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# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from datetime import datetime
import os
from unittest import TestCase
from django.utils import html, safestring
from django.utils._os import upath
from django.utils.encoding import force_text
class TestUtilsHtml(TestCase):
def check_output(self, f... | errx/django | tests/utils_tests/test_html.py | Python | bsd-3-clause | 7,061 | [
"ADF"
] | 779ca181af51742c25d2dc9842f8bd1169af978918e84629c9b4321e927d3be3 |
from __future__ import division
import abc
import numpy as np
from menpo.transform import Scale, AlignmentAffine
from menpo.fitmultilevel.functions import noisy_align, align_shape_with_bb
from .algorithm import (StandardAAMInterface, LinearAAMInterface,
PartsAAMInterface, AIC_GN)
from .result ... | jalabort/ijcv-2014-aam | aam/fitter.py | Python | bsd-2-clause | 15,070 | [
"Gaussian"
] | 9b10d517da3978e8ee77aaf55599ba91bd5752b96005ad6eb305cb9b4b2a627e |
from property import *
# Layer GLu GABA
L1_ratio = (8, 0) #only glu
L2_ratio = (16, 4)
L3_ratio = (32, 0) #only glu
L4_ratio = (26, 6)
L5_ratio = (42, 0) #only glu
L6_ratio = (74, 0) #only glu
# Neuron number in layer
L1_NN = GlobalColumns * sum(L1_ratio)
L2_NN = GlobalColumns * sum(L2_ratio)
L3_NN = GlobalC... | research-team/NEUCOGAR | NEST/visual/association/scripts/data.py | Python | gpl-2.0 | 2,489 | [
"NEURON"
] | 9ae234ab0f27f3b0cfe26c9a7449b3192794eccea839ab5f58d5eb7f18bebfa0 |
"""
Statistics (:mod:`skbio.stats`)
===============================
.. currentmodule:: skbio.stats
This package contains various statistical methods, including ordination
techniques and distance matrix-based statistics.
Subpackages
-----------
.. autosummary::
:toctree: generated/
distance
evolve
ordin... | gregcaporaso/scikit-bio | skbio/stats/__init__.py | Python | bsd-3-clause | 919 | [
"scikit-bio"
] | ead30529b5ecd61690ab4d15f128f217880a4af5257d3730731f9b9cc10e3fd2 |
from ase import *
from gpaw.atom.all_electron import AllElectron
from gpaw.test import equal
data = []
def out(a,b,c,d,e,f):
data.append( (a,b,c,d,e,f) )
ETotal = {'Be': -14.572+0.012, 'Ne': -128.548 -0.029, 'Mg': -199.612 - 0.005 }
EX = {'Be': -2.666 - 0.010, 'Ne': -12.107 -0.122, 'Mg': -15.992 -0.092 }
EHOMO = ... | robwarm/gpaw-symm | gpaw/test/gllbatomic.py | Python | gpl-3.0 | 1,508 | [
"ASE",
"GPAW"
] | e6c4594ce08a16677a84c3f6b6957332be2e14849b407f1cdab6af37612dbb02 |
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Autodesk/molecular-design-toolkit | moldesign/molecules/molecule.py | Python | apache-2.0 | 45,660 | [
"GAMESS"
] | fe9cca4ad918565c269f7f7f0496c7af649e9ce3615bb827c5aad8397e13c6f1 |
#
# Adrian Soto
# 22-12-2014
# Stony Brook University
#
################################################
# Plot band structure and DOS from the
# output of the bands.x program in the
# Quantum Espresso package.
#
# Features:
# 1) Allows for scissor correction (band shift)
# 2)
#
###################################... | adrian-soto/QEdark_repo | tools/bandsndos/bandsndos_mirror.py | Python | gpl-2.0 | 20,068 | [
"Quantum ESPRESSO"
] | 6e5284327526cd5e125e056e57f35a95ddaa7735bfdb16ff783fc5be26bc2c44 |
# Copyright (c) 2006-2013 Regents of the University of Minnesota.
# For licensing terms, see the file LICENSE.
import datetime
import os
import sys
import time
import conf
import g
from grax.user import User
from item import item_user_access
from item.attc import post
from item.attc import thread
from item.feat impo... | lbouma/Cyclopath | pyserver/item/util/watcher_composer.py | Python | apache-2.0 | 26,320 | [
"VisIt"
] | 2fd0876e3fd55f8cec30beadef2170610cbac44b81c37545e6aad436e3ef4d7d |
class HelpMessage():
'''Carriers the help message that is available
to all classes
'''
help_message ="""
You should use the following commands ONLY:
\n\t 1. pomodoro create*<title>
\n\t 2. pomodoro config_time*<day:hrs:min:sec>
\n\t 3. pomodoro config_shortbreak*<hrs:min:... | Migwi-Ndungu/bc-9-Pomodoro-Timer | helpmessage.py | Python | mit | 760 | [
"VisIt"
] | e386e2e04936b436c194c2b32e80afd466018eb7fc5967d98d7ed75c76a14cc2 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import (
UniqueCourseTest,
EventsTestMixin,
... | rismalrv/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 46,640 | [
"VisIt"
] | 6b9cf55bc2a01b0ee927508aefc81da1485a5df5da7a9289eca65cefd1848fee |
# -*- coding: utf-8 -*-
'''
pyqz: a Python module to derive the ionization parameter and oxygen abundance of HII
regions, by comparing their strong emission line ratios with MAPPINGS photoionization
models.\n
Copyright (C) 2014-2016, F.P.A. Vogt
----------------------------------------------------------------... | fpavogt/pyqz | pyqz/pyqz_plots.py | Python | gpl-3.0 | 24,483 | [
"Gaussian"
] | 1497f5c02b0b9e20985a42d8212284124e2e6b0b4ee439019a2dc565dd354fda |
import numpy as np
from ase import Atom, Atoms
from ase.units import Hartree
from gpaw.mpi import size
from gpaw import GPAW
from gpaw.response.bse import BSE
GS = 1
bse = 1
casida = 1
compare = 1
if GS:
d = 2.89
cluster = Atoms([Atom('Na', (0, 0, 0)),
Atom('Na', (0, 0, d)),
... | ajylee/gpaw-rtxs | gpaw/test/bse_vs_lrtddft.py | Python | gpl-3.0 | 1,334 | [
"ASE",
"GPAW"
] | 35fd762368672cd5b60eb812d91d96f9f850798368b93d5a970c35fffd9dadf1 |
# region gplv3preamble
# The Medical Simulation Markup Language (MSML) - Simplifying the biomechanical modeling workflow
#
# MSML has been developed in the framework of 'SFB TRR 125 Cognition-Guided Surgery'
#
# If you use this software in academic work, please cite the paper:
# S. Suwelack, M. Stoll, S. Schalck, N.Sch... | CognitionGuidedSurgery/msml | src/msml/exporter/sofanew.py | Python | gpl-3.0 | 37,859 | [
"VTK"
] | 1260dd984c7e61c21277a9b2114dfd5389e3d1e79fc20e9c8a04dedb79207b3f |
"""Implementation of magic functions for interaction with the OS.
