Commit 2645e924 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.14.1

parent 13239c5c

.github/CONTRIBUTING.rst

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@@ -3,7 +3,8 @@ Contributing 
============



Contributions are welcome, and they are greatly appreciated! Every little bit

helps, and credit will always be given.

helps, and credit will always be given. For issues that contributors have 

experienced in the past, see the FAQ at the bottom of this document.



You can contribute in many ways:
@@ -240,3 +241,17 @@ Please use concise descriptive commit messages and consider using 
   instead of ``my_dict.iteritems()`` use ``six.iteritems(my_dict)``



Thank you very much for contributing to cobrapy!



FAQs

----

Q1. Why do all of the tests that involve loading a pickled model fail on my branch?

	A: Pickling is the standard method for serializing objects in python,

	which is commonly done during operations like multiprocessing.

	Because of this, we need to maintain tests that run on pickled

	models, otherwise contributors may inadvertantly break

	multiprocessing features. If changes you made to cobrapy

	modify attributes of the ``cobra.Model`` class, the pickled

	models stored in the repository won't contain those changes

	and may fail tests that you add or modify. To resolve these

	errors, just run ``cobra/test/data/update_pickles.py`` on your

	branch, which will repickle the models.

.travis.yml

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language: python

python: 3.5

sudo: false

cache:

  pip: true

python:

  - "2.7"

  - "3.5"

  - "3.6"

  - "3.7-dev"



git:

  depth: 2



cache:

  pip: true



branches:

 only:

 - master
@@ -18,54 +24,18 @@ env: 


matrix:

  fast_finish: true

  exclude:

    - python: 3.5

  include:

    - os: linux

      python: 3.5

      env:

        - TOXENV=pep8

    - os: linux

      python: 2.7

      env: TOXENV=py27

    - os: linux

      python: 3.5

      env: TOXENV=py35

    - os: linux

      python: 3.6

      env: TOXENV=py36

    - os: linux

      python: 3.7-dev

      env: TOXENV=py37

    - os: linux

      python: 3.5

      env: TOXENV=sbml

    - os: linux

      python: 3.5

      env: TOXENV=array

    #    - os: osx

    #      language: generic

    #      before_install:

    #        - brew update

    #        - brew install --without-readline --without-xz --without-gdbm --without-sqlite python3

    #        - virtualenv env -p python3

    #        - source env/bin/activate

    #    - os: osx

    #      language: generic

    #      before_install:

    #        - brew update

    #        - brew install --without-readline --without-xz --without-gdbm --without-sqlite python2

    #        - virtualenv env -p python2

    #        - source env/bin/activate



before_install:

  - travis_retry pip install -U pip setuptools wheel tox



before_cache:

  - set +e

install:

  - pip install --upgrade pip setuptools wheel tox tox-travis



script:

  - travis_wait tox

  - tox -- --benchmark-skip --cov-report xml --cov-report term

  - bash <(curl -s https://codecov.io/bash)



stages:

  - test

  - name: deploy

    if: tag IS present



# N.B.: Currently, Travis mangles (escapes) the release tag body badly.

#before_deploy:
@@ -75,27 +45,28 @@ deploy: 
  - provider: pypi

    skip_cleanup: true

    distributions: sdist bdist_wheel

    install: skip

    script:

      - echo "Deploying COBRApy to PyPI."

    on:

      tags: true

      repo: $GITHUB_REPO

      python: '3.6'

      condition: $TRAVIS_OS_NAME == "linux"

    user: cobrapy

    password: $PYPI_PASSWORD

  - provider: script

    skip_cleanup: true

    install: skip

    script: scripts/deploy_website.sh

    on:

      tags: true

      repo: $GITHUB_REPO

      python: '3.6'

      condition: $TRAVIS_OS_NAME == "linux"

  - provider: releases

    skip_cleanup: true

    install: skip

    script:

    - echo "Releasing COBRApy to GitHub."

    api_key: $GITHUB_TOKEN

    body: "Please see https://github.com/opencobra/cobrapy/tree/${TRAVIS_TAG}/release-notes/${TRAVIS_TAG}.md for the full release notes."

    on:

      tags: true

      repo: $GITHUB_REPO
 
      python: '3.6'

      condition: $TRAVIS_OS_NAME == "linux"

benchmarks/parallel_fva.ipynb

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cobra/__init__.py

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@@ -8,12 +8,14 @@ from os import name as _name 
from os.path import abspath as _abspath

from os.path import dirname as _dirname



from cobra import flux_analysis, io

from cobra.core import (

    DictList, Gene, Metabolite, Model, Object, Reaction, Species)

    Configuration, DictList, Gene, Metabolite, Model, Object, Reaction,

    Species)

from cobra import flux_analysis

from cobra import io

from cobra.util import show_versions



__version__ = "0.13.4"

__version__ = "0.14.1"



# set the warning format to be prettier and fit on one line

_cobra_path = _dirname(_abspath(__file__))

cobra/config.py

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# -*- coding: utf-8 -*-



from __future__ import absolute_import



import logging



log = logging.getLogger(__name__)



non_zero_flux_threshold = 1e-6

ndecimals = 6