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"""
Test the Studio help links.
"""
from unittest import skip
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.asset_index import AssetIndexPageStudioFrontend
from common.test.acceptance... | teltek/edx-platform | common/test/acceptance/tests/studio/test_studio_help.py | Python | agpl-3.0 | 41,125 | [
"VisIt"
] | b3be012a05ff3870892f26a1acda3fe0b2b9cc1def7b0dafea1a69038fb5a2bb |
'''
This module contains the `RBF` class, which is used to symbolically define and
numerically evaluate a radial basis function. `RBF` instances have been
predefined in this module for some of the commonly used radial basis functions.
The predefined radial basis functions are shown in the table below. For each
expressi... | treverhines/RBF | rbf/basis.py | Python | mit | 29,352 | [
"Gaussian"
] | f0c92c47170c62334c3cf6fa7217bbc2a018b05d87792a7c35775b976f02702f |
########################################################################
# File : CPUNormalization.py
# Author : Ricardo Graciani
########################################################################
""" DIRAC Workload Management System Client module that encapsulates all the
methods necessary to handle CPU... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/CPUNormalization.py | Python | gpl-3.0 | 10,878 | [
"DIRAC"
] | b3e42d1251d9027c71b4c80da7682709af65bfb165f5aaa48d8193c4e388986d |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/pmv_dev/APBSCommands_2x.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... | corredD/ePMV | pmv_dev/APBSCommands_2x.py | Python | gpl-3.0 | 238,741 | [
"Amber",
"CHARMM",
"VisIt"
] | 362cee4e6f40c240feb2cd39435ec61da159edff0d3bf60ae69af30aaff1c732 |
'''
Created on 18 may 2018
@author: Yonatan-Carlos Carranza-Alarcon
About how to use the Imprecise Gaussian Discriminant.
'''
import classifip
# We start by creating an instance of the base classifier we want to use
print("Example of Imprecise Linear Discriminant Analyse for Classification - Data set IRIS \n")
mode... | sdestercke/classifip | examples/classification/qdatest.py | Python | gpl-2.0 | 1,176 | [
"Gaussian"
] | ea3d9cf4031b0966ce66de338fd7c9f85afcc512a5a8cfe9b50797be8adea80e |
#! /usr/bin/env python
# linearizedGP -- Implementation of extended and unscented Gaussian processes.
# Copyright (C) 2014 National ICT Australia (NICTA)
#
# This file is part of linearizedGP.
#
# linearizedGP is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public... | NICTA/linearizedGP | experiments/datagen.py | Python | gpl-3.0 | 3,553 | [
"Gaussian"
] | 366d9fcede29ecaec5cc74e20864819f45b83d1ce2aa388745129f489d24499f |
"""
KeepNote
Notebook indexing
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# 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;... | vatslav/perfectnote | keepnote/notebook/index.py | Python | gpl-2.0 | 15,994 | [
"VisIt"
] | 304c9f20c9123c8540e7e4477d343d10b23b742e488c399dee32560c9bd7c966 |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | samples/lj-demo.py | Python | gpl-3.0 | 20,362 | [
"ESPResSo",
"Mayavi"
] | ba0e3e7c086c7bc1aca97e00e98bbb8a1720d56c56cf3ca4c55a51607d23ee62 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.core import m... | zerobatu/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 196,429 | [
"VisIt"
] | cc17eafee7e9589e532327e74e9d68da852c6033f37d649f68cc2af8f273bd3b |
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
import re
import os
import numpy
from cctbx import crystal
from cctbx import miller
from cctbx import uctbx
from cctbx.array_family import flex
from libtbx.utils import null_out
fro... | keitaroyam/yamtbx | yamtbx/dataproc/xds/xds_ascii.py | Python | bsd-3-clause | 12,714 | [
"CRYSTAL"
] | b9d3955ec895640750964ff533ff9c311041cd47701f4b656699c7491e2dde06 |
import pytest
@pytest.fixture(params=[True, False])
def raw(request):
return request.param
@pytest.fixture(
params=[
"triang",
"blackman",
"hamming",
"bartlett",
"bohman",
"blackmanharris",
"nuttall",
"barthann",
]
)
def win_types(request):... | toobaz/pandas | pandas/tests/window/conftest.py | Python | bsd-3-clause | 935 | [
"Gaussian"
] | 98406e5e247f9f33af0e80c4b065aa05de054bed33dc727fc0fc9796116f086e |
# coding: utf-8
from __future__ import division, unicode_literals
"""
TODO: Modify unittest doc.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "5/22/14"
import unittest
from p... | rousseab/pymatgen | pymatgen/analysis/diffraction/tests/test_xrd.py | Python | mit | 3,465 | [
"pymatgen"
] | 4194d7ed94d6e2b66845d54b4557e0c5143ed6a2809bdcd7101851332487c942 |
"""
Implements Autodock Vina's pose-generation in tensorflow.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import warnings
import numpy as np
... | Agent007/deepchem | contrib/vina_model/vina_model.py | Python | mit | 18,976 | [
"Gaussian",
"RDKit"
] | 9f3cc8afb832feea1c1b12a6bc1f1d4d13315b7a8a316c9f86cf25d4ee72095d |
"""
Visitor pattern for walking through a BaseNode AST.
"""
from collections import namedtuple
from .membership import AndNode
from .membership import OperatorNode
from .membership import OrNode
from .membership import RolesNode
from .membership import ValueNode
from .membership import XorNode
VisitedNode = namedtu... | counsyl/baya | baya/visitors.py | Python | mit | 6,755 | [
"VisIt"
] | c347337179bc8d319c0c86907b2c3ea1ade50b16502f25608466c498e11ea6d3 |
# -*- coding: utf-8 -*-
"""
This script contains the business logic for the sample ArcGIS Python Toolbox.
