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from __init__ import *
# determine the thermal state of the IGM due to photoheating
## blazar heating rate
#plheatbl = 10**(0.0315 * (1. + red)**3 - 0.512 * (1. + red)**2 + 2.27 * (1. + red) - 2.38) / 3.154e22 # [MeV/s]
#plheatbl[where(gdat.meanreds gt 5.7)] = 0.
## photoheating rate
# phhe... | tdaylan/tdgu | phot_ionz.py | Python | mit | 74,435 | [
"Galaxy"
] | d23622653f84661d22c166c9984ecc11ef12c6dec2f4c3fd85cf15f5845d9bb9 |
import pickle
from sklearn.cluster import KMeans
from image import *
def find_centroids(folder, n_images, n_centroids):
"""
find <n_centroids> centroids of descriptors of <n_images> in <folder> using KMeans
"""
print "Finding visual vocabulary, This may take a while..."
print "Getting descriptors..."
descriptors... | gabrielilharco/sketch-bot | src/visual_vocabulary.py | Python | mit | 2,430 | [
"Gaussian"
] | 933006143676e1ada0871a34e318928b076a3f5cdd5615dab297d97183159ecb |
"""Module containing element dict, species and reaction classes, and constants.
"""
# Python 2 compatibility
from __future__ import division
# Standard libraries
import math
import numpy as np
__all__ = ['RU', 'RUC', 'RU_JOUL', 'PA', 'get_elem_wt',
'ReacInfo', 'SpecInfo', 'calc_spec_smh']
# universal ga... | kyleniemeyer/pyJac | pyjac/core/chem_utilities.py | Python | mit | 10,063 | [
"Avogadro"
] | d01d5b88d4a46806819b5e52eaf02fbed63ad13e834bc26af99b284b8adaa85f |
#!/usr/bin/env python
# Copyright 2016 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... | mkumatag/origin | vendor/github.com/google/cadvisor/build/boilerplate/boilerplate.py | Python | apache-2.0 | 4,780 | [
"VisIt"
] | 071483c60e77a76944e155f7113cdd57b4ce52353ae8b256bd0fc959835f078d |
# pylint: disable=W0622,R0903,R0902,R0913,W0633
"""Functions and objects to manipulate materials.
A material is an object with a refractive index function.
"""
from builtins import str
from builtins import object
from functools import partial
import numpy
from scipy.integrate import quad
from EMpy.constants import ... | DavidRimel/EMpy | EMpy/materials.py | Python | mit | 10,639 | [
"CRYSTAL"
] | 9b78aaa5fafda1303ea2151bf1b5c9fcb9aeab65cdcef500908b6bafaac7e93e |
from django.db.models.query import QuerySet
from django.db.models import get_models, get_app, get_model
from edc.lab.lab_requisition.models import BaseRequisition
from edc_sync.models import BaseSyncUuidModel
from edc_consent.models import BaseConsent
from ..exceptions import (
AlreadyDispatchedItem, AlreadyRetur... | botswana-harvard/edc-dispatch | edc_dispatch/classes/base_dispatch_controller.py | Python | gpl-2.0 | 13,625 | [
"VisIt"
] | 0f22772b98eb4f2b8b7fd896b5359800205152ff2b8f139f6e8d5e91a32717ec |
import json
import logging
from datetime import datetime
import ddt
from django.urls import reverse
from django.http import Http404
from django.test.client import Client, RequestFactory
from django.test.utils import override_settings
from django.utils import translation
from edx_django_utils.cache import RequestCache
... | jolyonb/edx-platform | lms/djangoapps/discussion/tests/test_views.py | Python | agpl-3.0 | 86,375 | [
"VisIt"
] | 0b8ddcaa62bf62a5a3f18f9db8aa481ca10f27543d7281486072dcddc954a755 |
#! /usr/bin/python3.5m
#
# Copyright (C) 2016, Jaguar Land Rover. All Rights Reserved.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
#
from vsi_py import *... | rstreif/vehicle_signal_interface | python-interfaces/tests/send.py | Python | mpl-2.0 | 373 | [
"Jaguar"
] | 03bca6161fbae00e9f439a39a320795601a02e7a65dc84c11a9da7329274f392 |
r"""
variational formulation described at https://www.authorea.com/users/23640/articles/61529
Inspired from http://sfepy.org/doc-devel/examples/diffusion/poisson_field_dependent_material.html
Help thread: https://groups.google.com/forum/#!msg/sfepy-devel/dbEy3I3jSOg/mxQJEkpOCAAJ
cd ~bin/sfepy
./simple.py SEP_pdf/EnvG... | sergeetiparent/EnvGeotech | Richards-Buckingham_SfePy.py | Python | mit | 3,901 | [
"Mayavi",
"VTK"
] | 1924356d0771a70f918e0f1c1b562333f410e2378599454740e935d2574e0ae5 |
"""Gauss-Gegenbauer quadrature rule."""
import numpy
import chaospy
from .hypercube import hypercube_quadrature
def gegenbauer(order, alpha, lower=-1, upper=1, physicist=False):
"""
Gauss-Gegenbauer quadrature rule.
Compute the sample points and weights for Gauss-Gegenbauer quadrature. The
sample po... | jonathf/chaospy | chaospy/quadrature/gegenbauer.py | Python | mit | 2,162 | [
"Gaussian"
] | 636439f44cb0cd201f843da316d2c65eec25ade7f480c4afac9716805f7ddf0b |
#!/usr/bin/env python
'''
Scanning Cr2 molecule dissociation curve with regular CASSCF module (see
examples/mcscf/31-cr2_scan) is not a difficult task. The calculation becomes
challenge when large active space is required in the DMRG-CASSCF (or
FCIQMC-CASSCF, SHCI-CASSCF) methods. In this example, we demonstrated
ho... | gkc1000/pyscf | examples/dmrg/31-cr2_scan/cr2-scan.py | Python | apache-2.0 | 4,186 | [
"PySCF"
] | bfd511e8de9e84201b8e35d70899128b42effbd32572f9afced602daf8c50830 |
"""
Tests for conformers.py.
