text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
## INFO ########################################################################
## ##
## plastey ##
## ======= ... | kitchenbudapest/vr | sphere.py | Python | gpl-3.0 | 6,331 | [
"VisIt"
] | d0982fd28a29e97f20671f717000e9bfbbdd4b36c64fce2c424c4a3203b913ef |
from rdkit import Chem
from functools import total_ordering
import h5py
from progressbar import ProgressBar
import numpy
from tsp_solver.greedy import solve_tsp
import random
def fingerprint_with_new_index(smiles_file_path, random_order):
prefix = smiles_file_path[:smiles_file_path.rfind('.')]
smiles_file = ... | patrick-winter-knime/deep-learning-on-molecules | custom-fingerprints/neighborhoods/neighborhoods.py | Python | gpl-3.0 | 10,027 | [
"RDKit"
] | 7d9b54881564acb5a2018c11199738d881740d71b740d6c175f3096aaea0cf00 |
import httplib2
import os
import sys
from apiclient.discovery import build_from_document
from apiclient.errors import HttpError
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oauth2client.tools import run_flow
video_id = "IrPwZ7ejsw8"
channel_id = "UC5aFBZOvtseFQWib... | chihacknight/chihacknight-yt-interface | scrape.py | Python | mit | 6,026 | [
"VisIt"
] | 583253765033985f8abec909056c7c407fecf90c9754156025f0d7252b91f2bd |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# 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.
... | shawnsi/ansible | lib/ansible/plugins/cache/base.py | Python | gpl-3.0 | 1,480 | [
"Brian"
] | ca902ab4f063f2e6c11c5387ff0c34485f0ec65c693343565a5f5770e36c726c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2009-2010 Craig J. Anderson
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistr... | jralls/gramps | gramps/plugins/drawreport/descendtree.py | Python | gpl-2.0 | 69,344 | [
"Brian"
] | 1a0a8a8f234c0c19fb48ae6d0f0950818adcff02457030e9b9be0fd0e9665428 |
import _testcapi
import codecs
import io
import locale
import sys
import unittest
import warnings
from test import support
if sys.platform == 'win32':
VISTA_OR_LATER = (sys.getwindowsversion().major >= 6)
else:
VISTA_OR_LATER = False
try:
import ctypes
except ImportError:
ctypes = None
SIZEOF_WCH... | mancoast/CPythonPyc_test | fail/332_test_codecs.py | Python | gpl-3.0 | 91,385 | [
"FEFF"
] | fd68fde27696b154b7daa5d82cbf8af61112c4c016382e6a5ce58f26fe31f073 |
#
# 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 requir... | shiwalimohan/RLInfiniteMario | system/codecs/Python/examples/skeleton/skeleton_experiment.py | Python | gpl-2.0 | 3,245 | [
"Brian"
] | 23bca55c3861f3d85ea2c71ef573ed948d6ecdc41410993f282f7866ec0cf750 |
#########################################################################################
#
# ERA_INTERIM.py
#
# Download ERA Interim data and create a movie from it.
#
#
# bethan.perkins@assimila.eu
# May 2014
#
#########################################################################################
# Import librari... | joelfiddes/toposubv2 | getERA/ERA_INTERIMtest.py | Python | gpl-3.0 | 18,444 | [
"NetCDF"
] | 03641956e3dc24589807d4e5679812b7abed0f00f8eaf67dafd334c3b1ed1ed6 |
#!/usr/bin/env python
import os
import sys
import unittest
import shutil
from PyQt5 import QtWidgets
import vtk
import mock
from peacock.ExodusViewer.plugins.FilePlugin import main
from peacock.utils import Testing
class TestFilePlugin(Testing.PeacockImageTestCase):
"""
Testing for FileControl widget.
"""... | backmari/moose | python/peacock/tests/exodus_tab/test_FilePlugin.py | Python | lgpl-2.1 | 6,018 | [
"VTK"
] | f09fb75427d7a4377a0d2d01e7d52139b58b6e805a94853b781c0bb31a34de32 |
"""
[Deprecation warning]
`anaconda notebook` is going to be deprecated
use `anaconda upload/download` instead
"""
from __future__ import unicode_literals
import argparse
import logging
from binstar_client import errors
from binstar_client.utils import get_server_api
from binstar_client.utils.notebook import Uploader,... | Anaconda-Platform/anaconda-client | binstar_client/commands/notebook.py | Python | bsd-3-clause | 4,823 | [
"VisIt"
] | 60ea543486cad6d45cead99ca5812aa2f43e0b9897bd59c651811530e10c3879 |
from copy import copy
import six
from . import ast
from .visitor_meta import QUERY_DOCUMENT_KEYS, VisitorMeta
class Falsey(object):
def __nonzero__(self):
return False
def __bool__(self):
return False
BREAK = object()
REMOVE = Falsey()
class Stack(object):
__slots__ = 'in_array', '... | wandb/client | wandb/vendor/graphql-core-1.1/wandb_graphql/language/visitor.py | Python | mit | 6,276 | [
"VisIt"
] | 4b30f5e56755026b41124bc81b2b639de6c8ec24f10b07e21fd002357398e2b6 |
import itk
import possum.pos_itk_core
"""
http://www.vtk.org/doc/nightly/html/classvtkShepardMethod.html
http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_CreateVolume
http://www.itk.org/Doxygen/html/classitk_1_1DisplacementFieldTransform.html
http://www.itk.org/Doxygen/html/classitk_1_1CompositeTra... | pmajka/poSSum | possum/pos_itk_transforms.py | Python | mit | 15,486 | [
"VTK"
] | c4841331b88e8d6e95b5b85de0fa09488f1a8698595d429ecb61e1794c052975 |
#!/usr/bin/env python
""" load metabolome into OSDF using info from data file """
import os
import re
from cutlass.Metabolome import Metabolome
import settings
from cutlass_utils import \
load_data, get_parent_node_id, list_tags, format_query, \
write_csv_headers, values_to_node_dict, write_out_csv, ... | JAX-GM/osdf_submit | nodes/metabolome.py | Python | gpl-3.0 | 5,275 | [
"VisIt"
] | 968785259e5975a3a7b542e79e775890b7f5191428f47912731053b4cd4877ac |
# vclamp.py ---
#
# Filename: vclamp.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Sat Feb 2 19:16:54 2013 (+0530)
# Version:
# Last-Updated: Tue Jun 11 17:35:20 2013 (+0530)
# By: subha
# Update #: 178
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#... | BhallaLab/moose-examples | snippets/vclamp.py | Python | gpl-2.0 | 4,661 | [
"MOOSE",
"NEURON"
