mpkocher

from pymatgen.core.structure import Composition


ds = []
ds.append(dict(Mn=20, O=20))
ds.append(dict(Fe=3, O=4))
ds.append(dict(Li=2, Co=2, O=4))

for d in ds:
	c = Composition.from_dict(d)

mpkocher

import os
import sys
import types
import logging

log = logging.getLogger(__name__)


def _setup_log():
    log.setLevel(logging.DEBUG)

mpkocher

import sys
from bs4 import BeautifulSoup
html_file = sys.argv[1]
with open(html_file, 'r') as f:
    s = BeautifulSoup(f)
    print s.title.string
sys.exit(0)

mpkocher

from setuptools import setup, Command


class GetVersion(Command):
    """This must be defined"""
    user_options = []

    def initialize_options(self):
        pass
    

mpkocher

import sys

try:
    from setuptools import setup
except ImportError:
    from distutils.core import setup

if ("install" in sys.argv) and sys.version_info < (2, 7, 0):
    print "pbcore requires Python 2.7"
    sys.exit(-1)

mpkocher

"""Example taken from Raymond Hettinger's Pycon 2013 talk"""
import sys
import os
from contextlib import contextmanager

_file_name = "Exampl3.fil3.tmp"


def terrible_example():
    """Terrible. Race condition"""

mpkocher

# Use most recent gold build from SIV
function goldSeymour(){
        root=/mnt/secondary-siv/nightlytest/siv3
        changelist=`ls /home/UNIXHOME/secondarytest/gold_releases | sort -r | head -1 |  egrep --only-match "^[0-9]*"`
        seymour=${root}/smrtanalysis_${changelist}
        if [ -d "${seymour}" ]
        then
                echo "Loading changelist ${changelist} with SEYMOUR_HOME=${seymour}"
                export SEYMOUR_HOME=$seymour
                source $SEYMOUR_HOME/etc/setup.sh

mpkocher

import logging
import os

from pbsmrtpipe.resource_types import (MovieFofn, BarcodeFofn, BarcodeFasta,
                                       MappingCmph5, BarcodeFastq)
from pbsmrtpipe.model import (TaskTypes, TaskBase,
                              TaskOption, TaskChoiceOption,
                              P_Module, TempDir)

log = logging.getLogger(__name__)

mpkocher

import argparse

def get_parser():
    parser = argparse.ArgumentParser(version=__version__,
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    parser.add_argument('input_fofn', help="Path to bas.fofn",
                        type=validate_fofn)

    return parser

mpkocher

import abc
import functools
import logging
import warnings
import operator

log = logging.getLogger(__name__)


class RuleBase(object):