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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.io.cif import CifParser
from pymatgen.analysis.magnetism.jahnteller import *
import unittest
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
't... | gVallverdu/pymatgen | pymatgen/analysis/magnetism/tests/test_jahnteller.py | Python | mit | 5,029 | [
"pymatgen"
] | bce3c702e7b7ef2b4eee9d6d6ffc2e2cec5be123b6e9bbb6a67cb4266e60f68d |
#!/usr/bin/env python
from glob import glob
import numpy as np
import os
import sys
from horton import * # pylint: disable=wildcard-import,unused-wildcard-import
from horton.meanfield.test.common import check_cubic_wrapper
# log.set_level(log.high)
log.set_level(log.silent)
debug = True
def main(fns_fchk):
... | theochem/horton | data/examples/hf_compare/compare.py | Python | gpl-3.0 | 2,998 | [
"Gaussian"
] | 8bb4c1dabb6e83f384fc9451d00bfbbc36fec58eab40ecd52c3c093f86114cb8 |
import ocl
import pyocl
import camvtk
import time
import vtk
import datetime
if __name__ == "__main__":
print ocl.version()
myscreen = camvtk.VTKScreen()
stl = camvtk.STLSurf("../../stl/gnu_tux_mod.stl")
myscreen.addActor(stl)
stl.SetWireframe()
stl.SetColor((0.5,0.5,0.5))
polydata ... | JohnyEngine/CNC | opencamlib/scripts/drop-cutter/drop_cutter_tst_5.py | Python | apache-2.0 | 2,140 | [
"VTK"
] | 6507d6510b8cc5932b6e11f1fdea11608eaaa48c58909d18474c9f7d9798ee9c |
# Copyright 2013 Rackspace
#
# 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... | ostackbrian/rackspace-glanceclient | setup.py | Python | apache-2.0 | 1,464 | [
"Brian"
] | 1b3be3d4ff6377b5eb39d9a6134e3752aab226d090e5a63c7544002c99780d99 |
# Turta IoT HAT Helper for Raspbian
# Distributed under the terms of the MIT license.
# Python Driver for Bosch Sensortec BME280 Environmental Sensor
# Version 1.01
# Updated: July 14th, 2018
# Visit https://docs.turta.io for documentation.
import time
import math
from enum import IntEnum
from smbus import SMBus
#E... | Turta-io/IoTHAT | DriverSource/Raspbian/Python/Turta_BME280.py | Python | mit | 13,072 | [
"VisIt"
] | 8dcf9591f2cae337922bf8f98f92b2d44ab6e20bd4f57f6b2df16656cf45908a |
# ----------------------------------------------------------------------
# Star Catalog -- Bright Stars (J2000 coordinates)
# Name RA Dec Mag Constellation
data = { \
"33 Psc": ... | walterbender/starchart | stars1.py | Python | gpl-2.0 | 283,181 | [
"Psi4"
] | 2b4b90c663888934f1458b1857293b627e453b307804bcc8893c0b9f317df9fc |
"""This module defines an ASE interface to FLAPW code FLEUR.
http://www.flapw.de
"""
import os
from subprocess import Popen, PIPE
import re
import numpy as np
from ase.units import Hartree, Bohr
class FLEUR:
"""Class for doing FLEUR calculations.
In order to use fleur one has to define the following env... | grhawk/ASE | tools/ase/calculators/fleur.py | Python | gpl-2.0 | 20,391 | [
"ASE",
"FLEUR"
] | 8ef27cfe3c44dea164f522c91ece16d39c641fc8f32415339fdbc03297f7e779 |
import os
import sys
import glob
import re
import os.path as op
import shutil
from collections import Counter
try:
from dnapilib.apred import iterative_adapter_prediction
error_dnapi = None
except ImportError:
error_dnapi = ("No dnapi installed. Need to give adapter sequence."
"Please, i... | vladsaveliev/bcbio-nextgen | bcbio/srna/sample.py | Python | mit | 15,251 | [
"Bioconda"
] | e374aa71beb81c3c0175c445df4d553ffe4bba0b0fba3a881bac4a70c92826f3 |
import numpy as np
from datetime import datetime
import netCDF4 as netCDF
import pdb
import pyroms
import pyroms_toolbox
## create CI remap file for scrip
#print 'Create remap grid file for CI grid'
#dstgrd = pyroms.grid.get_ROMS_grid('CI')
#dstgrd.hgrid.mask_rho = np.ones(dstgrd.hgrid.mask_rho.shape)
#pyroms.remap... | kshedstrom/pyroms | examples/rivers/compute_hill_remap_weights_2.py | Python | bsd-3-clause | 1,046 | [
"NetCDF"
] | 352bbd8580633a0c68570fb0610c5164ee996ff1c97f7a9a2972e8c96ecd0d0b |
from __future__ import print_function
import os
from ase.structure import molecule
from ase.io.bader import attach_charges
fname = 'ACF.dat'
f = open(fname, 'w')
print("""
# X Y Z CHARGE MIN DIST
----------------------------------------------------------------
1 7.086... | suttond/MODOI | ase/test/bader.py | Python | lgpl-3.0 | 846 | [
"ASE"
] | 80b859cf474d72fe0d01212a4a356e676edc5c95e3a6fcac286525807198fdff |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This script helps to create a new branch for a new Odoo version from the
another existing branch, making the needed changes on contents.