It shows how to iterate a feature class and update a field.
You could more easily do this using a call to arcpy.CalculateField_management()
but that's not as interesting an example!
@author: Brian Wilson ... | brian32768/ArcGIS_Python_Template | some_sample_code.py | Python | mit | 2,412 | [
"Brian"
] | e504f393019960a22b3e286ddcd0a3d522c6058e355569699415870bc7870cea |
# Copyright (C) 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 versio... | psci2195/espresso-ffans | testsuite/python/unittest_decorators.py | Python | gpl-3.0 | 1,865 | [
"ESPResSo"
] | 6157db6767116948bd1b739d1e52b19e16634578d5f6153de0475a94cf3a5e59 |
#!/usr/bin/env python
from ase import *
# Read in the geometry from a xyz file, set the cell, boundary conditions and center
atoms = read('geom.xyz')
atoms.set_cell([7.66348,7.66348,7.66348*2])
atoms.set_pbc((1,1,1))
atoms.center()
# Set initial velocities for hydrogen atoms along the z-direction
p = atoms.get_moment... | freephys/python_ase | doc/exercises/siesta2/siesta2.py | Python | gpl-3.0 | 832 | [
"ASE",
"SIESTA"
] | 1297d5b8ecf0558d242f6a13bc3bc55ba6fddd83542e1a35c7d580b402835172 |
"""
Test the **drf_ember** ``utils`` modules. Several of the functions in this module are
critical to managing the transformation of data to bridge the Django REST Framework's serializer
approach and the JSON API.
"""
from django import test
from django.test.utils import override_settings
from rest_framework.compat imp... | symfonico/drf-ember | tests/test_utils.py | Python | mit | 28,960 | [
"Galaxy"
] | 0773744c184111891f80e230e8021cc6c49465a156f84a2a51c9511863d1806d |
import numpy
import os
import subprocess
# from time import sleep
# Rotates input xyz file and generates 100 output xyz files at random orientations along with input.scan for each of them to give as input to mechAFM
def makeIt(output_folder = "randomRotateOutput/"):
fileNumber = 0
for x in range(41):
... | SINGROUP/readAFM | databaseCode/toyDB/oneAtom/makeXYZ.py | Python | gpl-3.0 | 3,995 | [
"CHARMM"
] | 321b81404b8899d52a8e70a0354bdc38ce9b079b29bbb6b96799479c47c3aa60 |
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008-2015, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO
import copy
import numpy
import unittest
# Local imports.
from m... | dmsurti/mayavi | mayavi/tests/test_glyph.py | Python | bsd-3-clause | 7,394 | [
"Mayavi"
] | 327dc031f8cf1146bde75a97102449bf89b1589cee5324ef2e18effce66fcace |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# MIT License
#
# Copyright (c) 2018 Miha Purg <miha.purg@gmail.com>
#
# 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, in... | mpurg/qtools | packages/Qpyl/common.py | Python | mit | 12,947 | [
"Amber"
] | 1065e1cb00fa3524c412cbe51b875bbc0a10ed5594f200aedeb9c46950f65068 |
#!/usr/bin/python -tt
# Automated BLAST search of a FASTA file. Search defaults to blastx (Protein) search,
# blast type, database, e-value threshold and number of hits can be changed with
# commandline inputs.
# Any inputs with - or -- are optional and will default to certain values.
# Blast will be done locally for ... | calandryll/transcriptome | scripts/old/fasta_search.py | Python | gpl-2.0 | 4,017 | [
"BLAST"
] | 8ede91bf007b722f091fbfa19c736e28e00d377cd0dcce261de894e7b03a7371 |
'''Noddy output file analysis
Created on 24/03/2014
@author: Florian Wellmann, Sam Thiele
'''
import os
import numpy as np
class NoddyOutput(object):
"""Class definition for Noddy output analysis"""
def __init__(self, output_name):
"""Noddy output analysis
**Arguments**:
- *outpu... | Leguark/pynoddy | pynoddy/output.py | Python | gpl-2.0 | 86,360 | [
"Mayavi",
"ParaView",
"VTK"
] | 3d72c4117dd18b6884251750746d809a6de710491f6ceebac8002cf0793d5654 |
from rdkit import RDConfig,RDRandom
import unittest
from rdkit.ML.InfoTheory import rdInfoTheory as rdit
from rdkit import DataStructs
import numpy
import os,cPickle
def feq(a,b,tol=1e-4):
return abs(a-b)<tol
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test0GainFuns(self):
... | rdkit/rdkit-orig | Code/ML/InfoTheory/Wrap/testRanker.py | Python | bsd-3-clause | 4,870 | [
"RDKit"
] | 95bbf4caa46eb4e8feb30a35372497df680b053c7fc6c27d1566b18f03230328 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.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 published by
# the Free Software Foundation, either version 3 of the License... | bsmr-ansible/ansible-modules-core | system/systemd.py | Python | gpl-3.0 | 13,997 | [
"Brian"
] | dbb0fc93131a9b660d51fd94289ce27b9ed3eb384c5dda4f74baef93725b0a69 |
"""
Takes blast output and reformats it to prepare for iTOL
"""
import os,sys
import argparse
import re
from collections import Counter
from accessionMap import AccessionGG
accReg = re.compile("([A-Z]+_\d+.\d)")
def bacteriocinLengths(blastFile,lengthsOut,accTable):
lenCnts = Counter()
accTable = AccessionGG(... | idoerg/BOA | src/format/phyloformat.py | Python | gpl-3.0 | 3,843 | [
"BLAST"
] | 023ec0f813491ce0a86727ffd85a662a867ff914b4d8a7c48280a235de708740 |
"""
Test the command line script dials.scale, for successful completion.
