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 |
|---|---|---|---|---|---|---|---|
# File I/O class
# A wrapper around the NetCDF4 library, used by
# BOUT++ routines. This allows easily changing
# methods later.
#
# NOTE: NetCDF includes unlimited dimensions,
# but this library is just for very simple
# I/O operations. Educated guesses are made
# for the dimensions.
try:
import numpy as np
excep... | bendudson/BOUT-1.0 | tools/pylib/boututils/datafile.py | Python | gpl-3.0 | 6,594 | [
"NetCDF"
] | 7d258ad1ad7bfe3f50ecba250e705edcd6ff6b1e3205f899449ff29c70df0602 |
"""
Class description of a DNA chain built of base pairs
"""
from typing import List, Tuple, Union
from copy import deepcopy
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from mpl_toolkits.mplot3d import Axes3D # NOQA
from scipy.interpolate import interp1d
try:
from m... | natl/fractaldna | fractaldna/dna_models/dnachain.py | Python | mit | 57,363 | [
"Mayavi"
] | 9fa374338e2ac85d9bb0d377b301002fc70fe9a3b23add673a86713722a2e788 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from rest_framework_jwt.views import obtain_jwt_token
from nomadgram imp... | plusbeauxjours/nomadgram | config/urls.py | Python | mit | 1,813 | [
"VisIt"
] | de66aff480195a85e20985952edbbd6f74838e7eff52c900f27eddae16231121 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Soft... | bhdouglass/remindor-common | remindor_common/threads.py | Python | gpl-3.0 | 4,331 | [
"Brian"
] | 04730c29cbdba4b27ef99c0c83ff76a4fe81ff3c4e9c0878e2a0946a61605463 |
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2019-, Dilawar Singh"
__maintainer__ = "Dilawar Singh"
__email__ = "dilawars@ncbs.res.in"
import moose
if moose._moose.__generated_by__ != "pybind11":
print("These bindings are not generated by pybind11.")
quit(0)
import random
import numpy as... | dilawar/moose-core | tests/core/test_api.py | Python | gpl-3.0 | 6,080 | [
"MOOSE"
] | 08f91dd3de66fde0daec7f31e2862e7b6ef343f3b5dfc72ddc34f60576658c8f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/test_units.py | Python | gpl-2.0 | 4,653 | [
"Gromacs",
"MDAnalysis"
] | bad0d64c5cf4e1be2cc422f1f6cad2050b0b32b1395c2e83490ce5f2e41d9358 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/driver/util/tty/__init__.py | Python | lgpl-3.0 | 4,312 | [
"Psi4"
] | 3673cc5cb4d85125444e03e6309a50844484ba7d2decdd55ba7b4284368b6240 |
# coding=UTF-8
"""
Created on Mar 11, 2014
@author: rgeorgi
"""
import re
import unittest
import string
# ===============================================================================
# Sub-tasks of cleaning
# ===============================================================================
from intent.alignment.Ali... | rgeorgi/intent | intent/igt/igtutils.py | Python | mit | 15,737 | [
"VisIt"
] | 7b47cebbad512ae623a8c6bc313794b2d936aabc3b1a6f68d9e5416595dbda75 |
# 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.
from copy import copy
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBEx... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/Entity.py | Python | gpl-2.0 | 7,284 | [
"Biopython"
] | 618980f980ae08f2c37c34f46b9a242f5b674991ef7a57255723cd5f0f16c54b |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/soffice/braille_generator.py | Python | gpl-3.0 | 9,278 | [
"ORCA"
] | 85ce39e3cac0a79ee72e97dc9bff382fd3cdd6eb6aaa95cccf224dabdf62324f |
# $Id$
#
# 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.
#
""" unit testin... | rdkit/rdkit-orig | rdkit/Logger/UnitTestLogger.py | Python | bsd-3-clause | 2,842 | [
"RDKit"
] | 3ab098c0edcd09a4c638fa9151e38212db0b4ab1cd13799c2f235b60b4f2f057 |
#!/usr/bin/env python3
"""
script for fixing scaffolding errors by:
1. identifying errors based on stringent read mapping (stringent mapping for both reads in a pair)
2. collecting mapped reads (stringent mapping for one read in pair)
3. re-assembling collected reads
4. merging the new assembly with the old assemb... | christophertbrown/fix_assembly_errors | ctbRA/re_assemble_errors.py | Python | gpl-2.0 | 38,555 | [
"Bowtie"
] | f3584afa1d8c8e3d594a8a517967c5e0dbed879735fceb8e4c2aeaef049b5317 |
########################################################################
# $HeadURL $
# File: StorageElementProxyHandler.py
########################################################################
"""
:mod: StorageElementProxyHandler
.. module: StorageElementProxyHandler
:synopsis: This is a service which represe... | sposs/DIRAC | DataManagementSystem/Service/StorageElementProxyHandler.py | Python | gpl-3.0 | 11,822 | [
"DIRAC"
] | fc6a98cab0262a395a94c28d344b319d189baecb0c333184b02febb7db22d8b3 |
#!/usr/bin/python
"""Test of sayAll."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
sequence.append(utils.StartRecordingAction())
sequence.append(KeyComboAction("KP_Add"))
sequence.append(utils.AssertPresentationActio... | GNOME/orca | test/keystrokes/firefox/say_all_wiki_no_context.py | Python | lgpl-2.1 | 12,887 | [
"ORCA"
] | 5b4c63a9c02627fb7c325cf0f962a75282d80a50eabe53e8d009fd689104512c |
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import os
import logging
import unittest
from telemetry.core import util
from telemetry.core.platform.profiler import perf_profiler
from telemetry.unittest i... | androidarmv6/android_external_chromium_org | tools/telemetry/telemetry/core/platform/profiler/perf_profiler_unittest.py | Python | bsd-3-clause | 2,063 | [
"VisIt"
] | 3f045be1319ac3b3330f0dbafda3dcc4059a81ac93a49078dfdca6a50dd15486 |
""" Hello Service is an example of how to build services in the DIRAC framework
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHa... | yujikato/DIRAC | docs/source/DeveloperGuide/AddingNewComponents/DevelopingServices/HelloHandler.py | Python | gpl-3.0 | 1,047 | [
"DIRAC"
] | 8172ea2a25b1507ccabd188cb26240887ccd81cf8c81a18e279592bf629117d7 |
''' AccountingCacheCommand
The AccountingCacheCommand class is a command module that collects command
classes to store accounting results in the accounting cache.