Installation
============
For using this utility, you need to install these dependencies:
* github3.py library for handling Githu... | Endika/maintainer-tools | tools/migrate_branch.py | Python | agpl-3.0 | 12,351 | [
"VisIt"
] | 47e1ccacc939b05c4e9fc0b812c18d99c8533bd814fbc8d6820c81a435c5b96b |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QAD Quantum Aided Design plugin
classe per la gestione delle entità
-------------------
begin : 2013-08-22
copyright : iiiii
email... | geosim/QAD | qad_entity.py | Python | gpl-3.0 | 33,573 | [
"ESPResSo"
] | b01e9fd792438ade90e65b63c186b7d5301feff7719898f3659f0e2f24907150 |
# Lint as: python3
# Copyright 2020 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 ... | tensorflow/lingvo | lingvo/core/gshard_builder.py | Python | apache-2.0 | 165,742 | [
"Gaussian",
"MOE"
] | bf4e6f334dc9adabdaf4e8c8020b0bf730dd3be90af603385805f853700c47af |
import atexit
from contextlib import contextmanager
from selenium.common.exceptions import (
NoAlertPresentException,
NoSuchWindowException,
TimeoutException,
UnexpectedAlertPresentException,
WebDriverException)
from selenium.webdriver.common.desired_capabilities import DesiredCapabilities
from sele... | elliterate/capybara.py | capybara/selenium/driver.py | Python | mit | 11,398 | [
"VisIt"
] | 7684db133fe6f863ccc4305c3c875172a85a451ff968d79d63f7afa0ee8eab18 |
"""**Obsolete** Fit PSF and make smoothed maps."""
from __future__ import print_function
import argparse
import sys
from multiprocessing import Pool, Manager
import numpy as np
from astropy.io import fits
from opstats.fitting import fit_gaussian1d
from opstats.io import write_fits
from opstats.psf import gen_psf
fro... | piyanatk/sim | scripts/archive/fhdpost1.py | Python | mit | 8,329 | [
"Gaussian"
] | 85970268305fe038574e47574be0d49da33f261c16116ae0ef4da41e351704f9 |
#! /usr/bin/env python
########################################################################
# File : dirac-stager-monitor-jobs
# Author : Daniela Remenska
########################################################################
"""
Report the summary of the staging progress of jobs
Example:
$ dirac-stager-mo... | ic-hep/DIRAC | src/DIRAC/StorageManagementSystem/scripts/dirac_stager_monitor_jobs.py | Python | gpl-3.0 | 5,845 | [
"DIRAC"
] | 0185398319fee5362337d7a3a00a83e03acab1fdc414760738e56d4ef44852da |
"""Made by Charlie Sievers Ph.D. Candidate, UC Davis, Donadio Lab 2019"""
# from mpi4py import MPI
from lammps import lammps
import numpy as np
# comm = MPI.COMM_WORLD
# rank = comm.Get_rank()
""" LAMMPS VARIABLES """
# data files
infile = "silicon_input_file.lmp"
ff_file = "ff-silicon.lmp"
# full output useful fo... | pdebuyl/lammps | examples/USER/phonon/dynamical_matrix_command/python/dynmat.py | Python | gpl-2.0 | 1,034 | [
"LAMMPS"
] | ba4080d342969702b348e43b5342047c8b937cc2965ab49a3171e7ae77810d06 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
from __future__ import print_function
import json
import op... | endlessm/chromium-browser | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 24,316 | [
"Galaxy"
] | 99df0318803eeb10de21ad8a5d551490cedd4b72788aa781fee983cbfb56d304 |
import os
import pysam
import numpy as np
import pandas as pd
import multiprocessing
import collections
class single_coverage(object):
def __init__(self, bam):
self.bam = bam
bamFile = pysam.AlignmentFile(bam)
self.length = collections.OrderedDict(
zip(bamFile.references, b... | adam-rabinowitz/ngs_python | bam/pysam_coverage.py | Python | gpl-2.0 | 25,391 | [
"pysam"
] | 63dc191f900596087fd6eeb639fb7b446bd5fcfd6084291392523439df616f39 |
# Copyright 2016 ASLP@NPU. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | npuichigo/voicenet | src/export_inference_graph.py | Python | apache-2.0 | 6,966 | [
"Gaussian"
] | d5d697e6509fd651044cf564dfbdbf938c68e7b89f0cb7124286409018622bf6 |
#-------------------------------------------------------------------------------
#
# Define classes for (uni/multi)-variate kernel density estimation.
#
# Currently, only Gaussian kernels are implemented.
#
# Written by: Robert Kern
#
# Date: 2004-08-09
#
# Modified: 2005-02-10 by Robert Kern.
# Contr... | gatoravi/svviz | src/svviz/kde.py | Python | mit | 3,322 | [
"Gaussian"
] | fd5882a79517dbfdf3d3e29cb51207a4d238b9d3d7e5b2e77e329655b7fde870 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_productsearch.py | Python | gpl-2.0 | 21,341 | [
"VisIt"
] | 33ef35f616419f9610b453199a992aa331283488ad5b5dd5d1b7a9f7b16b2838 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
@package pyssw
@brief Python standalone program for ssw alignment using the C library
Complete-Striped-Smith-Waterman-Library
Biopython module is require for fastq/fastq parsing
@copyright [The MIT licence](http://opensource.org/licenses/MIT)
@author Adrien Leger ... | a-slide/pyDNA | Ssw/pyssw.py | Python | gpl-2.0 | 10,948 | [
"Biopython"
] | e64ad5e51d538762619fa6a266ca081bf924eed8d099178ac93714a3c3b1a615 |
#!/usr/bin/env python
import sys
import os
import cProfile
import pstats
import pygame
import pygame.locals as pl
# Add directories to python path
base = os.path.abspath(os.path.dirname(__file__))
sys.path.append(os.path.abspath(os.path.join(base, 'gamelib')))
sys.path.append(os.path.abspath(os.path.join(base, 'ga... | miketwo/Moose | rewrite.py | Python | gpl-2.0 | 9,563 | [
"MOOSE"
] | fccea90c6bbc5ff408bde13d086a3a0f8cf01ccbf6f56c03de9adacb90af99e3 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
className
A QGIS plugin
description
-------------------
begin : 2016-12-03
copyright : (C) 2016 by Nico
... | lennepkade/dzetsaka | processing/domainAdaptation.py | Python | gpl-3.0 | 10,604 | [
"Gaussian"
] | fb359e1223ca72b3e4b2666b169ff5d23394d32a594398a376d8ea42e5726aab |
from nn.layer import Layer
import numpy as np
from theano.tensor import tanh
class ConvolutionalLayer(Layer) :
'''This class describes a Convolutional Neural Layer which specifies
a series of kernels and subsample.