"""
from __future__ import annotations
import json
import platform
import sys
import procrunner
import pytest
import iotbx.merging_statistics
import iotbx.mtz
from cctbx import uctbx
from dxtbx.model import Beam, Crystal, Detector, Experiment,... | dials/dials | tests/algorithms/scaling/test_scale.py | Python | bsd-3-clause | 43,030 | [
"CRYSTAL"
] | 4a238730c9486be2c935042864afc898811128695795a549086c86eb8266e5af |
#!/usr/bin/env python3
"""
A recursive solution to the Pardoner's Puzzle from
http://math-fail.com/2015/02/the-pardoners-puzzle.html
Copyright (c) Vedran Šego <vsego@vsego.org>
"""
import sys
n = 8
pos = (6, 2) # starting position (col, row)
max_steps = 15
# The list of neighbour towns not directly connected
# Eac... | vsego/misc | pardoners_puzzle.py | Python | mit | 4,102 | [
"VisIt"
] | 935b0af88a5f0804673b9d08da87d6a0e0d8e2ffa28a9ccc56f3473d7205957e |
# smCounter: barcode-aware variant caller
# Chang Xu. 23May2016; online version of 10APR2017
import os
import datetime
import subprocess
import math
import operator
import argparse
import random
import multiprocessing
import traceback
from collections import defaultdict
# 3rd party modules
import pysam
import scipy.s... | xuchang116/smCounter | smCounter.py | Python | mit | 42,453 | [
"pysam"
] | 40a1ecba3d1a7ae90eebaeee291d24c65c7aa53e84b72261aef010a70fcfe497 |
"""
Filter factories and their associated functions for mlab.
Module functions meant to be applied to a data source object should take
only one positional argument, the data object, to be easily used in
helper functions.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Prabhu Ramachandran
# Copy... | dmsurti/mayavi | mayavi/tools/filters.py | Python | bsd-3-clause | 7,862 | [
"Mayavi",
"VTK"
] | 58e6d06cc98eb27be5fbe3c04087505f0fc2ca9d92ed9612ec922446d91b9ad3 |
#!/usr/bin/env python
# Copyright 2014-2020 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/scf/addons.py | Python | apache-2.0 | 35,857 | [
"PySCF"
] | 4faa3fd1f77ed1dfbeac5a553ebf9af656d33d6719e826d502e3f8951c7fd8e2 |
"""
code to extract a single cell from a set of alignments or reads marked via Valentine's umis
repository:
https://github.com/vals/umis
"""
import regex as re
import sys
from argparse import ArgumentParser
from pysam import AlignmentFile
def extract_barcode(sam, barcode):
parser_re = re.compile('.*:CELL_(?P<CB>... | roryk/junkdrawer | extract-barcode.py | Python | mit | 1,714 | [
"pysam"
] | b3b5183010243a461ce4f8b655deafd088934afe9893eb9200b4f65e2e46d881 |
from time import sleep
from lettuce import *
from rapidsms.contrib.locations.models import Location
from survey.features.page_objects.question import BatchQuestionsListPage, AddQuestionPage, ListAllQuestionsPage, CreateNewQuestionPage, CreateNewSubQuestionPage, EditQuestionPage
from survey.models import Batch, Question... | unicefuganda/uSurvey | survey/features/Question-steps.py | Python | bsd-3-clause | 21,446 | [
"VisIt"
] | 26dc046374916fa9f9e31be80f4dd6df4ed066b89f1500492dcc77ae300476dd |
"""
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Candy, adam.candy@im... | adamcandy/qgis-plugins-meshing | release/mesh_netcdf/meshnetcdf.py | Python | lgpl-2.1 | 8,544 | [
"NetCDF"
] | fc7c9e80a33dc1a00dd53e3f4dd4185534dba8d6648d4c8c32a7f820749e53d7 |
"""
Miscellaneous utility functions and classes.
**Mathematical functions**
* :func:`~fatiando.utils.normal`
* :func:`~fatiando.utils.gaussian`
* :func:`~fatiando.utils.gaussian2d`
* :func:`~fatiando.utils.safe_solve`
* :func:`~fatiando.utils.safe_dot`
* :func:`~fatiando.utils.safe_diagonal`
* :func:`~fatiando.utils.... | eusoubrasileiro/fatiando_seismic | fatiando/utils.py | Python | bsd-3-clause | 22,382 | [
"Gaussian"
] | b01dbcacabbcfa1cfe383d043110249f37db45ad86ebcf1dd5bc47999d47c224 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version][p... | FabioRosado/opsdroid | versioneer.py | Python | apache-2.0 | 69,159 | [
"Brian"
] | f8b81d9c4089007fa2c9905e1036e819daee743efe11761725a0824acd2c362c |
from collections import OrderedDict, defaultdict, namedtuple, Counter
from collections.abc import Iterable
from copy import deepcopy
from numbers import Real
from pathlib import Path
import re
import warnings
from xml.etree import ElementTree as ET
import numpy as np
import openmc
import openmc.data
import openmc.che... | nelsonag/openmc | openmc/material.py | Python | mit | 46,990 | [
"Avogadro"
] | d6bc65982d8441c94068cb23962ab364aa4fdc469c2f3238396a92238e94b0d2 |
"""Element support in foyer."""
import openmm.app.element as elem
class Element(elem.Element):
"""An Element represents a chemical element.