] | 2d6c7b14f515c1038e3d9344fb73ea90f9d3da845f968a0020ae4ddb50fdf8d6 |
# -*- Python -*-
# Configuration file for the 'lit' test runner.
import os
import sys
import re
import platform
import subprocess
import lit.util
import lit.formats
from lit.llvm import llvm_config
from lit.llvm.subst import FindTool
from lit.llvm.subst import ToolSubst
# name: The name of this test suite.
config.n... | endlessm/chromium-browser | third_party/llvm/llvm/test/lit.cfg.py | Python | bsd-3-clause | 13,213 | [
"cclib"
] | 569ae30f55549bc70c1f8475c121835d054d160ff0787165185d0d4fab81032e |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['ApM1', 'M1', 'M1_Watchpoint', 'Watchpoint', 'ApKB', 'VFM', 'VFM_HFM', 'HFM', 'HFM_Sam... | mrakitin/sirepo | tests/template/srw_generate_data/gaussian-x-ray-beam-through-a-beamline-containing-imperfect-mirrors.py | Python | apache-2.0 | 26,362 | [
"Gaussian"
] | 8bea21c2aa5a90914d3038e48b3a183c0b88873ff68755e65b10919a2517734e |
# Copyright 2010 by Andrea Pierleoni
# Revisions copyright 2010 by Peter Cock
# 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.
import sys
# Add path to Bio
sys.path.append('..... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SeqIO/UniprotIO.py | Python | gpl-2.0 | 25,350 | [
"Biopython"
] | 37090635548d0f6eeec97ec3642ab4ad4085d850ba446c0700f359be4b8264cd |
# $Id$
#
# Copyright (C) 2005-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
def ConstructEnsemble... | adalke/rdkit | rdkit/DataStructs/BitUtils.py | Python | bsd-3-clause | 1,061 | [
"RDKit"
] | a8a7cdb586c076b844cb54dcc7b58e0ded709f908610bc77e6be8ab9da1a7a92 |
# 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 PyWhatshap(PythonPackage):
"""WhatsHap is a software for phasing genomic variants using DN... | LLNL/spack | var/spack/repos/builtin/packages/py-whatshap/package.py | Python | lgpl-2.1 | 1,210 | [
"pysam"
] | 5bb7040d947ab4de6bf6a5a5d39f063eddd6a36bfd293dc560a103ab8344905d |
from __future__ import unicode_literals
from __future__ import absolute_import
import logging
from .service import Service
from .container import Container
from .packages.docker.errors import APIError
log = logging.getLogger(__name__)
def sort_service_dicts(services):
# Topological sort (Cormen/Tarjan algorithm)... | saulshanabrook/fig | fig/project.py | Python | apache-2.0 | 8,116 | [
"VisIt"
] | 4ef06ee5ba27274606717b8034bc3f7948309088b3a55efb78c72d63bebf5366 |
#!/usr/bin/env python
'''
Takes a phylogeny and a taxonomy and labels nodes representing higher-order
taxa in the phylogeny.
Both the phylogeny and the taxonomy should be trees in a format supported by
BioPython.
For help on usage, run `python phylolabel.py -h`
'''
import Bio.Phylo as bp
def convert_labels(t):
... | bendmorris/phylolabel | phylolabel.py | Python | mit | 5,933 | [
"Biopython"
] | 9b05203f88861507e0b56f087fdbd820f44499d1d0f1aa6da2c102d590b2aa51 |
#!/usr/bin/env python3
#
# (C) 2016, Markus Wildi, wildi.markus@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
... | jstrobl/rts2 | scripts/u_point/meteo/meteo_dome_c.py | Python | lgpl-3.0 | 3,811 | [
"VisIt"
] | 3ded75fcb6e5526f6ae6ee11dba157e9f5689888364649e02b5fd5393ad91fe2 |
"""
An attempt at a user friendly Cart3d GUI
"""
# -*- coding: utf-8 -*-
from __future__ import division, unicode_literals, print_function
#from six.moves import range
# standard library
import sys
import os.path
from pyNastran.gui.qt_version import qt_version
if qt_version == 4:
from PyQt4 import QtCore, QtGui
... | saullocastro/pyNastran | pyNastran/converters/cart3d/gui.py | Python | lgpl-3.0 | 6,462 | [
"VTK"
] | 7501a406f3de54374619a8db512933574a5b2f2f12908c165e2ea1cbc81d901d |
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from mutation_stability import mutation_stability
import os
class virus_stability(object):
def __init__(self, hash, strain, trunk, tip, date, seq, foldx_directory):
self.hash_code = hash
self.strain = strain
... | blab/stability | augur/stability-data/foldx_essentials/virus_stability.py | Python | agpl-3.0 | 13,310 | [
"FoldX"
] | 4ea33a95486eb2f93503d0ae4573fde67ba85a1afba704c409be169c32f5a9a4 |
import abc
import json
import math
from collections.abc import Mapping, Sequence
import pprint
import numpy as np
import hail as hl
from hail import genetics
from hail.expr.nat import NatBase, NatLiteral
from .type_parsing import type_grammar, type_node_visitor
from hail.genetics.reference_genome import reference_gen... | cseed/hail | hail/python/hail/expr/types.py | Python | mit | 50,690 | [
"VisIt"
] | 633f07596e34e781bd66f7005bd96e79909fef461b8c3ed26999d46c6ae26c7e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from docutils import nodes
from docutils.parsers.rst import Directive
class localvideo(nodes.General,nodes.Element):
pass
def visit(self, node):
filename = node.filename
content=u'''
<video controls="">
<source type="video/webm" src="/_st... | mthoretton/sphinxcontrib-localvideo | sphinxcontrib/localvideo/localvideo.py | Python | gpl-2.0 | 923 | [
"VisIt"
