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|---|---|---|---|---|---|---|---|
dictionary = {
"000000": "XEROX CORPORATION",
"000001": "XEROX CORPORATION",
"000002": "XEROX CORPORATION",
"000003": "XEROX CORPORATION",
"000004": "XEROX CORPORATION",
"000005": "XEROX CORPORATION",
"000006": "XEROX CORPORATION",
"000007": "XEROX CORPORATION",
"000008": "XE... | ninuxorg/netengine | netengine/resources/manufacturers.py | Python | mit | 761,686 | [
"ASE",
"Amber",
"BWA",
"CRYSTAL",
"Galaxy",
"Jaguar",
"NEURON",
"Octopus"
] | 2d8c0915ad204a3ee4297f6382ba177ff27dbfec43bf0ac714eaf0aef24e18ac |
__all__ = [
'ADJECTIVES',
'ANIMALS',
]
ADJECTIVES = [
'adorable',
'acrobatic',
'adaptable',
'adventurous',
'agile',
'alert',
'amiable',
'amused',
'arboreal',
'ardent',
'artful',
'astonishing',
'astute',
'attentive',
'authentic',
'avid',
'beard... | 2ps/djenga | djenga/animal_pairs/dictionary.py | Python | bsd-3-clause | 12,228 | [
"Elk",
"Firefly",
"GULP",
"Jaguar",
"MOOSE",
"ORCA",
"Octopus"
] | c40ea27e33ae16886a3c7748045e36b647a70a3ba8b51ff1a591846d4878dd2a |
#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""A quick and dirty example of using Mayavi to overlay anatomy and activation.
"""
#-----------------------------------------------------------------------------
# Imports
#----------... | bthirion/nipy | examples/fiac/view_contrasts_3d.py | Python | bsd-3-clause | 2,584 | [
"Mayavi"
] | 600cfdcd0f7d3ba13d019f07528c8ce22f2aab096a6f4db9f06dbc9e60c09632 |
# (C) British Crown Copyright 2016, Met Office.
"""
The package: `ASoP1_spectral` package contains methods for analysing precipitation
intensity at any given time resolution, as part of the Analysing Scale of Precipitation
v1.0 package described in Klingaman et al. (2016).
ASoP (v1.0): A set of methods for analyzing s... | gillmmartin/ASoP1-Spectral | ASoP1_Spectral/tests/__init__.py | Python | apache-2.0 | 612 | [
"NetCDF"
] | 7cd4de208af0bc6ad8503f1a5f7c325dd9aec87bf5b89dcbe39b562da600322b |
from paraview.simple import *
#reader = XDMFReader(FileNames=['/scratch/snx3000tds/piccinal/sphflow/rotating_square_patch_3D/015/RES/square200.h5.xmf'])
reader = XDMFReader(FileNames=['/scratch/snx3000tds/piccinal/sphflow/rotating_square_patch_3D/015/RES/square278.h5.xmf'])
reader.PointArrayStatus = ['DeltaX', 'ID', ... | jgphpc/linux | paraview/dom/pvbatch/0.py | Python | gpl-2.0 | 505 | [
"ParaView"
] | c5ac7f9fe64c793a3d893bbe0d3a4833c5d4aac0c8e9716534ac62d74b8e96fc |
#!/usr/bin/python
# 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, or
# (at your option) any later version.
#
# Ansible is distributed... | alxnov/ansible-modules-core | cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 43,768 | [
"Dalton"
] | 739b6f25d8e08ca3826a8e666e802afa52e46c44cae10cb9b3f01f88f48bbfb0 |
# -*- coding: utf-8 -*-
#
# hpc_benchmark.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, ... | lekshmideepu/nest-simulator | pynest/examples/hpc_benchmark.py | Python | gpl-2.0 | 16,266 | [
"NEURON"
] | c6a581e03f985fd827e106e06ee8380f727748fe2bf357c6141ef2c5fa5c264b |
#pylint: disable=missing-docstring
#* 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/... | harterj/moose | python/chigger/base/ChiggerFilterSourceBase.py | Python | lgpl-2.1 | 5,420 | [
"MOOSE",
"VTK"
] | 7d84f0bd94682fca115f94539f2ec9f4b59e60949772ea16507bbe7c9e13d606 |
import re
_csq_format_re = re.compile(r'.*Format:\s*((\S+\|)*\S+)')
# for capturing VEP CSQ format in Description field of metaheader
_ann_format_re = re.compile(
r".*Functional annotations:\s*'(([^\|]+\|)*[^\|]+)'")
# for capturing SnpEff ANN format in Description field of metaheader
_common_csq_fields = ['CSQ', ... | gantzgraf/vape | vase/vcf_header.py | Python | gpl-3.0 | 8,057 | [
"pysam"
] | 5bbfac9062c98aef61db9230d44439b98de51f9114289161e3b84696f12cb35b |
"""
===================================
Simple 1D Kernel Density Estimation
===================================
This example uses the :class:`sklearn.neighbors.KernelDensity` class to
demonstrate the principles of Kernel Density Estimation in one dimension.