The openmm.app.element module contains objects for all the standard chemical elements,
such as element.hydrogen or element.carbon. You can also call the static meth... | mosdef-hub/foyer | foyer/element.py | Python | mit | 1,589 | [
"OpenMM"
] | 4cb6898ee5d808a4bb0673b7f46aef2ff0d708cdfe4698961b326d681269dda0 |
# -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import, division
import numpy as np
import pandas as pd
from scipy import optimize
from scipy.stats import boxcox
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.externals import six
from sklearn.externals.joblib import Paral... | tgsmith61591/skutil | skutil/preprocessing/transform.py | Python | bsd-3-clause | 34,160 | [
"Gaussian"
] | de1389fd5123e4735b6ad93d30258ea35cf4635ee57f480a88a8b882c458c027 |
from ase import Atoms
from gpaw import FermiDirac, Mixer
from gpaw.transport.calculator import Transport
from gpaw.atom.basis import BasisMaker
from gpaw.poisson import PoissonSolver
import pickle
a = 3.6
L = 7.00
basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na12', pbc=(1, 1, 1), cell=[L,... | robwarm/gpaw-symm | gpaw/test/transport.py | Python | gpl-3.0 | 1,185 | [
"ASE",
"GPAW"
] | 7f09d57078f8f62b0acb5352bb2597048383ded26ccea4e2b422e78efba82ea6 |
__author__ = 'cdan'
import pandas as pd
import sqlalchemy
import pymssql
server =
database =
user =
password =
year = 2014
ase_sql = 'SELECT 14 as datasource_id, [estimates_year],1300000 + [mgra] as mgra_id,[ethnicity],[popm_0to4],[popm_5to9],[popm_10to14],[popm_15to17],[popm_18to19],[popm_20to24],[popm_25to29],... | SANDAG/DataSurfer | api/utilities/Estimates_ETL.py | Python | mit | 5,121 | [
"ASE"
] | a47791f41be5c2313a6b489678b0b3e62c1984275ae76ce6997f58b58e6b7d21 |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/samples/test_visualization_charged.py | Python | gpl-3.0 | 1,260 | [
"ESPResSo"
] | 021886d640cee8728b9471179b112eccff3f45f1849856e06fdaf2081a64afba |
import HTSeq
import numpy
from matplotlib import pyplot
bamfile = HTSeq.BAM_Reader( "SRR001432_head.bam" )
gtffile = HTSeq.GFF_Reader( "Homo_sapiens.GRCh37.56_chrom1.gtf" )
halfwinwidth = 3000
fragmentsize = 200
coverage = HTSeq.GenomicArray( "auto", stranded=False, typecode="i" )
for almnt in bamfile:
if almnt.al... | simon-anders/htseq | python3/doc/tss1.py | Python | gpl-3.0 | 887 | [
"HTSeq"
] | c20207e0eb0d6d1db004a395d6eb7c49be7363dbf54eda8f4aaeefed7d0c51ce |
from .bernoulli import Bernoulli
from .exponential import Exponential
from .gaussian import Gaussian, HeteroscedasticGaussian
from .gamma import Gamma
from .poisson import Poisson
from .student_t import StudentT
from .likelihood import Likelihood
from .mixed_noise import MixedNoise
from .binomial import Binomial
| beckdaniel/GPy | GPy/likelihoods/__init__.py | Python | bsd-3-clause | 315 | [
"Gaussian"
] | 914324e05a836440ff7efe4aedca2c84598463a8d8a405a50d135ef765b18e48 |
##
# Copyright 2021 Vrije Universiteit Brussel
#
# 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 Foundati... | akesandgren/easybuild-easyblocks | easybuild/easyblocks/o/orca.py | Python | gpl-2.0 | 7,049 | [
"ORCA"
] | 62b4c89cbc2c68c1020eeff6e5bc1ec2a233624b2992b0310e1eac093b4478dd |
visit_schedule_fields = ('visit_schedule_name', 'schedule_name', 'visit_code')
visit_schedule_fieldset_tuple = (
'Visit Schedule', {
'classes': ('collapse',),
'fields': visit_schedule_fields})
visit_schedule_only_fields = ('visit_schedule_name', 'schedule_name')
visit_schedule_only_fieldset_tuple... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/fieldsets.py | Python | gpl-2.0 | 430 | [
"VisIt"
] | 9bb2b9edc6c5673910ea4cad2108f1291693662429548ebcb87ebe6e8c04679b |
"""
Do the initial configuration of a DIRAC component
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
from DIRAC.Core.Base import Script
Script.setUsageMessage(
'\n'.join(
[
__doc__.split('\n')[1],
... | yujikato/DIRAC | tests/Jenkins/dirac-cfg-add-option.py | Python | gpl-3.0 | 1,540 | [
"DIRAC"
] | 02cb2d2f7bf525be0121e3de16257f0df74d520f6cbc8791dea431aa1bcb0757 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nanditav/15712-TensorFlow | tensorflow/contrib/learn/python/learn/learn_io/graph_io.py | Python | apache-2.0 | 35,129 | [
"VisIt"
] | 544c6af81361c645957177022cd89a5ebb390b42d5579ddc1e2af976954171d8 |
# -*- coding: utf-8 -*-
'''
ATTENTION:
If this is a new installation of pygenewiki, edit this file (settings.example.py)
with your username and password for wikipedia and any other custom settings
and save it as settings.py in this directory. Modules rely on settings.py
being present to operate.
'''
'''
Te... | SuLab/genewiki | old-assets/genewiki/.settings.unconf.py | Python | mit | 1,675 | [
"PyMOL"
] | 797c3dee7a1f20b7d796f885a68a1f57d2f8dc2f155c977057bdf0af6bb2cc7f |
"""Module that allows for imposing a kinetically connected network
structure of weighted ensemble simulation data.