Note: this module is named 'osm' instead of 'os' to avoid a collision with the
builtin.
"""
from __future__ import print_function
#-----------------------------------------------------------------------------
# Copyright (c) 2012 The IPython Developmen... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/IPython/core/magics/osm.py | Python | gpl-3.0 | 26,581 | [
"VisIt"
] | 42fc9ef0959ecce6b60cc6eaba8e88108a42763d96a10290f6cb90e4410e6f60 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/advancedtab.py | Python | gpl-2.0 | 41,706 | [
"Brian"
] | 1bab28d439d093228a1cb22fd520db67ad0a18c9cad88dfda0a2ab91a887d86d |
"""
ROHF
"""
import numpy as np
import scipy.linalg as slg
from frankenstein.sgscf import rhf, sgopt
from pyscf import scf
from pyscf.lib import logger
""" Methods for initialization
"""
def get_init_guess_DC(mf, dm0=None, mo_coeff0=None):
if mo_coeff0 is None:
raise ValueError("For ROHF, initial gues... | hongzhouye/frankenstein | sgscf/rohf.py | Python | bsd-3-clause | 23,828 | [
"MOE",
"PyMOL",
"PySCF"
] | 8f87307d12bdf9f6a60d8c321c23fe3975aaf4d1b8549bbc116f2cd500208b9f |
# -*- coding: utf-8 -*-
# $Id: manpage.py 6378 2010-07-12 19:30:24Z grubert $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module is put into the public domain.
"""
Simple man page writer for reStructuredText.
Man pages (short for "manual pages") contain system documentation on unix-li... | MichaelNedzelsky/intellij-community | python/helpers/py2only/docutils/writers/manpage.py | Python | apache-2.0 | 33,845 | [
"VisIt"
] | cb152b7c8aafeeeb99ab9f79a20a6864e60ea7cb9b3e3e510b43549b78e9ae61 |
# (c) 2014, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.... | ramondelafuente/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 3,968 | [
"Brian"
] | 239c34cb859ffe9d11ab15b8e590236e7e7b66a5c7553940aae37caade6ed55e |
#
# Copyright (C) 2010-2019 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# 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... | psci2195/espresso-ffans | doc/tutorials/02-charged_system/scripts/nacl_units.py | Python | gpl-3.0 | 5,816 | [
"ESPResSo"
] | 1d7ac234b8898fda1e17c5b2f57cf4fc4616ee022b1613b8f066d930bf8f977f |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | scipy/scipy | scipy/special/_add_newdocs.py | Python | bsd-3-clause | 293,442 | [
"Gaussian"
] | e3eaab9b3b7330cd6c8b4745bdfe41a548bcff4b4e85f5c2ae6e946c8bc30342 |
"""
Basis Abstract Domain
=====================
Interface of an abstract domain mapping variables to lattice elements.