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# FIXME: NOT Usable ATM
# missing doN... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Command/AccountingCacheCommand.py | Python | gpl-3.0 | 16,493 | [
"DIRAC"
] | 9b2f4ac8cb95462a4809dfbec7450699da2ed6bf7bb24d6cdffa2d4026da080a |
#!/usr/bin/env python
from __future__ import print_function
from future.standard_library import install_aliases
install_aliases()
from urllib.parse import urlparse, urlencode
from urllib.request import urlopen, Request
from urllib.error import HTTPError
import json
import os
import traceback
from flask import Flask... | ypalkar/apiai-bww-webhook-sample | app.py | Python | apache-2.0 | 6,975 | [
"VisIt"
] | 8f2745f21f693656919cc76041138c280a9dadec3ae3889842ef5215b878e98a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# rpcserver - minimal rpc benchmark server
# Copyright (C) 2003-2011 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 terms of the GNU General Public L... | heromod/migrid | mig/grsfs-fuse/benchmarks/code/rpcserver.py | Python | gpl-2.0 | 4,822 | [
"Brian"
] | 2391b82c76a4d956ea26f7b90be9c69593db0e54644a09f0bf7fc42fe2b6d2e8 |
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
# Plane wave cutoff
pwcutoff = 600.0
# NxNxN k-point sampling, gamma-centred grid
k = 4
# Si lattice constant
alat = 5.421
# bulk calculation
bulk_crystal = bulk('Si', 'diamond', a=alat)
bulk_calc = GPAW(
mode = P... | robwarm/gpaw-symm | doc/exercises/rpa/si.rpa_init_pbe.py | Python | gpl-3.0 | 907 | [
"ASE",
"GPAW"
] | 562c6a47c874efd3734b07fb063e81645ce737570598c4457a5314ef99cdd22b |
#!/usr/bin/env python2
from netCDF4 import Dataset
import numpy
from geopy.distance import vincenty
from wrfpy.config import config
from wrfpy import utils
from wrfpy.readObsTemperature import readObsTemperature
import os
from datetime import datetime
import operator
from numpy import unravel_index
from numpy import s... | ERA-URBAN/wrfpy | wrfpy/bumpskin.py | Python | apache-2.0 | 21,936 | [
"NetCDF"
] | 8ce0145d1d76634412b883b8a36d92a95f3024119ee31208a36d9d79d99fbccf |
import ply.lex as lex
import ply.yacc as yacc
import lan
import rewriter
from codegen import cgen
from host import boilerplategen, kernelgen
from processing import collect_id as ci
from transformation import define_arguments as darg
from transformation import stencil
from transformation import transpose as tp
filepre... | dikujepsen/OpenTran | src/framework/main.py | Python | mit | 3,760 | [
"Gaussian"
] | 28c8ba94140a3321c66235a1e35a9a9f7cba2bbd8b4f2ca7f30f328b654e8173 |
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
from pgmpy.factors.continuous import ContinuousFactor
from pgmpy.factors.continuous import JointGaussianDistribution
class CanonicalFactor(ContinuousFactor):
u"""
The intermediate factors in a Gaussian network can be described
c... | dungvtdev/upsbayescpm | pgmpy/factors/continuous/CanonicalFactor.py | Python | mit | 15,198 | [
"Gaussian"
] | 05d8750ae6ecbcc753e04a13aaee2eff28a5a0a4712b3a5cbff471633822a8ef |
#!/usr/bin/env python
from __future__ import print_function
from vtk import *
if __name__ == "__main__":
""" Main entry point of this python script """
#
# Load our table from a CSV file (covered in table2.py)
#
csv_source = vtkDelimitedTextReader()
csv_source.SetFieldDelimiterCharact... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/tables3.py | Python | bsd-3-clause | 1,093 | [
"VTK"
] | c9c0ed6b10dc793229561748e9a4fd03ae90f1cf68d67c90dfd0c600aaf22a65 |
import logging
import urllib
from functools import partial
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
from django.contrib.auth.decorators i... | pdehaye/theming-edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 32,013 | [
"VisIt"
] | 23a6548d3287e8c45cbb41642ee4a11c42e052c6797dba2f816ec6eeaf796273 |
#!/usr/bin/env python
import sys, os, random
from pprint import pprint, pformat
from LunchPlace import LunchPlace
from LunchVisit import LunchVisit
from LuncherPreferences import LuncherPreferences
def read_places(filename):
placenames = {}
places = []
with open(filename) as f:
for line in f:
... | ryanaustincarlson/markovlunch | pick_lunch.py | Python | mit | 5,036 | [
"VisIt"
] | 5ace1a27c81b63800f6799bf68198752c2409e2180315ce3bcc92e42348af27c |
#
# Copyright (C) 2007, Mark Lee
#
# http://rl-glue-ext.googlecode.com/
#
# 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 require... | evenmarbles/rlglued | rlglued/agent/agent.py | Python | bsd-3-clause | 1,340 | [
"Brian"
] | 32b17976adc4cbeb6ddf5781f7f12298d840228984850f718517175a2d7cb866 |
"""
MRS.api
-------
Functions and classes for representation and analysis of MRS data. This is the
main module to use when performing routine analysis of MRS data.