layerID : unique name identifier for this layer
inputSize :... | mbojrab/playbox | trunk/modules/python/nn/convolutionalLayer.py | Python | mit | 6,200 | [
"NEURON"
] | 132b395930f33926f3080d27ac51dc2203f6677bc10742eae1e9f7eef2f9e16a |
# 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... | jbedorf/tensorflow | tensorflow/python/autograph/converters/return_statements.py | Python | apache-2.0 | 13,356 | [
"VisIt"
] | 79e8467693c1fb67323e46c6e7b82edb52ef31c0f5468b4355421b7deeb6ecf8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for representing species substitution
probabilities.
"""
import functools
import itertools
import json
import logging
import math
import os
from collections import defaultdict
... | gmatteo/pymatgen | pymatgen/analysis/structure_prediction/substitution_probability.py | Python | mit | 9,437 | [
"pymatgen"
] | db13c5b697b2ff73e2cfcbafba4b6a8eace93b84881d1e2063ef95c642322dac |
# Copyright 2018 Google LLC. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | PAIR-code/interpretability | text-dream/python/dream/reconstruct_shifted_activation.py | Python | apache-2.0 | 12,102 | [
"NEURON"
] | e8f1129b5abbcb03019ffaf3b96fdfdd920d939f38ac063e11365ea617b25456 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# 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 PyBioMed source tree.
"""
#####... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/constitution.py | Python | bsd-3-clause | 17,549 | [
"RDKit"
] | e126faaae9523699a4d05dd7dcdae0ac2af8d9fd3d0da33ffff15dc845ff30e1 |
import operator
import xml.etree.ElementTree as ETree
from ucca import core, layer0, layer1, convert
"""Utilities for tests."""
def empty():
p = core.Passage(ID="1")
layer0.Layer0(p)
layer1.Layer1(p)
return p
def basic():
"""Creates a basic :class:`Passage` to tinker with.
Passage structu... | danielhers/ucca | ucca/tests/conftest.py | Python | gpl-3.0 | 13,092 | [
"TINKER"
] | d4a963c326b6236a840397146c9e984d1b1578e8c3eb1ff9ee3941bd03aa354f |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required... | shiwalimohan/RLInfiniteMario | system/codecs/Python/src/rlglue/RLGlue.py | Python | gpl-2.0 | 5,110 | [
"Brian"
] | 941c4a99fe3b709a5b491f99c59b45f521ddf9fdb349b19334323856782d0cc6 |
"""
==========================================
Outlier detection with several methods.
==========================================
When the amount of contamination is known, this example illustrates three
different ways of performing :ref:`outlier_detection`:
- based on a robust estimator of covariance, which is assum... | herilalaina/scikit-learn | examples/covariance/plot_outlier_detection.py | Python | bsd-3-clause | 5,242 | [
"Gaussian"
] | 2f7dd5deaffaacb8ac1b1487f60d14ae984217114571d3fcb62bdc0df319c127 |
#!/usr/bin/env python3
#
# Copyright (C) 2015 Zubax Robotics <info@zubax.com>
#
# This program is free software: you can redistribute it and/or modify it under the terms of the
# GNU General Public License as published by the Free Software Foundation, either version 3 of the License,
# or (at your option) any later ver... | Zubax/zubax_gnss | tools/drwatson/drwatson_zubax_gnss.py | Python | gpl-3.0 | 23,497 | [
"CRYSTAL"
] | 97df1636bef7f7abc94a5252d14a6d3efe56f0ae47d117257e6e496975faf750 |
# -*- coding: utf-8 -*-
#
# hl_api_spatial_distributions.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 o... | sdiazpier/nest-simulator | pynest/nest/spatial_distributions/hl_api_spatial_distributions.py | Python | gpl-2.0 | 3,755 | [
"Gaussian"
] | 02453b6a151189e221bfd542ef3d4661b8493b65bccde19cab0381e47364df81 |
#!/usr/bin/env python
#
# @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
#... | andysim/psi4 | psi4/share/psi4/fsapt/copy_pymol2.py | Python | gpl-2.0 | 1,374 | [
"Psi4",
"PyMOL"
] | 16ddbec8013c3231e608bd3b807529327a7c9a5dc6a7700ef0e6a3b3d289e0b6 |
# -*- coding: utf8 -*-
from functools import partial
from . import stack
class Modifier(object):
"""Visitor with rollback"""
def visit(self, visited):
"""do something on visited"""
msg = "[method visit] %s can't visit %s" %(self, visited)
raise NotImplementedError(msg)
def visit_al... | apieum/eventize | eventize/typing/modifiers.py | Python | lgpl-3.0 | 4,014 | [
"VisIt"
] | 010435444e87225ab8bd9ca698fec4f3e16dfd84788a120316423709bb9bfaf7 |
"""
:mod: DataManager
.. module: DataManager
:synopsis: DataManager links the functionalities of StorageElement and FileCatalog.
This module consists of DataManager and related classes.
"""
# # RSCID
__RCSID__ = "$Id$"
# # imports
from datetime import datetime, timedelta
import fnmatch, os, time
# # from DIRAC
imp... | marcelovilaca/DIRAC | DataManagementSystem/Client/DataManager.py | Python | gpl-3.0 | 71,947 | [
"DIRAC"
] | 279f3e6f2c8cfe9721167da1c08b52e37a718ad578e3fbdb7edeab240dae2bce |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2011, 2012 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... | CERNDocumentServer/invenio | modules/bibauthorid/lib/bibauthorid_webapi.py | Python | gpl-2.0 | 111,955 | [
"VisIt"
] | e36a425f7e2485ac0f2952a00a0b497c44b653a7d737d15f9708aef8d9370f31 |
"""
This module provides classes and functions for pass management.
