Commit 13239c5c authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.13.4

parent 30413e7b

.travis.yml

+3 −0
Original line number Diff line number Diff line
@@ -34,6 +34,9 @@ matrix: 
    - 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

cobra/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ from cobra.core import ( 
    DictList, Gene, Metabolite, Model, Object, Reaction, Species)

from cobra.util import show_versions



__version__ = "0.13.3"

__version__ = "0.13.4"



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

_cobra_path = _dirname(_abspath(__file__))

cobra/io/mat.py

+1 −1
Original line number Diff line number Diff line
@@ -24,7 +24,7 @@ except ImportError: 




# precompiled regular expressions

_bracket_re = re.compile("r\[[a-z]\]$")

_bracket_re = re.compile(r"\[[a-z]\]$")

_underscore_re = re.compile(r"_[a-z]$")

cobra/io/yaml.py

+25 −9
Original line number Diff line number Diff line
@@ -5,11 +5,26 @@ from __future__ import absolute_import 
import io



from six import string_types

from ruamel import yaml

from ruamel.yaml import YAML

from ruamel.yaml.compat import StringIO



from cobra.io.dict import model_to_dict, model_from_dict



YAML_SPEC = "1"

YAML_SPEC = "1.2"





class MyYAML(YAML):

    def dump(self, data, stream=None, **kwargs):

        inefficient = False

        if stream is None:

            inefficient = True

            stream = StringIO()

        YAML.dump(self, data, stream, **kwargs)

        if inefficient:

            return stream.getvalue()





yaml = MyYAML(typ="rt")





def to_yaml(model, sort=False, **kwargs):
@@ -36,9 +51,10 @@ def to_yaml(model, sort=False, **kwargs): 
    save_yaml_model : Write directly to a file.

    ruamel.yaml.dump : Base function.

    """



    obj = model_to_dict(model, sort=sort)

    obj["version"] = YAML_SPEC

    return yaml.dump(obj, Dumper=yaml.RoundTripDumper, **kwargs)

    return yaml.dump(obj, **kwargs)





def from_yaml(document):
@@ -59,7 +75,8 @@ def from_yaml(document): 
    --------

    load_yaml_model : Load directly from a file.

    """

    return model_from_dict(yaml.load(document, yaml.RoundTripLoader))

    content = StringIO(document)

    return model_from_dict(yaml.load(content))





def save_yaml_model(model, filename, sort=False, **kwargs):
@@ -88,9 +105,9 @@ def save_yaml_model(model, filename, sort=False, **kwargs): 
    obj["version"] = YAML_SPEC

    if isinstance(filename, string_types):

        with io.open(filename, "w") as file_handle:

            yaml.dump(obj, file_handle, Dumper=yaml.RoundTripDumper, **kwargs)

            yaml.dump(obj, file_handle, **kwargs)

    else:

        yaml.dump(obj, filename, Dumper=yaml.RoundTripDumper, **kwargs)

        yaml.dump(obj, filename, **kwargs)





def load_yaml_model(filename):
@@ -114,7 +131,6 @@ def load_yaml_model(filename): 
    """

    if isinstance(filename, string_types):

        with io.open(filename, "r") as file_handle:

            return model_from_dict(yaml.load(file_handle,

                                             yaml.RoundTripLoader))

            return model_from_dict(yaml.load(file_handle))

    else:

        return model_from_dict(yaml.load(filename, yaml.RoundTripLoader))
 
        return model_from_dict(yaml.load(filename))

cobra/test/test_flux_analysis.py

deleted100644 → 0
+0 −1219

File deleted.

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