"""
from collections import defaultdict
from copy import deepcopy
import gc
import numpy as np
import networkx as nx
from wepy.analysis.transitions import (
transition_counts,
counts_d_to_matrix... | ADicksonLab/wepy | src/wepy/analysis/network.py | Python | mit | 52,176 | [
"MDTraj"
] | a586331eb87194678a2714d35642c2d9a91474774983f7c97e0d86822491829e |
"""
Module to create mitonetwork in graph representation, with nodes, edges and
their respective attributes
"""
import os
import os.path as op
import cPickle as pickle
import numpy as np
import networkx as nx
import vtk
from tvtk.api import tvtk
import wrappers as wr
# pylint: disable=C0103
def find_edges(X, Y, M):
... | moosekaka/sweepython | pipeline/make_networkx.py | Python | mit | 5,684 | [
"VTK"
] | 1d57bec60915a40871b2c61bde9326fd417f2faecaa8a5e20400b1309090a926 |
# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ 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.
#
from __future__ import print_function
import unittest... | rvianello/rdkit | rdkit/DataStructs/UnitTestDocTests.py | Python | bsd-3-clause | 3,019 | [
"RDKit"
] | 6c9d3e6b2666bfbbea6e5207ebd465bf565615ac8198d34dd9ca5f1a135095ea |
##
# Copyright 2009-2013 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 (htt... | omula/easybuild-easyblocks | easybuild/easyblocks/l/libsmm.py | Python | gpl-2.0 | 8,289 | [
"CP2K"
] | 70abf99bd79d91673c5ad5fa1f29e04f66a98cbcdc70ef237ba21c4097af7cc6 |
"""The suite of window functions."""
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
def boxcar(M, sym=True):
"""The M-point boxcar window.
"""
return np.ones(M, float)
def triang(M, sym=True):
"""The M-point triangular window.
"""
if M < 1:
retur... | jasonmccampbell/scipy-refactor | scipy/signal/windows.py | Python | bsd-3-clause | 12,780 | [
"Gaussian"
] | 966a5d142ed434085ed74d5794057af80130394299f3f6a31757bc4e64dca263 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
import unittest
from parts_genie.rbs_calculator import RbsCalculator
import parts_genie.vienna_utils as uti... | neilswainston/PathwayGenie | parts_genie/test/test_rbs_calculator_vienna.py | Python | mit | 2,848 | [
"VisIt"
] | 7ee4a44c60f92a48e859ac199105b5fba466847f16449d5eff076155c4bd7aef |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | chatelak/RMG-Py | rmgpy/molecule/molecule.py | Python | mit | 60,426 | [
"RDKit",
"cclib"
] | 66ac3ec11c0a4da3a7cba1f6e79c56054acb4bd56644a768c377f9e9d89fc16e |
#!/usr/bin/env python3
#
# Tests the twisted gaussian logpdf toy distribution.
#
# This file is part of PINTS (https://github.com/pints-team/pints/) which is
# released under the BSD 3-clause license. See accompanying LICENSE.md for
# copyright notice and full license details.
#
import pints
import pints.toy
import uni... | martinjrobins/hobo | pints/tests/test_toy_twisted_gaussian_logpdf.py | Python | bsd-3-clause | 3,965 | [
"Gaussian"
] | 10b7563040489b7f63073b2c718d7e6d490d6db4098aa013b13e3e2d1a81360b |
import ast
import importlib
import importlib.machinery
import decimal
import sys
def _call_with_frames_removed(f, *args, **kwargs):
return f(*args, **kwargs)
class FloatLiteral(float):
def __new__(cls, *args):
obj = super().__new__(cls, *args)
if args and len(args) == 1 and isinstance(args[0],... | abarnert/floatliteralhack | floatliteral_ast.py | Python | mit | 2,069 | [
"VisIt"
] | 0cddd2dccfe56299c3fe0d372c01ca8347276a2ab17834493f86626aceaa7cf3 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('get_invocation_report')
@click.argument("invocation_id", type=str)
@pass_context
@custom_exception
@json_output
def cli(ctx, invocation_id):
"""Get a Markdown report for an invo... | galaxy-iuc/parsec | parsec/commands/invocations/get_invocation_report.py | Python | apache-2.0 | 836 | [
"Galaxy"
] | d3f422db29c83eb6a11a910cc3fc7d930d23aa0d1a3fdbf150478450640822b3 |
import sys, os, math, time
import arcpy
from arcpy import env
from arcpy.sa import *
arcpy.CheckOutExtension("spatial")
#Metadata exists in one of two standard formats (finds the correct name for each field)
def acquireMetadata(metadata, band):
band = str(band)
metadatalist = []
if ("RADIANCE_M... | ColorTyWorld/GISRS | src/python/landsat/ndvi.py | Python | gpl-3.0 | 8,766 | [
"Brian"
] | 5614222ed2d06e6a229aa0d8f8b097afd20286f3f9a594fcb0b1607791f51949 |
"""Test the DataRecoveryAgent"""
import unittest
from collections import defaultdict
from mock import MagicMock as Mock, patch, ANY
from parameterized import parameterized, param
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.TransformationSystem.Agent.DataRecoveryAgent import DataRecoveryAgent
fro... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/test/Test_DRA.py | Python | gpl-3.0 | 27,210 | [
"DIRAC"
] | ca599a275403cec2c0fb5d0b3ac14c631766b16e7471ddcb132e5dc31ab521d0 |
########################################################################
# $Id$
########################################################################
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.List import intListToString
from ... | miloszz/DIRAC | DataManagementSystem/DB/FileCatalogComponents/FileManagerBase.py | Python | gpl-3.0 | 56,703 | [
"DIRAC"
] | 9b5d961f23a9686cf49626c5faacd8b720552acbacec9f955bf8fc38f4228adc |
"""
End-to-end tests for Student's Profile Page.
"""
from datetime import datetime
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.lms.learner_profile import LearnerProfilePage
from common.test.... | edx/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 6,461 | [
"VisIt"
] | 7c5b33d38db0eeb48aef067ea351176edb3b92a3b9d5f15050b300a8e66fc454 |
import numpy as np
import scipy.sparse
import pytest
from sklearn.datasets import load_digits, load_iris
from sklearn.model_selection import train_test_split
from sklearn.model_selection import cross_val_score
from sklearn.utils._testing import assert_almost_equal
from sklearn.utils._testing import assert_array_equ... | anntzer/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 34,620 | [
"Gaussian"
] | 19e21e42b0ce9fc8201e03370b7434a43a1d9179096925a8524663ca825c3630 |
"""
Module containing many types of goodness-of-fit test methods.
