[Debian-med-packaging] Bug#1009111: python-cobra: (autopkgtest) needs update for python3.10: module 'collections' has no attribute 'Iterable'

Thu Apr 7 12:03:05 BST 2022

Source: python-cobra
Version: 0.23.0-1
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: needs-update
User: debian-python at lists.debian.org
Usertags: python3.10
Control: affects -1 src:python3-defaults

Dear maintainer(s),

We are in the transition of making python3.10 the default Python 
versions [0]. With a recent upload of python3-defaults the autopkgtest 
of python-cobra fails in testing when that autopkgtest is run with the 
binary packages of python3-defaults from unstable. It passes when run 
with only packages from testing. In tabular form:

                        pass            fail
python3-defaults       from testing    3.10.4-1
python-cobra           from testing    0.23.0-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of python3-defaults 
to testing [1]. https://docs.python.org/3/whatsnew/3.10.html lists 
what's new in Python3.10, it may help to identify what needs to be 
updated. https://docs.python.org/3.9/library/collections.html says:
"""
Deprecated since version 3.3, will be removed in version 3.10: Moved 
Collections Abstract Base Classes to the collections.abc module. For 
backwards compatibility, they continue to be visible in this module 
through Python 3.9.
"""
Time to move on.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] https://bugs.debian.org/1006836
[1] https://qa.debian.org/excuses.php?package=python3-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-cobra/20649526/log.gz

==================================== ERRORS 
====================================
____________________ ERROR at setup of test_sbo_annotation 
_____________________

filename = '/usr/lib/python3/dist-packages/cobra/test/data/textbook.xml.gz'
number = <class 'float'>
f_replace = {'F_GENE': <function _f_gene at 0x7f121f630550>, 
'F_GENE_REV': <function _f_gene_rev at 0x7f121f6305e0>, 'F_GROUP': 
<function _f_group at 0x7f121f6308b0>, 'F_GROUP_REV': <function 
_f_group_rev at 0x7f121f630940>, ...}
kwargs = {}
doc = <libsbml.SBMLDocument; proxy of <Swig Object of type 'SBMLDocument 
*' at 0x7f121e2ce610> >
cobra_error = CobraSBMLError('Something went wrong reading the SBML 
model. Most likely the SBML model is not valid. Please check 
tha...ame)`\nIf the model is valid and cannot be read please open an 
issue at https://github.com/opencobra/cobrapy/issues .')

     def read_sbml_model(filename, number=float, f_replace=F_REPLACE, 
**kwargs):
         """Reads SBML model from given filename.
             If the given filename ends with the suffix ''.gz'' (for 
example,
         ''myfile.xml.gz'),' the file is assumed to be compressed in gzip
         format and will be automatically decompressed upon reading. 
Similarly,
         if the given filename ends with ''.zip'' or ''.bz2',' the file is
         assumed to be compressed in zip or bzip2 format (respectively). 
  Files
         whose names lack these suffixes will be read uncompressed. 
Note that
         if the file is in zip format but the archive contains more than one
         file, only the first file in the archive will be read and the rest
         ignored.
             To read a gzip/zip file, libSBML needs to be configured and 
linked
         with the zlib library at compile time.  It also needs to be linked
         with the bzip2 library to read files in bzip2 format.  (Both of 
these
         are the default configurations for libSBML.)
             This function supports SBML with FBC-v1 and FBC-v2. FBC-v1 
models
         are converted to FBC-v2 models before reading.
             The parser tries to fall back to information in notes 
dictionaries
         if information is not available in the FBC packages, e.g.,
         CHARGE, FORMULA on species, or GENE_ASSOCIATION, SUBSYSTEM on 
reactions.
             Parameters
         ----------
         filename : path to SBML file, or SBML string, or SBML file handle
             SBML which is read into cobra model
         number: data type of stoichiometry: {float, int}
             In which data type should the stoichiometry be parsed.
         f_replace : dict of replacement functions for id replacement
             Dictionary of replacement functions for gene, specie, and 
reaction.
             By default the following id changes are performed on import:
             clip G_ from genes, clip M_ from species, clip R_ from 
reactions
             If no replacements should be performed, set f_replace={}, None
             Returns
         -------
         cobra.core.Model
             Notes
         -----
         Provided file handles cannot be opened in binary mode, i.e., use
             with open(path, "r" as f):
                 read_sbml_model(f)
         File handles to compressed files are not supported yet.
         """
         try:
             doc = _get_doc_from_filename(filename)
>           return _sbml_to_model(doc, number=number, f_replace=f_replace, **kwargs)