:Author: Caterina Urban
"""
from abc import ABCMeta
from ast import literal_eval
from copy import deepcopy
from typing import Set, Dict, Type, Any, Union, List
from lyra.abstract_domains.container.i... | caterinaurban/Lyra | src/lyra/abstract_domains/basis.py | Python | mpl-2.0 | 99,669 | [
"VisIt"
] | 3d0290cac1ef286798a457fa60d6bdac6755218d4f54c0900f751318562d098e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/procrouting/__init__.py | Python | lgpl-3.0 | 1,221 | [
"Psi4"
] | 6f3c52bcfadf4640c63bd2e74a97cb881fe104b3eb4b217951fc45ec054bf33b |
#!/usr/bin/env python
import sys
import os.path
from optparse import OptionParser
from scipy.optimize import curve_fit
from numpy import (exp, cos, pi, tri, argsort, asarray, arange, mean, isnan,
zeros, square)
from qiime.parse import parse_distmat
__author__ = "Antonio Gonzalez Pena"
__copyright_... | antgonza/qiime | qiime/plot_semivariogram.py | Python | gpl-2.0 | 5,408 | [
"Gaussian"
] | 934086cfec96f203a7dd02d8d57a91f897771963570fff533fde5e1471d83e90 |
"""
Disclaimer
==========
This software was developed at the National Institute of Standards and Technology at the NIST Center for Neutron Research by employees of the Federal Government in the course of their official duties. Pursuant to title 17 section 105* of the United States Code this software is not subject to ... | bmazin/ARCONS-pipeline | legacy/arcons_control/lib/mpfit.py | Python | gpl-2.0 | 78,881 | [
"Gaussian"
] | 89aaee7fd97f48fbfd4873d348b3b6100993d7200e634a7cd1d92cf8864b9cea |
import os
import csv
import numpy
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from Utils.mixins import ModuleWidgetMixin
#
# NeedleGuideTemplate
#
class NeedleGuideTemplate(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.co... | tokjun/NeedleGuideTemplate | NeedleGuideTemplate/NeedleGuideTemplate.py | Python | bsd-3-clause | 22,110 | [
"VTK"
] | 701efe5630453518eb5748134704524b7163c5088d4be64f64e3fe7bfef8ec4d |
from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.simpleapi import logger
import AbinsModules
class AbinsLoadDMOL3Test(unittest.TestCase, AbinsModules.GeneralLoadDFTTester):
def tearDown(self):
AbinsModules.AbinsTestHelpers.remove_output_files(list_of_names=["... | dymkowsk/mantid | scripts/test/AbinsLoadDMOL3Test.py | Python | gpl-3.0 | 1,017 | [
"DMol3"
] | d7d0d62b2b07520b8755554ffcf1063640030cc63778d0778d380fd3054f3a03 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# Copyright (C) 2001-2008 greg Landrum
#
""" unit testing code for the Stats module
"""
import unittest, sys
from rdkit import RDConfig
from rdkit.ML.Data import Stats
import numpy
FLOAT_TOL = 1e-4
def feq(x, y, tol=FLOAT_TOL):
return abs(x - y... | jandom/rdkit | rdkit/ML/Data/UnitTestStats.py | Python | bsd-3-clause | 5,754 | [
"RDKit"
] | 530ae513dfa86a5d63697c1908c1530b692ead198799a04742cc65915a69ce99 |
#!/usr/bin/env python
"""
filt.py
Functions for quickly filtering time-series of data.
Written by Brian Powell on 02/09/16
Copyright (c)2010--2021 University of Hawaii under the MIT-License.
"""
import numpy as np
import seapy
import scipy.signal
def average_err(x, window=5):
"""
Generate a moving ... | powellb/seapy | seapy/filt.py | Python | mit | 5,197 | [
"Brian"
] | 15abb98c505265e43f586cadb9fa4b8c9e637a817da67d41db7c428c3dae31a0 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
import requests
from monty.os.path import which
from pymatgen.ext.cod import COD
website_is_up = requests.get("https://www.crystallography.net").status_code == 200
@unittest.skipIf(not we... | vorwerkc/pymatgen | pymatgen/ext/tests/test_cod.py | Python | mit | 1,199 | [
"pymatgen"
] | 420fa7d2ebdef30f39257f774e12d149a95b12282296bb65f836d5d5d8211be2 |
#!/usr/bin/env python3
import os
import unittest
import logging
import shutil
import tempfile
import ciftify.config
from ciftify.utils import run
import pytest
from pytest import raises
from unittest.mock import patch
def get_test_data_path():
return os.path.join(os.path.dirname(os.path.dirname(__file__)), 'data')... | edickie/ciftify | tests/functional/test_ciftify_surface_rois.py | Python | mit | 2,519 | [
"Gaussian"
] | 88229b442e7401421806a1829a4646c6e1ad10e099e4a1480f1238622422b439 |
from django.db import transaction
from django.db.models.signals import post_save
from django.dispatch import receiver
from django.utils import timezone
from edc_identifier.subject.classes import InfantIdentifier
from edc_registration.models import RegisteredSubject
from edc_appointment.models.appointment import Appoin... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/models/signals.py | Python | gpl-2.0 | 13,693 | [
"VisIt"
] | 69f2c6dc53fad3a9fc329f6cfea311be940bf49fac23f56d3d101d66adce15db |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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... | googleapis/python-datacatalog | tests/unit/gapic/datacatalog_v1beta1/test_policy_tag_manager_serialization.py | Python | apache-2.0 | 61,491 | [
"Octopus"
] | 930cf643d0b0dbeac81179297673edd2b9f115691197125c7585935d824808b5 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | ThomasYeoLab/CBIG | external_packages/python/yapf-master/yapf/yapflib/split_penalty.py | Python | mit | 24,031 | [
"VisIt"
] | d31584e80fe63b5310493a0b973ace203342b7dd7f7a44d81b58826c998ad4b4 |
#
# 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)... | tbereau/espresso | samples/python/lj_liquid_distribution.py | Python | gpl-3.0 | 7,570 | [
"ESPResSo"
] | 0a3939b723760d3af46671cb7364f7fa532a6b7c7ce8e708ae2cb7225532e57e |
###############################################################################