] | 5d54408384a3fa49112f8bd6286ed4a8decd3c38c967277ba5bd99c554ef5e8e |
#!/usr/bin/env python
# This script generates C++ source for parse tree syntax nodes from a data file.
import argparse
import os
class TypeInfo:
def __init__(self, processedMembers, members, pointerMembers, optionalMembers,
final, constructorArgs, argNames, base, combinedMembers, notNullMembers):
... | MikePopoloski/slang | scripts/syntax_gen.py | Python | mit | 17,774 | [
"VisIt"
] | 6735f34d3b4648b3d9fb6df27bad44eec928bd70c69dde03fef0277e4c00a1e9 |
# User scratch directory
SCRATCH_DIR = "/home/andersx/scr"
# Executable for CHARMM
CHARMM_EXE = "/home/andersx/dev/charmm_cpe/exec/gnu/charmm"
# Executable for CHARMM
CRD2XYZ_EXE = "/home/andersx/charmm-dftb-py/crd2xyz"
# This directory
D3H4_BIN_DIR = "/home/andersx/dev/charmm-dftb-py/d3h4_bin"
# Directory for the ... | andersx/charmm-dftb-py | sccdftb_config.py | Python | unlicense | 2,011 | [
"CHARMM"
] | d6b998615670b7a79e6b64fce123636e67197b15f61d2f49268700840ec1e7a9 |
#!/usr/bin/env python
"""Parse tracelog output for analysis/diagrams.
NOTE: tracelog is still in development.
Usage:
./client/tools/tracelog-tool.py
./client/tools/tracelog-tool.py --logdir logdir/
./client/tools/tracelog-tool.py --format plantuml
"""
import argparse
from dataclasses import dataclass
imp... | wandb/client | tools/tracelog-tool.py | Python | mit | 4,481 | [
"Amber"
] | 76b3d60e807103ccf4b2ed41434c755e5c0888cf2d11a3a7407ea3ef33231ea7 |
import pylab as plt
import numpy as np
from astrometry.util.plotutils import dimshow
from legacypipe.survey import get_rgb, tim_get_resamp
from legacypipe.coadds import quick_coadds
def fitblobs_plots_2(blobs, refstars, ps):
plt.clf()
dimshow(blobs>=0, vmin=0, vmax=1)
ax = plt.axis()
plt.plot(refstars.... | legacysurvey/legacypipe | py/legacypipe/runbrick_plots.py | Python | bsd-3-clause | 19,199 | [
"Galaxy"
] | a46532314f3623171a00cc3dc51a29c0d7a4b0dd6a0f21d82b89a5d2605c7a1d |
"""Save pairwise RMSD between conformers.
Authors: Seth Axen
E-mail: seth.axen@gmail.com
"""
import os
import sys
import struct
import itertools
import logging
import argparse
import numpy as np
import rdkit.Chem
from rdkit.Chem import rdMolAlign, rdFMCS
from python_utilities.scripting import setup_logging
from pytho... | keiserlab/e3fp-paper | project/fingerprint_comparison/get_rmsd.py | Python | lgpl-3.0 | 6,764 | [
"RDKit"
] | 2a9c1c7a2c4cf2a3fe5dff6a3a1d9e7e7ab5c439c21875b76e37e174e8b7e5a7 |
# $HeadURL: $
''' BaseAction
Base class for Actions.
'''
from DIRAC import gLogger
__RCSID__ = '$Id: $'
class BaseAction( object ):
'''
Base class for all actions. It defines a constructor an a run main method.
'''
def __init__( self, name, decisionParams, enforcementResult, singlePolicyResul... | marcelovilaca/DIRAC | ResourceStatusSystem/PolicySystem/Actions/BaseAction.py | Python | gpl-3.0 | 1,372 | [
"DIRAC"
] | e8ff57e224c6f0a0fc24972224d3b7d0fe4eea33c812a78739d3b4fbfbe31939 |
class Solution(object):
def ladderLength(self, beginWord, endWord, wordList):
"""
:type beginWord: str
:type endWord: str
:type wordList: Set[str]
:rtype: int
"""
bwset=set()
ewset=set()
bwset.add(beginWord)
ewset.add(endWord)
#... | Tanych/CodeTracking | 127-Word-Ladder/solution.py | Python | mit | 1,731 | [
"VisIt"
] | 5cdca92fecfaba28d86a910dfcd8cc9f186e2172e0d5d235b9861ce35a76118f |
from django.contrib import admin
from analytics.models import Visit, Visitor
class VisitAdmin(admin.ModelAdmin):
list_display = ('url','date','get_visitor')
class VisitorAdmin(admin.ModelAdmin):
list_display = ('ip','user_agent','visit_count','list_visits')
admin.site.register(Visit,VisitAdmin)
admin.site.register... | joeyuan19/flaming-bear | PersonalSite/analytics/admin.py | Python | apache-2.0 | 346 | [
"VisIt"
] | 2273e90ca79ae90beedc54a2c4772198f9cac1c8578de93827610b45f6d79e94 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
"""
Input sets for VASP GW calculations
Single vasp GW work: Creates input and jobscripts from the input sets for a specific job
"""
__author... | xhqu1981/pymatgen | pymatgen/io/vasp/GWvaspinputsets.py | Python | mit | 26,739 | [
"ABINIT",
"VASP",
"Wannier90",
"pymatgen"
] | cadeaf18d8d0057d47c73232584950f6cfb9868f0ec6768dbfc545189be3dfe5 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/interaction/Zero.py | Python | gpl-3.0 | 9,801 | [
"ESPResSo"
] | bc4a4281d3a3c5f3b3e1733c191176d06dd6d994b311335fbe6b557e5f64b897 |
# -*- coding: utf8 -*-
"""
Kernel Density Estimation
"""
from pyFTS.common import Transformations
import numpy as np