"""
import numpy as np
import unittest
from rdkit import Chem
from rdkit_utils import conformers
class TestConformerGenerator(unittest.TestCase):
"""
Tests for ConformerGenerator.
"""
def setUp(self):
"""
Set up tests.
"""
aspirin_smiles =... | skearnes/rdkit-utils | rdkit_utils/tests/test_conformers.py | Python | bsd-3-clause | 4,565 | [
"RDKit"
] | f05b7d4349419a1d3199e535b9ac649095a7c3ea6f50b33bcb601a79d3fb2ffe |
# $HeadURL: $
''' LogPolicyResultAction
'''
from DIRAC import S_OK, S_ERROR
from DIRAC.ResourceStatusSystem.Client.ResourceManagementClient import ResourceManagementClient
from DIRAC.ResourceStatusSystem.PolicySystem.Actions.BaseAction import BaseAction
__RCSID__... | marcelovilaca/DIRAC | ResourceStatusSystem/PolicySystem/Actions/LogPolicyResultAction.py | Python | gpl-3.0 | 2,850 | [
"DIRAC"
] | 733768d27b798706ac585049cc9b05540b838377de4fc31f869282f6a5133d5b |
"""
Migration script to add the repository_review, component_review and component tables and the Repository Reviewer group and role.
"""
import datetime, logging, sys
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
# Need our custom types, but don't import any... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py | Python | gpl-3.0 | 9,186 | [
"Galaxy"
] | 14aa7db4bbcabd4010ce8f09730c519b87cf1d08d8306d3e22197b8e3eaad1a0 |
import os
import subprocess
from itertools import chain
from pathlib import Path
import pytest
from netCDF4 import Dataset
from pkg_resources import resource_filename
from compliance_checker.cf import CF1_6Check, CF1_7Check, util
from compliance_checker.suite import CheckSuite
def glob_down(pth, suffix, lvls):
... | ioos/compliance-checker | compliance_checker/tests/conftest.py | Python | apache-2.0 | 2,945 | [
"NetCDF"
] | f1b0e3241ec36424c5106e2c3d6b326bdbe8df4090c9af6264601d90c7dfa1e5 |
"""
Convenience functions for the construction of spatial weights based on
contiguity and distance criteria
"""
__author__ = "Sergio J. Rey <srey@asu.edu> "
__all__ = ['queen_from_shapefile', 'rook_from_shapefile', 'knnW_from_array', 'knnW_from_shapefile', 'threshold_binaryW_from_array', 'threshold_binaryW_from_shapef... | anitagraser/processing_pysal | ext-libs/pysal/weights/user.py | Python | gpl-2.0 | 33,894 | [
"COLUMBUS",
"Gaussian"
] | 78584ed20f9b51b44bf7b395b01e428395d4b18afe16556bd1bb9a25cc24f2bd |
from django.utils.translation import ugettext_lazy as _
from corehq.apps.app_manager import id_strings
from corehq.apps.app_manager.const import (
SCHEDULE_DATE_CASE_OPENED, SCHEDULE_LAST_VISIT, SCHEDULE_LAST_VISIT_DATE,
SCHEDULE_GLOBAL_NEXT_VISIT_DATE, SCHEDULE_NEXT_DUE
)
from corehq.apps.app_manager.exception... | qedsoftware/commcare-hq | corehq/apps/app_manager/suite_xml/features/scheduler.py | Python | bsd-3-clause | 5,692 | [
"VisIt"
] | fa1bf5cf854af02561bb7aa944e2df1cd559c634b52ffed01766afc5c52e8e0a |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon
#
# MDTraj i... | daviddesancho/mdtraj | mdtraj/nmr/shift_wrappers.py | Python | lgpl-2.1 | 12,675 | [
"MDTraj"
] | 0e0d00cad144bc50d07c95f05fc1f3c44cbffb9d104a8df7ae28cd69d9e3e7cf |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/autograph/converters/slices.py | Python | apache-2.0 | 2,836 | [
"VisIt"
] | 1fb50756e60e9fda4d4fedcb7a537ecbdd864ccedc1a4251d67d6a131fd04dd4 |
#!/usr/bin/env python
"""
"""
import vtk
def view_frog(fileName, tissues):
colors = vtk.vtkNamedColors()
tissueMap = CreateTissueMap()
colorLut = CreateFrogLut()
# Setup render window, renderer, and interactor.
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWind... | lorensen/VTKExamples | src/Python/Visualization/ViewFrog.py | Python | apache-2.0 | 5,808 | [
"Gaussian",
"VTK"
] | 03b35fccf71e751fb1e2c912c7b39c2713e1c4cef65dabf90291ff6552293654 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/scf/stability.py | Python | apache-2.0 | 11,808 | [
"PySCF"