# Python Script to Combine Fasta or Qual Files Using BioPython
###############################################################################
# Written by Mario Muscarella
# Last Update 25 Apr 2013
# Directions:
# use the following comma... | mmuscarella/StarvationTraits | bin/MergeSeqs.py | Python | gpl-3.0 | 750 | [
"Biopython"
] | 6febcf3f2c2ffee770aeb0f3dc7b5867e49781775a359134463a620b9ac59382 |
#
# Copyright (C) 2008, Brian Tanner
#
#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 requ... | pclarke91/rl-glue-ext | projects/codecs/Python/src/tests/test_1_agent.py | Python | apache-2.0 | 1,831 | [
"Brian"
] | 31e7775917d1ead6368f41ffaf08b397115bb835133a798f0e131b231a99607c |
import copy
from SDWLE.cards.base import SpellCard, MinionCard
from SDWLE.cards.minions.priest import ShadowOfNothing
from SDWLE.cards.minions.neutral import Lightwarden
from SDWLE.tags.base import BuffUntil, Buff
from SDWLE.tags.event import TurnEnded
from SDWLE.tags.status import Stolen, SpellDamage
import SDWLE.tar... | jomyhuang/sdwle | SDWLE/cards_copy/spells/priest.py | Python | mit | 11,872 | [
"BLAST"
] | f892b6234f82a113b09ac06ca9146c8032f748b24e0f2a9bde16c1aa6548be6e |
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
# create a new 'XML Unstructured Grid Reader'
calc_test_node_statsvtu = XMLUnstructuredGridReader(FileName=['/raid/home/ksansom/caseFiles/mri/VWI_... | kayarre/Tools | vtk/paraview_case1_2.py | Python | bsd-2-clause | 32,966 | [
"ParaView"
] | 551a0379cb11bb036e475025afd0e5d082812778f33fc3e800930972077117d2 |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import re
import warnings
import numpy.core.... | WillieMaddox/numpy | numpy/lib/polynomial.py | Python | bsd-3-clause | 38,023 | [
"Gaussian"
] | 1d7c57091aebf2ab7b26d31c2925a41cf9e807f5e76937a1d6a56deea375accd |
#!/usr/bin/python -u
from argparse import Namespace
from gmx_lib import run_setup, gro_and_top, box, water
from gmx_lib import counterions, local_energy_minimum
from gmx_lib import solvent_equilibration, production
from gmx_lib import postproduction
from gmx_lib.run_setup import WorkdirStructure
from gmx_lib.gmx_engi... | ivanamihalek/smallmol | gmx01_core.py | Python | gpl-2.0 | 2,556 | [
"Gromacs"
] | 4e8a5db6558ec0b44f1f3e69194e524280587c5248bdf21c3ff4cd35d8f750af |
# -*- coding: utf-8 -*-
#
# Copyright (C) Pootle contributors.
#
# This file is a part of the Pootle project. It is distributed under the GPL3
# or later license. See the LICENSE file for a copy of the license and the
# AUTHORS file for copyright and authorship information.
import locale
from collections import Ordere... | pavels/pootle | pootle/apps/pootle_language/models.py | Python | gpl-3.0 | 7,470 | [
"VisIt"
] | 2c97920d59e87ec4925d6e088b6da7b5a83ed4dc37c365ea2854a67b190cd7d6 |
import os
import platform
from setuptools import find_packages
from setuptools import setup
import subprocess
import sys
requirements = [
"pycurl",
"pyyaml == 3.10",
"tornado >= 1.1, <2.0",
]
# python-rrdtool doesn't install cleanly out of the box on OS X
# TODO: python-rrdtool not compiling cleanly on l... | Yelp/firefly | setup.py | Python | isc | 1,470 | [
"Firefly"
] | e7803c8c531404064dd23e7e4d8e1735ac9612c8a02a00d0113837224925759b |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/lib/gto/test/test_gridao.py | Python | apache-2.0 | 9,167 | [
"PySCF"
] | 507282388c97caf0f0296d840a4e3b495a8400f40f750e546a6c0b67d80bfc16 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/Switch.py | Python | gpl-3.0 | 7,433 | [
"ORCA"
] | e2960443769e6d2f82b8dff43b327cd18320e58abf5a44de4094dd5d9f15b0f8 |
import numpy as np
from ..core import indexing
from ..core.utils import Frozen, FrozenDict, close_on_error
from ..core.variable import Variable
from .common import (
BACKEND_ENTRYPOINTS,
AbstractDataStore,
BackendArray,
BackendEntrypoint,
_normalize_path,
)
from .file_manager import CachingFileMana... | pydata/xarray | xarray/backends/pseudonetcdf_.py | Python | apache-2.0 | 4,555 | [
"NetCDF"
] | 47e581ec382bb78652d4722513bf057b4128019fa3df0f0e6e9b3b5d290e3524 |
from __future__ import print_function, division
__all__ = ['load', 'clone', 'Compound', 'Particle']
import collections
from collections import OrderedDict, defaultdict
from copy import deepcopy
import itertools
import os
import sys
import tempfile
from warnings import warn
import mdtraj as md
import numpy as np
from... | tcmoore3/mbuild | mbuild/compound.py | Python | mit | 75,385 | [
"Amber",
"LAMMPS",
"MDTraj",
"Open Babel",
"OpenMM"
] | e67913215f5087e903206650c3d57a8633364abb832b7e1f48cea9038bebc3e5 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016 Wil Clouser <clouserw@micropipes.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the ri... | qguv/config | weechat/plugins/python/emoji2alias.py | Python | gpl-3.0 | 41,578 | [
"FLEUR",
"Octopus"
] | a486bd0eb4e58bb198d3c25e6ebecc2918e3233670f1c9a38199f5e9733356e6 |
#
# $Revision: 738 $
# $Date: 2009-02-12 23:32:12 +0100 (Thu, 12 Feb 2009) $
# $Author: brian@tannerpages.com $
# $HeadURL: http://rl-glue-ext.googlecode.com/svn/trunk/projects/codecs/Python/src/rlglue/versions.py $
def get_svn_codec_version():
SVN_GLUE_VERSION="$Revision: 738 $"
justTheNumber=SVN_... | steckdenis/rlglue-py3 | rlglue/versions.py | Python | apache-2.0 | 437 | [
"Brian"
] | 13f49c78fb6e903c659f1eca7eb07ef5a205fd2b941f572e7cf15f84b4b996f8 |
# Copyright 2019 Microsoft Corporation
#
# 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 wri... | Sutto/cloud-custodian | tools/c7n_azure/c7n_azure/constants.py | Python | apache-2.0 | 4,310 | [
"ASE"
] | 2d767fb5918dc02e3e644b71cbb30502cfaf10a4e614f5e8039ed0c379dc2ed4 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""Tests for computing the overlap."""