class KernelSmoothing(object):
"""Kernel Density Estimation"""
def __init__(self, **kwargs):
self.h = kwargs.get('h',.5)
"""Width parameter"""
self.kernel = kwargs.ge... | petroniocandido/pyFTS | pyFTS/probabilistic/kde.py | Python | gpl-3.0 | 2,000 | [
"Gaussian"
] | 54c2e628e567b295515add653b4abcda068783494fe9199da58a49658290b2eb |
from datetime import datetime, timedelta
import re
from zk.model import Person, PasswordResetConfirmation
from routes import url_for
from .fixtures import PersonFactory, PasswordResetConfirmationFactory
from .utils import do_login, isSignedIn
class TestPersonController(object):
def test_registration_confirmation... | zookeepr/zookeepr | zkpylons/tests/functional/test_account.py | Python | gpl-2.0 | 15,167 | [
"VisIt"
] | f0d42ce5453c032188254c8524c4310ce8e01ae324d26c6293e474302083f7c3 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/gto/basis/__init__.py | Python | apache-2.0 | 4,185 | [
"CP2K",
"PySCF"
] | 5a1d8ce2917af0cdb5f3f2bca5c94bc15367f547ef7fad9b62f8029f84adc19b |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
from six.moves import xrange
import warnings
import numpy as np
from matplotlib.testing.decorators import image_comparison, knownfailureif
from matplotlib.cbook import MatplotlibDeprecationWarning
... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/tests/test_delaunay.py | Python | bsd-2-clause | 7,090 | [
"Gaussian"
] | bc1f049e60ddeca9c54388bc8354b3f6c7c7dac0fb3cab58f267204ae977661e |
from __future__ import absolute_import
import fluent.syntax.ast as FTL
from fluent.migrate.helpers import transforms_from
from fluent.migrate.helpers import VARIABLE_REFERENCE, TERM_REFERENCE
from fluent.migrate import REPLACE, COPY
newsletters = "mozorg/newsletters.lang"
def migrate(ctx):
"""Migrate bedrock/news... | MichaelKohler/bedrock | lib/fluent_migrations/newsletter/index.py | Python | mpl-2.0 | 36,945 | [
"VisIt"
] | 61e17b9c1510f98f9e214d3d26268cd71d738c9392066f18f880ddffcf3f4d7e |
import pysproto
from sys import getrefcount
from pysproto import sproto_create, sproto_type, sproto_encode, sproto_decode, sproto_pack, sproto_unpack, sproto_protocol, sproto_dump, sproto_name
from binascii import b2a_hex, a2b_hex
import unittest
class TestPySproto(unittest.TestCase):
def get_st_sp(self):
... | spin6lock/python-sproto | test.py | Python | mit | 9,209 | [
"CRYSTAL"
] | 6e1615a5625cbeb598ca6372de1218316e7aa62224614c2d8e65fe29bff0275a |
#!/usr/bin/env python
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/setup.py | Python | apache-2.0 | 6,974 | [
"ORCA"
] | ab2b033ce8c0fcda18621d6713ade713e598a21f528245175ba2871cc7c8c55a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.alchemy.filters import ContainsSpecieFilter, \
SpecieProximityFilter, RemoveDuplicatesFilter, RemoveExistingFilter
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure impor... | dongsenfo/pymatgen | pymatgen/alchemy/tests/test_filters.py | Python | mit | 5,248 | [
"pymatgen"
] | c19a47c484d87216afce6627c6bb627f45ec9a360c1d28cf5809fe356d95ba65 |
#!/usr/bin/env python
import sys
import argparse
import json
import logging
from Bio.Blast import NCBIXML
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger()
def parse_blast(blast, isXML = False):
res = []
finalRes = []
if isXML:
for iter_num, blast_record in enumerate(NCBIXML.parse(b... | TAMU-CPT/galaxy-tools | tools/blast/relatedness_prot.py | Python | gpl-3.0 | 7,784 | [
"BLAST"
] | ea223a14aaf7b6f5bf404a984e5b6af2b1281ce31818696921e7e751a36715df |
# Copyright 2021, 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 agreed to in writing... | tensorflow/federated | tensorflow_federated/python/aggregators/distributed_dp.py | Python | apache-2.0 | 31,668 | [
"Gaussian"
] | 9e315c068ef5752f0eeaa5fd997fd9367f130f69fe2aa0a4b5543cd166409e13 |
from dateutil.relativedelta import relativedelta
from datetime import datetime, date
from django.utils import timezone
from edc_registration.models import RegisteredSubject
from edc_identifier.models import SubjectIdentifier
from edc_constants.constants import FAILED_ELIGIBILITY, OFF_STUDY, SCHEDULED, POS, YES, NO, NO... | TshepangRas/tshilo-dikotla | td_infant/tests/test_infant_feeding_form.py | Python | gpl-2.0 | 14,488 | [
"VisIt"
] | 793c798d58606f117e23aa5f38512b89e60717a21bb610586e4545e4f53dfa78 |
#
# data.py
#
# Reads the dump files.
import numpy as np
import pyvtk as vtk
from vtk import vtkStructuredPointsReader, vtkStructuredGridReader
from vtk.util import numpy_support as VN
class readB0:
"""
readB0 -- Holds the initial magnetic field.