The first plot shows one of the problems with using histogram... | vortex-ape/scikit-learn | examples/neighbors/plot_kde_1d.py | Python | bsd-3-clause | 5,119 | [
"Gaussian"
] | 9369f4c85f289a71f00493e7b26cd108bcb05ad99cca65aaf51bbddf10300233 |
import numpy as np
from SimPEG import Mesh
from SimPEG import Problem
from SimPEG import Survey
from SimPEG import DataMisfit
from SimPEG import Directives
from SimPEG import Optimization
from SimPEG import Regularization
from SimPEG import InvProblem
from SimPEG import Inversion
import matplotlib.pyplot as plt
import ... | geoscixyz/em_examples | em_examples/LinearInversion.py | Python | mit | 17,361 | [
"Gaussian"
] | 858fbd86cd116b5eecd3d4750f101aa2882dbae7eec55e63e49642eddc9bdf81 |
import math
import numpy
class ElasticNet:
def __init__(self, cities, param):
self._cities = cities
self._param = param
self._num_iter = 0
self._k = self._param['init_k']
self._num_neurons = int(self._param['num_neurons_factor'] \
* self._... | larose/ena | elastic_net.py | Python | bsd-2-clause | 4,067 | [
"NEURON"
] | f137edffc1292d50c64d199a6a58b966798df513ac16eca8c29604a6fed8820a |
from .properties import Align, Bool, DataSpec, Enum, HasProps, Size, Any, Color
from .mixins import FillProps, LineProps, TextProps
from .enums import Units, AngleUnits, Direction
from .plot_object import Viewable
from six import add_metaclass, iteritems
# Size is a way to preserve a data-space-related metric all the... | jakevdp/bokeh | bokeh/glyphs.py | Python | bsd-3-clause | 8,148 | [
"Gaussian"
] | 151f658645cc43d634b523092dee664c5b557bd3c5749db1aab2a227374c50a6 |
#!/usr/bin/env python
# This script checks and can optionally update MOOSE source files.
# You should always run this script without the "-u" option
# first to make sure there is a clean dry run of the files that should
# be updated
import os, string
from optparse import OptionParser
global_ignores = ['contrib', '.s... | zzyfisherman/moose | framework/scripts/fixup_headers.py | Python | lgpl-2.1 | 2,599 | [
"MOOSE"
] | 906a9402b943390b83b3a1f570b5694f2cc738bc642549a495ed666aa7ae98f3 |
import numpy as np
import bayesianoracle as bo
import bayesianoracle.plot as boplotter
# Import function information
from function_data import *
import os
os.system("function_data.py")
def plot_kernels(bmao, X, x0, kernel_ranges, colors):
""" Auxillary plotting function
Parameters
----------
bmao... | altaetran/bayesianoracle | tests/quadraticBayesianAveraging/paper_examples/KernelDisplay.py | Python | apache-2.0 | 4,106 | [
"Gaussian"
] | 8b9d543f1ac7c1811088fe6311ad6c6d13d67b199bd79082bc6176aea11911ea |
"""
:mod: ReqClient
.. module: ReqClient
:synopsis: implementation of client for RequestDB using DISET framework
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
import os
import time
import random
import json
import datetime
# # from DI... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/Client/ReqClient.py | Python | gpl-3.0 | 25,398 | [
"DIRAC"
] | 79fd0ad9f12b3c33651cd53a5e4c28b0a972a528404ca5995a043e1f929c240b |
from flask import Flask, render_template, redirect, session, request
import random, datetime
app = Flask(__name__)
app.secret_key = "Felipe"
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_template('index.html', ... | jiobert/python | Velez_Felipe/assignments/Ninja/ninja_gold.py | Python | mit | 974 | [
"CASINO"
] | 0fd5fe8ba6b685a7ea6a4fabdc2b8b36a0f1351535699e601c6099eae94b8099 |
import mdpow.equil
S = mdpow.equil.WaterSimulation(molecule="BNZ")
S.topology("benzene.itp")
S.solvate(struct="benzene.pdb")
S.energy_minimize()
S.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps
# run simulation externally or use MDrunner
# (see docs for using mpi etc)
import gromacs
r... | Becksteinlab/MDPOW | doc/examples/benzene/session.py | Python | gpl-3.0 | 1,018 | [
"Gromacs"
] | 63d5c9c16e38407c92fd919e443e07c9661a2425eb003c470d8f75c12014392c |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | PatrickOReilly/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 68,627 | [
"Brian"
] | 0746fbc6b8650a90fef7240b8ab15b164d71534f033889c9f64af5f7f84ec244 |
#
# 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 | testsuite/python/interactions_non-bonded_interface.py | Python | gpl-3.0 | 7,883 | [
"ESPResSo"
] | fdf3d55bdc497d7c2133a26d2f84f2c17c182d82f3a313a2084298571f001ca2 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import pytest
import spack.util.spack_yaml as syaml
@pytest.fixture()
def minimal_configuration():
return {
... | rspavel/spack | lib/spack/spack/test/container/conftest.py | Python | lgpl-2.1 | 1,160 | [
"Gromacs"
] | 18b12fa6fa14141476852655cecec27af8955932f960c6d2448e002f8ad049e3 |
import sys
def set_help(input_write,dataname):
""" When using the help flag. It assists in writing all your files for you"""
print "\nIf you dont know parameters for these inputs, please refer to https://github.com/sipjca/cmlparser_py/blob/master/lammps_params.md\n"
print "Input the whole string you i... | sipjca/cmlparser_py | setparams.py | Python | apache-2.0 | 5,206 | [
"LAMMPS"
] | bf427ff98396789e069da3d063192438a8ebc9bfc9470667073e97301d7b08c9 |
# import shutil # not used
from collections import Counter
import string, re
import os, os.path, sys, subprocess, inspect
import pickle
import yaml
#import getopt # not used
from optparse import OptionParser
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast import NCBIXML
from Bio import... | phe-bioinformatics/emm-typing-tool | modules/EMM_determiner_functions.py | Python | gpl-3.0 | 54,076 | [
"BLAST",
"Biopython",
"Bowtie"
] | 1bb5132479b50fee43c776bf7c72d15a7e9a6ec01afb8cbbd567a05aa6b00bac |
"""
Tests for models.py.
