Merge 8c899a9 into 974abf7

.travis.yml

@@ -1,9 +1,7 @@
 language: python
 python:
  - "2.7"
-# command to install dependencies
-virtualenv:
-  system_site_packages: true
+ - "3.4"
 before_install:
   - sudo apt-get install swig redis-server libzmq3-dev libgmp-dev
   - sudo service redis-server start
@@ -19,8 +17,7 @@ before_install:
   - sudo ldconfig
   - sudo ln -s /run/shm /dev/shm
 install:
-  #glpk for cobra
-  - pip install glpk
+  - if [[ $TRAVIS_PYTHON_VERSION == "3.4" ]]; then pip install pyzmq pandas bokeh; fi
   - pip install python-libsbml-experimental cython numpy scipy pyzmq pandas bokeh -f https://dl.dropboxusercontent.com/u/22461024/pypi.drosophi.la/index.html --no-index
   - pip install coveralls coverage
   - pip install redis

cameo/__init__.py

@@ -47,13 +47,16 @@
        mutation_rate=0.3, view=cameo.parallel.SequentialView(),
        product="EX_succ_lp_e_rp_", num_elites=1)
 """
+from __future__ import absolute_import, print_function
 
 import os
 
 _cameo_path = __path__[0]
 _cameo_data_path = os.path.join(_cameo_path, 'data')
 
-from util import get_system_info
+from cameo import config
+
+from .util import get_system_info
 
 system_info = get_system_info()
 
@@ -67,8 +70,6 @@
 except ImportError:
     pass
 
-import config
-
 from cameo.core.solver_based_model import SolverBasedModel as Model
 from cameo.core.reaction import Reaction
 from cobra.core import Metabolite

cameo/api/__init__.py

@@ -4,23 +4,15 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#   http://www.apache.org/licenses/LICENSE-2.0
+#     http://www.apache.org/licenses/LICENSE-2.0
 #
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# import logging
-# logging.basicConfig(level=logging.INFO)
-# logger = logging.getLogger(__name__)
-#
-# logger.info('Initializing cameo advanced programming interface. Be patient this might take a while ...')
-
-import os
-import cPickle as pickle
-import cameo
+from __future__ import absolute_import
 
 import logging
 logger = logging.getLogger(__name__)

cameo/api/designer.py

@@ -12,7 +12,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from types import StringType
+from __future__ import absolute_import, print_function
+
 from functools import partial
 import progressbar
 from cameo import Metabolite, Model
@@ -21,6 +22,7 @@
 from cameo.api.products import products
 from cameo.strain_design.pathway_prediction import PathwayPredictor
 from cameo.util import TimeMachine, DisplayItemsWidget
+import six
 
 
 class Designs(object):
@@ -99,7 +101,7 @@ def predict_pathways(self, product, hosts=hosts):  #TODO: make this work with a
 
     def calculate_maximum_yields(self, pathways):
         """"""
-        for (host, model), pathway in pathways.iteritems():
+        for (host, model), pathway in six.iteritems(pathways):
             tm = TimeMachine()
             tm(do=partial(model.add_reactions, pathway), undo=partial(model.remove_reactions, pathway))
             maximum_theoretical_yield()
@@ -108,11 +110,11 @@ def calculate_maximum_yields(self, pathways):
     def __translate_product_to_universal_reactions_model_metabolite(self, product):
         if isinstance(product, Metabolite):
             return product
-        elif isinstance(product, StringType):
+        elif isinstance(product, str):
             search_result = products.search(product)
-            print "Found %d compounds that match query '%s'" % (len(search_result), product)
-            print repr(search_result)
-            print "Choosing best match (%s) ... please interrupt if this is not the desired compound." % search_result.name[0]
+            print("Found %d compounds that match query '%s'" % (len(search_result), product))
+            print(repr(search_result))
+            print("Choosing best match (%s) ... please interrupt if this is not the desired compound." % search_result.name[0])
             return METANETX['universal_model'].metabolites.get_by_id(search_result.index[0])
 
 design = Designer()

cameo/api/hosts.py

@@ -12,12 +12,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import absolute_import, print_function
 
 import os
 import optlang
 import cameo
 from cameo.util import IntelliContainer
 from cameo import load_model
+import six
 
