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

.travis.yml

@@ -21,7 +21,6 @@ addons:
     - pandoc
     - openbabel
 before_install:
-#- if [ ! -d "cplex/python/$TRAVIS_PYTHON_VERSION/x86-64_linux/" ]; then curl -L SECRET_CPLEX_LINK -o cplex.tar.gz && tar xvf cplex.tar.gz; fi
 - pip install pip --upgrade
 - pip install codecov
 - curl -L $SECRET_CPLEX_LINK -o cplex.tar.gz
@@ -37,25 +36,36 @@ install:
 - pip install flake8
 - pip install .[swiglpk,test,parallel]
 before_script:
-- "flake8 ."
+- flake8 .
 script: nosetests
 after_success:
 - codecov
 notifications:
   slack: biosustain:UGm09rOjMCgXko3rS3wUivoX
 before_deploy:
   - pip install twine
-deploy:
-  provider: pypi
-  user: Nikolaus.Sonnenschein
-  password:
-    secure: nxjszXtUzQfnLlfg0cmFjd9gRekXDog6dkkN1rMc7CIWH2gZ1gAX4sNETVChnuSmu9egzhuIkviHstRrdyGoEZ7ZkHlTXmpVAs9AY96eMSejnwHHODhYno0jB7DjGcfejodLF+lo6lWz7S7mXXwML6YLM3xxG+AOjLHlHbPTaKc=
-  distributions: sdist bdist_wheel
-  on:
-    branch: master
-    tags: true
-    repo: biosustain/cameo
-  docs_dir: docs/_build/html
+  - python setup.py sdist bdist_wheel
 env:
   global:
     secure: QgrOXEgpcH6xgToVfWIX6j6CPvycKMPtNnoYAxPrZjkMzd2aCHHeokv0FZkCn3uePO0I8W8TkKBxilGZbWYoseDq+Snds18sBTG9u2NHvYHnDQb4Oki7+NoxhlnGIOj/8ADONOpc0n7PyFDPK8zmKVZvv9p78OHZO5CmV/ktOeg=
+deploy:
+  - provider: releases
+    api_key:
+      secure: VsKdkwYvp7lf65S/pzLWbrk8PaRAzBVClB57s4jYepx+BbJdPJi5Zwz4zmu0Ifa1K7K2Jh0rITV9GZAyC+0Eq2ffXtZsBOsC5+2yKaWV5WiU7kNdUVhD9EFkUaNknT8+B2/sjPsl+GP8DTzCqstgdGo5EAAnvpV53qIAwwF9n0U=
+    file_glob: true
+    file: dist/cameo*.whl
+    skip_cleanup: true
+    on:
+      branch: master
+      tags: true
+      repo: biosustain/cameo
+  - provider: pypi
+    user: Nikolaus.Sonnenschein
+    password:
+      secure: nxjszXtUzQfnLlfg0cmFjd9gRekXDog6dkkN1rMc7CIWH2gZ1gAX4sNETVChnuSmu9egzhuIkviHstRrdyGoEZ7ZkHlTXmpVAs9AY96eMSejnwHHODhYno0jB7DjGcfejodLF+lo6lWz7S7mXXwML6YLM3xxG+AOjLHlHbPTaKc=
+    distributions: sdist bdist_wheel
+    on:
+      branch: master
+      tags: true
+      repo: biosustain/cameo
+    docs_dir: docs/_build/html

cameo/core/solver_based_model.py

@@ -307,13 +307,22 @@ def remove_reactions(self, the_reactions, delete=True, remove_orphans=False):
         super(SolverBasedModel, self).remove_reactions(the_reactions, delete=delete, remove_orphans=remove_orphans)
 
     def add_demand(self, metabolite, prefix="DM_", time_machine=None):
-        """Add a demand reaction for a metabolite (metabolite --> Ø)
+        from warnings import warn
+        warn('"add_demand" function is replaced with "add_exchange".', PendingDeprecationWarning)
+        return self.add_exchange(metabolite, prefix=prefix, time_machine=time_machine)
+
+    def add_exchange(self, metabolite, demand=True, prefix='DM_', bound=1000.0, time_machine=None):
+        """Add an exchange reaction for a metabolite (demand=TRUE: metabolite --> Ø or demand=False: 0 --> metabolite )
 
         Parameters
         ----------
         metabolite : Metabolite
+        demand : bool, optional
+            True for sink type exchange, False for uptake type exchange
         prefix : str, optional
             A prefix that will be added to the metabolite ID to be used as the demand reaction's ID (defaults to 'DM_').
+        bound : float, optional
+            Upper bound for sink reaction / lower bound for uptake (multiplied by -1)
         time_machine : TimeMachine, optional
             A TimeMachine instance that enables undoing.
 