"""
from __future__ import division
from builtins import zip
from builtins import str
from builtins import range
from past.utils import old_div
from builtins import object
from future.utils import with_metaclass
__author__ = 'wittawat'
from abc import ... | wittawatj/kernel-gof | kgof/goftest.py | Python | mit | 41,550 | [
"Gaussian"
] | ab85cf746b43449d0ab830b1a47b0c662edd12bfe6fba54d00dbc6af8bb7537f |
""" @package antlr3.tree
@brief ANTLR3 runtime package, treewizard module
A utility module to create ASTs at runtime.
See <http://www.antlr.org/wiki/display/~admin/2007/07/02/Exploring+Concept+of+TreeWizard> for an overview. Note that the API of the Python implementation is slightly different.
"""
# begin[licence]
#... | leriomaggio/code-coherence-evaluation-tool | code_comments_coherence/source_code_analysis/code_analysis/antlr3/treewizard.py | Python | bsd-3-clause | 18,025 | [
"VisIt"
] | 2ba7566b9d61866aa430fdbfb92d0464324c4e6e8339282948b38d18622c0dbe |
from test import test_support
import unittest
import codecs
import locale
import sys, StringIO
def coding_checker(self, coder):
def check(input, expect):
self.assertEqual(coder(input), (expect, len(input)))
return check
class Queue(object):
"""
queue: write bytes at one end, read ... | Jeff-Tian/mybnb | Python27/Lib/test/test_codecs.py | Python | apache-2.0 | 82,840 | [
"FEFF"
] | 352d901de7740a6624c839e17f0fe3f88106cadf61446cc4726e4d4521185609 |
# (C) British Crown Copyright 2010 - 2014, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | scollis/iris | lib/iris/tests/test_pickling.py | Python | gpl-3.0 | 4,584 | [
"NetCDF"
] | c8ea6cdb2fdb6ee7c7926142c26b8d6d8057c20c3ecd5f02c7cb4bcaf4f0ef8b |
"""feedfinder: Find the Web feed for a Web page
http://www.aaronsw.com/2002/feedfinder/
Usage:
feed(uri) - returns feed found for a URI
feeds(uri) - returns all feeds found for a URI
>>> import feedfinder
>>> feedfinder.feed('scripting.com')
'http://scripting.com/rss.xml'
>>>
>>> feedfinder.fe... | lerouxb/seymour | thirdparty/feedfinder.py | Python | mit | 12,984 | [
"Brian"
] | bdaab14acc7b580e789f457a908ec0c48dd3ec770293dcc708f03055be408829 |
"""
Author: Eric J. Ma
Purpose:
This Python module provides a dictionary for retrieving plasmid backbones as a
list of BioPython SeqRecord object.
"""
import os
from Bio import SeqIO
plasmid_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'plasmid_backbones')
plasmids = {f.... | ericmjl/flu-gibson | FluGibson/plasmids.py | Python | mit | 541 | [
"Biopython"
] | 09445572f4c8e26b87c6337e83d7ced97d7b956fca7bd1fbbc77f4b0c6f6bc50 |
#
# Copyright (c) 2016, 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 2 only, as
# published by the Free Softwar... | jjfumero/fastr | mx.fastr/mx_fastr_dists.py | Python | gpl-2.0 | 13,996 | [
"VisIt"
] | 39fc0231fe6569506cf709d30ca3d4b09364aba29ccd424ba555ca4a8560629c |
#!/usr/bin/env python3
"""
Copyright 2020 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 ... | pwillworth/galaxyharvester | html/checkOldResource.py | Python | gpl-3.0 | 2,945 | [
"Galaxy"