 MODEL_DIRECTORY = os.path.join(os.path.join(os.path.split(cameo.__path__[0])[0]), 'tests/data')
 
@@ -58,7 +60,7 @@ class Hosts(object):
     def __init__(self, host_spec):
         self._host_spec = host_spec
         self._hosts = list()
-        for host_id, information in self._host_spec.iteritems():
+        for host_id, information in six.iteritems(self._host_spec):
             host = Host(**information)
             self._hosts.append(host)
             setattr(self, host_id, host)
@@ -67,7 +69,7 @@ def __iter__(self):
         return iter(self._hosts)
 
     def __dir__(self):
-        return self._host_spec.keys()
+        return list(self._host_spec.keys())
 
 
 HOST_SPECS = {'ecoli': {'name': 'Escherichia coli', 'models': ('iJO1366',)}, #  'iAF1260', 'iJO1366', 'EcoliCore'

cameo/api/products.py

@@ -12,15 +12,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import absolute_import, print_function
+
 import difflib
 from cameo.data import metanetx
 
 
 def inchi_to_svg(inchi, file=None):
     try:
         import openbabel
-    except ImportError, e:
-        print e
+    except ImportError as e:
+        print(e)
         raise ImportError("OpenBabel seems to be not installed.")
     convert = openbabel.OBConversion()
     convert.SetInFormat("inchi")

cameo/config.py

@@ -12,6 +12,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import absolute_import, print_function
+
 non_zero_flux_threshold = 1e-6
 ndecimals = 6
 

cameo/core/reaction.py

@@ -13,6 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import absolute_import, print_function
+
 from functools import partial
 import hashlib
 import cobra as _cobrapy
@@ -23,7 +25,9 @@
 from cameo.parallel import SequentialView
 
 import logging
+import six
 logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
 
 
 class Reaction(_cobrapy.core.Reaction):
@@ -49,11 +53,13 @@ def clone(cls, reaction, model=None):
 
         """
         new_reaction = cls(name=reaction.name)
-        for attribute, value in reaction.__dict__.iteritems():
+        for attribute, value in six.iteritems(reaction.__dict__):
+            if attribute == '_model':  # _model needs to be set after all other attributes have been set.
+                continue
             try:
                 setattr(new_reaction, attribute, value)
             except AttributeError:
-                logger.debug("Can't set attribute %s for reaction %s (while cloning it to a cameo style reaction). Skipping it ..." % (attribute, reaction))
+                logger.info("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
         if model is not None:
@@ -97,7 +103,7 @@ def reversibility(self):
 
     def _get_reverse_id(self):
         """Generate the id of revers_variable from the reaction's id."""
-        return '_'.join((self.id, 'reverse', hashlib.md5(self.id).hexdigest()[0:5]))
+        return '_'.join((self.id, 'reverse', hashlib.md5(self.id.encode('utf-8')).hexdigest()[0:5]))
 
     @property
     def reverse_variable(self):
@@ -128,7 +134,7 @@ def lower_bound(self, value):
             elif value < 0 and self._lower_bound >= 0 and self.reverse_variable is None:  # self._lower_bound >= 0 implies self._upper_bound >= 0
                 reverse_variable = model.solver._add_variable(
                     model.solver.interface.Variable(self._get_reverse_id(), lb=0, ub=0))
-                for met, coeff in self._metabolites.iteritems():
+                for met, coeff in six.iteritems(self._metabolites):
                     model.solver.constraints[met.id] += sympy.Mul._from_args((-1 * sympy.RealNumber(coeff), reverse_variable))
 