"""
import json
import os
from django.conf import settings
from django.test import TestCase
from utils.import_util import import_reference_genome_from_local_file
from utils.import_util import copy_dataset_to_entity_data_dir
from main.models import AlignmentGroup
from main.models import Chrom... | woodymit/millstone_accidental_source | genome_designer/main/tests/test_models.py | Python | mit | 12,943 | [
"BWA"
] | 753e1221b2c2036d776b25dc41a468d2baafbd42d24c9b756321f8957f6de039 |
"""
Copyright (C) 2017 Roberto Bruttomesso <roberto.bruttomesso@gmail.com>
This file is distributed under the terms of the 3-clause BSD License.
A copy of the license can be found in the root directory or at
https://opensource.org/licenses/BSD-3-Clause.
Author: Roberto Bruttomesso <roberto.bruttomesso@gmail.com>
Da... | formalmethods/intrepyd | intrepyd/visitable.py | Python | bsd-3-clause | 669 | [
"VisIt"
] | 8720f113fb62b7a8a5024f2b5f8803a20cc3d4ff96aa68006e6752f40d6e3745 |
import dataclasses
from dataclasses import dataclass
from typing import Any
import typing
import sys
import numpy as np
import h5py
import Pyro5.api
# metadata support
from .mupifobject import MupifObject
from . import units, pyroutil, dumpable
from . import dataid
from .heavydata import HeavyDataBase, HeavyDataBase_Mo... | mupif/mupif | mupif/heavystruct.py | Python | lgpl-3.0 | 46,818 | [
"Dalton"
] | 36b54db37fc75bd91818e76413980b42e889a24f4e992990cab81c7c95195aa1 |
import logging
import random
import numpy as np
from ray.rllib.agents import with_common_config
from ray.rllib.agents.dreamer.dreamer_torch_policy import DreamerTorchPolicy
from ray.rllib.agents.trainer_template import build_trainer
from ray.rllib.execution.common import STEPS_SAMPLED_COUNTER, \
LEARNER_INFO, _ge... | pcmoritz/ray-1 | rllib/agents/dreamer/dreamer.py | Python | apache-2.0 | 9,028 | [
"Gaussian"
] | 044ccba1331ef60590669098c1308a624e9a0413206f831f4804c187ccef5c8e |
#!/usr/bin/env python
# =============================================================================
# Initialization
# =============================================================================
from active_worker.task import task
from task_types import TaskTypes as tt
import numpy as np
import h5py
num_surrs = ... | jakobj/UP-Tasks | Elephant/crosscorrelogram_task/crosscorrelogram_task.py | Python | gpl-2.0 | 10,090 | [
"NEURON"
] | 487cce2d8f47c92705c1f7c1de2e98ef5965835709d5601703694edb58b06b50 |
#!/usr/bin/env python
# -*- 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 ... | kain88-de/mdanalysis | package/setup.py | Python | gpl-2.0 | 22,850 | [
"Amber",
"Biopython",
"CHARMM",
"Gromacs",
"LAMMPS",
"MDAnalysis",
"NAMD",
"NetCDF"
] | cd129645f77b4a8ef5ae58eef59bfe9164f3e45ec59de671c6f227be47021d8f |
from functools import wraps
import os
import random
import re
import pytest
from flask.testing import FlaskClient
from flask import session
os.environ['PYDRILL_CONFIG'] = os.path.join(os.path.dirname(__file__), 'pydrill.cfg')
from pydrill import app, db, redis_store
from pydrill import models
from pydrill.jinja_env i... | alexandershov/pydrill | tests/test_pydrill.py | Python | mit | 9,111 | [
"VisIt"
] | ccc4d23540f0c085a11f987b90e8afdb83f98b009dcdb64d2e6c53fb6cdb1ec1 |
# Please do not change the configuration file quisk_conf_defaults.py.
# Instead copy one of the other quisk_conf_*.py files to your own
# .quisk_conf.py and make changes there. For a normal sound card
# configuration, copy quisk_conf_model.py to your .quisk_conf.py.
#
# PLEASE DO **NOT** COPY THIS FILE AND USE IT AS A... | shenki/quisk | quisk_conf_defaults.py | Python | gpl-2.0 | 39,603 | [
"CRYSTAL"
] | 3eb5dba55135fd65e5efd66f3db66e2684aa347774a412d80f5c31a8bdc62021 |
# -*- coding: utf-8 -*-
import numpy as np
from numpy.linalg import matrix_rank
from joblib import Parallel, delayed
from scipy.stats import multivariate_normal as _N
from scipy.optimize import minimize
from fitr.stats import lme
from fitr.stats import bic
from fitr.inference import OptimizationResult
def l_bfgs_b(f,
... | ComputationalPsychiatry/fitr | fitr/inference/mle_parallel.py | Python | gpl-3.0 | 10,027 | [
"Gaussian"
] | 5bfcc9601f60a22cabe857c555b20faf90651c191e102d68e2581c9546b4ae27 |
# coding: utf-8
# # Pollen
# This is the time of year when even thinking about flowers makes my eyes water.
# While it doesn't completely stop me from enjoying the outdoors, I find forecasts useful for planning and setting expectations.