"""
import numpy as np
import scipy.stats as stats
import nibabel as nib
import warnings
import MRS.analysis as ana
import MRS.utils as ut
import MRS.fre... | arokem/MRS-old | MRS/api.py | Python | mit | 31,407 | [
"Gaussian"
] | 682188465ba0a10cd6a59baa0823282b273c61d21d61d55041a9bc0206b65958 |
import ast
import datetime
import re
import secrets
import time
from collections import defaultdict
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
DefaultDict,
Dict,
Iterable,
List,
Optional,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
im... | kou/zulip | zerver/models.py | Python | apache-2.0 | 130,540 | [
"VisIt"
] | 8e3b60fedffde2f3b4c22dfe4b6af9870ce155d5686f046aa4017906fe4770b3 |
"""
====================================================================
Probabilistic predictions with Gaussian process classification (GPC)
====================================================================
This example illustrates the predicted probability of GPC for an RBF kernel
with different choices of the hy... | manhhomienbienthuy/scikit-learn | examples/gaussian_process/plot_gpc.py | Python | bsd-3-clause | 3,999 | [
"Gaussian"
] | c8e9ead4eec364b492fd944d43f41939733410580e55530ac6f9031c0f8b2f07 |
# -*- coding: utf-8 -*-
# HiPart is a program to analyze the electronic structure of molecules with
# fuzzy-atom partitioning methods.
# Copyright (C) 2007 - 2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>
#
# This file is part of HiPart.
#
# HiPart is free software; you can redistribute it and/or
# modify it under t... | molmod/hipart | hipart/schemes.py | Python | gpl-3.0 | 44,551 | [
"CP2K",
"CPMD",
"GAMESS",
"Gaussian"
] | 861484eae3121edb0c80855611e0d6860f06418386d3b8d4e725ca60ca914a53 |
from datetime import datetime
import logging
from time import time
from sqlalchemy.exc import IntegrityError, OperationalError
from sqlalchemy.sql import and_, or_
from .select_or_insert import SelectOrInsert
from .stripXML import strip as stripXML
from .tables import AdmissionSource, SpecimenSource
from .tables impo... | pbugni/pheme.longitudinal | pheme/longitudinal/longitudinal_worker.py | Python | bsd-3-clause | 69,014 | [
"VisIt"
] | 75d0b65c239ea942d74b070447a51e11a1c2621768d38fa309bdded5844cf1f5 |
# #
# Copyright 2009-2015 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://vscentrum.be/nl/en),
# the Hercules foundation (ht... | pneerincx/easybuild-framework | easybuild/tools/filetools.py | Python | gpl-2.0 | 36,453 | [
"NetCDF"
] | 68ea2e4c399e62c25b25a8fc3ad3ab50692cdcb498f01c79b5ae015751742cbe |
# -*- coding: utf-8 -*-
#
# CMS documentation build configuration file, created by
# sphinx-quickstart on Mon Apr 6 14:12:39 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | broadinstitute/cms | docs/conf.py | Python | bsd-2-clause | 10,185 | [
"pysam"
] | 1775cc28c14e9bafa4e98a6f2c7327032938539658c15fd71bbf12f3ba36de78 |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest
import os
import json
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import AngleNbSetWeight
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import ... | dongsenfo/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py | Python | mit | 34,458 | [
"pymatgen"
] | cda54eab77e1a84980c253c14c0318062f1eaa331faa3692816bfe15e383a049 |
##
# Copyright 2009-2016 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... | hpcleuven/easybuild-easyblocks | easybuild/easyblocks/a/aladin.py | Python | gpl-2.0 | 15,321 | [
"NetCDF"
] | 2e03fdb516e2c9576d2d335e69b0c2dbf5395ce2e68cbce03316c30f334ad969 |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/epmvGui.py is part of ePMV.
ePMV 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)... | corredD/ePMV | epmvGui.py | Python | gpl-3.0 | 184,458 | [
"CRYSTAL",
"Gromacs",
"PyMOL"
] | f9f8f563d598d1d2dc1248fff09ecdb722ffc0e3cc2f3d440c0eda73eb631b93 |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | barnabytprowe/great3-public | inputs/galdata/run_props.py | Python | bsd-3-clause | 4,678 | [
"Galaxy",
"Gaussian"
] | 08b82801f3debf51b0eff6a26bc7627320494e45014e98870f483567fe2bca15 |
import numpy as np
def gaussian_peak(grid, x0, FWHM):
""" Return a normalized gaussian peak with FWHM=width
in the given grid. """
a = np.sqrt(4*np.log(2)/np.pi)/FWHM
b = 4*np.log(2)/FWHM**2
return a*np.exp( - b*(grid-x0)**2 )
def broaden(grid, values, width, weights=None):
""" Broaden g... | pekkosk/hotbit | box/broaden.py | Python | gpl-2.0 | 1,774 | [
"Gaussian"
] | 855a2188c4b28b265aa9a8db5e4988fbf0876daf143c67a0bedabcfba347cfc3 |
# Copyright 2019 Google 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
#
# Unless required by applicable law or a... | google/timesketch | api_client/python/timesketch_api_client/sketch.py | Python | apache-2.0 | 66,968 | [
"Elk"
] | 88017a294dc0557a72e285682c073905f1fedb79be7d5d2cd160726b6cf7eaf7 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getp... | DivineHime/seishirou | lib/youtube_dl/extractor/common.py | Python | gpl-3.0 | 119,472 | [
"VisIt"