/usr/lib/python3/dist-packages/cobra/io/sbml.py:249: _ _ _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
doc = <libsbml.SBMLDocument; proxy of <Swig Object of type 'SBMLDocument 
*' at 0x7f121e2ce610> >
number = <class 'float'>
f_replace = {'F_GENE': <function _f_gene at 0x7f121f630550>, 
'F_GENE_REV': <function _f_gene_rev at 0x7f121f6305e0>, 'F_GROUP': 
<function _f_group at 0x7f121f6308b0>, 'F_GROUP_REV': <function 
_f_group_rev at 0x7f121f630940>, ...}
set_missing_bounds = False, kwargs = {}
model = <libsbml.Model; proxy of <Swig Object of type 'Model_t *' at 
0x7f121e2cd890> >
model_fbc = <libsbml.FbcModelPlugin; proxy of <Swig Object of type 
'FbcModelPlugin *' at 0x7f121e2cda70> >
doc_fbc = <libsbml.FbcSBMLDocumentPlugin; proxy of <Swig Object of type 
'FbcSBMLDocumentPlugin *' at 0x7f121e2cda40> >
fbc_version = 2, model_id = 'e_coli_core'

     def _sbml_to_model(
         doc, number=float, f_replace=F_REPLACE, 
set_missing_bounds=False, **kwargs
     ):
         """Creates cobra model from SBMLDocument.
             Parameters
         ----------
         doc: libsbml.SBMLDocument
         number: data type of stoichiometry: {float, int}
             In which data type should the stoichiometry be parsed.
         f_replace : dict of replacement functions for id replacement
         set_missing_bounds : flag to set missing bounds
             Returns
         -------
         cobra.core.Model
         """
         if f_replace is None:
             f_replace = {}
             # SBML model
         model = doc.getModel()  # type: libsbml.Model
         if model is None:
             raise CobraSBMLError("No SBML model detected in file.")
         model_fbc = model.getPlugin("fbc")  # type: libsbml.FbcModelPlugin
             if not model_fbc:
             LOGGER.warning("Model does not contain SBML fbc package 
information.")
         else:
             if not model_fbc.isSetStrict():
                 LOGGER.warning('Loading SBML model without 
fbc:strict="true"')
                 # fbc-v1 (legacy)
             doc_fbc = doc.getPlugin("fbc")  # type: 
libsbml.FbcSBMLDocumentPlugin
             fbc_version = doc_fbc.getPackageVersion()
                 if fbc_version == 1:
                 LOGGER.warning(
                     "Loading SBML with fbc-v1 (models should be 
encoded" " using fbc-v2)"
                 )
                 conversion_properties = libsbml.ConversionProperties()
                 conversion_properties.addOption(
                     "convert fbc v1 to fbc v2", True, "Convert FBC-v1 
model to FBC-v2"
                 )
                 result = doc.convert(conversion_properties)
                 if result != libsbml.LIBSBML_OPERATION_SUCCESS:
                     raise Exception("Conversion of SBML fbc v1 to fbc 
v2 failed")
             # Model
         model_id = model.getIdAttribute()
         if not libsbml.SyntaxChecker.isValidSBMLSId(model_id):
             LOGGER.error("'%s' is not a valid SBML 'SId'." % model_id)
>       cobra_model = Model(model_id)