] | af2b78561e35b2d29119aee6bce3807d372872f244904ab9a6c1f693f82c3be5 |
#
# This file is part of Healpy.
#
# Healpy 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.
#
# Healpy is distributed in the h... | zonca/healpy | healpy/sphtfunc.py | Python | gpl-2.0 | 33,454 | [
"Gaussian"
] | 08d8008540b7cfd91ca420db0ddd9b5a5d468bee96318f55494019db6c1c3d35 |
# 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... | wvangeit/python-mode | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/variables.py | Python | lgpl-3.0 | 30,288 | [
"VisIt"
] | a562261180b333bcc958e5c886b9f847b2d9a1b6ee388bf26835f7571f0034ee |
# Copyright 2016 James Hensman
#
# 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, so... | jameshensman/VFF | experiments/setting_a_b_M/gpr_special.py | Python | apache-2.0 | 4,803 | [
"Gaussian"
] | 264ad2de2d9e15c3c11df3e06d41eefcb45b7faa611b9c1433f50bfad39e963b |
"""
GSIServer - Contributed by Ivan R. Judson <judson@mcs.anl.gov>
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# ... | xyproto/turbine | djl/libs/SOAPpy/GSIServer.py | Python | gpl-3.0 | 5,031 | [
"Brian"
] | cfd927dd518a7eefe8e715b1de444902adc5cf8b9ddf26dbbf84ab6031c89f26 |
# -*- coding: utf-8 -*-
# (c) Nelen & Schuurmans. GPL licensed, see LICENSE.rst.
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import division
from openradar import calc
from openradar import config
from openradar import io
from openradar import utils
from openradar i... | tomvansteijn/openradar | openradar/scans.py | Python | gpl-3.0 | 39,459 | [
"ASE"
] | 4ba5f5d4abfb35729415f995d16ba75a0bde867d699c2cf1b71d45a211ce005a |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | samples/immersed_boundary/addBending.py | Python | gpl-3.0 | 1,445 | [
"ESPResSo"
] | 272b67b3de743ec5145e5c6bec51939ca3b34779a8dd799d1474d5b02174778d |
########################################################################
# File : ServerUtils.py
# Author : Ricardo Graciani
########################################################################
"""
Provide uniform interface to backend for local and remote clients (ie Director Agents)
"""
__RCSID__ = "$Id$"
de... | arrabito/DIRAC | WorkloadManagementSystem/Client/ServerUtils.py | Python | gpl-3.0 | 1,610 | [
"DIRAC"
] | 1f7c2563293db0efa38cd3647bd9393586cb82a929709bd106c7309b332a5447 |
#! /usr/bin/env python
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
import nose
from nose.tools import assert_equal, assert_true
import numpy as np
import pymatgen as pmg
from sknano.core import rezero_array
from sknano.core.crystallography import Crystal2... | scikit-nano/scikit-nano | sknano/core/crystallography/tests/test_xtal_lattices.py | Python | bsd-2-clause | 23,776 | [
"pymatgen"
] | e12dc2e574490d24d625447d0d7e890d1869e807d4e13c8f8d2acfe7e337d829 |
GREEK = {
r"\alpha" : ("mi", {}, "var", "α"),
r"\beta" : ("mi", {}, "var", "β"),
r"\gamma" : ("mi", {}, "var", "γ"),
r"\digamma" : ("mi", {}, "var", "ϝ"),
r"\delta" : ("mi", {}, "var", "δ"),
r"\epsilon" : ("mi", {}, "var", "ϵ"),
r"\varepsilon" ... | fourpoints/addup | mumath/Context/UNICODE.py | Python | mit | 15,088 | [
"Bowtie"
] | 62b2171896ba3bea89e88eb229d9f7192fe8c73b4996ff1f08638ffe081416ce |
###############################################################################
# TriaxialGaussianPotential.py: Potential of a triaxial Gaussian stratified
# on similar ellipsoids
#
# \rho(x,y,z) ~ exp(-m^2/[2\sigma^2])
#
# ... | jobovy/galpy | galpy/potential/TriaxialGaussianPotential.py | Python | bsd-3-clause | 4,023 | [
"Gaussian"
] | b5ffc2044a0a3fbe553cfb6809a294a2940111acbf78ebf97eba5e8d3d8f9189 |
# Copyright 2020 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, ... | google-research/dice_rl | environments/env_policies.py | Python | apache-2.0 | 18,345 | [
"Gaussian"
] | 1803fee54366434db58aba8935b71f5c538c49b52d859e70ed25899590eae1f3 |
#!/usr/bin/env python2
import sys
sys.path.append('../../../src/')
import cgmap as cg
import mdtraj as md
import md_check as check
############################### config #####################################
input_traj = "dppc.trr"
input_top = "dppc.pdb"
input_maps = ["mapping_bead_1_dppc",
"mapping_... | uchicago-voth/cgmap | test/molecular_map_test/same_molecules_shared_map_naive_com/test_same_molecules_shared_map_naive_com.py | Python | apache-2.0 | 2,338 | [
"MDTraj"
] | c26cf9c944ff2fb224735643d605bd58d28af641af1f40badff76e53ea0dfbb4 |
from distutils.core import setup
from ductape import __version__
from os import path
here = path.abspath(path.dirname(__file__))
with open(path.join(here, 'README.md')) as f:
long_description = f.read()
setup(
name = 'DuctApe',
version = __version__,
author = 'Marco Galardini',
author_email ... | combogenomics/DuctApe | setup.py | Python | bsd-2-clause | 1,083 | [
"Biopython"
] | 11f91cebb9ec6259626a883e1fe0f1a34492d9ddcf485c9858ca6dfdfe18de5d |
import os
import shutil
import math
import torch
import numpy as np
import matplotlib.pyplot as plt
import pyprob
from pyprob import Model, InferenceEngine
from pyprob.distributions import Uniform, Normal
plt.switch_backend('agg')
class GaussianWithUnknownMeanMarsaglia(Model):
def __init__(self, prior_mean=1, pr... | probprog/pyprob | tests/extra/inference_compilation/gum_marsaglia.py | Python | bsd-2-clause | 6,116 | [
"Gaussian"
] | a2ba7bc86f57c8f99739d82d2a33153012e4cd0d0682864d9cb19d4580d930d0 |
import json
import logging
from difflib import ndiff
import waffle
from django import forms
from django.conf import settings
from django.core.exceptions import ObjectDoesNotExist
from django.forms.widgets import CheckboxSelectMultiple
from django.template.loader import render_to_string
from django.utils import transla... | yfdyh000/kuma | kuma/wiki/forms.py | Python | mpl-2.0 | 37,655 | [
"VisIt"
] | 1e91b3865f243861de8417c9c0442e163399db14c432414ffb26003d68c75383 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
float_or_none,
int_or_none,
parse_duration,
parse_iso8601,
remove_end,
unescapeHTML,
)
from ..compat import (
compat_etree_fromstring,
compat_HT... | AMOboxTV/AMOBox.LegoBuild | script.module.youtube.dl/lib/youtube_dl/extractor/bbc.py | Python | gpl-2.0 | 41,565 | [
"VisIt"
] | 9f14bbeca23d21a8cc376d72462c2444dafc062528d134b0ed8b336626f45c6b |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy as np
node = import_file("../../files/CFG/shear.void.120.cfg")