#
# There are pollen tracking services that I find useful, but have shortcomin... | d10genes/pollen | pollen2.py | Python | mit | 21,073 | [
"Gaussian"
] | 181be1499b46ca92cf7b9ba7c9af39a46627dfa7a01d938b580528df0f636bb2 |
from datetime import datetime, date
from django.contrib.auth.models import User
from django.forms import (
BooleanField,
CharField,
CheckboxInput,
ChoiceField,
EmailField,
FileField,
Form,
ModelForm,
Select,
SelectMultiple,
Textarea,
ValidationError,
)
from datetimewidg... | softwaresaved/fat | lowfat/forms.py | Python | bsd-3-clause | 40,592 | [
"VisIt"
] | 6ad8f285381852d21f1966492b1c28ad941e8f81651fb43f3f0ce072bb51ceb2 |
########################################################################
# File: Operation.py
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implementation
Operation implementation
"""
from __future_... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 10,783 | [
"DIRAC"
] | 9f34204433c62d5696027f0b122590aea904425cdccee9157018a00f2ca11e7d |
from math import sqrt
import numpy as np
from ase.atoms import Atoms
from ase.units import Bohr, Hartree
from ase.dft.stm import STM
from ase.io.cube import write_cube
from ase.io.plt import write_plt
import gpaw.mpi as mpi
from gpaw.mpi import MASTER
from gpaw.io.plt import read_plt
from gpaw.grid_descriptor impor... | robwarm/gpaw-symm | gpaw/analyse/simple_stm.py | Python | gpl-3.0 | 10,576 | [
"ASE",
"GPAW"
] | 7f1d5458fcead3c00ad153ee90efc235c82e9acec66756c4727eea5cbbca79d6 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
from nose.plugins.attrib import attr
from unittest import skipIf, skip
from ..helpers import UniqueCourseTest, is_youtube_available, YouTubeStubConfig
from ...pages.lms.video.video import VideoPage
from ...pages.lms.tab_nav import TabNavPage
from ...pages.lms... | zerobatu/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 41,492 | [
"VisIt"
] | 76740d0cf1572d39ae951d5ebcca3f57d3a4d630faf577bc7f184ccc0b7eef52 |
"""Test that compute_delta_cchalf returns required values"""
from __future__ import annotations
import json
from unittest import mock
from dxtbx.model import Crystal, Experiment, Scan
from dxtbx.model.experiment_list import ExperimentList
from libtbx import phil
from dials.algorithms.scaling.model.model import KBSca... | dials/dials | tests/algorithms/scaling/test_scale_and_filter.py | Python | bsd-3-clause | 8,168 | [
"CRYSTAL"
] | 1edaf40c11ec874ea8bebf395a6522ebfc1f891d7c6e2b300937eb761ea15b5d |
#!/usr/bin/python
import os
import itertools
experiments = [
[1,"gaussian",1.5],
[0,"mixture",1,0.005],
[0.7,"mixture",1,0.1],
[0.7,"mixture",1,0.075],
[0.7,"mixture",2,0.05],
[0.7,"mixture",2,0.075]
]
os.chdir("../dboost")
for e in experiments:
if e[1] == "gaussian":
f = "sensors_... | cpitclaudel/dBoost | scripts/run_sensor_experiments.py | Python | gpl-3.0 | 888 | [
"Gaussian"
] | 39c881e62185bc2751f31fe0642299e1a484d1bec9fbcb82044130fdc97d71e2 |
import numpy as N
from image import *
import mylogger
from copy import deepcopy as cp
from . import has_pl
if has_pl:
import matplotlib.pyplot as pl
import scipy
import scipy.signal as S
import _cbdsm
import functions as func
import _pytesselate as _pytess
import shapelets as sh
from scipy.optimize import leastsq
... | jjdmol/LOFAR | CEP/PyBDSM/src/python/psf_vary.py | Python | gpl-3.0 | 48,910 | [
"Gaussian"
] | 4abe0d40eb88ff081f22b182bea7e249f2315a4762eaf67196556ce244b9ff84 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | Forage/Gramps | gramps/gen/filters/rules/event/_hasnote.py | Python | gpl-2.0 | 1,764 | [
"Brian"
] | 377319d86fb6f725efc69658e3a4b795f7771b8960b38051b0070590b626082a |
"""
==============================================
Visualizing the enegy-sensor-weather structure
==============================================
This example employs several unsupervised learning techniques to extract
the energy data structure from variations in Building Automation System (BAS)
and historial weather ... | TinyOS-Camp/DDEA-DEV | Development/plot_csv.py | Python | gpl-2.0 | 27,192 | [
"Gaussian"
] | 26728dcf6988faf4196c34ef18d3eb40375a6efc93ec9d3495115c34ddba919a |
"""
"""
from abc import ABCMeta, abstractmethod
PULSAR_UNKNOWN_RETURN_CODE = '__unknown__'
class ManagerInterface(object):
"""
Defines the interface to various job managers.
"""
__metaclass__ = ABCMeta
@abstractmethod
def setup_job(self, input_job_id, tool_id, tool_version):
"""
... | jmchilton/pulsar | pulsar/managers/__init__.py | Python | apache-2.0 | 3,493 | [
"Galaxy"
] | 50cbe84f70f54fa08a8b16655b47d894ca9c09f39a8d1e4efffc4043882f2f70 |
# This python script contains functions and classes used in the
# two synthetic galaxy model notebooks in this directory.
import astropy.io.ascii as asciitable
from scipy import interpolate
import numpy as np
def LoadData(galaxy_datafile, HIrad, ddensdR):
# Read the galaxy description file which contains rotatio... | JuanCab/synthetic_HI_models | galaxyparam.py | Python | gpl-3.0 | 3,144 | [
"Galaxy"
] | 8fa8acec8aa55b652378d520eb8c2c09c0fddeab760f63e541cbcaf98d3c80bd |
import os
import sys
import json
from datamanagerpkg import ProtonCommunication_data_manager
from datamanagerpkg import GalaxyCommunication_data_manager
from sequencer.models import Experiments, GalaxyUsers
from sequencer.models import GalaxyJobs, ExperimentRawData
##########################
#URL SEQUENCER
####... | CARPEM/GalaxyDocker | data-manager-hegp/analysisManager/analysismanager/addPlasmaMutation_Information.py | Python | mit | 4,872 | [
"Galaxy"
] | 6a3f07bcc7b2b508e7311eb63c95a313e4ba71175535b37c8d9ba23c32803da3 |
"""
A simple VTK widget for PyQt v4, the Qt v4 bindings for Python.