There are two kinds of passes: transformations and analysis.
* ModuleAnalysis, FunctionAnalysis and NodeAnalysis are to be
subclassed by any pass that collects information about the AST.
* gather is used to gather (!) the result of an an... | artas360/pythran | pythran/passmanager.py | Python | bsd-3-clause | 5,987 | [
"VisIt"
] | bc6e1d1ab249d1b8449127ceb2cddb8c2b31fa74819bd72a4bbbae095e1c846a |
# coding: utf-8
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>,
# <d.desvillechabrol@gmail.com>
#
# Distributed under the terms of the 3-clause BSD license.
# The full licen... | sequana/sequana | sequana/modules_report/coverage.py | Python | bsd-3-clause | 27,762 | [
"Gaussian"
] | d454ce0f8e33918565eb7149579856a63444c19d26397f838ca67491323c2a05 |
"""Test automagical calculation of wfs"""
import os
import sys
import time
from gpaw import GPAW
from ase import Atom, Atoms
from gpaw.test import equal
from ase.parallel import rank, barrier, size
txt=None
ending = 'gpw'
restart = 'gpaw-restart.' + ending
# H2
H = Atoms([Atom('H', (0, 0, 0)), Atom('H', (0, 0, 1))])... | qsnake/gpaw | gpaw/test/wfs_auto.py | Python | gpl-3.0 | 689 | [
"ASE",
"GPAW"
] | 8a9c75f56749590107e4007dd97bcf9c78e7b21ad5eea796fdec6f6b3f23a240 |
"""
##########################################################################
#
# 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-initial | dev/plugins/mesh_netcdf/scripts/PreMeshingFunctions.py | Python | lgpl-2.1 | 7,137 | [
"NetCDF"
] | 9a429e635ea2fa0d588033759eeb616ee584df247369250c2724694e63c4361a |
from django.core.management.base import BaseCommand, CommandError
from django.conf import settings
from django.db import connection
from django.db.models import Q
from build.management.commands.build_human_proteins import Command as BuildHumanProteins
from residue.functions import *
from structure.functions import Bla... | cmunk/protwis | build/management/commands/build_other_proteins.py | Python | apache-2.0 | 12,938 | [
"BLAST"
] | a097b25bf5eb121a2a90e2a94978aae6f560fc2aa197ac400b63c7b7bb61e6ad |
# -*- coding: utf-8 -*-
"""
morphsnakes
===========
This is a Python implementation of the algorithms introduced in the paper
Márquez-Neila, P., Baumela, L., Álvarez, L., "A morphological approach
to curvature-based evolution of curves and surfaces". IEEE Transactions
on Pattern Analysis and Machine Intelligence... | braysia/CellTK | celltk/utils/morphsnakes.py | Python | mit | 11,905 | [
"Mayavi"
] | e354a61841f7572a52e28568a32c475b816a43861ce6734d2027f1d9c4ad2264 |
import sys,os,unittest
from lammps import PyLammps
class PythonPyLammps(unittest.TestCase):
def setUp(self):
machine = None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
self.pylmp = PyLammps(name=machine, cmdargs=['-nocite', '-log','none', '... | jeremiahyan/lammps | unittest/python/python-pylammps.py | Python | gpl-2.0 | 5,280 | [
"LAMMPS"
] | ae9811890fa7640e1bb3c0c61ab404b5f05d9699f647ec50bd09ac9b73c580bd |
from mumax2 import *
from math import *
from mumax2_geom import *
# Test for LLB with 2TM
# Ni, just like in PRB 81, 174401 (2010)
Nx = 64
Ny = 64
Nz = 4
sX = 640e-9
sY = 640e-9
sZ = 20e-9
hsX = 0.5 * sX
hsY = 0.5 * sY
hsZ = 0.5 * sZ
csX = sX/Nx
csY = sY/Ny
csZ = sZ/Nz
setgridsize(Nx, Ny, Nz)
setcellsize(csX, c... | mumax/2 | tests/heat-demag.py | Python | gpl-3.0 | 2,910 | [
"Gaussian"
] | 1b027f119d044a938fa6cac5947c10f97ee810d5fda63cdaddb702da03173aae |
""" DIRAC.Resources.Catalog.test package """
| calancha/DIRAC | Resources/Catalog/test/__init__.py | Python | gpl-3.0 | 45 | [
"DIRAC"
] | 120034d717e972902df3a52bc9cc6ba4075569f26e98ad7311fa8a451c1c063a |
#!/usr/bin/env python
"""
Implement classes for several Path loss models.