# Apply smoe strain to the atoms.
node.modifiers.append(AffineTransformationModifier(
transformation = [[1,0.1,0,0],[0,1,0,0.8],[0,0,1,0]],
transform_box = True
... | srinath-chakravarthy/ovito | tests/scripts/test_suite/atomic_strain_modifier.py | Python | gpl-3.0 | 2,045 | [
"OVITO"
] | ba4711bf21aa7556dd097707a1861d5fc2ab795d3bf3a1dee553ecb67393b6dd |
#!/usr/bin/env python
#
# IThugAPI.py
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; ... | palaniyappanBala/thug | src/ThugAPI/IThugAPI.py | Python | gpl-2.0 | 12,995 | [
"Galaxy"
] | fb8f65de1772226b0d74008cdf01d7af8f849304188e55bf74bf368ec43de7d2 |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
"""
Django settings for rvi p... | rstreif/rvi_backend | settings.py | Python | mpl-2.0 | 6,670 | [
"Jaguar"
] | 8b963d26101dd0c658c14d7c45a4f3b9891514efde7bf1da9642288b7b12fe0f |
"""
Provides factory methods to assemble the Galaxy web application
"""
import sys
import os
import os.path
import atexit
import warnings
import glob
from paste import httpexceptions
import pkg_resources
import galaxy.model
import galaxy.model.mapping
import galaxy.datatypes.registry
import galaxy.web.framework
impo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py | Python | gpl-3.0 | 31,390 | [
"Galaxy"
] | cc0bfa927990f45b2d1e82bd524ed98a73b7013f2921551eab328b877adb3c0c |
#
# Copyright 2021 Lars Pastewka (U. Freiburg)
# 2021 Jan Griesser (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licen... | libAtoms/matscipy | tests/test_bulk_properties.py | Python | lgpl-2.1 | 6,833 | [
"ASE",
"Matscipy"
] | 824ff3ea053127dfc39ad50e8e551322a8218aa69bb78a3afc351266db8161de |
""" FTS3Job module containing only the FTS3Job class """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id $"
import datetime
import errno
# Requires at least version 3.3.3
import fts3.rest.client.easy as fts3
from fts3.rest.client.exception... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Client/FTS3Job.py | Python | gpl-3.0 | 31,176 | [
"DIRAC"
] | 7cff80b89e7f724141ede09550c0f636da03654717aa2c071cb5e4adf669efe5 |
# -*- coding: utf-8 -*-
__version__ = '0.4.0.dev0'
PROJECT_NAME = "starforge"
PROJECT_OWNER = PROJECT_USERNAME = "galaxyproject"
PROJECT_AUTHOR = 'Galaxy Project and Community'
PROJECT_EMAIL = 'nate@bx.psu.edu'
PROJECT_URL = "https://github.com/%s/%s" % (PROJECT_OWNER, PROJECT_NAME)
RAW_CONTENT_URL = "https://raw.gi... | galaxyproject/starforge | starforge/__init__.py | Python | mit | 385 | [
"Galaxy"
] | ee7b7b16c23063a360d7649e8605aa10cfc5edc81654737c1b2d234aa8c6875c |
# Copyright (c) 2016 Claudiu Popa <pcmanticore@gmail.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""Module to add McCabe checker class for pylint. """
from __future__ import absolute_import
from mccabe impor... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/pylint/extensions/mccabe.py | Python | apache-2.0 | 5,836 | [
"VisIt"
] | 1b31ed8cb2e0c7067590551e4e9b49e053cbaa18bdc8c6e70d93547a05bc4a54 |
import json
import math
from django.core.management.base import BaseCommand
from django.conf import settings
from django.db.models import Count
from django.utils import timezone
from twitterbot.bot import TwitterBot
from visitors.models import Visitor, Statistic, Statistic_detail, Institution, VisitorScrapeProgress
... | aniversarioperu/django-manolo | visitors/management/commands/run_statistics.py | Python | bsd-3-clause | 4,316 | [
"VisIt"
] | df4742995d42004bc5df99260a0aaa4d03caaf0cd21cf155aa6d92ebd68067d8 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-anaquin/package.py | Python | lgpl-2.1 | 2,204 | [
"Bioconductor"
] | efee8ea297606a4863f683319269c3b288ae611ac3eee6ce5a54b57a78652eed |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# XCode Project Creator
#
import os, sys, re, shutil, codecs
from shutil import copyfile
from os.path import join, splitext, split, exists
from datetime import date
template_dir = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
from tools import *... | xissy/titanium-mobile-sdk | iphone/projector.py | Python | apache-2.0 | 8,292 | [
"VisIt"
] | 108c956ed598a62dd957dde4e668cb8de3548be2cb75548cba813f8e0ef08dc4 |
import numpy as np
import bayesianoracle as bo
import bayesianoracle.plot as boplotter
# Import function information
from function_data import *
execfile("function_data.py")
def plot(bmao, X, k_fig):
""" Auxillary plotting function
Parameters
----------
bma : EnrichedBayesianModelAveraging object... | altaetran/bayesianoracle | tests/quadraticBayesianAveraging/paper_examples/FullyBayesianBMADecomposition.py | Python | apache-2.0 | 10,922 | [
"Gaussian"
] | 26b77a80af83db891155bfb11b1050d8f8624369b1b9916f940534986f3391a6 |
#!/usr/bin/env python
from __future__ import absolute_import, unicode_literals
import os
import sys
if __name__ == "__main__":
if os.environ.get('AMBERHERBERT_ENV') == 'PROD':
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "amber.settings.production")
else:
os.environ.setdefault("DJANGO_SETTI... | Taywee/amberherbert.com | manage.py | Python | mit | 462 | [
"Amber"
] | 177449294acd6c1c97ae0b77ab2363f5017b07bfeff34784e47aa6c9285a6bd1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
GridPP and DIRAC: adding CERN@school cluster metadata.