] | eefaa1e91e3f7dce05e1763f37fcf3292bb1d2481c5ba809db8c0592c1dd53bf |
# 1-text becomes instructions (as chunks) becomes/generates text
# 2-also as genetic algo.
# so: how to train on wounds...? tag it first
# and what we expect to achieve? by training rather than just recognition of injury phrases
# ballardian noun phrase?
#catting texts such as crash excerpts with paget report, rippe... | microresearch/diana | discard.py | Python | gpl-2.0 | 10,970 | [
"VisIt"
] | 2ec91e063e567dff0a5b578dd00b875b88d11e293d683e5490f2beed84d89ce9 |
# Copyright 2012 OpenStack Foundation
# 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 requ... | JioCloud/neutron | neutron/tests/unit/agent/linux/test_ip_lib.py | Python | apache-2.0 | 45,248 | [
"Brian"
] | 1ae31512f5a86fdbfae81f0cf37ba6d9cc44100e3347e53f16d188762e0aa944 |
# 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... | pkreissl/espresso | testsuite/python/dipolar_mdlc_p3m_scafacos_p2nfft.py | Python | gpl-3.0 | 7,707 | [
"ESPResSo"
] | 13007b86bdcb55aa60838619fb0837a2b264fa6907cae2ed10f519ad5a46a576 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008,2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | beernarrd/gramps | gramps/plugins/textreport/custombooktext.py | Python | gpl-2.0 | 6,829 | [
"Brian"
] | 73b3e6982f7d957a5a71ad34a657a2aecca83bb4f27a3eea0eade3aad1c7a150 |
# -*- coding: utf-8 -*-
import os
import sys
import array
import numpy as np
import scipy.ndimage
import scipy.interpolate
from scipy.interpolate import UnivariateSpline
from matplotlib.pyplot import *
from matplotlib.mlab import *
####### Check for h5py to Read AMR data ######
#try:
# import h5py as h5
# hasH5 ... | aywander/pluto-outflows | Tools/pyPLUTO/pyPLUTO/pyPLUTO.py | Python | gpl-2.0 | 63,895 | [
"VTK"
] | 534176c0856b2c4a0f3faf78137df27e98fe9f8072fa6e3c541120932f1df01a |
from django.db import models
from django.contrib.auth.models import (
BaseUserManager, AbstractBaseUser, PermissionsMixin,
)
from django.contrib.auth.models import Group
from django.core.validators import RegexValidator
from django.utils import timezone
from datetime import datetime, timedelta
from django.conf ... | fenglb/mysite | accounts/models.py | Python | cc0-1.0 | 6,595 | [
"VisIt"
] | d48387a9035c7c686db42ddbb089a90eae41df45180f54ec97ed0aadaa540641 |
def sizeof_fmt(num, suffix='B'):
for unit in ['', 'Ki', 'Mi', 'Gi', 'Ti', 'Pi', 'Ei', 'Zi']:
if abs(num) < 1024.0:
return "%3.1f%s%s" % (num, unit, suffix)
num /= 1024.0
return "%.1f%s%s" % (num, 'Yi', suffix)
def _check_for_local_file(name, path):
import os
"""Checks if th... | AWI-Paleodyn/Python_Helpers | custom_io/get_remote_data.py | Python | gpl-2.0 | 11,352 | [
"NetCDF"
] | a70006951ea33a9bf002c73ed550d5bc095953d7bbeea98a9b3e838931e3bf20 |
'''
@author Ivehui
@time 2016/05/18
@function copy caffenet model to other net
'''
import caffe
from caffe import layers as L
from caffe.proto import caffe_pb2
import parameters as pms
import random
weight_param = dict(lr_mult=1, decay_mult=1)
bias_param = dict(lr_mult=1, decay_mult=0)
learned_param = [weight_param, ... | Ivehui/DQN | creatNet.py | Python | mit | 5,380 | [
"Gaussian"
] | c19940d3da7265e107943360b861fa9e9202b9376926d2ca430d681747142ac9 |
#!/usr/bin/env python
"""
Do the initial installation and configuration of a DIRAC component
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import exit as DIRACexit
from DIRAC import gConfig, gLogger, S_OK
from DIRAC.Core.Utilities.DIRACScri... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_install_component.py | Python | gpl-3.0 | 4,598 | [
"DIRAC"
] | b2cf98f91b4b8902af774f035aaef7c3f3dd31b9eb1686dfba4d1a72ba8bd1af |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/storage/Storage.py | Python | gpl-3.0 | 15,816 | [
"ESPResSo"
] | 2e33ab93d7086ab9c3a1be2ca6d0dc13272a0765509687ba0ad41d01affabecc |
#!/usr/bin/env python
"""
Remove the given file replica or a list of file replicas from the File Catalog
This script should be used with great care as it may leave dark data in the storage!
Use dirac-dms-remove-replicas instead
"""
from __future__ import print_function
from __future__ import absolute_import
from __futu... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_remove_catalog_replicas.py | Python | gpl-3.0 | 2,410 | [
"DIRAC"
] | 9b0efd5220630076549242db3eec487c56946a5886f063e085cd95b72ce0d137 |
r"""
This module is a VTK Web server application.
The following command line illustrate how to use it::
$ vtkpython .../vtk_web_phylogenetic_tree.py --tree /.../data.phy --table /.../data.csv
Set of expected arguments:
--tree /file/path/to/anolis.phy
--table /file/path/to... | timkrentz/SunTracker | IMU/VTK-6.2.0/Web/Applications/PhylogeneticTree/server/vtk_web_phylogenetic_tree.py | Python | mit | 5,415 | [
"VTK"
] | d41cba8676b53b9444679d425d4324885bdddbcbdbbab304e7d6c69710d14ea2 |
#!/usr/bin/env python
from numpy import *
import pylo
import visit
import sys
import os
from glob import glob
filelist = sys.argv[1:]
zipped = False
name,sep,ext = filelist[0].rpartition('.')
if ext == 'lzma':
os.system('tar -xaf '+filelist[0])
filelist = glob('*.silo')
zipped = True
#create a .visit file
... | rogersce/fts | scripts/plot_visit.py | Python | mit | 708 | [
"VisIt"
] | 048378b3a317ed4dd765332a96931e2c6215e16a805f22d548639ddbd207328c |
import os
import glob
import warnings
import logging
import re
import atexit
logger = logging.getLogger(__name__)
@atexit.register
def cleanup():
for f in glob.glob('/sys/class/tacho-motor/motor*/command'):
with open(f, 'w') as f:
f.write('stop')
for f in glob.glob('/sys/class/leds/*/trig... | MaxNoe/python-ev3 | ev3/ev3dev.py | Python | apache-2.0 | 19,911 | [
"Amber"
] | e48576a95c44d4542d409793ffaef2edb0ac9173f56ce034142484ed6a3bbd93 |
import espressopp as sxx
from momo import osio, endl, flush
import mpi4py.MPI as MPI
import os
osio << "Running on %d cores ..." % MPI.COMM_WORLD.size << endl
# COLLECT CONFIG FILES FROM FOLDER
config_file_dir = './configs'
osio.cd(config_file_dir)
config_files = sorted(os.listdir('./'))
config_list = sxx.tools.conve... | capoe/espressopp.soap | examples/soap/test.py | Python | gpl-3.0 | 4,413 | [
"LAMMPS"
] | 12b5ab13c938f8a54a88151b79cd9b99f049396e432314072214d29a3ee0a286 |
<<<<<<< HEAD
<<<<<<< HEAD
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also imp... | ArcherSys/ArcherSys | Lib/email/_header_value_parser.py | Python | mit | 311,765 | [
"CRYSTAL"
] | 6da25e83ae6d7d83c74598f2310b7416e4931c1388f02b022349fbc0dad9a988 |
# 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.
"""Turn an mmCIF file into a dictionary."""
