Merge branch 'devel' of https://github.com/biosustain/cameo into devel

.travis.yml

@@ -15,8 +15,6 @@ matrix:
       env: TOXENV=py36
     - python: '3.7'
       env: TOXENV=py37
-    - python: '3.8'
-      env: TOXENV=py38
 
 branches:
  only:

cameo/core/strain_design.py

@@ -23,7 +23,6 @@
 
 from cameo.core.result import Result
 from cameo.core.target import EnsembleTarget, Target
-from cameo.visualization.plotting import plotter
 
 from gnomic import Genotype
 
@@ -180,7 +179,7 @@ def __add__(self, other):
     def _repr_html_(self):
         return self.data_frame._repr_html_()
 
-    def plot(self, grid=None, width=None, height=None, title=None, *args, **kwargs):
+    def plot(self, plotter, grid=None, width=None, height=None, title=None, *args, **kwargs):
         if title is None:
             title = "Target frequency plot for %s result" % self.__method_name__
 

cameo/flux_analysis/analysis.py

@@ -29,18 +29,16 @@
 from cobra.util import fix_objective_as_constraint, get_context
 from cobra.exceptions import OptimizationError
 from numpy import trapz
-from sympy import S
 from optlang.interface import UNBOUNDED, OPTIMAL
+from optlang.symbolics import Zero
 
-import cameo
 from cameo import config
 from cameo.core.result import Result
 from cameo.flux_analysis.util import remove_infeasible_cycles, fix_pfba_as_constraint
 from cameo.parallel import SequentialView
 from cameo.ui import notice
 from cameo.util import partition, _BIOMASS_RE_
 from cameo.core.utils import get_reaction_for
-from cameo.visualization.plotting import plotter
 
 logger = logging.getLogger(__name__)
 
@@ -203,8 +201,9 @@ def flux_variability_analysis(model, reactions=None, fraction_of_optimum=0., pfb
 
     Returns
     -------
-    pandas.DataFrame
-        Pandas DataFrame containing the results of the flux variability analysis.
+    FluxVariabilityResult
+        FluxVariabilityResult with DataFrame data_frame property containing the results of the flux variability
+        analysis.
 
     """
     if view is None:
@@ -357,7 +356,7 @@ def _flux_variability_analysis(model, reactions=None):
     fva_sol = OrderedDict()
     lb_flags = dict()
     with model:
-        model.objective = S.Zero
+        model.objective = Zero
 
         model.objective.direction = 'min'
         for reaction in reactions:
@@ -760,7 +759,7 @@ def __init__(self, phase_plane, variable_ids, objective,
     def data_frame(self):
         return pandas.DataFrame(self._phase_plane)
 
-    def plot(self, grid=None, width=None, height=None, title=None, axis_font_size=None, palette=None,
+    def plot(self, plotter, grid=None, width=None, height=None, title=None, axis_font_size=None, palette=None,
              points=None, points_colors=None, estimate='flux', **kwargs):
         """plot phenotypic phase plane result
 
@@ -882,7 +881,7 @@ def __init__(self, data_frame, *args, **kwargs):
     def data_frame(self):
         return self._data_frame
 
-    def plot(self, index=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
+    def plot(self, plotter, index=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
         if index is None:
             index = self.data_frame.index[0:10]
         fva_result = self.data_frame.loc[index]

cameo/flux_analysis/simulation.py

@@ -48,8 +48,8 @@
 
 add = Add._from_args
 mul = Mul._from_args
-NegativeOne = sympy.singleton.S.NegativeOne
-One = sympy.singleton.S.One
+NegativeOne = sympy.S.NegativeOne
+One = sympy.S.One
 FloatOne = sympy.Float(1)
 RealNumber = sympy.RealNumber
 

cameo/strain_design/deterministic/flux_variability_based.py

@@ -37,7 +37,6 @@
 from cobra import Reaction, Metabolite
 from cobra.util import fix_objective_as_constraint
 
-from cameo.visualization.plotting import plotter
 from cameo import config
 
 from cameo.ui import notice
@@ -633,7 +632,7 @@ def plot(self, index=None, variables=None, grid=None, width=None, height=None, t
         else:
             self._plot_production_envelope(title=title, grid=grid, width=width, height=height)
 
-    def _plot_flux_variability_analysis(self, index, variables=None, title=None,
+    def _plot_flux_variability_analysis(self, plotter, index, variables=None, title=None,
                                         width=None, height=None, palette=None, grid=None):
         if variables is None:
             variables = self.reference_fva.index[0:10]
@@ -1008,7 +1007,7 @@ class FSEOFResult(StrainDesignMethodResult):
 
     __method_name__ = "FSEOF"
 
-    def plot(self, grid=None, width=None, height=None, title=None, *args, **kwargs):
+    def plot(self, plotter, grid=None, width=None, height=None, title=None, *args, **kwargs):
         if title is None:
             title = "FSEOF fluxes"
 

cameo/strain_design/deterministic/linear_programming.py

@@ -41,7 +41,6 @@
 from cameo.flux_analysis.simulation import fba
 from cameo.flux_analysis.structural import find_coupled_reactions_nullspace
 from cameo.util import reduce_reaction_set, decompose_reaction_groups
-from cameo.visualization.plotting import plotter
 
 logger = logging.getLogger(__name__)
 