See http://www.trolltech.com for Qt documentation, and
http://www.riverbankcomputing.co.uk for PyQt.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
vtk3DWidget ... | timkrentz/SunTracker | IMU/VTK-6.2.0/Wrapping/Python/vtk/qt4/QVTKRenderWindowInteractor.py | Python | mit | 14,630 | [
"CRYSTAL",
"VTK"
] | 57cee05725deb35e7fd3e9780074a9916d112e211549ba0a090c5014a6ac5dfc |
"""Generators for geometric graphs.
"""
from bisect import bisect_left
from itertools import accumulate, combinations, product
from math import sqrt
import math
try:
from scipy.spatial import cKDTree as KDTree
except ImportError:
_is_scipy_available = False
else:
_is_scipy_available = True
import network... | SpaceGroupUCL/qgisSpaceSyntaxToolkit | esstoolkit/external/networkx/generators/geometric.py | Python | gpl-3.0 | 28,960 | [
"Gaussian"
] | a517d8a2d0d3867c5876eff37e568d44c852589933bb5637b4c9449ccd85b1a2 |
#!/usr/bin/env python
import sys, os
from argparse import ArgumentParser, FileType
def get_data(small = False):
data_root = "http://www.ccb.jhu.edu/software/hisat2/downloads/evaluation"
# Download the reference human genome, SNPs, and gene annotations
if not os.path.exists("data"):
os.mkdir("... | infphilo/hisat2 | evaluation/get_data.py | Python | gpl-3.0 | 3,781 | [
"Bowtie"
] | 1e0e8df3017445271da4de1e4e63a9abca55765d227daf4fca0b8ec39afaf627 |
#!/usr/bin/env python
#
# AST.py
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; witho... | qistoph/thug | src/AST/AST.py | Python | gpl-2.0 | 10,198 | [
"VisIt"
] | aded855bd0880bc47cd3fbccd664ef7636498a13473d80924f92eecb0c348786 |
#!/usr/bin/python
import os, subprocess
import textwrap, argparse
if __name__ == '__main__':
argument_parser = argparse.ArgumentParser(
prog='stability_multiple_files.py',
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''\
create a graphical... | daniparera/MCR | Senses/analisys/others/stability_multiple_files.py | Python | gpl-2.0 | 3,732 | [
"VisIt"
] | 20509b749f594c268086890d73c32126f7487e3a89add5aefed3692a37aa5066 |
#!/usr/bin/env python
#
# E-Mail post-processing script for NZBGet
#
# Copyright (C) 2013-2017 Andrey Prygunkov <hugbug@users.sourceforge.net>
#
# 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; e... | nzbget/nzbget | scripts/EMail.py | Python | gpl-2.0 | 10,475 | [
"VisIt"
] | 14b9192cfb4b13d715866c3ae31cbc55052da2ea0272ebd6aeb8d741ca58ca5b |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkMedicalImageReader2(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkMedicalImageReader2.py | Python | bsd-3-clause | 486 | [
"VTK"
] | d88b6762995d9a702587597572829c04c588a824268cf0514d3676a5d1698396 |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.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 ... | crafty78/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 32,305 | [
"Galaxy"
] | 81fddfcf0d7a3fd538f5467d702d6e091bfdfa396df3043b1a3e2a8260c77183 |
import time
import argparse
import numpy as np
import tensorflow as tf
import reader
import model
import pickle
import os
def parsing_args():
parser = argparse.ArgumentParser()
parser.add_argument('--mode', type=str, default='train',
help='train or test')
parser.add_argument('--i... | darongliu/Lstm_Turing_LM_tf | exp_merge_method/LSTM+att_fix+matrix_concat/run.py | Python | mit | 13,336 | [
"NEURON"
] | ffdd850a030e80eb43edd58a55b923f8d518a9030d1565d97033233be4703d12 |
# -*- coding: utf-8 -*-
#
# hl_api_models.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, ... | hakonsbm/nest-simulator | pynest/nest/lib/hl_api_models.py | Python | gpl-2.0 | 5,333 | [
"NEURON"
] | a72f930125c36ed1e4e7ddc1d206fa0481742dddf46e7ed0f03f99f8cda71554 |
from django.conf import settings
from django.db import models
from reviews.models import Review, ReviewSegment
"""
These models extend the basic review models with new fields. You do not need to
do this, but you can do it.
Take a look at the forms.py, too.
Also visit the __init__.py.
This all works only if the REVIEW... | shockflash/reviews | testapp/testdata/models.py | Python | bsd-3-clause | 1,308 | [
"VisIt"
] | 958937a55a0870d954622b9dd9b6293f6a20cbe73db5d878605fd3a17ca75e73 |
# Tests writing amber format with amber parameters
# Special isopeptide bond between two residues
import os
from vmd import atomsel, molecule
dir = os.path.dirname(__file__)
#==============================================================================
def test_amber_custom_residues(tmpdir):
from Dabble.param im... | drorlab/dabble | test/3NOB/test_3nob.py | Python | gpl-2.0 | 1,849 | [
"Amber",
"VMD"
] | 005fe33e2022f55cacd3041aba3cd42e067ae4b6f8a72899bc4bc4f29be0ef7a |
# Authors:
# Martin Kosek <mkosek@redhat.com>
# Pavel Zuna <pzuna@redhat.com>
#
# Copyright (C) 2010 Red Hat
# see file 'COPYING' for use and warranty information
#
# 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 Fr... | pspacek/freeipa | ipalib/plugins/dns.py | Python | gpl-3.0 | 168,418 | [
"VisIt"
] | a3b50959ecd9756cfee5063d953b81e4155e4196cdc20079dd0d2c8f342f009c |
#!/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... | sunqm/pyscf | pyscf/lo/test/test_orth.py | Python | apache-2.0 | 4,348 | [
"PySCF"
] | c23c5a7399fd1d1859cd661db19b267682a520a255dc863dcefcff5c22762137 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
try:
import json
except:
import simplejson as json
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','versi... | meeech/Titanium-Mixpanel-Module | build.py | Python | mit | 6,445 | [
"VisIt"
] | 1834be6bff81678da1ac9a4fce147478e64fc7cb8c3d03f7c2c9ff0da4604ceb |
# -*- mode: python; -*-
##
## Utilities for working with paired-end reads and
## fragment distributions
##
import os
import sys
import glob
import time
import pysam
from scipy import *
from numpy import *
import misopy
from misopy.parse_csv import *
import misopy.Gene as gene_utils
import misopy.sam_utils as sam_uti... | Xinglab/rmats2sashimiplot | src/MISO/misopy/pe_utils.py | Python | gpl-2.0 | 19,818 | [
"pysam"
] | 044a1b8ef86b9bf18a189ecc37186e9a296deb74335c943d664b106e886adf48 |
"""Code for checking for local names and superfluous import statements.