from __future__ import print_function
from B... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/PDB/MMCIF2Dict.py | Python | gpl-2.0 | 2,809 | [
"Biopython"
] | c0cf9b0bdbf3b11abcd0709ecab0419f0f4bec55785d10ff5b610d99832bb65d |
from aces.materials import Material
from aces.modify import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt,atan
import numpy as np
class structure(Material):
def set_parameters(self):
pass
def setup(self):
pass
def lmp_structure(self):
col=self.unitcell(self.laty,self.latx)
col.set... | vanceeasleaf/aces | aces/materials/CN-rotate.py | Python | gpl-2.0 | 2,009 | [
"ASE"
] | e1e3502fbca6d0ac1c192ceb044a42119e66fd6b9cd80c330476cc2a3e7fa2bb |
"""
Miscellaneous tools for the pipeline. Some may eventually be refactored into their own modules.
"""
import re
import itertools
import argparse
import pysam
import pandas as pd
import os
import procOps
from pipeline import ProcException, Procline
from cat.exceptions import ToolMissingException
from distutils.versio... | ucsc-mus-strain-cactus/Comparative-Annotation-Toolkit | tools/misc.py | Python | apache-2.0 | 5,114 | [
"pysam"
] | 04fdbd58ebfa7cc1ebea4cd85a421f2950078e7b09f0aa2549d9be3999dd0010 |
import pytest
from boltons.dictutils import OMD
from boltons.iterutils import (first,
remap,
default_enter,
default_exit,
get_path)
from boltons.namedutils import namedtuple
isbool = lambda x:... | suranap/boltons | tests/test_iterutils.py | Python | bsd-3-clause | 11,404 | [
"VisIt"
] | 9d3d2b92d46df0df77bd3c91cbd858c0c44e4e81fdb92342e57fe8ca8360bea4 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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 ... | mhlechner/psi4 | psi4/driver/__init__.py | Python | gpl-2.0 | 1,624 | [
"Psi4"
] | 19928c40539796d32a5230a6db75ebde02016870a079f29d5dabe65fb73afe1d |
from .util import make_enum, get_value_by_version, OS_NAME
OUTPUT_FILES_LAYOUTS = make_enum(
"eplusout", # {simulation_dir_path}/eplusout.{extension}
"simu", # {simulation_dir_path}/{simulation_base_name}.{extension}
"output_simu", # {simulation_dir_path}/Output/{simulation_base_name}.{extension}
"s... | Openergy/oplus | oplus/compatibility/outputs.py | Python | mpl-2.0 | 1,958 | [
"EPW"
] | 9a2c260d498c05368f3d197639bee72d0f0b45b2b6a16e0ebd1561858ea33dc0 |
# Author : Kevin Murphy(@murphyk), Aleyna Kara(@karalleyna)
# import superimport
import jax
import jax.numpy as jnp
from jax import jit, value_and_grad, tree_leaves, tree_map
from jax import random
from jax.random import split, permutation
from jax.nn import one_hot
from jax.lax import scan
import optax
from functo... | probml/pyprobml | old/subspace_opt_lib.py | Python | mit | 4,515 | [
"Gaussian"
] | 5c71fa832091c61fe787b243ad34979de251d9a710d5c3c81b073f9d77528415 |
#* 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/lgpl-2.1.html
import subp... | harterj/moose | python/TestHarness/tests/test_ShouldExecute.py | Python | lgpl-2.1 | 973 | [
"MOOSE"
] | 11a18c252f0a88fd8e6cdc792a6c66d2b56e5223bc1f35833b2a2f0527053d94 |
# -*- coding: utf-8 -*-
"""
edacc.ranking
-------------
This module implements some possible ranking schemes that can be used
by the ranking view in the analysis module.
:copyright: (c) 2010 by Daniel Diepold.
:license: MIT, see LICENSE for details.
"""
import numpy, math
from scipy.stats.msta... | EDACC/edacc_web | edacc/ranking.py | Python | mit | 34,854 | [
"VisIt"
] | df4503802b526327ed90b576f2f1835cf10c90969fd8f6d1cfd1d12cfbe39f45 |
# encoding: utf-8
__author__ = 'Olivier Mangin <olivier.mangin@inria.fr>'
__date__ = '06/2012'
"""Module to convert frame representation as output by kinect recording
to angle and/or angle velocity histogram representations.
"""
import numpy as np
from scipy.cluster.vq import kmeans, whiten
from ..lib.transforma... | omangin/multimodal | multimodal/features/angle_histograms.py | Python | bsd-3-clause | 7,555 | [
"Gaussian"
] | 80443951a1413b5634152180f5850c3ac6c0e10071774271f7551e527f0ba199 |
## This file is part of Invenio.
## Copyright (C) 2011, 2012, 2013 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later versio... | MSusik/invenio | modules/webauthorlist/lib/authorlist_engine.py | Python | gpl-2.0 | 34,357 | [
"VisIt"
] | 3df11137e44db416d4d8207823cd208aa6ec4498d01f3394495c48da450d8074 |
# Copyright (C) 2015 Ivan Pechenezhskiy
#
# 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 License, or
# (at your option) any later version.
#
# This program is distribute... | McDermott-Group/LabRAD | LabRAD/Measurements/General/server_interfaces.py | Python | gpl-2.0 | 46,740 | [
"Gaussian"
] | 79ac2e0265cfcc9e40a485b822ff9df2aaaefd352e0c1b932d77e7bbe05d0065 |
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