"""
def __init__(self, dataDir = 'data', fileName... | SimonCan/glemur | python/glemur/data.py | Python | gpl-2.0 | 6,178 | [
"VTK"
] | a81af8c834d0e38cce99bb7ed5740ebc1be3e14424bfda2821b191d1f0c8b76d |
import os
import time
import math
import director.vtkAll as vtk
import PythonQt
from PythonQt import QtCore
from PythonQt import QtGui
from director import getDRCBaseDir as getDRCBase
from director import botspy
from director import openscope
import functools
_mainWindow = None
_defaultRenderView = None
def getMainW... | RobotLocomotion/director | src/python/director/applogic.py | Python | bsd-3-clause | 8,190 | [
"VTK"
] | c5f7cad7f689fcfb3177bfcf520ad45c64e4a0cc79af674e31f38f3433a80306 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from logging import warning
from zeroinstall import _
from zeroinstall import support
def get_fetch_info(config, impl):
"""Get the text for a Fetch column."""
if impl is None:
return ""
elif impl.is_... | linuxmidhun/0install | zeroinstall/gui/utils.py | Python | lgpl-2.1 | 1,232 | [
"VisIt"
] | aa463163d2ef1db895fdf69515d94347f0f74e8631c97842c30f5872929006dd |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | samples/visualization_elc.py | Python | gpl-3.0 | 2,920 | [
"ESPResSo"
] | 90d366dd123b6bef984f2a091c5e4ecf9d0c89e535b235c35fbd0e27cd817ca3 |
###############################################################################
# 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/dataSelection/datasetInfoEditorWidget.py | Python | gpl-3.0 | 41,133 | [
"VisIt"
] | 2179495ce1d507f56ee686b7923f69b087a2443a239fef29eb3c06999c6454b0 |
#!/usr/bin/env python
"""Load a texture with alpha from a file and draw with mask."""
import os
import VisionEgg
VisionEgg.start_default_logging(); VisionEgg.watch_exceptions()
from VisionEgg.Core import *
from VisionEgg.Textures import *
import pygame
from pygame.locals import *
filename = os.path.join(VisionEgg.co... | visionegg/visionegg | demo/spiral.py | Python | lgpl-2.1 | 1,893 | [
"Gaussian"
] | 48ddea08a702a6eb0e35c2b643899922b8bf08f3aaddbd91261c38850e764b9a |
# 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... | karllessard/tensorflow | tensorflow/python/keras/activations.py | Python | apache-2.0 | 18,188 | [
"Gaussian"
] | c3f0d73547b36ffe4216d744274c3c3c836c69313b2c72c2401b3f258c283f01 |
#!/usr/bin/python
import os, sys, getopt
import datetime
__version__ = 0.2
#################### UNITS ####################
# Only used with --units flag
econv = 1.0 # Additional Factor for unit conversion if needed (energies)
lconv = 1.0 # Additional Factor for unit conversion if neededa (lengths)
dconv = 1.0 # Addi... | ramisetti/lammps | tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py | Python | gpl-2.0 | 24,135 | [
"LAMMPS"
] | 1cd9a8a344c33e7baa6a83f4c7fd5abc93fc6ab4f4d683a3c339edd9f0c496e6 |
"""
Support for Google - Calendar Event Devices.
For more details about this platform, please refer to the documentation at
https://home-assistant.io/components/google/
NOTE TO OTHER DEVELOPERS: IF YOU ADD MORE SCOPES TO THE OAUTH THAN JUST
CALENDAR THEN USERS WILL NEED TO DELETE THEIR TOKEN_FILE. THEY WILL LOSE THEI... | ewandor/home-assistant | homeassistant/components/google.py | Python | apache-2.0 | 9,604 | [
"VisIt"
] | 12c4e9d06d44badf58b02874130b144dc29cee7c3a14cf8ba31df917fec64881 |
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
""" Contains functionality for doing tree pruning
"""
import copy
import numpy
from rdkit.ML.DecTree import CrossValidate, DecTree
_verbose = 0
def MaxCount(examples):
""" given a set of examples, returns the most common result code
... | ptosco/rdkit | rdkit/ML/DecTree/PruneTree.py | Python | bsd-3-clause | 9,403 | [
"RDKit"
] | 1c7a9666f751425bd0f5945d3e6e17dee4b3983644b37f12232fb5af776ae91c |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 encoded w... | unreal666/outwiker | plugins/webpage/webpage/libs/email/_header_value_parser.py | Python | gpl-3.0 | 105,092 | [
"CRYSTAL"
] | b83111cd29d2389fe10ba7de3dcc946eb85d61a6fc464e669c44e2e9c14f5e85 |
#=== SHADER ==========================================================================================
# Fragment shaders, filters, Frame Buffer Object (FBO)
# Authors: Tom De Smedt, Frederik De Bleser
# License: BSD (see LICENSE.txt for details).
# Copyright (c) 2008 City In A Bottle (cityinabottle.org)
# http://cityi... | est/nodebox-gl | graphics/shader.py | Python | bsd-3-clause | 59,842 | [
"Gaussian"
] | 3b064307a6f0238ada6611c6465c647a2e25f5253fc4764a9af5d05d2ecf43c1 |
# Copyright 2021 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 agreed to in writing, ... | datacommonsorg/data | scripts/us_eia/opendata/process/nuclear.py | Python | apache-2.0 | 5,171 | [
"VisIt"
] | cfa1401a2271678b1ee974faca020909f78d08ab9651e88f41f388463cd77827 |
#!/usr/bin/env python
# HedgehogHD - Vector Graphics Platform Game Engine
# Copyright (C) 2010 Andrew Clunis <andrew@orospakr.ca>
# 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 versio... | orospakr/hedgehoghd | hedgehoghd/importer/sonic2.py | Python | gpl-3.0 | 8,411 | [
"CASINO"
] | 1d72456eef207c3295b9f30726c99cb4d9ed98b0aa00bc812b95fc55c7ef52a3 |
# Definition for a binary tree node
# class TreeNode:
# def __init__(self, x):
# self.val = x
# self.left = None
# self.right = None
# Iterative implementation. This postorder version is more complicated than preorder
# and inorder traversal. More delicate handling of stack is needed.
# ... | lijunxyz/leetcode_practice | binary_tree_postorder_traversal_medium/Solution2.py | Python | mit | 1,549 | [
"VisIt"
] | 347724b882250cae7f4da540984f919510e7899f04c21e9a5bf434ecdce8ac1b |
#!/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/dft/gen_xcfun_param.py | Python | apache-2.0 | 5,050 | [
"PySCF"
] | 7451462edc0af250924e4ddbd07982a30db963c76792ff62d74c6bfbbcbaa91a |
#! /usr/bin/env python
# coding=utf8
# ECDSA BTC of FastSignVerify
# Copyright (C) 2014 Antoine FERRON
# Some portions based on :
# "python-ecdsa" Copyright (C) 2010 Brian Warner (MIT Licence)
# "Simple Python elliptic curves and ECDSA" Copyright (C) 2005 Peter Pearson (public domain)
# "Electrum" Copyright (C) 2011... | antonio-fr/AddressGen_BTChip | ECDSA_BTC.py | Python | gpl-3.0 | 12,133 | [
"Brian"
] | 3390f87ca038fef4355af88b6b52e45436d7c197e7912fa3327dc319602968f1 |
"""
Module to build install the azorange package.