@@ -385,7 +384,7 @@ def display_on_map(self, index=0, map_name=None, palette="YlGnBu"):
             fluxes = fba(self._model)
             fluxes.display_on_map(map_name=map_name, palette=palette)
 
-    def plot(self, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
+    def plot(self, plotter, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
         wt_production = phenotypic_phase_plane(self._model, objective=self._target, variables=[self._biomass.id])
         with self._model:
             for ko in self.data_frame.loc[index, "reactions"]:

cameo/strain_design/heuristic/evolutionary_based.py

@@ -38,7 +38,6 @@
 from cameo.strain_design.heuristic.evolutionary.processing import process_reaction_knockout_solution, \
     process_gene_knockout_solution, process_reaction_swap_solution
 from cameo.util import TimeMachine
-from cameo.visualization.plotting import plotter
 from cameo.core.utils import get_reaction_for
 
 __all__ = ["OptGene"]
@@ -294,7 +293,7 @@ def display_on_map(self, index=0, map_name=None, palette="YlGnBu"):
             fluxes = self._simulation_method(self._model, **self._simulation_kwargs)
             fluxes.display_on_map(map_name=map_name, palette=palette)
 
-    def plot(self, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
+    def plot(self, plotter, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
         wt_production = phenotypic_phase_plane(self._model, objective=self._target, variables=[self._biomass])
         with self._model:
             for ko in self.data_frame.loc[index, "reactions"]:
@@ -483,7 +482,7 @@ def display_on_map(self, index=0, map_name=None, palette="YlGnBu"):
             fluxes = self._simulation_method(self._model, **self._simulation_kwargs)
             fluxes.display_on_map(map_name=map_name, palette=palette)
 
-    def plot(self, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
+    def plot(self, plotter, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
         wt_production = phenotypic_phase_plane(self._model, objective=self._target, variables=[self._biomass])
         with self._model:
             for ko in self.data_frame.loc[index, "reactions"]:

cameo/strain_design/pathway_prediction/pathway_predictor.py

@@ -39,7 +39,6 @@
 from cameo.data import metanetx
 from cameo.strain_design.pathway_prediction import util
 from cameo.util import TimeMachine
-from cameo.visualization.plotting import plotter
 
 __all__ = ['PathwayPredictor']
 
@@ -172,7 +171,9 @@ def plot(self, grid=None, width=None, height=None, title=None):
         # TODO: small pathway visualizations would be great.
         raise NotImplementedError
 
-    def plot_production_envelopes(self, model, objective=None, title=None):
+    def plot_production_envelopes(
+        self, plotter, model, objective=None, title=None
+    ):
         rows = int(ceil(len(self.pathways) / 2.0))
         title = "Production envelops for %s" % self.pathways[0].product.name if title is None else title
         grid = plotter.grid(n_rows=rows, title=title)

cameo/visualization/plotting/__init__.py

@@ -11,68 +11,3 @@
 # 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.
-from __future__ import absolute_import
-
-from warnings import warn
-
-from cameo.visualization.plotting.abstract import AbstractPlotter
-
-__all__ = ["plotter"]
-
-_engine = None
-_engines = {}
-
-try:
-    from cameo.visualization.plotting.with_bokeh import BokehPlotter
-
-    _engine = BokehPlotter() if _engine is None else _engine
-    _engines["bokeh"] = BokehPlotter
-except ImportError:
-    pass
-
-try:
-    from cameo.visualization.plotting.with_plotly import PlotlyPlotter
-
-    _engine = PlotlyPlotter(mode='offline') if _engine is None else _engine
-    _engines["plotly"] = PlotlyPlotter
-except ImportError:
-    pass
-
-try:
-    from cameo.visualization.plotting.with_plotly import GGPlotPlotter
-
-    _engine = GGPlotPlotter() if _engine is None else _engine
-    _engines["ggplot"] = GGPlotPlotter
-except ImportError:
-    pass
-
-if _engine is None:
-    warn("Cannot import any plotting library. Please install one of 'plotly', 'bokeh' or 'ggplot' if you want to"
-         " use any plotting function.")
-    _engine = AbstractPlotter()
-
-
-class _plotting:
-    def __init__(self, engine):
-        self.__dict__['_engine'] = engine
-
-    def __getattr__(self, item):
-        if item not in ["_engine", "engine"]:
-            return getattr(self.__dict__['_engine'], item)
-        else:
-            return self.__dict__['_engine']
-
-    def __setattr__(self, key, item):
-        if key not in ["_engine", "engine"]:
-            raise KeyError(key)
-        else:
-            if isinstance(item, str):
-                item = _engines[item]()
-
-            if not isinstance(item, AbstractPlotter):
-                raise AssertionError("Invalid engine %s" % item)
-
-            self.__dict__['_engine'] = item
-
-
-plotter = _plotting(_engine)