@@ -323,22 +332,30 @@ def add_demand(self, metabolite, prefix="DM_", time_machine=None):
             The created demand reaction.
         """
         id = str(prefix + metabolite.id)
-        name = "Exchange %s" % metabolite.name if prefix == "EX_" else "Demand %s" % metabolite.name
+        name = "Exchange %s" % metabolite.name if prefix != "DM_" else "Demand %s" % metabolite.name
         if id in self.reactions:
             raise ValueError("The metabolite already has a demand reaction.")
 
-        demand_reaction = Reaction()
-        demand_reaction.id = id
-        demand_reaction.name = name
-        demand_reaction.add_metabolites({metabolite: -1})
-        demand_reaction.lower_bound = 0
-        demand_reaction.upper_bound = 1000
+        reaction = Reaction()
+        reaction.id = id
+        reaction.name = name
+
+        reaction.add_metabolites({metabolite: -1})
+        if demand:
+            reaction.upper_bound = bound
+            reaction.lower_bound = 0
+        else:
+            reaction.upper_bound = 0
+            reaction.lower_bound = -bound
+
+
+
         if time_machine is not None:
-            time_machine(do=partial(self.add_reactions, [demand_reaction]),
-                         undo=partial(self.remove_reactions, [demand_reaction], delete=False))
+            time_machine(do=partial(self.add_reactions, [reaction]),
+                         undo=partial(self.remove_reactions, [reaction], delete=False))
         else:
-            self.add_reactions([demand_reaction])
-        return demand_reaction
+            self.add_reactions([reaction])
+        return reaction
 
     def fix_objective_as_constraint(self, time_machine=None, fraction=1):
         """Fix current objective as an additional constraint (e.g., ..math`c^T v >= max c^T v`).

docs/Makefile

@@ -47,13 +47,17 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 	@echo "  ipy2rst    to convert ipython notebooks in to rst files"
 	@echo "  apidoc     to autogenerate API "
+	@echo "  updatenb   to update the notebooks git submodule"
+
+updatenb:
+	git submodule update --remote --merge
 
 ipy2rst:
 	for i in notebooks/*.ipynb; do if [ $$i != "notebooks/index.ipynb" ] ; then jupyter nbconvert $$i --to rst; fi done
 	sed -i '' 's/``/`/g' *.rst
 
 apidoc:
-	sphinx-apidoc --no-toc -f -o apidoc_output/ ../cameo ../cameo/strain_design/heuristic/multiprocess ../cameo/stuff ../cameo/strain_design/heuristic/evolutionary
+	sphinx-apidoc --no-toc -f -o apidoc_output/ ../cameo ../cameo/strain_design/heuristic/multiprocess ../cameo/stuff ../cameo/strain_design/heuristic/evolutionary ../cameo/visualization/plotting
 