Specific versions of dependencies are needed, eg gcc.
"""
import commands
import os
from optparse import OptionParser
import string
import sys
import traceback
import types
# Needed for modules to be loaded.
def module(command, *arguments):
#status = commands.gets... | AZCompTox/AZOrange | setup.py | Python | lgpl-3.0 | 58,633 | [
"CDK",
"RDKit"
] | a93e59c55f9f011807e791246a5f76fb255e63c0ac6d35120f30424b5f96aca7 |
"""
Tests for django.utils.
"""
from unittest import TestCase
from django.utils import html, checksums
import timesince
import datastructures
from decorators import DecoratorFromMiddlewareTests
# Extra tests
__test__ = {
'timesince': timesince,
'datastructures': datastructures,
}
class TestUtilsHtml(TestCa... | paulsmith/geodjango | tests/regressiontests/utils/tests.py | Python | bsd-3-clause | 5,384 | [
"ADF"
] | 0005a0e3e09379698b74d1dbc261e56aa6ea970705c6544f8a6b62d17a13d1fd |
#!/usr/bin/env python3
# This Script is FAR from complete, and may or may not ever get completed...
# Copyright (C) Jacob J. Walker
#
# The code was influenced by Simon Law's apt-rdepends pearl script
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Publ... | JacobJWalker/DescartesDaemon | tools/create_udpkg_commands.py | Python | gpl-2.0 | 4,442 | [
"Brian"
] | e4f32173df0fea953906296ab5e251b705b7ab7cae3e3cecc7ec269f0970d931 |
"""
.. class:: LineFittingLibrary
.. moduleauthor:: Johan Comparat <johan.comparat__at__gmail.com>
This class contains a variety of function to fit emission or absorption lines in galaxy spectra.
"""
from scipy.optimize import curve_fit
import numpy as n
import matplotlib
matplotlib.use('pdf')
import matplotlib.pypl... | JohanComparat/pySU | galaxy/python/LineFittingLibrary.py | Python | cc0-1.0 | 49,598 | [
"Galaxy",
"Gaussian"
] | b51cc0e15d36e040a9e70f58624739da31b90a129225ad87d01a0580394e4888 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/single_feature/best_kNN_PCA/test11_cross_validate_objects_1200ms_scaled_method_v_area.py | Python | mit | 4,922 | [
"Mayavi"
] | 53bc98ff4e285d3dbfbdf048d4b32e9d7c2174401f2aff49785ad501889bcd21 |
from os.path import join
from contextlib import contextmanager
from galaxy.util import parse_xml_string
from tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
TEST_DEPENDENCIES_DIR = "/opt/galaxy/depen... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/tool_shed_unit_tests/test_td_common_util.py | Python | gpl-3.0 | 3,594 | [
"Galaxy"
] | 11ec1b6d1b704e9cc1baa4f8fb4917458d0bb2c3abab4bb17323b23f00c7c913 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | uflow/uflow_utils.py | Python | apache-2.0 | 50,720 | [
"Gaussian"
] | d14336fdca7d1338d557ea1d888b0d9c5299cf26ae8ce76d23ab21129b79846d |
# ----------------------------------------------------------------------------
# pyglet
# Copyright (c) 2006-2008 Alex Holkner
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistribu... | NiclasEriksen/py-towerwars | src/pyglet/graphics/__init__.py | Python | cc0-1.0 | 26,048 | [
"VisIt"
] | 705d57cbacd146a1adfd7900988ec4b8d386d207ed8cd21813a1df4ef1f6b632 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Constant-Q transforms"""
from __future__ import division
import warnings
import numpy as np
from numba import jit
from . import audio
from .fft import get_fftlib
from .convert import cqt_frequencies, note_to_hz
from .spectrum import stft, istft
from .pitch import estim... | bmcfee/librosa | librosa/core/constantq.py | Python | isc | 42,171 | [
"Brian"
] | 3f98b02fe80fb0dbab154d5bd7a815d2ace896bb7c6d797bf1e46879712e05aa |
'''
This library is used to manipulate the sam and bam files. You can merge bams and
add some xtra information to sams
Created on 05/01/2010
@author: peio
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of franklin.