             variable = self.variable
@@ -178,7 +184,7 @@ def upper_bound(self, value):
                 if self.reverse_variable is None:
                     reverse_variable = model.solver._add_variable(
                         model.solver.interface.Variable(self._get_reverse_id(), lb=0, ub=0))
-                    for met, coeff in self._metabolites.iteritems():
+                    for met, coeff in six.iteritems(self._metabolites):
                         model.solver.constraints[met.id] += sympy.Mul._from_args((-1 * sympy.RealNumber(coeff), reverse_variable))
                 else:
                     reverse_variable = self.reverse_variable
@@ -249,7 +255,7 @@ def add_metabolites(self, metabolites, **kwargs):
         super(Reaction, self).add_metabolites(metabolites, **kwargs)
         model = self.model
         if model is not None:
-            for metabolite, coefficient in metabolites.iteritems():
+            for metabolite, coefficient in six.iteritems(metabolites):
                 model.solver.constraints[metabolite.id] += coefficient*self.variable
 
     def knock_out(self, time_machine=None):

cameo/core/result.py

@@ -13,6 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import absolute_import, print_function
+
 import time
 from datetime import datetime
 from cameo import system_info
@@ -71,7 +73,7 @@ def __init__(self, solution, *args, **kwargs):
 
     @property
     def data_frame(self):
-        return pandas.DataFrame(self._fluxes.values(), index=self._fluxes.keys(), columns=['flux'])
+        return pandas.DataFrame(list(self._fluxes.values()), index=list(self._fluxes.keys()), columns=['flux'])
 
     @property
     def fluxes(self):
@@ -90,8 +92,8 @@ def objective_value(self):
     from cameo.util import Timer
     with Timer():
         result = FluxDistributionResult(solution)
-        print result.meta_information.system_info
-        print result.meta_information.responsible
-        print result.meta_information.timestamp
-        print result.meta_information.human_readable_timestamp
-        print result.data_frame
+        print(result.meta_information.system_info)
+        print(result.meta_information.responsible)
+        print(result.meta_information.timestamp)
+        print(result.meta_information.human_readable_timestamp)
+        print(result.data_frame)

cameo/core/solution.py

@@ -13,6 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import absolute_import, print_function
+
 from collections import OrderedDict
 
 import time
@@ -22,6 +24,7 @@
 from cameo.exceptions import UndefinedSolution
 
 import logging
+from six.moves import zip
 logger = logging.getLogger(__name__)
 
 
@@ -99,11 +102,11 @@ def __init__(self, model, *args, **kwargs):
 
     @property
     def x_dict(self):
-        return OrderedDict(zip(self._reaction_ids, self.x))
+        return OrderedDict(list(zip(self._reaction_ids, self.x)))
 
     @property
     def y_dict(self):
-        return OrderedDict(zip(self._reaction_ids, self.y))
+        return OrderedDict(list(zip(self._reaction_ids, self.y)))
 
     @property
     def fluxes(self):
@@ -115,7 +118,7 @@ def reduced_costs(self):
 
     def __dir__(self):
         # Hide 'cobrapy' attributes and methods from user.
-        fields = sorted(dir(type(self)) + self.__dict__.keys())
+        fields = sorted(dir(type(self)) + list(self.__dict__.keys()))
         fields.remove('x')
         fields.remove('y')
         fields.remove('x_dict')
@@ -184,7 +187,7 @@ def f(self, value):
     @property
     def x(self):
         self._check_freshness()
-        return self.x_dict.values()
+        return list(self.x_dict.values())
 
     @property
     def x_dict(self):
@@ -199,7 +202,7 @@ def x_dict(self):
     @property
     def y(self):
         self._check_freshness()
-        return self.y_dict.values()
+        return list(self.y_dict.values())
 
     @property
     def y_dict(self):
@@ -227,7 +230,7 @@ def reduced_costs(self):
 
     def __dir__(self):
         # Hide 'cobrapy' attributes and methods from user.
-        fields = sorted(dir(type(self)) + self.__dict__.keys())
+        fields = sorted(dir(type(self)) + list(self.__dict__.keys()))
         fields.remove('x')
         fields.remove('y')
         fields.remove('x_dict')