This code provides searches for local symbols in the AST, assignments and such
things.
"""
# This file is part of the Snakefood open source package.
# See http://furius.ca/snakefood/ for licensing details.
# stdlib imports
import compiler
__all_... | GreatFruitOmsk/snakefood | lib/python/snakefood/local.py | Python | gpl-2.0 | 4,247 | [
"VisIt"
] | e305eaa39611663c1710a4b5d49c7d03e7b60c25f07f9787134c1f4461dd429e |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class VotcaCsg(CMakePackage):
"""Versatile Object-oriented Toolkit for Coarse-graining
A... | iulian787/spack | var/spack/repos/builtin/packages/votca-csg/package.py | Python | lgpl-2.1 | 1,911 | [
"Gromacs"
] | 6385154c910e7725aa9faf2744066b07886556b457c2bb46875d1d42b867a362 |
from catkit import Gratoms
import numpy as np
import ase
import re
try:
from math import gcd
except ImportError:
from fractions import gcd
def running_mean(array, N=5):
"""Calculate the running mean of array for N instances.
Parameters
----------
array : array_like | ndarray (N,)
Arra... | jboes/CatKit | catkit/gen/utils/utilities.py | Python | gpl-3.0 | 4,498 | [
"ASE"
] | 01bdb9f6f7ec38a07802e86795703de8abb174de6b1a9bd43e4438ac13255c59 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from .fake_webapp import EXAMPLE_APP
class StatusCodeTest(object):
def test_should_visit_index_of_example_app_and_get_200_status_c... | bmcculley/splinter | tests/status_code.py | Python | bsd-3-clause | 767 | [
"VisIt"
] | 6aa7c8921e1133a26457405ed4a243ad19ec7b847fea47a4c5b7056a29117366 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
This example shows how to specify auxiliary basis for density fitting integrals.
The format and input convention of auxbasis are the same to the AO basis.
See also examples/gto/04-input_basis.py
'''
import tempfile
from pyscf import gto, scf, ... | gkc1000/pyscf | examples/df/01-auxbasis.py | Python | apache-2.0 | 2,034 | [
"Gaussian",
"PySCF"
] | c3392b6feed2d9c7c63ff83a37453f9e4b3241f056a51e1ac41fb56231b9c444 |
import os
import vtk
import csv
import math
from vtk.util.numpy_support import numpy_to_vtk, vtk_to_numpy
import numpy as np
import sklearn.utils
#-----------------------------------------------------------------------
# SPECIFIC FUNCTIONS
#-----------------------------------------------------------------------
def c... | catactg/lasc | code/lasc_benchmark_tools.py | Python | bsd-2-clause | 40,887 | [
"VTK"
] | edb021a96aea31aaf0347cd43c431b933d98fd1243010d63ec44aeb39f426572 |
#!/usr/bin/env python
import json
import logging
import os
import string
import subprocess
import sys
import time
import uuid
from random import choice
from twisted.internet import reactor, defer
from twisted.internet.task import deferLater
from twisted.internet.defer import CancelledError
from twisted.python import... | ashray/VTK-EVM | Web/Python/vtk/web/launcher.py | Python | bsd-3-clause | 26,500 | [
"ParaView",
"VTK"
] | bffc798cbc661f94eaa2d5f03893f3ed6361a056b0984b70c0ff0e7500248b5f |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | Chuban/moose | python/MooseDocs/tests/sqa/test_sqa.py | Python | lgpl-2.1 | 4,670 | [
"MOOSE"
] | 8601f0bf50599a5d859a7ab893d12a3bee96fccbd693d9a8c357848a1c3f7cd1 |
########################################################################
# File: RegisterOperation.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/19 13:55:14
########################################################################
""" :mod: RegisterFile
==================
.. module: RegisterFile
... | miloszz/DIRAC | DataManagementSystem/Agent/RequestOperations/RegisterFile.py | Python | gpl-3.0 | 3,811 | [
"DIRAC"
] | 766bcba8b68a4ce1daae2c0a75c1272b3787c7c2f03c0d0db874fc0be4679e68 |
from openanalysis.base_data_structures import UnionFind, PriorityQueue
import openanalysis.tree_growth as TreeGrowth
def kruskal_mst(G):
"""
Finds Minimum Spanning Tree of graph by Kruskal's Algorithm
:param G: networkx graph
:return: iterator through edges of Minimum spanning Tree
"""
edge_li... | OpenWeavers/openanalysis | analysistest/tree_growth.py | Python | gpl-3.0 | 4,835 | [
"VisIt"
] | 6fe6e8705028547f2047fb40792b41707849fc1291ae220460335102edf7fa80 |
# Copyright 2017 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... | kevin-coder/tensorflow-fork | tensorflow/python/data/experimental/kernel_tests/sql_dataset_test.py | Python | apache-2.0 | 22,191 | [
"MOE"