# franklin is free software: you can redistrib... | JoseBlanca/franklin | franklin/sam.py | Python | agpl-3.0 | 26,699 | [
"pysam"
] | 0b07fa028d8f0f812e6571191d85279be02daf7bef817be3638038b2c3352428 |
import pickle
import gzip
import os, sys, errno
import time
import math
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy itself
import numpy.distut... | bajibabu/merlin | src/work_in_progress/oliver/run_dnn_hourly_check.py | Python | apache-2.0 | 52,699 | [
"NEURON"
] | dd5282347f49a2b25bd6bb9dfe9fa0e0a273704c0f11346d72bc411a308ebd5c |
"""A GTK dialog which lets the user add a new application to their desktop."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os
import gtk
from zeroinstall.gtkui import gtkutils
from zeroinstall.support.tasks import get_loop
fro... | turtledb/0install | zeroinstall/gtkui/addbox.py | Python | lgpl-2.1 | 5,035 | [
"VisIt"
] | 590b1bdf02668382da9413bf73b0ad33ee1adb07c33c85c528d0c2dea3ba96db |
#!/usr/bin/python
# 04.10.2005
# last revision: 03.09.2007
import sys
import os.path as op
if (len( sys.argv ) == 3):
filename_in = sys.argv[1];
filename_out = sys.argv[2];
else:
print 'Usage: ', sys.argv[0], 'file.mesh file.vtk'
sys.exit()
if (filename_in == '-'):
file_in = sys.stdin
else:
fi... | certik/sfepy | script/mesh_to_vtk.py | Python | bsd-3-clause | 2,962 | [
"VTK"
] | 5eb69e99971345fbc67f8cab42d8edb20b3daf13749adc1fb9ca69531e5f6a56 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | tlksio/tlksio | env/lib/python3.4/site-packages/pylint/utils.py | Python | mit | 23,940 | [
"VisIt"
] | 8b5c010761f27c79755a14928dd04656f5fd05e00f17ff906b04f640b47401c2 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | hryamzik/ansible | lib/ansible/modules/network/avi/avi_hardwaresecuritymodulegroup.py | Python | gpl-3.0 | 3,636 | [
"VisIt"
] | 2bc19441947a97f4a3017d126c8b03f29e9d835f4acb31606ffb6e4f42b260ba |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.util.string import formula_double_format, latexify, \
latexify_spacegroup, transformation_to_string, htmlify, unicodeify, \
disordered_formula, unicodeify_spacegroup, uni... | fraricci/pymatgen | pymatgen/util/tests/test_string_utils.py | Python | mit | 3,333 | [
"pymatgen"
] | 7e13c6da17a916f9529be87f5fed0e54b5e74f83f580d96b7cd7229e875fecf7 |
"""
Serializes a Cython code tree to Cython code. This is primarily useful for
debugging and testing purposes.
The output is in a strict format, no whitespace or comments from the input
is preserved (and it could not be as it is not present in the code tree).
"""
from Cython.Compiler.Visitor import TreeVisitor
from C... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/Cython/CodeWriter.py | Python | agpl-3.0 | 15,220 | [
"VisIt"
] | 4faaf2f7ffae75f8cab088f9f6db4f35526459fd4dcc7ffa544be421fe1d8740 |
#!/usr/bin/env python
'''
File name: main_make_MAP_PAXINO.py
Author: Guillaume Viejo
Date created: 28/09/2017
Python Version: 3.5.2
'''
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
from pylab import *
from sklearn.decompositio... | gviejo/ThalamusPhysio | python/main_make_MAP_PAXINO.py | Python | gpl-3.0 | 8,302 | [
"Gaussian"
] | 931bdf6bcdaab5e07476fdd30a8b37ee7cbdda170e4f1753e0eea156d68c796e |
import os
from bs4 import BeautifulSoup
from decimal import Decimal as D
from ..base import BaseAccountScraper
class UbankAccountScraper(BaseAccountScraper):
scrape_code = 'ubank'
default_currency = 'AUD'
def login(self):
self.browser.visit('https://www.ubank.com.au')
with self.browser.... | elbaschid/geldmaschine | geldmaschine/scrapers/au/ubank.py | Python | mit | 1,753 | [
"VisIt"
] | 09f4aba7e896de34ab4e664e76d92ad1a02f8ab79ef53d30c43cf8698b3d751e |
'''Single neuron models.
.. inheritance-diagram:: NeuronAndGenerator
:parts: 2
.. autosummary::
OneNeuronNetwork
NeuronAndGenerator
'''
import numpy as np
import logging as lg
from numpy.random import rand, randn
from . import gc_neurons
from .gc_net import GridCellNetwork
from simtools.storage i... | MattNolanLab/ei-attractor | grid_cell_model/models/gc_single_neuron.py | Python | gpl-3.0 | 7,015 | [
"NEURON"
] | 11822ccacb5f6448c9f92466ae8df948f75447f8db72336acf60763a69d22a82 |
#!/usr/bin/env python
"""
Visualize and modify Parameters, PDFs and Response Functions
This file is part of PUQ
Copyright (c) 2013-2016 PUQ Authors
See LICENSE file for terms.
"""
from __future__ import absolute_import, division, print_function
import matplotlib
matplotlib.use('TkAgg', warn=False)
import scipy
impor... | c-PRIMED/puq | puq/read.py | Python | mit | 36,764 | [
"Gaussian"