"""
#...for operating system stuff.
import os
#...for parsing the arguments.
import argparse
#...for the logging.
import logging as lg
# Import the JSON library.
import json
# The DIRAC imports.
from DIRAC.... | gridpp/dirac-getting-started | add_cluster_metadata.py | Python | mit | 2,620 | [
"DIRAC"
] | 2f5d45a25a463cf97635d05bb7f7de70baf42837a8fa76ec2027de75e838fe7b |
""" This module exposes the BaseClient class,
which serves as base for InnerRPCClient and TransferClient.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import time
from six.moves import _thread as thread
import DIRA... | yujikato/DIRAC | src/DIRAC/Core/DISET/private/BaseClient.py | Python | gpl-3.0 | 26,661 | [
"DIRAC"
] | ba1f55638f075a03c0e60ecd62efe32821dbd3f476db6623a3511466935e7505 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/modelchems.py | Python | gpl-2.0 | 30,689 | [
"CHARMM",
"Psi4"
] | b4c78bc452fea8bf1f627fc41831a76059a3fdfb26bd976dd7807b734a8eea01 |
# -*- coding: utf-8 -*-
#@author: ilyass.tabiai@polymtl.ca
#@author: rolland.delorme@polymtl.ca
#@author: patrickdiehl@lsu.edu
import sys
import numpy as np
from scipy import linalg
np.set_printoptions(precision=8, threshold=sys.maxsize)
from ..util import functions
## Class to compute the well-known strain and stress... | lm2-poly/PeriPyDIC | peripydic/IO/ccm.py | Python | gpl-3.0 | 12,948 | [
"DIRAC"
] | 33fd15ebbef45c19b136529789abfa29602bbe03b95d1a87939be9bc0702750f |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
n0=100
n1=100
output = False
display = False
... | mcopik/Elemental | examples/interface/BPComplex.py | Python | bsd-3-clause | 2,537 | [
"Gaussian"
] | f0cd79497cd53218a761361ce33b918ab8d8989217b3cad709c9e5b4cb8ada13 |
#
# The Python Imaging Library.
# $Id$
#
# standard filters
#
# History:
# 1995-11-27 fl Created
# 2002-06-08 fl Added rank and mode filters
# 2003-09-15 fl Fixed rank calculation in rank filter; added expand call
#
# Copyright (c) 1997-2003 by Secret Labs AB.
# Copyright (c) 1995-2002 by Fredrik Lundh.
#
# See t... | bzennn/blog_flask | python/lib/python3.5/site-packages/PIL/ImageFilter.py | Python | gpl-3.0 | 7,406 | [
"Gaussian"
] | bfeeca1ac392834c1bc8d4f608739df9455e3b1b7ae123d92df41f740d8b25fd |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/share/psi4/databases/HTBH.py | Python | gpl-2.0 | 38,497 | [
"Psi4"
] | 48ddfe30c315b275a4eef119fbd40d3968199934618242909e66e82795c96505 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-allelicimbalance/package.py | Python | lgpl-2.1 | 2,701 | [
"Bioconductor"
] | 463899e7e2934f705d5034b7be42ebd82d9b7f8e8245a2ce4bcec4720c570fb1 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | rsepassi/tensor2tensor | tensor2tensor/models/research/attention_lm_moe.py | Python | apache-2.0 | 28,325 | [
"MOE"
] | ddbb2f39e4ed9f42d0618fb118cddd6d9e51d3ea40f05a86f59091d3aa9ccdc9 |
# Copyright (C) 2016 Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in t... | bema-ligo/pycbc | pycbc/inference/likelihood.py | Python | gpl-3.0 | 24,120 | [
"Gaussian"
] | c68f00f43064dc52781d69119b15bbc8f66d37d186145f8f6afc5eac00f8c5dc |
from rdkit import RDConfig
from rdkit import Chem
import unittest, os.path
import sascorer
print(sascorer.__file__)
class TestCase(unittest.TestCase):
def test1(self):
with open('data/zim.100.txt') as f:
testData = [x.strip().split('\t') for x in f]
testData.pop(0)
for row in testData:
smi... | bp-kelley/rdkit | Contrib/SA_Score/UnitTestSAScore.py | Python | bsd-3-clause | 930 | [
"RDKit"
] | 621d6370399d981a9500c7a1470a778ae7cdadfa07ab7e1ceb12cd3657eb145c |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max-Planck-Institute of Neurobiology, Munich, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
from mayavi import mlab
import functools
#import sys
#sys.setrecursionlimit(500)
#import numba
#print('test0')
im... | StructuralNeurobiologyLab/SyConn | syconn/analysis/bio_interface.py | Python | gpl-2.0 | 63,052 | [
"Mayavi",
"NEURON"
] | 0abf2f7c02c766f27f866a22270f9855dc9ee24df119658c31e7ba9194c174a3 |
"""
At_initial_setup module template
Custom at_initial_setup method. This allows you to hook special
modifications to the initial server startup process. Note that this
will only be run once - when the server starts up for the very first
time! It is called last in the startup process and can thus be used to
overload t... | MarsZone/DreamLand | muddery/server/conf/at_initial_setup.py | Python | bsd-3-clause | 3,763 | [
"VisIt"