] | 35e3e76c1d08656f0f5db9fd7f6609988b6909377413bde625fcc75b258bda44 |
#
# Copyright (C) 2015-2021 University of Oxford
#
# This file is part of msprime.
#
# msprime 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... | jeromekelleher/msprime | msprime/ancestry.py | Python | gpl-3.0 | 74,467 | [
"DIRAC"
] | d1ab078ed1d32b8e43cffbc6b6c4dcf822859a6255b454fc2ab28fbe2f0f926f |
import pandas as pd
import nmrpystar
import mdtraj as md
t0 = md.load("./Trajectories/1am7_1.dcd", top="./1am7_fixed.pdb")[0:50]
t1 = md.load("./Trajectories/1am7_1.dcd", top="./1am7_fixed.pdb")[-50:]
prediction0 = md.nmr.chemical_shifts_shiftx2(t0).mean(1) # Average over time dimensions
prediction1 = md.nmr.chemica... | hainm/open-forcefield-group | nmr/code/compare_shifts_T4_test.py | Python | gpl-2.0 | 1,238 | [
"MDTraj"
] | cd8339b37bbcf30079aa864c19dca216197d8f14456688da4d00c6d6726c6f29 |
# Version: 0.15+dev
"""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, and pypy
* [![Latest Version]
(https... | lbdreyer/nc-time-axis | versioneer.py | Python | bsd-3-clause | 72,477 | [
"Brian"
] | d2ac4c3371c86ea58ebbfb3371c9bf54bc72b5314b5c2103c459ebb813e369ea |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# (converting to a object-oriented, more modular design)
# Licence: BSD 3 clause
"""
The built-in correlation mod... | jmetzen/skgp | skgp/correlation_models/stationary.py | Python | bsd-3-clause | 21,469 | [
"Gaussian"
] | 0a3c490339b97cdfd030e23b4712f7a631c718713df2536ba33453e8603f803e |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/py-netcdf4/package.py | Python | lgpl-2.1 | 1,807 | [
"NetCDF"
] | 6ccbe3b8324d5977cf80fbbbc29b05765efcb5d03a3f3ebe066524c6ecb1bdcf |
###############################
# 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/vasp/extract/mixin.py | Python | gpl-3.0 | 3,547 | [
"CRYSTAL",
"VASP"
] | ea02425fddce7d2eb97ca3e8ed0df1f9198a3abc53ca3d78e38d7bf5758cc4a3 |
# -*- coding: utf-8 -*-
#*******************************************************************
# * File: merge.py
# * Description:
# * Author: HarshaRani
# * E-mail: hrani@ncbs.res.in
# ********************************************************************/
# ***********************************... | dharmasam9/moose-core | python/moose/merge/merge.py | Python | gpl-3.0 | 28,641 | [
"MOOSE"
] | 5a90cbb2de812274a85d94af91c33fdce76fb2f796d48fdf06b770c3f9c6b2ce |
#
# Copyright (C) 2013,2014,2015,2016 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... | KonradBreitsprecher/espresso | doc/tutorials/01-lennard_jones/scripts/two-component-visualization.py | Python | gpl-3.0 | 4,208 | [
"ESPResSo"
] | c8224aab5f4eb379a8d166f0de41aff6a0de293101f1549c25e8cd648f6160e0 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | eerorika/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 92,348 | [
"VisIt"
] | 35b968e0aafdd8e1954440b7470a6fbe706ca4d92d907c8060d06ec82b4e972e |
from collections import namedtuple
from ua_parser import user_agent_parser
from .compat import string_types
MOBILE_DEVICE_FAMILIES = (
'iPhone',
'iPod',
'Generic Smartphone',
'Generic Feature Phone',
'PlayStation Vita',
'iOS-Device'
)
PC_OS_FAMILIES = (
'Windows 95',
'Windows 98',
... | public-ink/public-ink | server/appengine/lib/user_agents/parsers.py | Python | gpl-3.0 | 7,813 | [
"Galaxy"
] | 73c17577e931d663d462d0fcd8f3dfcfde47b2c7a3befe24dd74303aa663c27f |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for Entrance exams in the LMS
"""
from __future__ import absolute_import
from textwrap import dedent
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from com... | ESOedX/edx-platform | common/test/acceptance/tests/lms/test_lms_entrance_exams.py | Python | agpl-3.0 | 3,073 | [
"VisIt"
] | 28c92e9240ca453de8a900b6a829f306dfa0e3daed83238f069ae15a092c3e0a |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import copy
import json
import os
import py... | kvar/ansible | test/units/galaxy/test_collection_install.py | Python | gpl-3.0 | 31,481 | [
"Galaxy"
] | d3401cbce8e96cc32304bc7a52cec337f2c4d04116954ac62d727e3589c89c2c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/client/graphs.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, th... | hdemeyer/king-phisher | king_phisher/client/graphs.py | Python | bsd-3-clause | 33,983 | [
"VisIt"
] | 8904e023ac5166cf81128057504e09fa41f93a7b8b3202f90eb933ecaba58511 |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
import warnings
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import ndarray, ufunc, asarray
import numpy as np
# getargspec and formatargspec were removed in Python... | bringingheavendown/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 36,347 | [
"VisIt"
] | 6f16d31c5e703b59247056c0474d5d02edd68620f3b59e43013ccd1e07541760 |
# coding: utf-8
from __future__ import unicode_literals
import binascii
import collections
import email
import getpass
import io
import itertools
import optparse
import os
import re
import shlex
import shutil
import socket
import struct
import subprocess
import sys
import xml.etree.ElementTree
try:
import urllib... | phihag/youtube-dl | youtube_dl/compat.py | Python | unlicense | 90,595 | [
"Bowtie"
] | 664e6e37ddc2c9b857ec9b60f12794fcd46fedc16db5272bad3507cabfa44bfd |
#DeepLearning Demo in Python3
# notes xrange is named range
# print requires parenthisis ()
from numpy import exp, array, random, dot
class NeuralNetwork():
def __init__(self):