The :class:`PathLossBase` class implements the common code to every path loss model and
only two methods need to be implemented in subclasses: the
:meth:`PathLossBase.which_distance_dB` and the
:meth:`PathLossBase._calc_deterministic_path_loss_d... | darcamo/pyphysim | pyphysim/channels/pathloss.py | Python | gpl-2.0 | 53,936 | [
"Gaussian"
] | c246890b7e799a5a1a3e6429f51a3aa9da87ac3e701cb609e3fb02457037db1a |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/share/psi4/databases/HTBH.py | Python | lgpl-3.0 | 38,462 | [
"Psi4"
] | fbf9c23d82ec964574705e3132179dc9c513d4b3fe6d58842ba06de77b0e4498 |
"""
:mod: FTS3ManagerHandler
.. module: FTS3ManagerHandler
:synopsis: handler for FTS3DB using DISET
Service handler for FT3SDB using DISET
"""
__RCSID__ = "$Id$"
import json
# from DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.DISET.RequestHandler import RequestHandler, getServiceOption
from ... | andresailer/DIRAC | DataManagementSystem/Service/FTS3ManagerHandler.py | Python | gpl-3.0 | 4,636 | [
"DIRAC"
] | 9f240679ad76da42cd9ac85978e2eec9c6f8ebbae072fa015ba120ef19421f72 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2012-2013 Esteban Tovagliari, Jupiter Jazz Limited
# Copyright (c) 2014-2018 Esteban Tovagliari, The appleseedhq Organization
#
# ... | est77/appleseed | src/appleseed.python/logtarget.py | Python | mit | 2,861 | [
"VisIt"
] | f850f4622cd1722c03038bc76206cd07e93e82f348e2867fdb792ed4fc57f9c0 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Denominator.slug'
db.add_column(u'profiles_denominator', 'slug', self.gf('django.db.models... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0076_auto__add_field_denominator_slug.py | Python | mit | 23,934 | [
"MOE"
] | dd77ec8eac9c277c6578ae965c9ab0cdaf5011be2ab95b281ff6ae08a8aa7b76 |
import math
import numpy
import logging
import scipy.stats
from atnr import constants
from atnr.util import Profile
from skimage import filter
from skimage import measure
from skimage import transform
from skimage import morphology
# abstractions
class BaseOperation(object):
__abstract__ = True
__inputs__ ... | kevinjdolan/Automated-Tail-Number-Recognition | atnr/operations.py | Python | mit | 19,796 | [
"Gaussian"
] | 9c787e51aa66313cfb6dcbe2f997e07cc01c8a6314c78475d9bcadc423233b0a |
from __future__ import unicode_literals
import json
import django
from django.test import TransactionTestCase
from rest_framework import status
from mock import patch
import util.rest as rest_util
from rest_framework.test import APITransactionTestCase
from util import rest
class TestQueueScaleBakeView(APITransacti... | ngageoint/scale | scale/diagnostic/test/test_views.py | Python | apache-2.0 | 4,708 | [
"CASINO"
] | 274a6ae4dad6327eee5d0226aa20b81553298681584c10b2cda74be700769426 |
#!/usr/bin/env python
"""
Creates a mpileup file from a bam file and a reference.
usage: %prog [options]
-p, --input1=p: bam file
-o, --output1=o: Output pileup
-R, --ref=R: Reference file type
-n, --ownFile=n: User-supplied fasta reference file
-d, --dbkey=d: dbkey of user-supplied file
-x, --index... | maxplanck-ie/Megamapper | mpileup_VCF.py | Python | bsd-3-clause | 13,822 | [
"BWA",
"Galaxy"
] | 03c24d2720979da1f120ebc7b08c9a1c53dab3f112b6af84f1964ec6f5215145 |
#!/usr/bin/env python
# test_cursor.py - unit test for cursor attributes
#
# Copyright (C) 2010-2011 Daniele Varrazzo <daniele.varrazzo@gmail.com>
#
# psycopg2 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 Foun... | KrzysztofStachanczyk/Sensors-WWW-website | www/env/lib/python2.7/site-packages/psycopg2/tests/test_cursor.py | Python | gpl-3.0 | 21,326 | [
"GULP"
] | b76da815eb8d93229a459dea354a8d4dc6b94f4cf926fc7c9db47aee1e43991d |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-03-08 18:08:34
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-08-14 18:10:06
from __future__ import print_function, division, absolute_import
import pytest
import os
i... | albireox/marvin | python/marvin/tests/core/test_config.py | Python | bsd-3-clause | 8,038 | [
"Brian"
] | dcb60aa0c34987394dad165d8cb9436e37919d053e4d8c423cad90cb0639928d |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | CodeMonkeyJan/hyperspy | hyperspy/io.py | Python | gpl-3.0 | 20,171 | [
"NetCDF"
] | 01ca96892a11295d855ee89a37acbcae7df7713d930ff72f79240b2ddfc9894d |
""" JobPolicy encapsulates authorization rules for different groups
with respect to job related operations
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Security import Properties
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import (
getUsernameForDN,
getGroupsForUser,
getProper... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Service/JobPolicy.py | Python | gpl-3.0 | 8,250 | [
"DIRAC"
] | 55b9087649646ce701690cf0139c951a5dce1aa85fdd2a27823e4218e473685f |
# Copyright 2013-2021 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 RGenemeta(RPackage):
"""MetaAnalysis for High Throughput Experiments
A collection ... | LLNL/spack | var/spack/repos/builtin/packages/r-genemeta/package.py | Python | lgpl-2.1 | 1,131 | [
"Bioconductor"
] | baea87c610c56f344e4cfe8f296465f43a2cb2bcb050a425f2498ff5a46325d9 |
# -*- coding: utf-8 -*-
# AwesomeTTS text-to-speech add-on for Anki
# Copyright (C) 2010-Present Anki AwesomeTTS Development Team
#
# 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 versi... | AwesomeTTS/awesometts-anki-addon | __init__.py | Python | gpl-3.0 | 2,336 | [
"VisIt"
] | 220b8eb77112403a024342f7f68f4a489d508ac7ba10f71a03d68f871f4a800b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup
import os
import subprocess
from setuptools.command import easy_install
def parse_requirements(filename):
