refactor: add a compartment class

This represents the state of the work done by @MaxGreil.

refactor: add methods

feat: mimic previous behaviour when comparing compartments with strings

fix: use compartment IDs instead of objects when converting model to dict

fix: ensure backwards compatibility when importing JSON following the previous schema

fix: add importlib-resources to setup

chore: regenerate pickle models and fix SBML and mat importer

fix: update compartment handling on mat and sbml input

fix: change version type in json schema from int to str

fix: satisfy flake8

fix: better checking for sane IDs

chore: update pickels again

fix: update documentation notebooks building_model and getting_started

test: add tests for compartments and metabolites

fix: flake8 is a cruel mistress

style: add blank line in test_compartment

Author: Midnighter

cobra/__init__.py

@@ -10,7 +10,7 @@
 
 from cobra import flux_analysis, io
 from cobra.core import (
-    DictList, Gene, Metabolite, Model, Object, Reaction, Species)
+    DictList, Gene, Metabolite, Model, Object, Reaction, Species, Compartment)
 from cobra.util import show_versions
 
 __version__ = "0.13.4"

cobra/core/__init__.py

@@ -10,3 +10,4 @@
 from cobra.core.reaction import Reaction
 from cobra.core.solution import Solution, LegacySolution, get_solution
 from cobra.core.species import Species
+from cobra.core.compartment import Compartment

cobra/core/compartment.py

@@ -0,0 +1,76 @@
+# -*- coding: utf-8 -*-
+
+"""Provide a class for compartments."""
+
+from __future__ import absolute_import
+
+from copy import deepcopy
+from cobra.util import format_long_string, is_not_sane
+from six import string_types
+
+from cobra.core.object import Object
+
+
+class Compartment(Object):
+    """
+    Compartment is a class for holding information regarding
+    a compartment in a cobra.Model object
+
+    Parameters
+    ----------
+    id : string
+       An identifier for the compartment
+    name : string
+       A human readable name.
+
+    """
+    def __init__(self, id=None, name=""):
+        super(Compartment, self).__init__(id=id, name=name)
+        self._id = None
+        self.id = id
+
+    def __contains__(self, metabolite):
+        return metabolite.compartment is self
+
+    def __eq__(self, other):
+        if self is other:
+            return True
+        if isinstance(other, string_types):
+            return self._id == other
+        if isinstance(other, Compartment):
+            return self._id == other.id
+        else:
+            return False
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def __hash__(self):
+        return hash(self._id)
+
+    def copy(self):
+        return deepcopy(self)
+
+    @property
+    def id(self):
+        return self._id
+
+    @id.setter
+    def id(self, value):
+        if is_not_sane(value):
+            raise TypeError("The compartment ID must be a non-empty string")
+        self._id = value
+
+    def _repr_html_(self):
+        return """
+        <table>
+            <tr>
+                <td><strong>Compartment identifier</strong></td><td>{id}</td>
+            </tr><tr>
+                <td><strong>Name</strong></td><td>{name}</td>
+            </tr><tr>
+                <td><strong>Memory address</strong></td>
+                <td>{address}</td>
+            </tr>
+        </table>""".format(id=self.id, name=format_long_string(self.name),
+                           address='0x0%x' % id(self))

cobra/core/metabolite.py

@@ -12,7 +12,8 @@
 from cobra.core.formula import elements_and_molecular_weights
 from cobra.core.species import Species
 from cobra.util.solver import check_solver_status
-from cobra.util.util import format_long_string
+from cobra.util.util import format_long_string, is_not_sane
+from cobra.core.compartment import Compartment
 
 
 # Numbers are not required because of the |(?=[A-Z])? block. See the
@@ -35,15 +36,16 @@ class Metabolite(Species):
         A human readable name.
     charge : float
        The charge number of the metabolite
-    compartment: str or None
-       Compartment of the metabolite.
+    compartment: cobra.Compartment, str or None
+       Compartment or compartment ID that the the metabolite is in.
     """
 
     def __init__(self, id=None, formula=None, name="",
                  charge=None, compartment=None):
         Species.__init__(self, id, name)
         self.formula = formula
         # because in a Model a metabolite may participate in multiple Reactions
+        self._compartment = None
         self.compartment = compartment
         self.charge = charge
 
@@ -58,6 +60,28 @@ def _set_id_with_model(self, value):
         self._id = value
         self.model.metabolites._generate_index()
 
+    @property
+    def compartment(self):
+        return self._compartment
+
+    @compartment.setter
+    def compartment(self, value):
+        if value is None:
+            self._compartment = None
+        elif isinstance(value, Compartment):
+            if self._model and value.id in self._model.compartments:
+                self._compartment = \
+                    self._model.compartments.get_by_id(value.id)
+            else:
+                self._compartment = value
+        elif not is_not_sane(value):
+            if self._model and value in self._model.compartments:
+                self._compartment = self._model.compartments.get_by_id(value)
+            else:
+                self._compartment = Compartment(value)
+        else:
+            raise TypeError("The compartment ID must be a non-empty string")
+
     @property
     def constraint(self):
         """Get the constraints associated with this metabolite from the solve