import numpy as np
from unittest import TestCase
from exatomic.base import resource
from exatomic.core.basis import Overlap
from exatomic.molca... | avmarchenko/exatomic | exatomic/algorithms/tests/test_overlap.py | Python | apache-2.0 | 1,387 | [
"MOLCAS"
] | e9a7906a1b6e98fd06e7a6daa26f180a972e5cfad24e6f53521fa3cd54306016 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg
##
## 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
... | graik/biskit | biskit/atomCharger.py | Python | gpl-3.0 | 9,449 | [
"Amber"
] | 228cfa3baef3589fdd77f149ac6a4de90e837a2d67595cf5c17645457ce255c9 |
"""Handle running, parsing and manipulating metrics available through Picard.
"""
import contextlib
import glob
import json
import os
import subprocess
from bcbio.utils import tmpfile, file_exists
from bcbio.distributed.transaction import file_transaction
from bcbio.broad.picardrun import picard_rnaseq_metrics
import... | brainstorm/bcbio-nextgen | bcbio/broad/metrics.py | Python | mit | 21,507 | [
"pysam"
] | 68669bac4563fdb68a7d6a9c95c65042dc7792b4374b93e7aaa654e616698082 |
"""
=============================
Noise estimation using PIESNO
=============================
Often, one is interested in estimating the noise in the diffusion signal. One
of the methods to do this is the Probabilistic Identification and Estimation of
Noise (PIESNO) framework [Koay2009]_. Using this method, one can de... | jyeatman/dipy | doc/examples/piesno.py | Python | bsd-3-clause | 3,970 | [
"Gaussian"
] | e3242ead3e0d7c999171a83a5f218bcf9a6434a8539a55b279a7e78ef292ffad |
# 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 *
import os
import glob
from shutil import copyfile, Error
class NetcdfFortran(AutotoolsPackage):
... | iulian787/spack | var/spack/repos/builtin/packages/netcdf-fortran/package.py | Python | lgpl-2.1 | 7,222 | [
"NetCDF"
] | e200e9c6aabd183b6a2cd287034982b60b88f5d22cfeba2e5f3f3337278a2189 |
#
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | doc/tutorials/active_matter/exercises/enhanced_diffusion.py | Python | gpl-3.0 | 4,152 | [
"ESPResSo"
] | 121b588022b2e7a1bef527c7a9be49ca6fc7a5fc9133437e3bfeab24cdc9d664 |
from django.db import models
from django.db.models.deletion import PROTECT
from edc_base.model_mixins import BaseUuidModel
from edc_base.utils import get_utcnow
from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
from ..models import RequisitionIdentifierMixin, RequisitionModelMixin
from ..mod... | botswana-harvard/edc-lab | edc_lab/tests/models.py | Python | gpl-2.0 | 922 | [
"VisIt"
] | 60d3f05afa0d00b29861ca43075e3433e417c910d60aa975fcd2a50b0b0ba2c2 |
import numpy as np
from dipy.align.metrics import CCMetric, EMMetric, SSDMetric
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.imaffine import (transform_centers_of_mass,
AffineMap,
MutualInformationMetric,
... | arokem/AFQ-notebooks | tools.py | Python | mit | 6,112 | [
"Gaussian"
] | 2f50f77125a39f8dabffe83d5b0dfd4fcc228ce9cda0a8435c71faf09cd370a8 |
# Copyright 2002 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""handles true random numbers supplied from the web server of
fourmilab. Based on atmo... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/HotRand.py | Python | apache-2.0 | 2,539 | [
"Biopython"
] | 53a034d79cda0036709d2b250b88b316eac97df0040ac4fe01bca1ba1d648d63 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Molcas Output Parser
#####################
Multiple frames are not currently supported
"""
from __future__ import absolute_import
from __future__ import print_function
from __fut... | exa-analytics/exatomic | exatomic/molcas/output.py | Python | apache-2.0 | 24,368 | [
"Gaussian",
"MOLCAS"
] | de96d527d17d7c036e439d2e899532c2b07d2db9f205c3a01c15b6b98964981b |
import numpy as np
import scipy
import scipy.optimize as opt
import scipy.ndimage as ndimage
import scipy.ndimage.filters as filters
import matplotlib.pyplot as plt
import glob, os, sys, fnmatch
from astropy.io import fits as pyfits
from astropy.io import ascii
#define model Gaussian function and pass independent var... | kkozarev/mwacme | src/find_local_maxima_multi_integrated_subset.py | Python | gpl-2.0 | 8,760 | [
"Gaussian"
] | 834e965a7da3088d2bfb9db25625c2206bb2182ad0df0fdf5f0875b72582189e |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | jakereps/qiime2 | qiime2/core/type/tests/test_grammar.py | Python | bsd-3-clause | 23,607 | [
"scikit-bio"
] | e76fc820c13d6d50a66814770a75f1e4b3fc2f2235cf08f3df3f2cd78279f413 |
#! /usr/bin/python
# encoding: -*- utf-8 -*-
# sale_panel.py
# This file is part of miniPOS.
# miniPOS 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
# (... | nitheeshkl/miniPOS | mpos/pnl_sales.py | Python | gpl-3.0 | 35,483 | [
"VisIt"
] | bd6aa84c48df30ada577e3f5944d58791fa13d8fe78e954828faa30d19126ca1 |
#!/usr/bin/env python
# Various functions for tmi_viewer
# Copyright (C) 2016 Tristram Lett
# 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
... | trislett/tmi_viewer | tmi_viewer/tv_func.py | Python | gpl-3.0 | 20,600 | [
"Mayavi",
"Octopus"
] | 6d519d9d6342d279f41b31a693616759f07a28b6c999509f0e33a8e6c4dce9fe |
"""
DIRAC.DataManagementSystem.DB test package
"""
| marcelovilaca/DIRAC | DataManagementSystem/DB/test/__init__.py | Python | gpl-3.0 | 54 | [
"DIRAC"
] | 841ecd4e3e94178aa5f818228cf74e9421aa4c6db86708ed69b224740aabb03c |
"""Tool for sorting imports alphabetically, and automatically separated into sections."""
