#!/usr/bin/env python
#This script regenerates pickles of cobra Models. Should be
#performed after updating core classes to prevent subtle bugs.
from cPickle import load, dump
from cobra import Model
from cobra.version import get_version
from cobra.io import read_sbml_model, read_legacy_sbml
from cobra.test import create_test_model
model_names = ['salmonella', 'iJO1366', 'Yersinia_pestis_CO92_iPC815']
for model_name in model_names:
model_pickle = model_name + '.pickle'
old_model = create_test_model(model_pickle)
if model_name == "iJO1366":
new_model = read_legacy_sbml(model_name + '.xml')
else:
new_model = read_sbml_model(model_name + '.xml')
[setattr(x, 'name', old_model.genes.get_by_id(x.id).name)
for x in new_model.genes]
if hasattr(old_model, 'media_compositions'):
new_model.media_compositions = old_model.media_compositions
new_model._cobra_version = get_version()
dump(new_model, open(model_pickle, 'w'))
from os.path import isfile
from cobra import Model
from cobra.version import get_version
from cobra.io import read_sbml_model, read_legacy_sbml
from cobra.test import create_test_model
model_names = ['salmonella', 'iJO1366', 'Yersinia_pestis_CO92_iPC815']
for model_name in model_names:
# read in old pickle and model from sbml
model_pickle = model_name + '.pickle'
if model_name == "iJO1366":
new_model = read_legacy_sbml(model_name + '.xml')
else:
new_model = read_sbml_model(model_name + '.xml')
# update other attributes
if isfile(model_name + ".genes"):
with open(model_name + ".genes") as infile:
gene_names = load(infile)
for gene in new_model.genes:
gene.name = gene_names[gene.id]
if isfile(model_name + ".media"):
with open(model_name + ".media", "rb") as infile:
new_model.media_compositions = load(infile)
new_model._cobra_version = get_version()
# write out new pickle
with open(model_pickle, 'wb') as outfile:
dump(new_model, outfile, protocol=2)
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'cobra'
copyright = u'2016, Daniel Robert Hyduke and Ali Ebrahim'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
from cobra.version import get_version, read_release_version
version = read_release_version()
# The full version, including alpha/beta/rc tags.
release = get_version()
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build', 'version.py', '.ipynb_checkpoints']
pygments_style = 'sphinx'
# -- Options for HTML output --------------------------------------------------
mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
# -- Options for LaTeX output --------------------------------------------------
latex_elements = {
# The master toctree document. master_doc = 'index' # General information about the project. project = u'cobra' copyright = u'2015, Daniel Robert Hyduke and Ali Ebrahim' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. from cobra.version import get_version, read_release_version version = read_release_version() # The full version, including alpha/beta/rc tags. release = get_version() # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = ['_build', 'version.py']
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup, find_packages
from cobra.version import get_version
__version = get_version()
setup(
name = "cobra",
version = __version,
packages = find_packages(exclude=['cobra.oven', 'cobra.oven*']),
#scripts = [''],
#put in numpy, scipy, libsbml, and pyglpk
setup_requires = [],
#install_requires = ['numpy>=1.6', 'scipy>=0.10'],
#leave blank because it tries to build scipy/numpy on os x when they are
#installed by the superpack. And these are not really essential for core functions.
install_requires = [],
extras_require = {
'parallel': ['pp>=1.6.0'],
'matlab': ["mlabwrap>=1.1"],
'R': ["rpy2>=2.2.2"]
},
package_data = {
'': ['test/data/*',
'examples/*py',
'mlab/matlab_scripts/*m']},
author = "Daniel Robert Hyduke",
author_email = "*****@*****.**",
description = "COBRApy is a package for constraints-based modeling of biological networks",
try:
import setuptools
except ImportError:
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup, find_packages
from sys import argv
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
from cobra.version import get_version
__version = get_version(pep440=True)
setup_kwargs = {}
# for running parallel tests due to a bug in python 2.7.3
# http://bugs.python.org/issue15881#msg170215
try:
import multiprocessing
except:
None
# cython is optional for building. The c file can be used directly. However,
# to run sdist, the c file must be generated, which requires cython.
try:
from Cython.Build import cythonize
except ImportError:
cythonize = None
if "sdist" in argv:
raise Exception("cython required for sdist")
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup, find_packages
from cobra.version import get_version
__version = get_version()
setup_kwargs = {}
try:
from Cython.Build import cythonize
from distutils.extension import Extension
from distutils.command.build_ext import build_ext
from os.path import isfile, abspath, dirname
from platform import system
class FailBuild(build_ext):
"""allow building of the C extension to fail"""
def run(self):
try:
build_ext.run(self)
except:
None
def build_extension(self, ext):
try:
build_ext.build_extension(self, ext)
except:
None
sources = ["cobra/solvers/cglpk.pyx"]
build_args = {}
try:
import setuptools
except ImportError:
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup, find_packages
from sys import argv
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
from cobra.version import get_version
__version = get_version(pep440=True)
setup_kwargs = {}
# for running parallel tests due to a bug in python 2.7.3
# http://bugs.python.org/issue15881#msg170215
try:
import multiprocessing
except:
None
# cython is optional for building. The c file can be used directly. However,
# to run sdist, the c file must be generated, which requires cython.
try:
from Cython.Build import cythonize
except ImportError:
cythonize = None
if "sdist" in argv:
raise Exception("cython required for sdist")
