or modify
#* it under the terms of the GNU General Public Licens... | kkarrancsu/copula-bayesian-networks | copulamnsig.py | Python | gpl-3.0 | 24,012 | [
"Gaussian"
] | 7a946273f02945245c6f49a120f30d23bd0689f83ac1361f098cd2b81b823324 |
#
# Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyrigh... | bp-kelley/rdkit | rdkit/Chem/SaltRemover.py | Python | bsd-3-clause | 10,659 | [
"RDKit"
] | adc0740fb9dfd09dbb362edd33a1095ff6191c4f3231ec155d56fc052f644235 |
#!/usr/bin/python
import sys
import inspect
import re
import pysam
import os
import numpy as np
import heapq
import matplotlib
import matplotlib.cm as cm
import pylab
import argparse
# realpath() will make your script run, even if you symlink it :)
cmd_folder = os.path.realpath(os.path.abspath(os.path.split(inspect.... | batxes/4Cin | src/paint_model.py | Python | gpl-3.0 | 15,498 | [
"pysam"
] | 2dc1185c5c796d1ddc425d74798a99f5c0d0b3e1cbad5bef4162c8e3399cd419 |
# coding=utf-8
# Copyright 2022 The Google Research 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 required by applicab... | google-research/google-research | smu/find_noncanonical_smiles.py | Python | apache-2.0 | 4,872 | [
"RDKit"
] | d1d5b49898ba0e45fd35dbbfd8f6e06eea8ec0a3ba53f6f724c2a8210609e8d5 |
from theano import function
import theano
from theano import tensor as T
from numpy import *
class neuron(object):
def __init__(self, args, w = None, active_fun = T.tanh):
if w == None:
self.w = asarray( random.uniform(low = -1.0,
high = 1.0,
... | PiscesDream/Ideas | ML/single_ann/test.py | Python | apache-2.0 | 914 | [
"NEURON"
] | 5926150441bb07adbf21aee44e341e7ddc34e6c172c04e61e4e716fd41d815b2 |
"""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 ... | Tong-Chen/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 47,814 | [
"Brian"
] | 3ad55b7887cba95e1341ebec67f2a8a4a1d2f358e911b8d50bb69ed1308978c9 |
#!/usr/bin/python
#
# Copyright © 2014 Brian E Hoch
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This pr... | hochbrian/bridal_party | bridal_party.py | Python | gpl-3.0 | 8,812 | [
"Brian"
] | 02445a77db3d4c705d7997478c329b397775a0577b51abe42fd3de5f64d13430 |
# Copyright 2011-2016, Damian Johnson and The Tor Project
# See LICENSE for licensing information
"""
Basic enumeration, providing ordered types for collections. These can be
constructed as simple type listings...
::
>>> from stem.util import enum
>>> insects = enum.Enum('ANT', 'WASP', 'LADYBUG', 'FIREFLY')
>>... | sammyshj/stem | stem/util/enum.py | Python | lgpl-3.0 | 4,385 | [
"Firefly"
] | 0dcfb38ede7ff9b50a90dffd6a216b09b65b99e0886d0a5494f66ce3d748e6e5 |
#!/usr/bin/env python
'''
Different ways to input density fitting auxiliary basis for PBC Gaussian
density fitting.
See also pyscf/examples/df/01-auxbasis.py for more auxiliary basis input
methods.
'''
import numpy as np
from pyscf import gto as mol_gto
from pyscf.pbc import gto, scf, cc, df
cell = gto.Cell()
cell.... | sunqm/pyscf | examples/pbc/35-gaussian_density_fit.py | Python | apache-2.0 | 3,584 | [
"Gaussian",
"PySCF"
] | ba20642232ad18ee1900d08b99a84342b2873e085dd19b0040b01ad0c24a2923 |
from unittest import mock
from nimoy.ast_tools import ast_chain
from nimoy.runner.metadata import RunnerContext
from nimoy.runner.spec_finder import Location
from nimoy.specification import Specification
class AstChainSpec(Specification):
@mock.patch('nimoy.ast_tools.ast_chain.SpecTransformer')
def apply_ch... | browncoat-ninjas/nimoy | specs/nimoy/ast_tools/ast_chain_spec.py | Python | apache-2.0 | 642 | [
"VisIt"
] | fcec7c53ef34732fbe69b787b8dfdc227ad9c67241fa47f0bcb1b75200dd23ce |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-agilp/package.py | Python | lgpl-2.1 | 1,627 | [
"Bioconductor"
] | 12b8995f5e6eec6674c7d0f27db376e946aff9e71018925072b050ea51f5d1d1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Some reimplementation of Henkelman's Transition State Analysis utilities,
which are originally in Perl. Additional features beyond those offered by
Henkelman's utilities will be added.
This allows the usag... | gVallverdu/pymatgen | pymatgen/analysis/transition_state.py | Python | mit | 17,151 | [
"VASP",
"pymatgen"
] | e7dd43464539a5979958ba962460c63dfb7e78f3e13ce752d5531f12d6b22548 |
# coding=utf-8
"""
How much do you win if you never lose a bet?
How to detect if someone is winning all the
bets so you can throw them out of the casino?
"""
from __future__ import print_function, unicode_literals, absolute_import
# configure logging for file and console output.
import logging
import os.path
if os.pa... | matthewdeanmartin/kata-python | kata/never_lose/main.py | Python | gpl-3.0 | 1,407 | [
"CASINO"
] | 9d8c42d6a42afddce4b9719196d74bf55c583eb5491e430e741506c08b15791c |
'''
drivers to prepare the data for scaffolding
'''
import sys
import logging
import string
import subprocess
import os
from utils.misc import *
## private functions ##
## public functions ##
def prep_silp(work_dir, ant_dir, prep_sh, ctg_fasta, read1_sam, read2_sam, ins_size, std_dev, bundle_size, pair_mode, args):
... | jim-bo/scafathon | utils/prep.py | Python | mit | 9,362 | [
"Bowtie"
] | 8fd37787a2f00a3a9c6b0138b613ef97429c145bf3b08572cd2bb592b19cf5af |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""Module for `Latent Semantic Analysis (aka Latent Semantic Indexing)
<https://en.wikipedia.org/wiki/Latent_semantic_analysis#Latent_s... | RaRe-Technologies/gensim | gensim/models/lsimodel.py | Python | lgpl-2.1 | 44,906 | [
"Gaussian"
] | c85b9a5fb65f0734d3e7e24ff62a05554c6b0a1537a4edf4dff745573a655932 |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | Eric89GXL/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 134,490 | [
"Elk"
] | 45c16f271c3de165f17f219b2859403fdb7ea1390c4c8885138c7b7933fa5145 |
#!/usr/bin/env python
import os,sys,csv,re
from sqlalchemy.sql import select
from htsint.database import db_connect,Taxon,Gene
def get_blast_map(resultsFilePath,evalue=0.00001,taxaList=None,asGenes=False,append=False):
"""
load assembly blast results into dictionary
if taxaList is provided then only gen... | ajrichards/htsint | htsint/blast/BlastTools.py | Python | bsd-3-clause | 7,565 | [
"BLAST"
] | 63ea68f03516044776a1adfecf2021c70803f52b70f365bb92c69f066689fa08 |
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