import argparse
import functools
import json
import os
import sys
from gettext import gettext as _
from io import TextIOWrapper
from pathlib import Path
from typing import Any, Dict, List, Optional, Sequence, Union
from warnings i... | PyCQA/isort | isort/main.py | Python | mit | 46,574 | [
"VisIt"
] | c011dcb020e2ab048f0ccd609d7e7fd00e7bccceb267d7b7627f488ea5cca8d3 |
#!/bin/env python
import numpy, sys, vtk, wx
from PyQt4 import QtCore, QtGui
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from vtk.volumerendering import *
try:
from transfer_function import TransferFunctionWidget
except ImportError:
print 'You need to get the TransferFunction from: "... | chapering/PyVolRender | imgVolRender_GPU.py | Python | gpl-2.0 | 7,766 | [
"VTK"
] | c7bcd0ca4095c36687145fdf5fb53bf0ed82007e91ab5f50a029305e164eb7d3 |
import jsonpickle
import requests
from colorker.core import Query
GALILEO_SERVICE_HOST = 'http://tomcat.columbus.cs.colostate.edu/galileo-web-service'
polygons = [[{"lat": "40.597792003905454", "lon": "-104.77729797363281"},
{"lat": "40.43545015171254", "lon": "-104.77729797363281"},
{"lat":... | jkachika/columbus | pyedf/tests.py | Python | mit | 14,815 | [
"COLUMBUS"
] | a335722a8d41151fb5e3b47e7db3e6b7f2f48f005066a524d6b696cd12dd2b5a |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageIdealLowPass(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkImageIdealLowPass.py | Python | bsd-3-clause | 497 | [
"VTK"
] | d1f15ab0bc0d67c14e07517f3f165724833b6f3378a5b31105a20cf9d6e42545 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010-2018 (ita)
"""
Classes and functions enabling the command system
"""
import os, re, imp, sys
from waflib import Utils, Errors, Logs
import waflib.Node
# the following 3 constants are updated on each new release (do not touch)
HEXVERSION=0x2000f00
"""Constan... | drobilla/pugl | waflib/Context.py | Python | isc | 21,029 | [
"VisIt"
] | 40af4ebe0bed4159a9ab6e3cbd7bc672f78cc27ed28af8ae723ba1561b67b436 |
#!/usr/bin/env python
#encoding:utf8
#====================================================
# FILE: img2sdat.py
# AUTHORS: xpirt - luxi78 - howellzhu
# DATE: 2015-10-11 14:37:22 CST
#====================================================
import sys, blockimgdiff, sparse_img, os
def main(sysimg, o... | FlymeOS/tools | reverses/de-dat/img2sdat.py | Python | apache-2.0 | 1,296 | [
"VisIt"
] | 6c2d25ab128026618fab47807f59b8ac667f83348034d49c4de964d38792dcfc |
import numpy as np
from astropy.modeling import models, fitting
__all__ = ["sinc_square_model", "sinc_square_deriv", "fit_sinc",
"fit_gaussian", "SincSquareModel"]
def sinc(x):
"""
Calculate a sinc function.
sinc(x)=sin(x)/x
Parameters
----------
x : array-like
Returns
... | StingraySoftware/stingray | stingray/pulse/modeling.py | Python | mit | 5,000 | [
"Gaussian"
] | 50e1d5205a43bdcd3e3733d80cf2e1a336c0dd4e7b50be6e5a7b5b6056f5fa80 |
#########################################################################
## rdesigneur0_4.py ---
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU General Public ... | subhacom/moose-core | python/rdesigneur/rmoogli.py | Python | gpl-3.0 | 6,261 | [
"MOOSE"
] | b6bdd51671da4797cf88d13f6bd86df78323a0bac44c3fc85e88fded9a8062e9 |
# Copyright (C) 2006-2011 Canonical Ltd
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distribute... | stewartsmith/bzr | bzrlib/knit.py | Python | gpl-2.0 | 146,948 | [
"VisIt"
] | c24a86121555ad35e20becfbaed9b30260b964007244aac28a3c1ce28d8b640a |
import hashlib
import datetime
from tornado import web, gen
from RESTDIRAC.RESTSystem.Base.RESTHandler import WErr, WOK, TmpDir, RESTHandler
from DIRAC.WorkloadManagementSystem.Client.SandboxStoreClient import SandboxStoreClient
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities.JDL import load... | DIRACGrid/RESTDIRAC | RESTSystem/API/Job/JobStuffHandler.py | Python | gpl-3.0 | 2,830 | [
"DIRAC"
] | 024655faee0924e26f3a2c89666a7a52962a7903feb2cd2606b98553fdb2e302 |
"""
=======================================
Signal processing (:mod:`scipy.signal`)
=======================================
Convolution
===========
.. autosummary::
:toctree: generated/
convolve -- N-dimensional convolution.
correlate -- N-dimensional correlation.