] | 71a0bdb8674751445691f0bc5d07574bd732427d827305d6abb1beb81077780c |
# Copyright 2008 by Norbert Dojer. All rights reserved.
# Adapted by Bartek Wilczynski.
# 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.
"""Approximate calculation of appropriate thresholds for motif ... | zjuchenyuan/BioWeb | Lib/Bio/motifs/thresholds.py | Python | mit | 4,516 | [
"Biopython"
] | 98c9733e57eddcc4ddd6694f1b0308b62f6ae1bfaa0b93441ec92c959af254d8 |
import suspect.basis
import numpy
def gaussian_window(t, params):
"""
Calculates a Gaussian window function in the time domain which will broaden
peaks in the frequency domain by params["line_broadening"] Hertz.
:param t:
:param params:
:return:
"""
window = suspect.basis.gaussian(t, ... | bennyrowland/suspect | suspect/processing/_apodize.py | Python | mit | 693 | [
"Gaussian"
] | 7e3db6f197fe364d33dc40eeb21d59ff246cfa209f6ed3cb79f8e7ce20ebdf11 |
# copyright 2003-2015 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of astroid.
#
# astroid is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
#... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/astroid/tests/unittest_transforms.py | Python | apache-2.0 | 8,625 | [
"VisIt"
] | 412d7bd10b2535576034e55a2baa8a18f2d9b941266ae82fc9e0e00fda3742f2 |
import Avogadro
import unittest
from numpy import *
class TestResidue(unittest.TestCase):
def setUp(self):
self.molecule = Avogadro.molecules.addMolecule()
def test_number(self):
residue = self.molecule.addResidue()
residue.number = "5A"
self.assertEqual(residue.number, "5A")
def test_chainNumb... | rcplane/periodicdisplay | reference/avogadro/libavogadro/src/python/unittest/residue.py | Python | gpl-2.0 | 1,095 | [
"Avogadro"
] | 9c0ec0464463c52615201d3b037841bd4b915da627a661a51ddf9db63c22492f |
# 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)
import os
from spack import *
class HoomdBlue(CMakePackage):
"""HOOMD-blue is a general-purpose particle simulation... | LLNL/spack | var/spack/repos/builtin/packages/hoomd-blue/package.py | Python | lgpl-2.1 | 3,802 | [
"HOOMD-blue"
] | cfce1f0993176f2dd74874014ce744b9187f0456ff9be28d4c703e851d61f8d7 |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.
pK values and the methos are taken from::
* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
J.-Ch., Frutige... | zjuchenyuan/BioWeb | Lib/Bio/SeqUtils/IsoelectricPoint.py | Python | mit | 4,290 | [
"Biopython"
] | c44c39ca153377a116e0d5fe691c5d3019a036a3ba920008b22186158854de6e |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/solvent/ddcosmo.py | Python | apache-2.0 | 36,047 | [
"Gaussian",
"PySCF"
] | 5276dc66bc111e96c50c11b891637ca90daf6b46ceb3401083a45c266e80a567 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | lukecwik/incubator-beam | sdks/python/apache_beam/examples/snippets/snippets.py | Python | apache-2.0 | 62,270 | [
"VisIt"
] | e4f4b467bfed735ddf9a8c82477ff61a51bb162e4135629f230b62585f9f9ade |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2012 OpenPlans
#
# 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... | Phil-LiDAR2-Geonode/pl2-geonode | geonode/base/enumerations.py | Python | gpl-3.0 | 13,736 | [
"BWA"
] | c851834fdc5f8f7d54dab56b60c848980530cbe4e78055c317173c2d69ca9806 |
"""TODO: DOC."""
import array
import mathutils
import bpy
import bmesh
from bpy_extras.io_utils import unpack_list
from . import nvb_def
from . import nvb_utils
from . import nvb_parse
from . import nvb_aabb
from . import nvb_material
class Node(object):
"""TODO: DOC."""
nodetype = 'undefined'
def __... | gyoerkaa/mdltools | neverblender/nvb_node.py | Python | gpl-2.0 | 69,344 | [
"BLAST"
] | 168f04445f0098a671c154dde35808554a7618b98164ff903104fc4874b606f4 |
# #
# Copyright 2009-2014 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (ht... | gc3-uzh-ch/easybuild-framework | easybuild/tools/filetools.py | Python | gpl-2.0 | 34,673 | [
"NetCDF"
] | f45b349be57ac14b37f0ad8eee3eb504cd31effd853230c34e09d509e756312b |
import copy
INF = 99999
def main():
_input = None
with open('input.txt') as input_file:
_input = [line.strip() for line in input_file]
part_1(_input)
part_2(_input)
class SearchState(object):
def __init__(self):
self.path = []
self.distance = 0
def __repr__(self):
return str(self.distance) + ' ' + ... | T-R0D/JustForFun | adventofcode/Day09/all_in_one_night.py | Python | gpl-2.0 | 3,612 | [
"VisIt"
] | 26158cdf05a469f82bd359e30a1b5dadf85dd718dd49cfebc693ed97fd428acc |
# Copyright: 2005,2010 Gentoo Foundation
# Author(s): Nicholas Carpaski (carpaski@gentoo.org), Brian Harring (ferringb@gentoo.org)
# License: GPL2
__all__ = ["cache"]
import stat
import sys
from portage.util import normalize_path
import errno
from portage.exception import PermissionDenied
from portage import os
if s... | Neuvoo/legacy-portage | pym/portage/eclass_cache.py | Python | gpl-2.0 | 3,937 | [
"Brian"
] | a5355c97cad9fcd84355a8a13a51ecd2fcb9c08cf6430ee7b85ea5ed1197a2cb |
"""
Testing code.