/usr/lib/python3/dist-packages/cobra/io/sbml.py:371: _ _ _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0x7f121e2cd540>, id_or_model = 'e_coli_core'
name = None

     def __init__(self, id_or_model=None, name=None):
         if isinstance(id_or_model, Model):
             Object.__init__(self, name=name)
             self.__setstate__(id_or_model.__dict__)
             if not hasattr(self, "name"):
                 self.name = None
             self._solver = id_or_model.solver
         else:
             Object.__init__(self, id_or_model, name=name)
             self._trimmed = False
             self._trimmed_genes = []
             self._trimmed_reactions = {}
             self.genes = DictList()
             self.reactions = DictList()  # A list of cobra.Reactions
             self.metabolites = DictList()  # A list of cobra.Metabolites
             self.groups = DictList()  # A list of cobra.Groups
             # genes based on their ids {Gene.id: Gene}
             self._compartments = {}
             self._contexts = []
                 # from cameo ...
                 # if not hasattr(self, '_solver'):  # backwards 
compatibility
             # with older cobrapy pickles?
                 interface = check_solver(configuration.solver)
             self._solver = interface.Model()
             self._solver.objective = interface.Objective(Zero)
>           self._populate_solver(self.reactions, self.metabolites)

/usr/lib/python3/dist-packages/cobra/core/model.py:115: _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0x7f121e2cd540>, reaction_list = []
metabolite_list = []

     def _populate_solver(self, reaction_list, metabolite_list=None):
         """Populate attached solver with constraints and variables that
         model the provided reactions.
         """
         constraint_terms = AutoVivification()
         to_add = []
         if metabolite_list is not None:
             for met in metabolite_list:
                 to_add += [self.problem.Constraint(Zero, name=met.id, 
lb=0, ub=0)]
>       self.add_cons_vars(to_add)

/usr/lib/python3/dist-packages/cobra/core/model.py:1003: _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0x7f121e2cd540>, what = [], kwargs = {}

     def add_cons_vars(self, what, **kwargs):
         """Add constraints and variables to the model's mathematical 
problem.
             Useful for variables and constraints that can not be 
expressed with
         reactions and simple lower and upper bounds.
             Additions are reversed upon exit if the model itself is used as
         context.
             Parameters
         ----------
         what : list or tuple of optlang variables or constraints.
            The variables or constraints to add to the model. Must be of
            class `optlang.interface.Variable` or
            `optlang.interface.Constraint`.
         **kwargs : keyword arguments
            Passed to solver.add()
         """
>       add_cons_vars_to_problem(self, what, **kwargs)

/usr/lib/python3/dist-packages/cobra/core/model.py:895: _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
model = <Model e_coli_core at 0x7f121e2cd540>, what = [], kwargs = {}

     def add_cons_vars_to_problem(
         model: "Model",
         what: Union[List[CONS_VARS], Tuple[CONS_VARS], Components],
         **kwargs,
     ) -> None:
         """Add variables and constraints to a model's solver object.
             Useful for variables and constraints that can not be 
expressed with
         reactions and lower/upper bounds. It will integrate with the 
model's
         context manager in order to revert changes upon leaving the 
context.
             Parameters
         ----------
         model : cobra.Model
            The model to which to add the variables and constraints.
         what : list or tuple of optlang.interface.Variable or
                optlang.interface.Constraint
            The variables and constraints to add to the model.
         **kwargs : keyword arguments
            Keyword arguments passed to solver's add() method.
             """
>       model.solver.add(what, **kwargs)

/usr/lib/python3/dist-packages/cobra/util/solver.py:384: _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <optlang.glpk_interface.Model object at 0x7f121e2cd600>, stuff = []
sloppy = False

     def add(self, stuff, sloppy=False):
         """Add variables and constraints.
             Parameters
         ----------
         stuff : iterable, Variable, Constraint
             Either an iterable containing variables and constraints or 
a single variable or constraint.
             sloppy : bool
             Check constraints for variables that are not part of the 
model yet.
             Returns
         -------
         None
         """
         if self._pending_modifications.toggle == 'remove':
             self.update()
             self._pending_modifications.toggle = 'add'
>       if isinstance(stuff, collections.Iterable):
E       AttributeError: module 'collections' has no attribute 'Iterable'

/usr/lib/python3/dist-packages/optlang/interface.py:1358: AttributeError