] | 3d60d1a23bfd6173cb438cccca6b3826cd7f8f712d351798c49121059eaaba95 |
import os
import sys
import re
import glob
import string
import traceback
import time
# list of tests to run ...
# prefixes
# C = command line scripts
# G = graphics and internal GUI
standard_prefixes = ['C', 'G' ]
# uniform parameter handling
argv = sys.argv
if len(argv):
if re.search("\.py$",argv[0]):
... | gratefulfrog/lib | python/pymol/pymol_path/test/win.py | Python | gpl-2.0 | 1,943 | [
"PyMOL"
] | a94d09b43cab4937fb69ba4d64d7c301753d1350d9d6e1e72156f53bcfcab69a |
#!/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... | kbrebanov/ansible | lib/ansible/modules/network/cnos/cnos_vlan.py | Python | gpl-3.0 | 11,632 | [
"VisIt"
] | 2aaec32097dee7f11dcb83b49095f3a416215e24d941bc3a64c7ea84fdb5ac3c |
#!/usr/bin/env python
'''
IP/EA-ADC calculations for closed-shell N2
'''
from pyscf import gto, scf, adc
mol = gto.Mole()
r = 1.098
mol.atom = [
['N', ( 0., 0. , -r/2 )],
['N', ( 0., 0. , r/2)],]
mol.basis = {'N':'aug-cc-pvdz'}
mol.build()
mf = scf.RHF(mol)
mf.conv_tol = 1e-12
mf.kernel()
myadc = ... | sunqm/pyscf | examples/adc/03-closed_shell_different_setup.py | Python | apache-2.0 | 801 | [
"PySCF"
] | ba561c450d82a0832ba4b508ac9fabf85755393f0536eca8f33c7fb271f0d99c |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_C3H8_emissions_n96e_360d.py | Python | gpl-3.0 | 19,239 | [
"NetCDF"
] | 939761a3d1ec3bffec49a531859ae67db44c0270553cdb9164894203b3d3c378 |
"""
tune_combat.py
Copyright 2016 Brian Romanchuk
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 i... | brianr747/Simple4Xpygame | tune_combat.py | Python | apache-2.0 | 1,484 | [
"Brian"
] | 7a41e03ec0974036a7d89a0c62105dc6b97e8b9aecf4c8046943e7005cfcd6d0 |
#!/usr/bin/env python3
########################################################################
# Solves problem 1 from projectEuler.net.
# Sums all the multiples of 3 or 5 from 1 to 1000(exclusive)
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or modi... | sanSS/programming-contests | project-euler/problem001.py | Python | gpl-3.0 | 1,240 | [
"VisIt"
] | a79ba0398f1e6dd03f92b0814d7f3eace92fe8b448d3686b6fdf8841888220c7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 19 11:20:48 2020
@author: tommy
"""
if __name__ == "__main__":
from KDEpy import FFTKDE
import matplotlib.pyplot as plt
customer_ages = [40, 56, 20, 35, 27, 24, 29, 37, 39, 46]
# Distribution of customers
x, y = FFTKDE(kernel=... | tommyod/KDEpy | docs/source/README_examples.py | Python | gpl-3.0 | 2,299 | [
"Gaussian"
] | 54adf2dad703a0d1aaca4ae64a978eef4154184c7d02b4bb96a269ce8fb437e0 |
from functools import partial
from kivy.properties import ObjectProperty, StringProperty, OptionProperty
from kivy.uix.accordion import AccordionItem
from kivy.uix.button import Button
from kivy.uix.gridlayout import GridLayout
from kivy.uix.modalview import ModalView
from kivy.uix.togglebutton import ToggleButton
cl... | MiyamotoAkira/kivy-designer | designer/uix/playground_size_selector.py | Python | mit | 8,095 | [
"Galaxy"
] | d8359bbf438abbf87956660db3a6d1d7bb533da272cd3adbca7d9478220bb74f |
#
# 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 n... | lhfei/spark-in-action | spark-2.x/src/main/python/ml/gaussian_mixture_example.py | Python | apache-2.0 | 1,616 | [
"Gaussian"
] | d38ebbc090bd05aec963427affb2beb7fb94ea0eea0b2c4d253470928df504e4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A Flow is a container for Works, and works consist of tasks.
Flows are the final objects that can be dumped directly to a pickle file on disk
Flows are executed using abirun (abipy).
"""
from __future__ impo... | tallakahath/pymatgen | pymatgen/io/abinit/flows.py | Python | mit | 106,450 | [
"ABINIT",
"pymatgen"
] | 76628aa965dbdf4f553dca1034b8ab2632f732bdcdab3bcef73cee6bd992ed04 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# jobscriptgenerator - dynamically generate job script right before job handout
# Copyright (C) 2003-2014 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 th... | heromod/migrid | mig/server/jobscriptgenerator.py | Python | gpl-2.0 | 35,103 | [
"Brian"
] | 8dd460e28e04ac3dbfa58b08190c106f6b2b510549586ab4aab8dda3a05e6f5d |
"""Various tools for surface desciption"""
import numpy as np
def spectrum(wk, sh, cl, th, n=1, kind='isotropic gaussian', **kwargs):
"""Surface roughness spectrum at at order n
"""
if kind == 'isotropic gaussian':
out = np.float64(cl)**2/n*np.exp(-(wk*cl*np.sin(th))**2/n) /2.
else:
r... | cgrima/subradar | subradar/roughness.py | Python | mit | 391 | [
"Gaussian"
] | 381c48accee411d841f8bcd12dae60280f939415fae3f3c5c9e2d13bfc3176e5 |
"""deployment scripts for researchcompendia
with credit to scipy-2014 fabric.py
fab <dev|staging|prod|vagrant> <deploy|provision>[:<git ref>]
deploy: deploys the site to the specified environment. if no git ref is provided, deploys head
provision: provisions a box to run the site. is not idempotent. do not rerun.
git... | researchcompendia/researchcompendia-deployment | fabfile.py | Python | mit | 17,507 | [
"VisIt"
] | dcb1ae527788bdab2df971e64154fdb4c1efe36f982b9838ba9511f4df74de2d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 Red Hat, Inc.
