text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This programme illustrates buildi... | BhallaLab/moose | moose-examples/paper-2015/Fig2_elecModels/Fig2C.py | Python | gpl-3.0 | 14,223 | [
"MOOSE",
"NEURON"
] | 5eb6a5a439a675762a02c12cdff996e6a0d98f6ee874773cba2951727562aac5 |
# creates: N.LDA
import os
from gpaw.test import gen
gen('N')
os.system('cp N.LDA ../_build')
| qsnake/gpaw | doc/setups/N.py | Python | gpl-3.0 | 94 | [
"GPAW"
] | ad7d53917d97406476db3321deeeb0fb89711b3341fa301373e89d7cf3800a42 |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems 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 copy of the License at
#
# http://www.apache.o... | misko/neon | tests/test_model.py | Python | apache-2.0 | 5,468 | [
"Gaussian"
] | 3bfd6fb19f3b714563f6e85de7e32ae6cf3194700cb2bc8edfd82d289f9d24bc |
#!/usr/bin/env python
"""Extract read start from BAM files to Wig format for PAUSE.
Usage:
bam_to_wiggle.py <BAM file>
"""
import os
import tempfile
from contextlib import contextmanager
import pysam
import subprocess
import argparse
@contextmanager
def indexed_bam(bam_file):
if not os.path.exists(bam_file.... | TAMU-CPT/galaxy-tools | tools/pause/pause_starts_to_wiggle.py | Python | gpl-3.0 | 4,610 | [
"Galaxy",
"pysam"
] | 7a17a731153d43766a00672d66cbc22da6041df4aad39283a34c65b81a35440d |
#!/usr/bin/env python
""" check_pseudo.py calculates energy for 7 alat points near SIESTA equilibrium to fine tune the delta-factor.
"""
import os
import sys
import uuid
import glob
import numpy as np
import shutil
import matplotlib.pyplot as plt
from generate import PGInputFile, PTInputFile
from get_energies import... | ansobolev/PseudoGenerator | pseudogen/check_pseudo.py | Python | mit | 2,386 | [
"SIESTA",
"WIEN2k"
] | 2286a65136ae498e930e31d1f7c6bfcf92c0cc82d6b4540635ee0de03e12cad9 |
from copy import deepcopy as dc
from itertools import combinations
import ase.io as aseio
import numpy as np
from ase.atoms import Atoms as AAtoms
from pyiid.asa import calculate_asa, get_neighbor_list, get_coordination
__author__ = 'christopher'
def convert_stru_to_atoms(stru):
symbols = []
xyz = []
t... | CJ-Wright/pyIID | pyiid/utils.py | Python | bsd-3-clause | 5,803 | [
"ASE"
] | 5e32988f1ea4991d436343938a03c8967054e4336fc3660a3273e5bdda9ddf19 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A app configuration defines the user-tunable parameters of the application and also the quality evaluation such as the:
* Amazon Mechanical Turk HIT description, pricing, keywords, etc.
* The description and instructions of the task
* The configuration of the type of t... | mcartwright/CAQE | src/caqe/configuration.py | Python | mit | 19,785 | [
"VisIt"
] | 60f1965a4f5b55df7d2bb1ddb9a6d553291e0b68e9e279e55f56f6f2698d3754 |
#!/usr/bin/env python
#
# Wrapper script for Java Conda packages that ensures that the java runtime is invoked with the right options.
# Adapted from https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/1.16.16/peptide-shaker.py (accessed June, 21th 2019).
#
# Program Parameters
#
import os
... | cokelaer/bioconda-recipes | recipes/gemoma/GeMoMa.py | Python | mit | 3,169 | [
"Bioconda"
] | 018ca2619f82a0002e2334d695e8fe532aec2293d4d5bda0711ecab68d30118d |
# sql/elements.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnEle... | alex/sqlalchemy | lib/sqlalchemy/sql/elements.py | Python | mit | 80,420 | [
"VisIt"
] | 86bfc65f9d734ee04a7c2773fb927f89f54190ec9301257a444d40b24eadaa09 |
from .base import *
class session(object):
"""
cytoscape session interface as shown in CyREST's swagger documentation for 'session'.
:param url: an url of the type 'http://' + host + ':' + str(port) + '/' + version + '/'.
"""
def __init__(self, url):
self.__url = url + 'commands/session'
... | idekerlab/py2cytoscape | py2cytoscape/cyrest/session.py | Python | mit | 4,191 | [
"Cytoscape"
] | fe26253e7102c00f30e59407705c422f04c4aea74d370ec2e61a6ff1b43b3e24 |
#!/usr/bin/env python3
from abc import ABC, abstractproperty
import torch
from .. import settings
from ..distributions import Delta, MultivariateNormal
from ..module import Module
from ..utils.broadcasting import _mul_broadcast_shape
from ..utils.memoize import cached, clear_cache_hook
class _VariationalStrategy(M... | jrg365/gpytorch | gpytorch/variational/_variational_strategy.py | Python | mit | 6,122 | [
"Gaussian"
] | cbf329ff3ac64378b8e2456fbfd4a4611c6f179ada0ab8216307b67e4a26bc48 |
from __future__ import division, unicode_literals
import warnings
import matplotlib
matplotlib.use('pdf')
import unittest as unittest
import numpy as np
from pymatgen import Composition
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.analysis.phase_diagram import PhaseDiagram, \
GrandP... | nisse3000/pymatgen | pymatgen/analysis/tests/test_interface_reactions.py | Python | mit | 17,218 | [
"pymatgen"
] | 5ab5543c3163c6a13a930820d2e2aad8e90291dea8fb5580e6fc7d826acf1d31 |
from __future__ import unicode_literals
import datetime
import requests
from requests_oauthlib import OAuth1
from oauthlib.oauth1 import (SIGNATURE_RSA, SIGNATURE_TYPE_AUTH_HEADER,
SIGNATURE_HMAC)
from six.moves.urllib.parse import urlencode, parse_qs
from .constants import (XERO_BASE_URL,... | MJMortimer/pyxero | xero/auth.py | Python | bsd-3-clause | 13,625 | [
"VisIt"
] | e7c50eaf91b091a9ca538d2b45240df1a54ccca446f71eff0b782f19c8a6baa2 |
import ast
import collections
from ..visitor import ClassVisitor, handle
from . import Metric
class _TypeCountVisitor(ClassVisitor):
@handle(ast.AST)
def __visit_ast(self, node):
return (node.__class__,) + tuple(cls for name in node._fields for cls in self.visit(getattr(node, name)))
@handle(co... | herczy/pydepend | pydepend/metric/cyclomatic.py | Python | bsd-3-clause | 1,908 | [
"VisIt"
] | c66a25e202655c7f073a823fb8d8dccc257ea7f48e319421947bec27c7206669 |
from django.conf import settings
from django.contrib.sites.models import get_current_site
from django.core.urlresolvers import reverse
from django.http import Http404, HttpResponse
from django.shortcuts import redirect
from .models import APIKey, Short, Visit
def _record_visit(request, short):
remote_addr = (
... | sneeu/little | little/views.py | Python | mit | 1,560 | [
"VisIt"
] | 5044b35c3eb85a66e78dc6ba0307c40f432a7e54e2055aee67a8bee015916f5c |
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