Updated BSM February 2017
"""
import sys
import os
import numpy as np
import pytest
from pytest import approx
from numpy.testing import assert_allclose
from scipy.spatial.distance import cdist
from pykrige import kriging_tools as kt
from pykrige import core
from pykrige import variogram_models
from ... | bsmurphy/PyKrige | tests/test_core.py | Python | bsd-3-clause | 95,232 | [
"Gaussian"
] | 4af2d06290c2af7f69aab8b486dfc28398e7500125cf3e7a6bbee942474db5c7 |
#### PATTERN | GRAPH ###############################################################################
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
####################################... | decebel/dataAtom_alpha | bin/plug/py/external/pattern/graph/__init__.py | Python | apache-2.0 | 60,204 | [
"VisIt"
] | db91c55e84975cbc5cad9b997cfae2ee85e2d0a595fa1bd55f36edb45948df65 |
"""
Provides analysis of site symmetries.
"""
import numpy as np
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
def get_site_symmetries(struc, precision=0.1):
"""
Get all the point group operations centered on each atomic site
in the form [[p... | davidwaroquiers/pymatgen | pymatgen/symmetry/site_symmetries.py | Python | mit | 2,727 | [
"pymatgen"
] | 65303933d31cdefe885e9f8408ff868fd5ed19b1fadfc70042559d432b2417c5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import numpy as np, scipy as sp
import orthAE as ae
import scipy.io
import matplotlib.pyplot as plt
from sklearn.cross_decomposition import CCA
import argparse, sys
__author__ = "TengQ... | tengerye/orthogonal-denoising-autoencoder | python/demo.py | Python | apache-2.0 | 3,566 | [
"Gaussian"
] | 218c5b7adb7d28eb96e58c156f3d3b613be5341f7fedba3f191fd11f548cc2b0 |
"""
`nappy` provides python scripts related to programs in the *nap* package.
"""
from __future__ import print_function
__all__ = ['pmd','napsys','atom','common','io','rdf','adf','msd','gaussian_smear',
'util','vasp','mkcell','manipulate','units']
from . import *
_nappy_dir = '.nappy'
def get_nappy_dir()... | ryokbys/nap | nappy/__init__.py | Python | mit | 407 | [
"ADF",
"VASP"
] | 797a206c8dc83020c14b069c0e086f4863f9a1a0de110ba7e695710e8157a771 |
#!/usr/bin/env pypy
import random
import math
import argparse
import cPickle as pickle
import logging
import os
import sys
import re
import colorsys
import bisect
import operator
from xml.dom.minidom import parse
InkscapePath = "/Applications/Inkscape.app/Contents/Resources/bin/inkscape"
try:
import Image
im... | vishnubob/snowflake | src/engine.py | Python | mit | 27,185 | [
"CRYSTAL"
] | f48771d03c049e8b33a2cf9879929d265df21fd37c12356b99cb3497667dfbd8 |
class mesh:
def __init__(self):
self.position = []
self.normal = []
self.uvw = []
self.faces = []
self.texture = []
self.smoothing = []
class program:
def __init__(self):
self.meshes = {}
def open(self,path):
importFile = open(path)
findName = False
current = None
for line in importFile:
lin... | burzumishi/dragonballworld | Tools/ASE2OBJ/ase2obj.py | Python | gpl-2.0 | 3,507 | [
"ASE"
] | 01f4b92a6829f276571f840fd35491d3e38fc28c61d7a27d16a8178f8dc20302 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | QuantumElephant/horton | horton/gbasis/test/test_iobas.py | Python | gpl-3.0 | 8,184 | [
"NWChem"
] | 548ed1199e5049d062e89a3b83d3d47f5b8512a02ef0b9335a9029b0a8d5141b |
#!/usr/bin/python
# defect.py v0.1 5/22/2012 Jeff Doak jeff.w.doak@gmail.com
# Change Log:
import numpy as np
BOLTZCONST = 8.617e-5 #eV/K
class Defect():
"""
Class containing the energetic, compositional, and structural data about
a defect structure. Defect class has the following attributes:
... | jeffwdoak/free_energies | free_energies/defect.py | Python | mit | 3,374 | [
"CRYSTAL"
] | aea967a5aca3cdf7d9e75931b2667f914103a6419d0a6f95ad73612d7e980ccc |
"""
desisim.scripts.quickgen
========================
Quickgen quickly simulates pipeline outputs if given input files.
- must provide simspec and fibermap files via newexp script
- Number of spectra to be simulated can be given as an argument for quickgen,
but the number of spectra in the simspec file is tak... | desihub/desisim | py/desisim/scripts/quickgen.py | Python | bsd-3-clause | 31,215 | [
"Galaxy",
"Gaussian"
] | dac1dae4d18ddb47303e755c45bdc8e34ae29ba921422ec85c89a94299487b36 |
#!/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/chkfile.py | Python | apache-2.0 | 5,801 | [
"PySCF"
] | baa46a5eb9df204dba66172fc2c73618cd735276cfd1dddd28d0347bab2c84a7 |
########################################################################
#
# (C) 2015, Chris Houseknecht <chouse@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 Fo... | j00bar/ansible | lib/ansible/galaxy/login.py | Python | gpl-3.0 | 4,500 | [
"Galaxy"
] | 902b74f486498712bcdf1876b00b9f5f64c53ffcbd0c6076331d8c5b8ff33246 |
# Copyright 2001 by Tarjei Mikkelsen. 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.
"""BioPython Pathway module.
Bio.Pathway is a lightweight class library designed to suppor... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Pathway/__init__.py | Python | gpl-2.0 | 10,793 | [
"Biopython"
] | af92ff9472cecf3cb7f546e898c6b261bd987dcc9d2055a0957cb82cf8b5f825 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This script helps to create a new branch for a new Odoo version from the
another existing branch, making the needed changes on contents.