# Copyright (c) 2010 Ville Skyttä
# Copyright (c) 2009 Tim Lauridsen
# Copyright (c) 2007 Marcus Kuhn
#
# kitchen 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
# ... | fedora-infra/kitchen | kitchen2/kitchen/text/display.py | Python | lgpl-2.1 | 40,137 | [
"NetCDF"
] | ed22fe11db84bedca4511113813d2b6fa947abb978d0efb68b3c0a9acf6c6c8d |
class ASTVisitor():
def visit(self, astnode):
'A read-only function which looks at a single AST node.'
pass
def return_value(self):
return None
class ASTModVisitor(ASTVisitor):
'''A visitor class that can also construct a new, modified AST.
Two methods are offered: the normal visit() method, which ... | cs207-project/TimeSeries | pype/ast.py | Python | mit | 5,420 | [
"VisIt"
] | dc5ed9baa6f651f760ab74dfd5e17c23d262545ef5d62420ac48f7a69c41675e |
#! /usr/bin/env python
"""Usage: AsapFileToTrajectory.py oldfile newfile [frame1 [frame2]]
Converts an Asap version 1.x netcdf file to an ASE version 2
trajectory file. If a single frame number is given, only that frame
is converted. If two frame numbers are given, all frame from the
first to the last are converted... | auag92/n2dm | Asap-3.8.4/Python/asap3/Tools/AsapFileToTrajectory.py | Python | mit | 4,899 | [
"ASE",
"NetCDF"
] | 7db528cf68e4c0b0328e187e0ced91aa0b06983cb301f5ac39b378d9ef17fdbc |
#
# Author: Pearu Peterson, March 2002
#
# w/ additions by Travis Oliphant, March 2002
# and Jake Vanderplas, August 2012
from warnings import warn
import numpy as np
from numpy import atleast_1d, atleast_2d
from .flinalg import get_flinalg_funcs
from .lapack import get_lapack_funcs, _compute_lwork
from .... | WarrenWeckesser/scipy | scipy/linalg/basic.py | Python | bsd-3-clause | 67,094 | [
"Gaussian"
] | 7b26113bd184e50a751252119b04932ea046cf8f358d28fb30b1b9c1ec177f6d |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | lothian/psi4 | psi4/driver/driver_findif.py | Python | lgpl-3.0 | 38,143 | [
"Psi4"
] | 1f4ac51b3d2a8f7b2f7071f21ffdcc48dafbfada83719a188704bcd14d0d18b7 |
#!/usr/bin/env python
import unittest
from MooseDocs.testing import MarkdownTestCase
class TestMarkdownExtensions(MarkdownTestCase):
"""
Tests that the 'moosedocs.yml' configuration file sets up the markdown conversion, including
that the basic (i.e., non-MOOSE) extensions are working.
"""
def tes... | backmari/moose | docs/tests/markdown_extensions/test_markdown_extensions.py | Python | lgpl-2.1 | 3,380 | [
"MOOSE"
] | 24f8904bca44bbb0b7063648c51c41847d95b9159d03d6b396dd22d268286ca4 |
import numpy as np
from scipy.linalg import cholesky, qr, lstsq
"""
The Q_discrete_white_noise function is taken from filterpy by Roger R Labbe Jr. (MIT Licensed)
"""
def Q_discrete_white_noise(dim, dt=1., var=1.):
""" Returns the Q matrix for the Discrete Constant White Noise
Model. dim may be either 2 or 3, ... | zelmon64/PSMoveService | misc/python/pypsmove/srukf.py | Python | apache-2.0 | 11,894 | [
"Gaussian"
] | 761c95d288e5bd20142f4544d1ba72999f341282cddf390781dbdc0174d00e90 |
# Orca
#
# Copyright (C) 2013-2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/gtk/script.py | Python | gpl-3.0 | 7,150 | [
"ORCA"
] | 8df44fd3ba1fee434d58347990f3282c9890b2ea4949717645357bde2bd4e40a |
"""MPF plugin for sounds. Includes SoundController, Channel, Sound, Track, and
StreamTrack parent classes."""