return list(filter(lambda line: (line.strip())[0] != '#',
[line.strip() for line in open(filename).readlines()... | gersolar/goesdownloader | setup.py | Python | mit | 2,849 | [
"NetCDF"
] | e8a50827191b1c02b60d41fa39454b31535329df0ce3ca351d3f7678467a448c |
#!/usr/bin/env python
# for python 2 / 3 compatibility
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
try :
range = xrange
except NameError :
pass
import phasing_3d
def config_iters_to_alg_num(string):
... | andyofmelbourne/crappy-crystals | utils/phase_new.py | Python | gpl-3.0 | 2,099 | [
"CRYSTAL"
] | c9aebed917faaf421f475b4d948ecd6bda374318a9df6fa283ef0b5da4d2ec65 |
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import cv2
import sys
np.set_printoptions(threshold=np.nan)
try:
image = mpimg.imread('test.jpg')
except FileNotFoundError as e:
print(e)
sys.exit(1)
gray = cv2.cvtColor(image, cv2.COLOR_RGB2GRAY) # 8-bit image
kernel_s... | akshaybabloo/Car-ND | Term_1/Finding_Lane_Lines_1/5_hough_transform_masked.py | Python | mit | 2,555 | [
"Gaussian"
] | 55b8c447b7f7c07c0b09bf0a50265899a4a7076639ac9d440fa4250285c24208 |
# -*- coding: utf-8 -*-
import logging
import os
import re
import socket
import sys
import time
from django.conf import settings
from django.core.management.base import BaseCommand, CommandError
from django.db import connections, DEFAULT_DB_ALIAS
from django.db.backends import utils
from django.db.migrations.executor ... | neilpelow/wmap-django | venv/lib/python3.5/site-packages/django_extensions/management/commands/runserver_plus.py | Python | gpl-3.0 | 18,650 | [
"VisIt"
] | d4cc5050adef6d410499dd36830d4c75d49acd72ac539bb34926ffb0eccb1b12 |
#!/usr/bin/env python
# coding=utf-8
# ly2video - generate performances video from LilyPond source files
# Copyright (C) 2012 Jiri "FireTight" Szabo
# Copyright (C) 2012 Adam Spiers
# Copyright (C) 2014 Emmanuel Leguy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the ... | algomus/ly2video | ly2video.py | Python | gpl-3.0 | 55,502 | [
"VisIt"
] | 0e7fbb2219322185679b233eb078d781526884ca72ca512e64cc5e10a2810041 |
import itertools
from sqltxt.column import ColumnName
from sqltxt.util import PriorityContainer, Queue
def plan(tables, join_conditions, where_conditions):
"""Given a list of tables and a list of conditions across those tables, return a list
of relation indices in an optimized join order."""
graph = build... | shahin/sqltxt | sqltxt/plan.py | Python | mit | 2,787 | [
"VisIt"
] | 29bbed1f137c20cf404f69c1eb61af7da7329ee99c5536bee027cdf25bfe093e |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.core import Structure
from pymatgen.util.string import (
disordered_formula,
formula_double_format,
charge_string,
htmlify,
latexify,
latexify_spacegroup,
transformat... | vorwerkc/pymatgen | pymatgen/util/tests/test_string.py | Python | mit | 4,743 | [
"pymatgen"
] | 7ccdca2306509cf37f1d97d8357859880a0dab4788d35956bee71d9ad1f3178f |
# -*- coding: utf-8 -*-
"""
***************************************************************************
dataobject.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
****************************... | pavlova-marina/QGIS | python/plugins/processing/tools/dataobjects.py | Python | gpl-2.0 | 15,508 | [
"NetCDF"
] | 369c38cc44c648385d1a14ffe3595ac5ef46c14a7eb2e1314e2587369a6c92d8 |
# -*- coding: utf-8 -*-
__author__ = 'Olivier Mangin <olivier.mangin@inria.fr>'
__date__ = '02/2011'
"""One dimensional kernel density estimation.
"""
import numpy as np
from scipy import convolve as convolve_1d
from scipy.integrate import trapz
from scipy.signal import fftconvolve
def get_bins_1d(x, nb_bins, bo... | omangin/multimodal | multimodal/lib/kde1d.py | Python | bsd-3-clause | 5,423 | [
"Gaussian"
] | bb55dff094f7c440acf4def57374381956df472bb76f6c3316ac164e09f358cd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import logging
import math
import itertools
import warnings
from collections import OrderedDict
import six
import numpy as np
from monty.json ... | nisse3000/pymatgen | pymatgen/electronic_structure/plotter.py | Python | mit | 183,163 | [
"BoltzTrap",
"CRYSTAL",
"Gaussian",
"Mayavi",
"VASP",
"pymatgen"
] | 692fb753e1343a6301d2e516f934b39e5a43342eefee0ea25ddc899576e48180 |
##
## Draw gene structure from a GFF file
##
import os, sys, operator, subprocess
import math
import pysam
import glob
from pylab import *
from matplotlib.patches import PathPatch
from matplotlib.path import Path
import misopy
import misopy.gff_utils as gff_utils
import misopy.sam_utils as sam_utils
from misopy.sash... | kdaily/altanalyze | misopy/sashimi_plot/plot_utils/plot_gene.py | Python | apache-2.0 | 29,067 | [
"pysam"
] | 80c39b0cdc6a1a4480bcff7535c802492de4b39316e714a8a0b4e4857b26cff8 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 153,845 | [
"Gaussian"
] | a00143dff679180d803fd11c0e2ad90a13da57f09063212cce96f5663c8ee0f1 |
"""
API for initiating and tracking requests for credit from a provider.
"""
import datetime
import logging
import uuid
import pytz
from django.db import transaction
from lms.djangoapps.django_comment_client.utils import JsonResponse
from edx_proctoring.api import get_last_exam_completion_date
from openedx.core.djan... | Learningtribes/edx-platform | openedx/core/djangoapps/credit/api/provider.py | Python | agpl-3.0 | 16,211 | [
"VisIt"
] | bbab55b1f561b4ea6daa74fdf2fec75457927116e29f45e43cdf2d29251178c0 |
# Author: David Goodger
# Contact: goodger@users.sourceforge.net
# Revision: $Revision: 4242 $
# Date: $Date: 2006-01-06 00:28:53 +0100 (Fri, 06 Jan 2006) $
# Copyright: This module has been placed in the public domain.
"""
Parser for Python modules. Requires Python 2.2 or higher.