fftconvolve --... | matthewalbani/scipy | scipy/signal/__init__.py | Python | bsd-3-clause | 12,578 | [
"Gaussian"
] | 5ac81b8a1ef375a25ad0a5c2028bc7b8d413a98fad84c2ac33082e989a956184 |
# ******************************************************************************
# Copyright 2017-2018 Intel Corporation
#
# 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.apa... | NervanaSystems/neon | tests/test_dilated_conv.py | Python | apache-2.0 | 6,039 | [
"Gaussian"
] | b756c2fa4166c11ac2e12cef0766e395e50070dc98f2df028f8498ee3599511b |
# -*- coding: utf-8 -*-
"""
Master Dictionary
Translations
0: English
1: Chinese
2: Dutch
3: French
4: Italian
5: Japanese
6: Korean
7: Portuguese
8: Russian
9: Spanish
"""
class MD_F:
# Master Dictionary Functions
def get_languages_list():
languages = []
languages.append("English")
... | mdmintz/SeleniumBase | seleniumbase/translate/master_dict.py | Python | mit | 99,028 | [
"VisIt"
] | b76dcb7328e53d36fd74ec4c16a79347ff86ccbe2a0874d1ca25284fd4600bba |
# -*- coding:utf-8 -*-
"""
Utilities not related to neuronal network simulation.
"""
from numpy import linspace
from os import path, listdir
from importlib import import_module
import itertools
def path_to_modline(filepath):
"""Returns a string representation for module import of a file."""
# Import the set ... | neuro-lyon/multiglom-model | src/utils.py | Python | mit | 7,140 | [
"Brian"
] | e1534bbbf6c7f27a5b01e350d88605947348e2929d2b92e11ecebd6afe4c252c |
#!/usr/bin/env python3
"""
If you have a large FASTA file with a great number of entries, this script is used to
split the file into multiple new files with an even number of records (or as close
as possible.)
Use case example: I have a reference genome collection with 2000 genomes and want to
search this using bowt... | jorvis/biocode | fasta/split_fasta_into_even_files.py | Python | mit | 3,580 | [
"Bowtie"
] | 94c9732050aeb3fc1b2e36c16f2ee3dec72249d9fbe9a59e93813b4c6f892a06 |
import os
from setuptools import setup
setup(
name = "prometheus_client",
version = "0.0.13",
author = "Brian Brazil",
author_email = "brian.brazil@robustperception.io",
description = ("Python client for the Prometheus monitoring system."),
long_description = ("See https://github.com/prometheus... | thomaso-mirodin/client_python | setup.py | Python | apache-2.0 | 1,046 | [
"Brian"
] | 61b8ecfc70bbc09a94594b1bd23bd9136705697e97a454da127ed585fc887c79 |
#./parallel_manager.sh ./create_skysub_delink_para.sh ${SUBARUDIR}/${cluster}/${filter} SCIENCE ${ending} ".sub" TWOPASS
global tmpdir
import os
#os.system('mkdir -p ' + tmpdir)
astrom = 'solve-field'
import traceback, tempfile
def fix_table():
import MySQLdb, sys, os, re, time, utilities, pyfits ... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_test_save.6.25.py | Python | mit | 315,503 | [
"Galaxy"
] | 41655fc0c78cd421927dc23b2e5a18eee0d325fd4d1429ee2afbdd2328d367ef |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | ilastikdev/ilastik | ilastik/applets/counting/countingGui.py | Python | gpl-3.0 | 69,303 | [
"Gaussian"
] | addbd14743b7d49dcd474f5c6d30dc13230726551132524e875a8cc9267449a7 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/share/psi4/databases/S22.py | Python | lgpl-3.0 | 43,408 | [
"Psi4"
] | e7d0c48d60ba5b55b6c31b0c2c5892b0013348f8f8793d10af36b8ba082c5d00 |
# Player: A player in this game. Every AI controls one player.
# DO NOT MODIFY THIS FILE
# Never try to directly create an instance of this class, or modify its member variables.
# Instead, you should only be reading its variables and calling its functions.
from typing import List
from games.saloon.game_object import... | JacobFischer/Joueur.py | games/saloon/player.py | Python | mit | 4,027 | [
"SIESTA"
] | 85d4430b4991e758f065cb42e6f33ef8aaa0e2d73d7780ea24e6d97d4d5446cc |
#!/usr/bin/env python
# Filename: util.py
'''
util
@author: Andrew Philpot
@version 0.79
collection of misc utils
Usage: python util.py
Options:
\t-h, --help:\tprint help to STDOUT and quit
\t-v, --verbose:\tverbose output
'''
import sys
import inspect
import types
import getopt
import fileinput
import tempfile
impo... | usc-isi-i2/dig-prep | python/dig/pymod/util.py | Python | apache-2.0 | 55,059 | [
"VisIt"
] | e6280b76ba4690ca908fd5f8d3aa929311d833aa985a78f090f7307e08c84ee7 |
# Copyright 2005-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# Author(s): Nicholas Carpaski (carpaski@gentoo.org), Brian Harring (ferringb@gentoo.org)
from __future__ import unicode_literals
__all__ = ["cache"]
import stat
import sys
import operator
import warnings
from ... | nullishzero/Portage | pym/portage/eclass_cache.py | Python | gpl-2.0 | 5,664 | [
"Brian"
] | ee09a520d2304e3c839735fc6f30d3fa8411c82892edbeb8176fc8b0e9873845 |
#!/usr/bin/env python
from __future__ import unicode_literals, print_function
import os
from discogs_client.exceptions import HTTPError
from six.moves import input
import discogs_client as dc
USER_AGENT = "discogstagger +http://github.com/jesseward"
class DiscogsWrapper(object):