# sound.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinbal... | spierepf/mpf | mpf/media_controller/core/sound.py | Python | mit | 33,528 | [
"Brian"
] | ca0fb779e49f8cfb0178f907c148411fd7d70af85412d8109adfba3b0279765b |
"""
Updated by Lin Xiong Oct-30, 2017
Modified by Lin Xiong Oct-31, 2017 (add SE building block)
"""
import argparse,logging,os
import mxnet as mx
from symbol_se_inception_resnet_v2 import get_symbol
logger = logging.getLogger()
logger.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s - %... | bruinxiong/SENet.mxnet | train_se_inception_resnet_v2.py | Python | apache-2.0 | 9,164 | [
"Gaussian"
] | 1d65f6b5d0531909c5f22954fe1b8b7a112c6542a5ce544f136f887ee81bfb14 |
from django.shortcuts import render
from rango.models import Category
from rango.models import Page
from rango.models import User
from rango.forms import CategoryForm
from rango.forms import PageForm
from rango.forms import UserForm, UserProfileForm
from django.contrib.auth import authenticate, login
from django.http i... | 2027205T/tango_with_django | tango_with_django_project/rango/views.py | Python | mit | 13,387 | [
"VisIt"
] | 83483ff6d67a9bbff078602d046d1b6033f8a89f573d5e4b7d5a58b62c86ebd8 |
''' COSMO-VIEW,
Quim Ballabrera, May 2017
Script for visualizing model outputs provided by various operational
systems
EGL, 06/2020: Changes:
No more support to python 2.7
Support to Basemap deprecated and updated to Cartopy system
Limited support to geographical projections. Everything is
p... | quimbp/cosmo | modules/cosmo/lagrangian.py | Python | mit | 28,012 | [
"NetCDF"
] | 48f3093a1733cd2076c96daf45798bf31e6c1a3ce024a88194d6466cd9daba23 |
# -*- coding: UTF-8 -*-
# Copyright (C) 2006, 2010 Hervé Cauwelier <herve@oursours.net>
# Copyright (C) 2006-2007, 2009-2011 J. David Ibáñez <jdavid.ibp@gmail.com>
# Copyright (C) 2007 Sylvain Taverne <taverne.sylvain@gmail.com>
# Copyright (C) 2009 David Versmisse <versmisse@lil.univ-littoral.fr>
# Copyright (C) 2009 ... | bepatient-fr/itools | itools/pkg/build.py | Python | gpl-3.0 | 6,574 | [
"GULP"
] | 7b27c8d9aa57633c6fed4e6e6b8834382071958a30d59cabc5a9ec224a912ea6 |
"""
Numerical python functions written for compatability with MATLAB
commands with the same names.
MATLAB compatible functions
-------------------------------
:func:`cohere`
Coherence (normalized cross spectral density)
:func:`csd`
Cross spectral density uing Welch's average periodogram
:func:`detrend`
... | rbalda/neural_ocr | env/lib/python2.7/site-packages/matplotlib/mlab.py | Python | mit | 125,545 | [
"Gaussian"
] | 60a82a91085c1a843251999696f8b93a5cf3c3d9d009e73bd2d99fca3bc420a8 |
# This file contains all the possible names used in toon name generation.
# Each name has a unique id and a category:
# 0 - boyTitle
# 1 - girlTitle
# 2 - neutralTitle
# 3 - bo... | silly-wacky-3-town-toon/SOURCE-COD | toontown/makeatoon/ToonNamesEnglish.py | Python | apache-2.0 | 8,178 | [
"MOE",
"TINKER"
] | efc8ba507015847dda5bc65075c7e8134d103046f4bd79d9280bc44348d3de64 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | modules/geochemistry/python/dbclass.py | Python | lgpl-2.1 | 5,668 | [
"MOOSE"
] | 64a8bc63d23cf24ad3103f5d5ae8266645c992e7378b54a7413500a52b8a9fba |
#! /usr/bin/env python3
import os
import matplotlib.pyplot as plt
import galore
import galore.formats
import galore.plot
from tempfile import mkstemp
fd, tmp = mkstemp(suffix='.txt', text=True)
os.close(fd)
sim_xvals = [10, 15, 19.5, 20, 20.5, 21]
sim_yvals = [12, 6, 3, 2, 1, 2]
galore.formats.write_txt(sim_xvals, ... | SMTG-UCL/galore | docs/source/figures/ir_schematic.py | Python | gpl-3.0 | 840 | [
"Gaussian"
] | c6d0ebd5c6330f63803687b7e2ff8cdf107dfbc63a255847ee615e285e6653f0 |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/symm/basis.py | Python | apache-2.0 | 20,142 | [
"PySCF"
] | d37551cf12c3953ee28c91b706532314cfd6900c4581d365a9ef1b7d545303a2 |
import requests
from Firefly import logging, scheduler
from Firefly.const import AUTHOR
from Firefly.helpers.device import *
from Firefly.helpers.device.device import Device
from Firefly.helpers.metadata.metadata import ColorMap, action_text
from .foobot_service import STATUS_URL
TITLE = 'Foobot Air Sensor'
DEVICE_TY... | Firefly-Automation/Firefly | Firefly/components/foobot/foobot.py | Python | apache-2.0 | 5,962 | [
"Firefly"
] | 39b837de6518b854f950a2942231202720fa31298d0b05b4d70925ebe45794d3 |
#!/usr/bin/env python
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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... | OuterDeepSpace/OuterDeepSpace | server/osclient.py | Python | gpl-2.0 | 13,338 | [
"Galaxy"
] | e9801fde16de86e0c373105ae78e6194d49a6af6563e9fa779729b2a4d8d773b |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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 ... | sam-m888/gprime | gprime/filters/rules/person/_searchname.py | Python | gpl-2.0 | 2,194 | [
"Brian"