] | d211eaaee49aad85e6699b24f7bcd0fdbf10a124281fe60c08c9fde0d323379e |
# Copyright(C) 2011-2019 by
# Ben Edwards <bedwards@cs.unm.edu>
# Aric Hagberg <hagberg@lanl.gov>
# Konstantinos Karakatsanis <dinoskarakas@gmail.com>
# All rights reserved.
# BSD license.
#
# Authors: Ben Edwards (bedwards@cs.unm.edu)
# Aric Hagberg (hagberg@lanl.gov)
# Konstanti... | sserrot/champion_relationships | venv/Lib/site-packages/networkx/generators/community.py | Python | mit | 34,998 | [
"Gaussian"
] | 7e2ae7bcdfc7cf8b539891c8ca3d5d0dd44f1255fd8246a824aeb3954c12a1b1 |
#!/usr/bin/env python3
# ver 0.1 - coding python by Hyuntae Jung on 02/25/2017
# ver 0.2 - support pdb and dcd files for openmm on 5/8/2017
# ver 0.3 - support xtc trajectory files for Monte Carlo using "reduce_unitcells_3d_to_1d" on 6/6/2017
# ver 0.4 - support block average module on 6/26/2017 and remove out agai... | jht0664/Utility_python_gromacs | python/conv_1d.py | Python | mit | 6,252 | [
"OpenMM"
] | d915a6baa5bcf529cc9e665986dc87eb3716d1f60abc9cae9df9905f1bb611c4 |
# -*- coding: utf-8 -*-
#
# test_sp_manager.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License... | sanjayankur31/nest-simulator | testsuite/pytests/test_sp/test_sp_manager.py | Python | gpl-2.0 | 5,678 | [
"Gaussian"
] | 2819d47b2d99f342cefa37c6f47db45f0c3f042b53849a403a13e2249ac7ed8d |
# Script to create a latitude-longitude plot of potential temperature
# from a NetCDF data file
import netCDF4
import matplotlib.pyplot as plt
# Open the data file
nc = netCDF4.Dataset('../data/pottmp.2014.1time.nc')
# Get a handle to the variable (this doesn't actually read any data yet)
pottmp = nc.variables['pottm... | jonblower/python-viz-intro | Lesson 3. Plotting data from NetCDF files/temperature.py | Python | bsd-3-clause | 914 | [
"NetCDF"
] | 44e119c58a1add3ad3e35d6b1dbec9d7725d6fa09a58fb289125c642e087cccf |
# author: brian dillmann
# for rscs
import RPi.GPIO as GPIO, time
class AnalogInput:
def __init__(self, name, loc):
if not isinstance(loc, (int, long)):
raise TypeError('Output Location must be an integer')
if not name.replace(' ', '').isalnum():
raise ValueError('Device names must only contain letters, n... | dillmann/rscs | lib/Devices/AnalogInput.py | Python | mit | 635 | [
"Brian"
] | 9777d4e1465b99256535e614dd774a853d213b125b0264143235185be2be7992 |
#!env/python3
# coding: utf-8
import os
import sys
import datetime
import sqlalchemy
import subprocess
import reprlib
import time
import psycopg2
import threading
from progress.bar import Bar
from sqlalchemy import Table, Column, Integer, String, Boolean, ForeignKey, Sequence, UniqueConstraint, Index, func, distinct... | REGOVAR/Sandbox | benchs/db/sandbox/poc_009.py | Python | agpl-3.0 | 7,532 | [
"pysam"
] | 83ec84595a8e823eec2ca45b19fc3f11d1e4db0489f06f1118c0460c0fa430d2 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | sam-m888/gramps | gramps/gen/filters/rules/place/_hassourcecount.py | Python | gpl-2.0 | 1,791 | [
"Brian"
] | 8639c9d4cac5213abecad60ab7cb8ca9697d6e3bfc4ca7deb6c04db379431d04 |
# Copyright (c) 2020, Michael Boyle
# See LICENSE file for details: <https://github.com/moble/scri/blob/master/LICENSE>
### NOTE: The functions in this file are intended purely for inclusion in the AsymptoticBondData
### class. In particular, they assume that the first argument, `self` is an instance of
### Asymptoti... | moble/scri | scri/asymptotic_bondi_data/constraints.py | Python | mit | 8,379 | [
"Psi4"
] | a6fd4f1eba4859bfd3a1986ace3541b34ab7eadc8c5391dfe8351d1d5aeaabd2 |
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.cos.AdaptiveNEB import AdaptiveNEB
from pysisyphus.optimizers.ConjugateGradient import ConjugateGradient
from pysisyphus.run import run_from_dict
from pysisyphus.testing import using
def test_anapot_aneb():
calc = AnaPot()
all_geoms = calc.get_p... | eljost/pysisyphus | tests/test_adaptive_neb/test_adaptive_neb.py | Python | gpl-3.0 | 1,348 | [
"PySCF"
] | d03efbf187a709ad955c924c21796df4f6062ef60cd3191a29e93baf3b25caaa |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import os, random, sys, time
import urllib.parse
from selenium import webdriver
from bs4 import BeautifulSoup
def Launch():
# Check if the file 'config' exists, otherwise quit
if os.path.isfile('config') == False:
print ('Error! No configuration file.')
... | HoussemCharf/FunUtils | Bots/linkedinViewerBot.py | Python | mit | 8,390 | [
"VisIt"
] | a0295005265df3767f90cb998443c7920ac1a8d85101a8a078ce3a35e72424eb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# Copyright 2015 Kitware Inc.
#
# 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 cop... | cjh1/cumulus | girder/cumulus/plugin_tests/aws_test.py | Python | apache-2.0 | 25,844 | [
"ParaView"
] | e839252c458fc19debae966247467615409c7b6fc24149fb0dbae3216d957e34 |
# -*- coding: utf-8 -*-
##
# Copyright (C) 2015 Jessica Tallon & Matt Molyneaux
#
# This file is part of Inboxen.
#
# Inboxen is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either versio... | Inboxen/Inboxen | inboxen/tests/example_emails.py | Python | agpl-3.0 | 105,372 | [
"VisIt"
] | 6c6ca693f686943010b1f56447f457e37b9c21944a88d196e2b5441fb99bcc3d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
### Simpificated buldozer simulation with VTK recorder
from woo import utils
from numpy import linspace
from numpy import arange
import gts
import itertools
from woo import geom,pack
###Initial Data
numKnifeParts = 10
radiusKnife=1
lengthKnife=2
buldozerHeight=1.2
radiusSph =... | woodem/woo | obsolete/examples/bulldozer/bulldozerVTK.py | Python | gpl-2.0 | 3,225 | [
"VTK"
] | e5ff7eb81410275e556a4f4d5779bce248701b02a6e33b0ead6858e66f1abae2 |
"""This module defines an ASE interface to NWchem
http://www.nwchem-sw.org/
"""
import os
import numpy as np
from ase.atoms import Atoms
from ase.units import Hartree, Bohr
from ase.io.nwchem import write_nwchem
from ase.calculators.calculator import FileIOCalculator, Parameters, ReadError
class KPoint:
def __... | grhawk/ASE | tools/ase/calculators/nwchem.py | Python | gpl-2.0 | 10,727 | [
"ASE",
"Gaussian",
"NWChem"
] | 89b12ba45da89f55c920f5d6449f89bb301ff5471cd88ec43a16b89374255306 |
import os
import sys
import glob
from ase.test.tasks.analyse import AnalyseOptimizersTask as Task
def get_optimizer_shortname(optimizer):
name = {
'FIREE19': 'FIRE\neigenstates 1.e-9',
'GoodOldQuasiNewtonD16': 'GoodOldQuasiNewton\ndensity 1.e-6',
'BFGSLineSearch': 'BFGSLineSearch',
... | robwarm/gpaw-symm | doc/devel/ase_optimize/task_analyse.py | Python | gpl-3.0 | 1,384 | [
"ASE"
] | ffaac36d62e645ae01571a6868af57a2028e95f328fb3cd72d84c9717c6fabcb |
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