''' Returns an OAuth authentic... | jesseward/discogstagger | discogstagger/discogswrapper.py | Python | mit | 2,977 | [
"VisIt"
] | ce7a393a3665884599b405032ad485673557dc56f1a0c6b8f744c92f0e02fa17 |
import ast
import operator
from fractions import Fraction
from artiq.transforms.tools import *
from artiq.language.core import int64, round64
_ast_unops = {
ast.Invert: operator.inv,
ast.Not: operator.not_,
ast.UAdd: operator.pos,
ast.USub: operator.neg
}
_ast_binops = {
ast.Add: operator.add,
... | kgilmo/penning_artiq | artiq/transforms/fold_constants.py | Python | gpl-3.0 | 4,462 | [
"VisIt"
] | 13613b3276dcb974ab1c54a34cd56cd1e9d4a4ce3efbca14b56d6baf3bf0a313 |
import numpy as np
import pychemia
import itertools
import scipy.spatial
from scipy.spatial import qhull
from pychemia.utils.periodic import covalent_radius
# return [x, y, d], that ax + by = d, d = gcd(a, b)
def ext_gcd(a, b):
v1 = [1, 0, a]
v2 = [0, 1, b]
if a > b:
a, b = b, a
while v1[2] ... | MaterialsDiscovery/PyChemia | pychemia/analysis/surface.py | Python | mit | 14,660 | [
"CRYSTAL"
] | 4f13bd40885b02e615da10e972d900fb6eb3e8c708f064d8b600bf5693623ace |
"""
font data tables for truetype and afm computer modern fonts
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
latex_to_bakoma = {
'\\__sqrt__' : ('cmex10', 0x70),
'\\bigcap' : ('cmex10', 0x5c),
... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/_mathtext_data.py | Python | bsd-2-clause | 89,645 | [
"Bowtie"
] | 72df117ff68dbdec7f52c7c1ce0193ecf1415b13412caea87e8b11f8727a0508 |
# Copyright (C) 2015
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free softw... | capoe/espressopp.soap | src/tools/convert/topology_helper.py | Python | gpl-3.0 | 12,248 | [
"ESPResSo",
"Gromacs"
] | 84e19c6eda35754a06c8ff56e329d05960c25effdb7b53f2ae7a2ccc33b96c3d |
import unittest
import warnings
import numpy as np
from boldsim import sim
class TestHelpers(unittest.TestCase):
"""Unit tests for sim helper functions"""
def test_handle_nscan_returns_ints(self):
"""Test _handle_nscan returns int with int or float input"""
self.assertEqual(10, sim._handle_ns... | adamatus/boldsim | tests/test_sim.py | Python | gpl-2.0 | 49,245 | [
"Gaussian"
] | 054193f497451648e2dd25adc8577517f3053d8bedf87cbb993b3de8ee3978bd |
# -*- coding: utf-8 -*-
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Authors: Aric Hagberg <hagberg@lanl.gov>
# Loïc Séguin-C. <loicseguin@gmail.com>
# Da... | goulu/networkx | networkx/algorithms/shortest_paths/weighted.py | Python | bsd-3-clause | 63,355 | [
"VisIt"
] | 2759b1e24007b1a173520f1f5c32a3546e9a1e2d834cf1dc4a81fc51aff32b2d |
#-------------------------------------------------------------------------------
#
# 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... | teoliphant/scipy | scipy/stats/kde.py | Python | bsd-3-clause | 17,245 | [
"Gaussian"
] | 7b552e1a30858377bcd5c5745ce2971ce1fbb5077074fa00ccd11854c2de77b1 |
#
# @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
#... | jturney/psi4 | psi4/driver/gaussian_n.py | Python | lgpl-3.0 | 7,116 | [
"Gaussian",
"Psi4"
] | 0181f11f7f496f06bf356583b700070fe1b5ab163670373a0421b4b7275a26e4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (c) 2014,2015,2016,2017 Jeremie DECOCK (http://www.jdhp.org)
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, ... | jeremiedecock/pyai | ailib/optimize/minimizers/cutting_plane.py | Python | mit | 40,577 | [
"Gaussian"
] | 3e2925543de304611fa4cb7cc12f786110d4d46f0ec14181ca5f942338739b3b |
#!/usr/bin/python
#
# 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 Jonathan Topf, Jupiter Jazz Limited
# Copyright (c) 2014-2018 Jonathan Topf, The appleseedhq Organizat... | luisbarrancos/appleseed | scripts/rendernode.py | Python | mit | 18,139 | [
"VisIt"
] | 332fc2237e1fa163d4c4d3f9b99677fe10527a062ef62916db4c3817fe5bc810 |
#########################################################
#
#EntropyCalculator calculates the entropy value for a SNP or pair of SNPs
#by using the phylogenetic tree to calculate the probabilities of each value
#(A, T, C, G, AA, AT, ect.), using the methods demonstrated in:
#http://www.ncbi.nlm.nih.gov/pmc/articles/PMC... | rsb93/Capstone | EntropyCalculator.py | Python | gpl-2.0 | 9,160 | [
"VisIt"
] | b324d4e9cc9f7ef37e32052ca808de4c97a505959ad99654b841d841c2e90f90 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 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/lib/test/test_fileutils.py | Python | gpl-2.0 | 1,888 | [
"VisIt"
] | 0e9ed9a88ac269731607b69e8482daf3cedbfe04f7635799a4a0c7ab54c41b2f |
"""Quality control and summary metrics for next-gen alignments and analysis.
"""
import collections
import contextlib
import csv
import os
import shutil
import subprocess
import pandas as pd
import lxml.html
import yaml
from datetime import datetime
# allow graceful during upgrades
try:
import matplotlib
matpl... | hjanime/bcbio-nextgen | bcbio/pipeline/qcsummary.py | Python | mit | 44,083 | [
"pysam"
] | 1277b104dbc23487daeae99eefb9a15b0033f04cb08784d16085213f33b87a10 |
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