The `parse_module()` function takes... | alon/polinax | libs/external_libs/docutils-0.4/docutils/readers/python/moduleparser.py | Python | gpl-2.0 | 25,842 | [
"CRYSTAL",
"VisIt"
] | 01580bcb3e380742086f9d07f13fd95db982d94d25d7bb8b7ab6c0242fac7e55 |
# coding=utf-8
# Copyright 2022 The TensorFlow Datasets 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 appl... | tensorflow/datasets | tensorflow_datasets/image_classification/cars196.py | Python | apache-2.0 | 12,364 | [
"Jaguar"
] | 378463d9ec40f936de1c4ba69056a87eae06f51b0c15c5577f649f572064cf27 |
import itertools
import unittest
from nose.tools import assert_true
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_raises)
from scipy import stats
from sklearn import mixture
from sklearn.datasets.samples_generator import make_spd_matrix
... | mrshu/scikit-learn | sklearn/mixture/tests/test_gmm.py | Python | bsd-3-clause | 12,398 | [
"Gaussian"
] | 371ac46cce38eadb1334680773a448c814731a41f90d0e2f61c6246a1cb57493 |
#!/usr/bin/env python
import pyemma
import numpy as np
import mdtraj
import os
# Source directory
source_directory = '/cbio/jclab/projects/fah/fah-data/munged/no-solvent/10471'
################################################################################
# Load discrete trajectories
##############################... | choderalab/MSMs | jchodera/src-10471/pyemma/analyze.py | Python | gpl-2.0 | 732 | [
"MDTraj"
] | 820b02f1a6360a5903b7145eb75ac8d116daa601b6f8884ad179b27615f5f716 |
#!/usr/bin/env python3
import cherrypy
from cherrypy import tools
import cherrypy_cors
from jinja2 import Environment, FileSystemLoader
import os
from collections import namedtuple, defaultdict
import json
import gzip
import numpy as np
import glob
import math
import argparse
from sqlalchemy import func, and_, or_
fr... | baliga-lab/cmonkey2 | cmonkey/cmviewer/webapp.py | Python | lgpl-3.0 | 42,105 | [
"Cytoscape"
] | aedec271cb9c608e123a5307ec1977fccda241bb48d014300623d91cc4653fa6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import json
import os
import sys
from pathlib import PurePath # nueva forma de trabajar con rutas
import requests
# Confirmamos que tenemos en el path la ruta de la aplicacion, para poder lanzarlo desde cualquier ruta
absolut_path: PurePath = PurePath(os.path.realpath(... | procamora/Gestor-Series | app/utils/telegram2.py | Python | gpl-3.0 | 4,146 | [
"ASE"
] | ba4564267482eda37d4e0d6027011ab32854b407e3da007ae47529a1127f4439 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/procrouting/findif_response_utils/data_collection_helper.py | Python | lgpl-3.0 | 4,173 | [
"Psi4"
] | 69841b24f77d6cec2e6c270de54a8d8c6743730f4a5f7b920615af357902b853 |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright (C) 2014, 2020 Dave Hocker
#
# 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, version 3 of t... | dhocker/athomepowerlineserver | commands/ActionFactory.py | Python | gpl-3.0 | 2,164 | [
"xTB"
] | 6a703ac0dda9cf681eb1f36894044098cab3ba43144d321b57be54f360dc86a9 |
import pytest
from graphapi.schema import schema
from openstates.data.models import Bill, Person
from .utils import populate_db
@pytest.mark.django_db
def setup():
populate_db()
@pytest.mark.django_db
def test_bill_by_id(django_assert_num_queries):
with django_assert_num_queries(17):
result = schema... | openstates/openstates.org | graphapi/tests/test_legislative.py | Python | mit | 22,303 | [
"MOOSE"
] | 278362a65a4588007b5c28abeb9f4831a456582ed3c71dc02be89ff85018e4a8 |
# (c) 2014 Michael DeHaan, <michael@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, or
# (at your option) any later ve... | ownport/ansiblite | src/ansiblite/playbook/role/metadata.py | Python | gpl-3.0 | 4,251 | [
"Galaxy"
] | c110cd06a93f13b1ae62399bdc5f4b0c7f27c2390ceff705968fe1fd3f1f7986 |
#Fits an emission ine with a Gaussian and returns the amplitude, standard deviation, and continuum line
#Usage: run FitEmission.py 'a6' 4861 to fit the lines at rest wavelengths 6563 (Ha) for the a6 mask.
#Typing run FitEmission.py 'a6' 'HaNII' will fit all three lines around Ha simulaaneously
import nump... | brianlorenz/COSMOS_IMACS_Redshifts | Emission_Fitting/FitEmission_MosaicByUsig.py | Python | mit | 41,785 | [
"Galaxy",
"Gaussian"
] | c48ebc5347bee58e08a65ea335d229b0af29b83719fe98cec842829dbc2dee37 |
import numpy as np
from numpy.random import default_rng, SeedSequence
class StochasticProcess(object):
"""
This is a base (parent) class for all the stochastic process models.
"""
__slots__ = ("xt", "tk", "rand_g", "single_dimension")
def __init__(self, r_seed=None, single_dim=True):
"""... | vrettasm/VGPA | code/dynamics/stochastic_process.py | Python | gpl-3.0 | 6,335 | [
"Gaussian"
] | f7f45f1660241a7b509a60ce8333b51b7e97ebdab1f7b6d9e736ad531f31b142 |
"""Reconstruct subclones and phylogenetic history using PhyloWGS.
PhyloWGS uses phylogenetic histories inferred through Battenberg CNV calls
along with variant frequencies.
https://github.com/morrislab/phylowgs
http://genomebiology.com/2015/16/1/35
"""
from __future__ import print_function
import collections
import o... | a113n/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | Python | mit | 12,141 | [
"pysam"
] | b59eeefb7b14d595b2f814f5534be51bc1a401b18a3403686fabbf04cd234e5e |
from django.test import TestCase
from django.core.urlresolvers import resolve
#from annotations.views import home
from annotations.models import Annotation, AnnotationShareMap
from django.contrib.auth.models import User
from django.contrib.contenttypes.models import ContentType
from django.contrib.contenttypes import... | PirateLearner/annotations | annotations/tests.py | Python | gpl-2.0 | 12,613 | [
"VisIt"
] | b8074940ddcd5fb7d98fba7b45cb3f66ab709dddab81d6057bfb34e4af9b52e7 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.metrics.pairwise` submodule implements utilities to evaluate
pairwise distances, paired distances or affinity of sets of samples.