Installation
============
For using this utility, you need to install these dependencies:
* github3.py library for handling Githu... | vauxoo-dev/maintainer-tools | tools/migrate_branch.py | Python | agpl-3.0 | 14,379 | [
"VisIt"
] | fe10fb58bf2e0878ed5fffab2a9975c790f8017e8a783f625207d56bc887ec78 |
#=================================
# AbinitStructureViewer.py
version = 'beta'
#=================================
# written by Benjamin Tardif
# benjamin.tardif@umontreal.ca
# last modified : october 25 2006 by Guillaume Dumont
# added support for default rprim
#=================================
headline = '\n========... | qsnake/abinit | util/users/AbinitStructureViewer.py | Python | gpl-3.0 | 28,946 | [
"ABINIT",
"Jmol"
] | 872788343e3881fb8d1c967656e20e26fdc58c5e220161b6120bcb0124c1eaf9 |
from __future__ import absolute_import, division, print_function, unicode_literals
class Subject(object):
"""The system, biological or artificial, which contains neuroids under study. """
def __init__(self, name, type):
self.name = name
self.type = type
class Neuroid(object):
"""The neu... | jjpr-mit/mkgu | mkgu/neuroids.py | Python | mit | 460 | [
"NEURON"
] | 29f4a1e4338f071ba032a88f8191cbf05f52cc9a7ca641174adfdef7a7a6ca35 |
#!/home/psilocaluser/toolchainconda/bin/python
#!/home/psilocaluser/bldmconda3/bin/python
#!/Users/github/bldmconda3/bin/python
#/usr/bin/env python3
# [LAB 4 Apr 2017]
# Adapt for Mac and Linux
# Separate psi4-core dest_channel from other defaults
# [LAB 24 Mar 2017]
# Confirmed a nightly build set
# Outputs stdou... | psi4/psi4meta | conda-recipes/pre-cb3-recipes-linux/kitandkapoodle_well_into_cb3_but_before_deletions.py | Python | gpl-2.0 | 25,609 | [
"Psi4"
] | 2a1dfc9974bdb72c6e94b854bd4e4b6d67e4174f30c60f0a99804fac1e26f19a |
#!/usr/bin/env python3
"""Contains `KappaComplex`, a class to represents a list of agents chained into a larger entity, and the `embed_and_map`
function."""
import re
import networkx as nx
import numpy as np
from collections import deque
from typing import Deque, Dict, List, FrozenSet, Set, Tuple, Union
from .KappaMu... | hmedina/KaSaAn | KaSaAn/core/KappaComplex.py | Python | mit | 21,549 | [
"Cytoscape"
] | c651a12cd12121c0c353b3aa0c82395373e531f85bb81a975cc5debe4598de77 |
# Lint as: python3
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | google/tf-quant-finance | tf_quant_finance/models/hjm/gaussian_hjm_test.py | Python | apache-2.0 | 9,226 | [
"Gaussian"
] | 4035648363325845e938f184b7c44c1dd3f36ee626a85c4b3c96b0b25a8e1575 |
import ast
import typedpython
class CollectNames(ast.NodeVisitor):
_names_ = []
def visit_Name(self, node):
self._names_.append( node )
def collect_names(node):
CollectNames._names_ = names = []
CollectNames().visit( node )
return names
class CollectReturns(ast.NodeVisitor):
_returns_ = []
def visit_Return... | pombredanne/PythonJS | pythonjs/ast_utils.py | Python | bsd-3-clause | 3,679 | [
"VisIt"
] | 7ef97613919ea92f050faa97ee297b8b6feb611892a680212885f2e16ff25897 |
from distutils.core import setup, Extension
from distutils.sysconfig import get_python_inc, get_python_lib
from glob import glob
import sys, os
try:
import numpy
except:
print '''
-- Error.
kmpfit requires NumPy, which seems to be unavailable here.
Please check your Python installation.
'''
sys.exit(1)
incl... | aoeftiger/kmpfit | setup.py | Python | bsd-3-clause | 1,650 | [
"Gaussian"
] | 5b63a720a9ba51a24479e6d6011170af77c350c33012849085ba0568be266cd0 |
"""========================================
RNA-Seq Differential expression pipeline
========================================
The RNA-Seq differential expression pipeline performs differential
expression analysis. It requires three inputs:
1. A geneset in :term:`gtf` formatted file
2. Mapped reads in :term:`ba... | CGATOxford/CGATPipelines | CGATPipelines/pipeline_rnaseqdiffexpression.py | Python | mit | 53,106 | [
"Bioconductor",
"Gaussian"
] | 5b018a75078102a6ea598c48c7d605db4c306c2096c2e47996a8b28925748efa |
import string
import random
import json
from collections import defaultdict
from django.conf import settings
from django.http import HttpResponse
from django.shortcuts import render_to_response
from django.template.context import RequestContext
from catmaid.fields import Double3D
from catmaid.models import Log, Neur... | dwitvliet/CATMAID | django/applications/catmaid/control/common.py | Python | gpl-3.0 | 9,404 | [
"NEURON"
] | 739ad7052d23b369cb89bcafdc8bdf7d2338b807f705a17dfa475976bcc689e9 |
import os
import re
import shutil
import sys
try:
from setuptools import setup
setup_params = {
'entry_points': {
'console_scripts': [
'virtualenv=virtualenv:main',
'virtualenv-%s.%s=virtualenv:main' % sys.version_info[:2]
],
},
'z... | craigkerstiens/gistlog | vendor/virtualenv-1.8.4/setup.py | Python | mit | 3,091 | [
"Brian"
] | 0f970a7f747a886a2241ceea1c50547db96fe5c916a372ae341c05f813b4c8ff |
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