Merge branch 'devel' into devel-nonfree

.gitignore

@@ -51,3 +51,5 @@ docs/_build
 .vagrant
 *~
 /.DS_Store
+.cache
+/coverage.xml

.travis.yml

@@ -1,5 +1,6 @@
 language: python
-sudo: false
+sudo: required
+dist: trusty
 
 python:
   - '2.7'
@@ -37,11 +38,11 @@ before_install:
 - 'echo "this is a build for: $TRAVIS_BRANCH"'
 - 'if [[ "$TRAVIS_BRANCH" != "devel" && ($TRAVIS_PYTHON_VERSION == "3.4" || $TRAVIS_PYTHON_VERSION == "2.7") ]]; then bash ./.travis/install_cplex.sh; fi'
 install:
-- pip install flake8 numpy scipy pyzmq pandas
+- pip install flake8 numpy scipy pyzmq pandas pytest pytest-cov
 - pip install .[swiglpk,test,parallel,cli]
 before_script:
 - if [[ $TRAVIS_PYTHON_VERSION == "3.6" ]]; then flake8 .; fi
-script: nosetests
+script: pytest -v -rsx --cov --cov-report=xml
 after_success:
 - codecov
 notifications:

cameo/cli/controllers.py

@@ -43,8 +43,10 @@ class Meta:
             (['-m', '--multiprocess'], dict(help='Run multiprocess mode', action='store_true')),
             (['-c', '--cores'], dict(help="Number of cores (if multiprocess)")),
             (['-o', '--output'], dict(help="Output file")),
-            (['-of', '--output-format'], dict(help="Output file format (default xlsx)\nOptions:%s" % VALID_OUTPUT_FORMATS)),
-            (['-y', '--yes-all'], dict(help="Auto select suggested options", action="store_true"))]
+            (['-of', '--output-format'], dict(help="Output file format (default xlsx)\nOptions:%s" %
+                                                   VALID_OUTPUT_FORMATS)),
+            (['-y', '--yes-all'], dict(help="Auto select suggested options", action="store_true")),
+            (['-t', '--test'], dict(help="Test mode", action="store_true"))]
 
     @expose(hide=True)
     def default(self):
@@ -105,9 +107,14 @@ def default(self):
         else:
             view = SequentialView()
 
+        design.debug = self.app.pargs.test
+
         results = design(product=product, hosts=_hosts,
                          view=view, aerobic=not self.app.pargs.anaerobic)
 
+        results['heterologous_pathway'] = results.heterologous_pathway.apply(str)
+        results['manipulations'] = results.manipulations.apply(str)
+
         OUTPUT_WRITER[output_format](results, output)
 
     @expose(help="Search for products in our internal database")

cameo/core/metabolite.py

@@ -25,7 +25,6 @@
 
 @six.add_metaclass(inheritdocstring)
 class Metabolite(cobra.core.Metabolite):
-
     # TODO: figure out how to handle the _reaction attribute
     @classmethod
     def clone(cls, metabolite, model=None):
@@ -35,7 +34,8 @@ def clone(cls, metabolite, model=None):
                 setattr(new_metabolite, attribute, value)
             except AttributeError:
                 logger.info(
-                    "Can't set attribute %s for metabolite %s (while cloning it to a cameo style metabolite). Skipping it ..." %
+                    "Can't set attribute %s for metabolite %s (while cloning it to a "
+                    "cameo style metabolite). Skipping it ..." %
                     (attribute, metabolite)
                 )
         if model is not None:

cameo/core/reaction.py

@@ -64,7 +64,8 @@ def clone(cls, reaction, model=None):
                 setattr(new_reaction, attribute, value)
             except AttributeError:
                 logger.info(
-                    "Can't set attribute %s for reaction %s (while cloning it to a cameo style reaction). Skipping it ..." % (
+                    "Can't set attribute %s for reaction %s (while cloning it to a "
+                    "cameo style reaction). Skipping it ..." % (
                         attribute, reaction))
         if not isinstance(reaction.model, cameo.core.solver_based_model.SolverBasedModel):
             new_reaction._model = None
@@ -333,7 +334,8 @@ def model(self, value):
 
     @property
     def objective_coefficient(self):
-        if self.model is not None and isinstance(self.model, cameo.core.SolverBasedModel) and self.model.objective is not None:
+        if self.model is not None and isinstance(self.model,
+                                                 cameo.core.SolverBasedModel) and self.model.objective is not None:
             coefficients_dict = self.model.objective.expression.as_coefficients_dict()
             forw_coef = coefficients_dict.get(self.forward_variable, 0)
             rev_coef = coefficients_dict.get(self.reverse_variable, 0)

cameo/core/solution.py

@@ -162,9 +162,11 @@ def __init__(self, model, *args, **kwargs):
         self._reduced_values = model.solver.reduced_costs
 
         for reaction in model.reactions:
-            self.fluxes[reaction.id] = self._primal_values[reaction._get_forward_id()] - self._primal_values[reaction._get_reverse_id()]
+            self.fluxes[reaction.id] = self._primal_values[reaction._get_forward_id()] - self._primal_values[
+                reaction._get_reverse_id()]
 