This module contains both distance metrics and kernels. A brief summary is
given on the two here.
Distance metrics are a function d(a, b) such... | treycausey/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 42,965 | [
"Gaussian"
] | e02a864f31310e30e66557ca4456f8bdebeb5a0f6b310e99bd9c26296923fd17 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
========================================================================
Gaussian Processes regression: goodness-of-fit on the 'diabetes' dataset
========================================================================
This example consists in fitting a Gaussian Process m... | joshbohde/scikit-learn | examples/gaussian_process/gp_diabetes_dataset.py | Python | bsd-3-clause | 2,011 | [
"Gaussian"
] | 028794026ffeedca0cfce093a3f18832a1e17063dc3415fb71534c84d537ee13 |
from kalliope.core.NeuronModule import NeuronModule, MissingParameterException
class Say(NeuronModule):
def __init__(self, **kwargs):
super(Say, self).__init__(**kwargs)
self.message = kwargs.get('message', None)
self.file_template = kwargs.get('file_template', None)
self.parameter... | kalliope-project/kalliope | kalliope/neurons/say/say.py | Python | gpl-3.0 | 1,086 | [
"NEURON"
] | 3d1beb928733c2f7ea03d8d9c77929e09e2c99e1882b387190a120b722f7a021 |
from rdkit import Chem
from rdkit.Chem import AllChem
inMols = Chem.SDMolSupplier("diazo.sdf")
inMols = Chem.SDMolSupplier("phosphine.sdf")
inMols = Chem.SDMolSupplier("nitro.sdf")
#rxn = AllChem.ReactionFromSmarts('[C:1]=[O,N:2]>>[C:1][*:2]')
#rxn = AllChem.ReactionFromSmarts('[S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:... | JonnaStalring/AZOrange | tests/standardizationTestSuite/testRxns.py | Python | lgpl-3.0 | 1,191 | [
"RDKit"
] | 95e3fff307cc7a39e91be6aede7b36340165acacf042ccb11b87452af5380936 |
import numpy as np
from math import exp, sqrt
from ase.calculators.lj import LennardJones
class MorsePotential(LennardJones):
"""Morse potential.
Default values chosen to be similar as Lennard-Jones.
"""
default_parameters = {'epsilon': 1.0,
'rho0': 6.0,
... | alexei-matveev/ase-local | ase/calculators/morse.py | Python | gpl-2.0 | 1,126 | [
"ASE"
] | 9dbc30d7a532d7624ecd0f8e5a64525eb53c53c51fa259febc2ba4a22bf4c088 |
# -*- coding: utf-8 -*-
"""
Write EC and SMC Meshes in legacy VTK format as .vtk.
"""
import os
import sys
# Run in current directory.
# os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Relative import path for the DumpMeshToLegacyFormat script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file_... | BlueFern/DBiharMesher | meshes/c4080Pulsatile/Dump4080MeshLegacyFormat.py | Python | gpl-2.0 | 895 | [
"VTK"
] | 6190b97677f8841df64c8fa1320c1008a7eb7203244941d05f4391bc34dc7662 |
#!/usr/bin/env python
# Copyright 2014-2019 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/pbc/scf/uhf.py | Python | apache-2.0 | 8,724 | [
"PySCF"
] | add9f8929c3a3dd55a7316f125d84768468316de632dca420e93ffd391fa5751 |
from .common import NetCDF4, expects_file_info
__all__ = [
'OceanRAIN',
]
class OceanRAIN(NetCDF4):
"""File handler that can read data from OceanRAIN NetCDF4 files.
This object handles OceanRAIN V1.0 NetCDF4 files such as they are
compatible with :mod:`typhon.collocations`, i.e.:
* rename *lati... | atmtools/typhon | typhon/files/handlers/ocean_rain.py | Python | mit | 3,663 | [
"NetCDF"
] | ca353c315137771df43720fe87bc763c387ce75f40738fb064f168a694baec64 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright (c), 2016-2017, Quantum Espresso Foundation and SISSA (Scuola
# Internazionale Superiore di Studi Avanzati). All rights reserved.
# This file is distributed under the terms of the LGPL-2.1 license. See the
# file 'LICENSE' in the root directory of the present... | QEF/postqe | postqe/api.py | Python | lgpl-2.1 | 7,867 | [
"ASE",
"ESPResSo",
"Gaussian",
"Quantum ESPRESSO"
] | 98b3e211b9fc3089e1af77eed620de63223e74b3f12a361a6061a1a1b2f673e1 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Patient.regiment'
db.add_column('core_patient', 'regiment', self.gf('django.db.models.fiel... | praekelt/txtalert | txtalert/core/migrations/0010_auto__add_field_patient_regiment__add_field_historicalpatient_regiment.py | Python | gpl-3.0 | 14,473 | [
"VisIt"
] | 6a9be8eb336c61f1ea934adfaffc57f5174caad702f946364a96cd066b7c0017 |
import logging
import re
from pycpt.build_visitor import BuildVisitor
import x11colors
logger = logging.getLogger('pycpt.cpt_reader')
from pycpt.ast import (CommentNode, CategoryNode, RGBColorNode, HSVColorNode,
CMYKColorNode, IntervalSpecNode)
FLOAT_PATTERN = r'([-+]?[0-9]*\.?[0-9]+([eE][-+]?... | rob-smallshire/pycpt | pycpt/cpt_reader.py | Python | mit | 8,793 | [
"VisIt"
] | 64ef060c2370e3411f995fbcb782dd0c55a156ffaf8c6ae17d2c48116b4db6f8 |
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