] | ba11762457605ac30ce1882493fe864cf319907da8020e8a116ab54ad6578bd2 |
# Copyright (c) 2020, Apple Inc. All rights reserved.
#
# Use of this source code is governed by a BSD-3-clause license that can be
# found in the LICENSE.txt file or at https://opensource.org/licenses/BSD-3-Clause
from coremltools.converters.mil.mil import types
class DotVisitor(object):
"""
Generates a ... | apple/coremltools | coremltools/converters/mil/frontend/tensorflow/dot_visitor.py | Python | bsd-3-clause | 4,552 | [
"VisIt"
] | 09003ede3951ed4f07ea7082a3a8998ce3f15528806edf8bfa8d879f144ec66f |
"""
============================================================
Sparse recovery: feature selection for sparse linear models
============================================================
Given a small number of observations, we want to recover which features
of X are relevant to explain y. For this :ref:`sparse linear ... | Titan-C/scikit-learn | examples/linear_model/plot_sparse_recovery.py | Python | bsd-3-clause | 7,453 | [
"Gaussian"
] | 18e3c3e52a55eb128843375546208610544ccab641b5fad89d6e2e9bd1da6d7d |
#!/usr/bin/env python
'''
Created on Jan 5, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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 Founda... | tectronics/chimerascan | chimerascan/deprecated/chimerascan_index_v2.py | Python | gpl-3.0 | 13,041 | [
"Bowtie",
"pysam"
] | a0ec567e1fb9f7a686db864928689899bc527f69407b599a340e2f9d9ca69e91 |
#!/usr/bin/env python
#JSON {"lot": "UHF/3-21G",
#JSON "scf": "PlainSCFSolver",
#JSON "er": "dense",
#JSON "difficulty": 1,
#JSON "description": "Basic UHF example with dense matrices"}
from horton import * # pylint: disable=wildcard-import,unused-wildcard-import
# Load the coordinates from file.
# Use the XYZ ... | theochem/horton | data/examples/hf_dft/uhf_methyl_dense.py | Python | gpl-3.0 | 3,305 | [
"Gaussian"
] | e7267279371564e2d97299497d363c4de6dab177fd3d446c6e2551d9060a28e9 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Carlos Hernande... | kyleabeauchamp/mdtraj | mdtraj/formats/pdb/pdbfile.py | Python | lgpl-2.1 | 27,393 | [
"MDTraj",
"OpenMM"
] | fc056e23710af75cb352fae74e1b717fc01ae183f488ae247be552c1cedede19 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/misc/__init__.py | Python | gpl-3.0 | 18,803 | [
"CRYSTAL",
"VASP"
] | 818bdbf247ec80439fb885dd245b83114a26971d8e39791c93656cb6b9857242 |
"""Pipeline utilities to retrieve FASTQ formatted files for processing.
"""
import os
import sys
from bcbio import bam, broad, utils
from bcbio.bam import fastq
from bcbio.bam import cram
from bcbio.distributed import objectstore
from bcbio.pipeline import alignment
from bcbio.utils import file_exists, safe_makedir, s... | lpantano/bcbio-nextgen | bcbio/pipeline/fastq.py | Python | mit | 5,917 | [
"Bowtie"
] | 279f411b1f61d6abfecb03f344db4b0532782b6247128b4021d9589738665955 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | doc/sphinxman/source/psi4doc/__init__.py | Python | gpl-2.0 | 1,500 | [
"Psi4"
] | 72e610df8c1a34bff15cd98259b83f234f890ca267052bcc116e971d594f566a |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | rapid_categorization/variable_length_training_data/hmm_force_two_objects.py | Python | mit | 26,303 | [
"Gaussian",
"Mayavi"
] | eec2ca03434cbad3cc9cce8f0b290ed93df99823b08debbd066d522311ae2032 |
#!/usr/bin/env python
# $Id: Compiler.py,v 1.69 2005/07/10 20:32:06 tavis_rudd Exp $
"""Compiler classes for Cheetah:
ModuleCompiler aka 'Compiler'
ClassCompiler
MethodCompiler
If you are trying to grok this code start with ModuleCompiler.__init__,
ModuleCompiler.compile, and ModuleCompiler.__getattr__.
Meta-Data
===... | jhjguxin/PyCDC | Karrigell-2.3.5/Cheetah/Compiler.py | Python | gpl-3.0 | 54,838 | [
"VisIt"
] | a86b1d1b6d9e7d6c72a7ccd5c32d59f2357af023420dd02795b6df77f12f43e6 |
__docformat__ = "restructuredtext en"
import mdp
from mdp import numx
from mdp.utils import mult, matmult, invert_exp_funcs2
from mdp.nodes import GrowingNeuralGasNode
def nmonomials(degree, nvariables):
"""Return the number of monomials of a given degree in a given number
of variables."""
return int(mdp.... | ME-ICA/me-ica | meica.libs/mdp/nodes/expansion_nodes.py | Python | lgpl-2.1 | 13,630 | [
"Gaussian"
] | 3dad45dfbb9016c2948b06222b668beb36ca5985319574c4492b2d87443e9239 |
"""Scraper for the Supreme Court of Ohio
CourtID: ohio
Court Short Name: Ohio
Author: Andrei Chelaru
Reviewer: mlr
History:
- Stubbed out by Brian Carver
- 2014-07-30: Finished by Andrei Chelaru
"""
from juriscraper.OpinionSite import OpinionSite
import time
from datetime import date
class Site(OpinionSite):
d... | brianwc/juriscraper | opinions/united_states/state/ohio.py | Python | bsd-2-clause | 3,141 | [
"Brian"
] | 101ee48f9bd72a46ca0ee1a3c575bb4ef8797d56223889996407e2e099305dd3 |
"""Miscellaneous functions and classes that dont fit into specific
categories."""
import sys, os, vtk
#----------------------------------------------------------------------
# the following functions are for the vtk regression testing and examples
def vtkGetDataRoot():
"""vtkGetDataRoot() -- return vtk example d... | collects/VTK | Wrapping/Python/vtk/util/misc.py | Python | bsd-3-clause | 2,365 | [
"VTK"
] | de227d0d19432c513556be5730763b0bee36abd82728c46aaa4a25de20f1d91a |
import MDAnalysis
import sys
# ----------------------------------------
# HOMEMADE ANALYSIS SELECTIONS
selections = []
selections.append(['aligned_CAs','protein and name CA and (resid 14:19 44:49 67:69 84:88 106:110 136:141 159:163 184:188 208:212 230:234 247:252 295:299)'])
selections.append(['aligned_betas','protei... | rbdavid/RMSD_analyses | Basic_RMSD/make_selections.py | Python | gpl-3.0 | 10,176 | [
"MDAnalysis"
] | 335376ae574aaef296ea8f294e713d6ac783f76dd36898167b97a131679364bf |
#
# Parse tree nodes for expressions
#
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, TempitaUtilityCode=object,
StringEncoding=object, operator=object,
Naming=object, Nodes=objec... | openilabs/falconlab | env/lib/python2.7/site-packages/Cython/Compiler/ExprNodes.py | Python | mit | 439,907 | [
"VisIt"
] | 309ac6642e0fa3d151dc9a2052f788b568d687f61e8582c82e818125e32f1e86 |
"""
Daemon to monitor a file hierarchy and create sequence reports.