-            self.reduced_costs[reaction.id] = self._reduced_values[reaction._get_forward_id()] - self._reduced_values[reaction._get_reverse_id()]
+            self.reduced_costs[reaction.id] = self._reduced_values[reaction._get_forward_id()] - self._reduced_values[
+                reaction._get_reverse_id()]
 
         self.status = model.solver.status
         self._reaction_ids = [r.id for r in self.model.reactions]
@@ -228,7 +230,8 @@ def timestamp_formatter(timestamp):
                     "%Y-%m-%d %H:%M:%S:%f")
 
             raise UndefinedSolution(
-                'The solution (captured around %s) has become invalid as the model has been re-optimized recently (%s).' % (
+                'The solution (captured around %s) has become invalid as the model has been '
+                're-optimized recently (%s).' % (
                     timestamp_formatter(self._time_stamp),
                     timestamp_formatter(self.model._timestamp_last_optimization))
             )
@@ -268,7 +271,8 @@ def reduced_costs(self):
 
         reduced_costs = OrderedDict()
         for reaction in self.model.reactions:
-            reduced_costs[reaction.id] = reduced_values[reaction._get_forward_id()] - reduced_values[reaction._get_reverse_id()]
+            reduced_costs[reaction.id] = reduced_values[reaction._get_forward_id()] - reduced_values[
+                reaction._get_reverse_id()]
         return reduced_costs
 
     @property

cameo/core/solver_based_model.py

@@ -315,7 +315,8 @@ def add_reactions(self, reaction_list):
             else:
                 cloned_reaction_list.append(reaction)
 
-        # cobrapy will raise an exceptions if one of the reactions already exists in the model (before adding any reactions)
+        # cobrapy will raise an exceptions if one of the reactions already exists in the model (before adding any
+        # reactions)
         super(SolverBasedModel, self).add_reactions(cloned_reaction_list)
         for reac in cloned_reaction_list:
             reac.model = self

cameo/core/strain_design.py

@@ -56,10 +56,10 @@ def __init__(self, targets):
         self.targets = DictList(targets)
 
     def __str__(self):
-        return "".join(str(t) for t in self.targets)
+        return ", ".join(str(t) for t in self.targets)
 
     def __repr__(self):
-        return str(self)
+        return "<StrainDesign [" + ";".join(repr(t) for t in self.targets) + "]>"
 
     def __iter__(self):
         return iter(self.targets)
@@ -92,35 +92,43 @@ def apply(self, model, time_machine=None):
             target.apply(model, time_machine)
 
     def __add__(self, other):
+        if not isinstance(other, StrainDesign):
+            raise AssertionError("Only instances of StrainDesign can be added together")
+
         targets = {}
         for target in self.targets:
             if target.id not in targets:
-                targets[target.id] = []
-            targets[target.id].append(target)
+                targets[target.id] = set()
+            targets[target.id].add(target)
 
         for target in other.targets:
             if target.id not in targets:
-                targets[target.id] = []
-            targets[target.id].append(target)
+                targets[target.id] = set()
+            targets[target.id].add(target)
 
-        targets = [t[0] if len(t) == 1 else EnsembleTarget(id, t) for id, t in six.iteritems(targets)]
+        targets = [next(iter(t)) if len(t) == 1 else EnsembleTarget(id, t) for id, t in six.iteritems(targets)]
 
         return StrainDesign(targets)
 
     def __iadd__(self, other):
+        if not isinstance(other, StrainDesign):
+            raise AssertionError("Only instances of StrainDesign can be added together")
+
         targets = {}
         for target in self.targets:
             if target.id not in targets:
-                targets[target.id] = []
-            targets[target.id].append(target)
+                targets[target.id] = set()
+            targets[target.id].add(target)
 
         for target in other.targets:
             if target.id not in targets:
-                targets[target.id] = []
-            targets[target.id].append(target)
+                targets[target.id] = set()
+            targets[target.id].add(target)
+
+        targets = [next(iter(t)) if len(t) == 1 else EnsembleTarget(id, t) for id, t in six.iteritems(targets)]
 
-        targets = [t[0] if len(t) == 1 else EnsembleTarget(id, t) for id, t in six.iteritems(targets)]
         self.targets = DictList(targets)
+
         return self
 
     def _repr_html_(self):