# Seed the random number generator, so it generates the same numbers
# every time the program runs.
random.see... | bluewitch/Code-Blue-Python | NeuralNetworkDemo.py | Python | mit | 3,145 | [
"NEURON"
] | 8316f0d547ab9007a2ac1367120d18aeed2ee7c23fda64165e14b0acd9d02e3b |
"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is ... | dwhswenson/mdtraj | setup.py | Python | lgpl-2.1 | 12,458 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | bc62426570250cababc492aa92d10edf16ea93d7d1885adcd799da0d5ccf90f0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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 aj... | c4sc/arividam | config/urls.py | Python | mit | 2,517 | [
"VisIt"
] | 870c32c51dc5dd9da31c04969cc6a5d38707bce0a7e0acad35340b30303ee753 |
from __future__ import unicode_literals
from frappe import _
def get_data():
return [
{
"label": _("Issues"),
"items": [
{
"type": "doctype",
"name": "Issue",
"description": _("Support queries from customers."),
"onboard": 1,
},
{
"type": "doctype",
"name": "Issue Typ... | ebukoz/thrive | erpnext/config/support.py | Python | gpl-3.0 | 1,960 | [
"VisIt"
] | 9c045241c05d3fdac6cc972a35648978fb44c56dfc9da1b428ef2d55975b5031 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest2 as unittest
from pymatgen.electronic_structure.core import Orbital, Spin
class SpinTest(unittest.TestCase):
def test_init(self):
self.as... | aykol/pymatgen | pymatgen/electronic_structure/tests/test_core.py | Python | mit | 969 | [
"pymatgen"
] | 18c380ab49da780ed1bb748f73d1ac45fc6b0ba863ef4f1dd9300dfc83588ce4 |
"""Base classes and utilities for readers and writers.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING,... | maximsch2/SublimeIPythonNotebook | external/nbformat/rwbase.py | Python | gpl-3.0 | 6,753 | [
"Brian"
] | 1e39838cb52af16c42b0861ab2f5f2795501875bc8135c3d9e2d1bb12e17061a |
""" TaskQueueDB class is a front-end to the task queues db
"""
__RCSID__ = "$Id"
import types
import random
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.private.SharesCorrector import SharesCorrector
from DIRAC.WorkloadManagementSystem.private.Queues import maxCPUSegments
fro... | marcelovilaca/DIRAC | WorkloadManagementSystem/DB/TaskQueueDB.py | Python | gpl-3.0 | 51,888 | [
"DIRAC"
] | 976429c6ec00ecff9e67e622c9328760278fb403d550836d682fbe6f93a1329e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import Tix
import tkFileDialog, tkMessageBox
import subprocess
from datetime import date
from fpdf import FPDF
from utils import settings
def main(_):
'''Currently aimed at producing product testing results for ASE
products but could change it to work fo... | Ripley6811/TAIMAU | src/pdf_tools/product_QC_report.py | Python | gpl-2.0 | 12,995 | [
"ASE"
] | dcd3ef9579442273fa50f263072c9b94d46bf714a5cc3de8786800a3109bb3fe |
##
# Copyright 2013-2020 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... | pescobar/easybuild-easyblocks | easybuild/easyblocks/p/psi.py | Python | gpl-2.0 | 11,207 | [
"Psi4"
] | b45dea1850dc551137dd3b4580887c121668765844ac1c0fc929dacf4fcdd21e |
import os
import sys
import argparse
import time
import glob
from farmpy import lsf
from farm_blast import blast, utils
class Error (Exception): pass
parser = argparse.ArgumentParser(
description = 'Run BLAST in parallel on the farm',
usage = '%(prog)s [options] <reference> <query>')
parser.add_argument('--n... | sanger-pathogens/Farm_blast | farm_blast/pipeline.py | Python | gpl-3.0 | 14,070 | [
"BLAST"
] | df8790e397fadfc9efe28dcc628c912551a34c120c8d27bd9de8bbc0efc022f3 |
'''
MFEM example 20p
See c++ version in the MFEM library for more detail
'''
import os
import mfem.par as mfem
from mfem.par import intArray
from os.path import expanduser, join, dirname
import numpy as np
from numpy import sin, cos, exp, sqrt, pi
from mpi4py import MPI
num_procs = MPI.COMM_WORLD.size
myid =... | mfem/PyMFEM | examples/ex20p.py | Python | bsd-3-clause | 7,072 | [
"Gaussian"
] | 1352ccf2e2fefac3bbb1bb76c7f155425a90728646d407fbd1553004ccf69eae |
"""Galaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import annotations
import os
import tempfile
from ....config import (
IntegrationConfig,
)
from ....docker_util import (
docker_cp_to,
)
from ....containers import (
run_support_container,
)
from . import (
CloudEnvironment... | mattclay/ansible | test/lib/ansible_test/_internal/commands/integration/cloud/galaxy.py | Python | gpl-3.0 | 6,384 | [
"Galaxy"
] | ddfd8b27944d63c7bf5a949496e8f26636b2e72e93c2bb646c120af73188de40 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/dl_cluster.py | Python | apache-2.0 | 4,240 | [
"ORCA"
] | 7a5ae963fa25a060e2ce793012b20f1594c29039b24832e095b9728d05c7c0e2 |
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