Any time 'workup.json' or any .ab1 file is added to a directory, check
if there is a usable set of files in that directory. If so, generate a
sequence report for them.
"""
import os
import pydaemonize
import pyinotify
import syslog
import json
import ... | madhadron/seqlabd | seqlab/daemons/sequencereportd.py | Python | gpl-3.0 | 3,937 | [
"BLAST"
] | 4af8127914fe43e5de6bb15d9c2e75f6effefce958d35152e3295649d89d23ce |
import array
import mysql.connector
def migration_name():
return "Adding crystal storage columns to char_points table"
def check_preconditions(cur):
return;
def needs_to_run(cur):
# Ensure crystal columns exist in char_points
cur.execute("SHOW COLUMNS FROM char_points LIKE 'fire_crystals'")
if not cur.fetchone(... | ffxijuggalo/darkstar | migrations/crystal_storage.py | Python | gpl-3.0 | 1,103 | [
"CRYSTAL"
] | 6ccddf1b2694301eb6bf4427f3ff23d91b12d57723c09dd30c07aa1b89acdc60 |
from distutils.core import setup
import os
def version():
setupDir = os.path.dirname(os.path.realpath(__file__))
versionFile = open(os.path.join(setupDir, 'checkm', 'VERSION'))
return versionFile.read().strip()
setup(
name='checkm-genome',
version=version(),
author='Donovan Parks, Michael Im... | hunter-cameron/CheckM | setup.py | Python | gpl-3.0 | 929 | [
"pysam"
] | 78a3508751d7b187101e03d8b166297c29ccb5f513a969311b69c6e5d2dc364c |
import numpy as np
import numpy.random as npr
import matplotlib.pyplot as plt
# Fancy plotting
try:
import seaborn as sns
sns.set_style("white")
sns.set_context("talk")
color_names = ["windows blue",
"red",
"amber",
"faded green",
... | mattjj/pylds | examples/simple_demo.py | Python | mit | 1,912 | [
"Amber"
] | a35405ebbb592cf4039fa133a978a9b76dbb1bd165faa035d58bf67dfd07f823 |
stations = { 'abagaqi': 'AQC',
'acheng': 'ACB',
'aershan': 'ART',
'aershanbei': 'ARX',
'aihe': 'AHP',
'aijiacun': 'AJJ',
'ajin': 'AJD',
'akesu': 'ASR',
'aketao': 'AER',
'alashankou': 'AKR',
'alihe': 'AHX',
'alongshan': 'ASX',
'amuer': 'JTX',
'ananzhuang': 'AZM',
... | fancyqlx/fancy12306 | fancy12306/stations.py | Python | mit | 58,597 | [
"ADF",
"ASE",
"VTK"
] | ea9221cce86739fe8e36422be7ebb14c934c57e83c09c5afee78cb12c73578a8 |
# Author: Carlos Xavier Hernandez <cxh@stanford.edu>
# Contributors:
# Copyright (c) 2016, Stanford University and the Authors
# All rights reserved.
from __future__ import print_function, division, absolute_import
import numpy as np
import collections
from ..base import BaseEstimator
from ..utils import check_iter_o... | mpharrigan/mixtape | msmbuilder/preprocessing/base.py | Python | lgpl-2.1 | 5,660 | [
"MDTraj"
] | 679d896b010de4dc9cd61e720a8f784b36bf678c065b20f168288c156ea7f6a8 |
import sys
import requests
from requests.exceptions import HTTPError
import os
import multiprocessing
import time
import queue
from ddsc.core.localstore import HashUtil
from ddsc.core.ddsapi import DDS_TOTAL_HEADER
from ddsc.core.util import humanize_bytes, transfer_speed_str
SWIFT_EXPIRED_STATUS_CODE = 401
S3_EXPIRED... | Duke-GCB/DukeDSClient | ddsc/core/download.py | Python | mit | 18,066 | [
"VisIt"
] | deab0ad832781932e9eb9285efbd6522ddff616d24effcfd9964ffe1e03c420d |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/timeraddbyeventid.py | Python | gpl-2.0 | 5,232 | [
"VisIt"
] | 570afb0f78a06bf1836a1683013d76b446dbfd5f25258fb51820553446dd706e |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended: CJKCodecs... | ingadhoc/odoo-help | document_page_adhoc/web/widgets/rss/feedparser.py | Python | agpl-3.0 | 122,515 | [
"NetCDF",
"VisIt"
] | 28cdd6e1960bd39474ad127b129908e11e6f5b40fcf62b5bc6bf27597fc8b308 |
"""
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 733 $"
import logging
import numpy
from calculationmethod import Method
class Population(Method):
"""A base class for all population-type ... | comocheng/RMG-Py | external/cclib/method/population.py | Python | mit | 2,808 | [
"cclib"
] | af89d1ecdc96643bb40c2fb517b0dae9aa865325d9dae561e5681684299ff334 |
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