 clean:
 	rm -rf $(BUILDDIR)/*

docs/README.md

@@ -4,6 +4,10 @@ Cameo tutorials come in the form of jupyter notebooks (./notebooks) that can be
 
 ```make ipy2rst```
 
+To update to the latest notebooks run
+
+```git submodule update --remote --merge```
+
 The notebooks folder is a git submodule pointing to [http://github.com/biosustain/cameo-notebooks](http://github.com/biosustain/cameo-notebooks).
 
 To regenerate the API docs run

docs/apidoc_output/cameo.core.rst

@@ -4,6 +4,22 @@ cameo.core package
 Submodules
 ----------
 
+cameo.core.gene module
+----------------------
+
+.. automodule:: cameo.core.gene
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cameo.core.metabolite module
+----------------------------
+
+.. automodule:: cameo.core.metabolite
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 cameo.core.pathway module
 -------------------------
 

docs/apidoc_output/cameo.flux_analysis.rst

@@ -20,6 +20,14 @@ cameo.flux_analysis.simulation module
     :undoc-members:
     :show-inheritance:
 
+cameo.flux_analysis.structural module
+-------------------------------------
+
+.. automodule:: cameo.flux_analysis.structural
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 cameo.flux_analysis.util module
 -------------------------------
 

docs/apidoc_output/cameo.visualization.rst

@@ -12,10 +12,18 @@ cameo.visualization.escher_ext module
     :undoc-members:
     :show-inheritance:
 
-cameo.visualization.plotting module
------------------------------------
+cameo.visualization.palette module
+----------------------------------
 
-.. automodule:: cameo.visualization.plotting
+.. automodule:: cameo.visualization.palette
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cameo.visualization.plotting_old module
+---------------------------------------
+
+.. automodule:: cameo.visualization.plotting_old
     :members:
     :undoc-members:
     :show-inheritance:

docs/conf.py

@@ -176,7 +176,7 @@
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-# html_favicon = None
+html_favicon = 'favicon.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/development.rst

@@ -114,7 +114,7 @@ The LP/MILP solver can be changed in the following way.
 
     model.solver = 'cplex'
 
-Currently ``cplex`` and ``glpk`` are supported.
+Currently `cplex` and `glpk` are supported.
 
 Manipulating the solver object
 ------------------------------

docs/index.rst

@@ -2,7 +2,7 @@
 Welcome to cameo!
 =================
 
-|Build Status| |Coverage Status| |DOI|
+|PyPI| |License| |Build Status| |Coverage Status| |DOI|
 
 **Cameo** is a high-level python library developed to aid the strain
 design process in metabolic engineering projects. The library provides a
@@ -61,9 +61,13 @@ Indices and tables
 * :ref:`search`
 
 
+.. |PyPI| image:: https://img.shields.io/pypi/v/cameo.svg
+   :target: https://pypi.python.org/pypi/cameo
+.. |License| image:: http://img.shields.io/badge/license-APACHE2-blue.svg
+   :target: http://img.shields.io/badge/license-APACHE2-blue.svg
 .. |Build Status| image:: https://travis-ci.org/biosustain/cameo.svg?branch=master
    :target: https://travis-ci.org/biosustain/cameo
-.. |Coverage Status| image:: https://codecov.io/github/biosustain/cameo/coverage.svg?branch=devel
-   :target: https://codecov.io/github/biosustain/cameo?branch=devel
-.. |DOI| image:: https://zenodo.org/badge/doi/10.5281/zenodo.19827.svg
-   :target: http://dx.doi.org/10.5281/zenodo.19827
+.. |Coverage Status| image:: https://coveralls.io/repos/biosustain/cameo/badge.svg?branch=devel
+   :target: https://coveralls.io/r/biosustain/cameo?branch=devel
+.. |DOI| image:: https://zenodo.org/badge/5031/biosustain/cameo.svg
+   :target: https://zenodo.org/badge/latestdoi/5031/biosustain/cameo

tests/test_solver_based_model.py

@@ -714,25 +714,27 @@ def test_remove_reactions(self):
             for reaction in reactions_to_remove:
                 self.assertIn(reaction, self.model.reactions)
 
-        def test_add_demand(self):
-            for metabolite in self.model.metabolites:
-                demand_reaction = self.model.add_demand(metabolite, prefix="DemandReaction_")
-                self.assertEqual(self.model.reactions.get_by_id(demand_reaction.id), demand_reaction)
-                self.assertEqual(demand_reaction.reactants, [metabolite])
-                self.assertTrue(self.model.solver.constraints[metabolite.id].expression.has(
-                    self.model.solver.variables["DemandReaction_" + metabolite.id]))
-
-        def test_add_demand_time_machine(self):
-            with TimeMachine() as tm:
+        def test_add_exchange(self):
+            for demand, prefix in {True: 'DemandReaction_', False: 'SupplyReaction_'}.items():
                 for metabolite in self.model.metabolites:
-                    demand_reaction = self.model.add_demand(metabolite, time_machine=tm)
+                    demand_reaction = self.model.add_exchange(metabolite, demand=demand, prefix=prefix)
                     self.assertEqual(self.model.reactions.get_by_id(demand_reaction.id), demand_reaction)
                     self.assertEqual(demand_reaction.reactants, [metabolite])
-                    self.assertTrue(-self.model.solver.constraints[metabolite.id].expression.has(
-                        self.model.solver.variables["DM_" + metabolite.id]))
-            for metabolite in self.model.metabolites:
-                self.assertNotIn("DM_" + metabolite.id, self.model.reactions)
-                self.assertNotIn("DM_" + metabolite.id, self.model.solver.variables.keys())
+                    self.assertTrue(self.model.solver.constraints[metabolite.id].expression.has(
+                        self.model.solver.variables[prefix + metabolite.id]))
+
+        def test_add_exchange_time_machine(self):
+            for demand, prefix in {True: 'DemandReaction_', False: 'SupplyReaction_'}.items():
+                with TimeMachine() as tm:
+                    for metabolite in self.model.metabolites:
+                        demand_reaction = self.model.add_exchange(metabolite, demand=demand, prefix=prefix, time_machine=tm)
+                        self.assertEqual(self.model.reactions.get_by_id(demand_reaction.id), demand_reaction)
+                        self.assertEqual(demand_reaction.reactants, [metabolite])
+                        self.assertTrue(-self.model.solver.constraints[metabolite.id].expression.has(
+                            self.model.solver.variables[prefix + metabolite.id]))
+                for metabolite in self.model.metabolites:
+                    self.assertNotIn(prefix + metabolite.id, self.model.reactions)
+                    self.assertNotIn(prefix + metabolite.id, self.model.solver.variables.keys())
 
         def test_objective(self):
             obj = self.model.objective