Merge branch 'master' into develop

NEWS.md

@@ -1,4 +1,47 @@
 
+v0.28 (2017-03-03)
+------------------
+
+- The YAML model format now allows users to specify compartment information and
+  compartment boundaries in the `model.yaml` file. See the file format
+  documentation for more information.
+- The `media` key in the `model.yaml` has changed name to `exchange` to
+  reflect the fact that not only uptake exchange must be defined here. The
+  `media` key is still supported but has been deprecated.
+- The gap-filling command `gapfill` and `fastgapfill` now use the compartment
+  information to determine which artificial transport and exchange reactions
+  to add. This means that a model *must* specify compartments and compartment
+  boundaries when using gap-filling commands.
+- The `gapcheck` command now has two new methods for detecting blocked
+  compounds. The new `prodcheck` is a more robust version of the GapFind check
+  which was previously used. The new `sinkcheck` method will find compounds
+  that cannot be produced in excess. This can find some additional blocked
+  compounds that were not detected by the other methods.
+- The `gapcheck` command now reports blocked compounds in the extracellular
+  space. Previously, these compounds were excluded. An option is available to
+  switch back the old behavior of excluding these from the final output.
+- The `gapcheck` command now has an option to run the check with unrestricted
+  exchange reactions.
+- The `gapfill` command can now be run without implicit sinks. This makes it
+  possible to use this command to solve additional model gaps. It is still
+  recommended to first solve gaps using implicit sinks, then later disable
+  implicit sinks when all other gaps have been closed.
+- The `gapfill` command now has an option to enable the bounds expansion
+  proposals (e.g. making irreversible reactions reversible). By default this
+  option is now off.
+- The `fastgapfill` has improved output that contains less superfluous
+  information. The output format is now identical to the `gapfill` command.
+  The `fastgapfill` also no longer runs an FBA on the induced model since this
+  caused some confusion.
+- Added new command `checkduplicates` which detects whether the model has
+  multiple reactions with the same (or similar) reaction equation.
+- The `sbmlexport` command now allows the user to specify a file path. The
+  command can also optionally output the SBML file in a more readable format
+  with an option.
+- Fixed support for the latest CPLEX release 12.7. A change in their API made
+  PSAMM incompatible with the 12.7 release. This is now fixed.
+- We now officially support Python 3.5 and Python 3.6.
+
 v0.27 (2016-12-23)
 ------------------
 

docs/commands.rst

@@ -381,7 +381,7 @@ to perform the gap check without implicit sinks.
 
 The gap check is performed with the medium that is defined in the model. It
 may be useful to run the gap check with every compound in the medium available.
-This can easily be done by specifying the ``--unrestricted-medium`` option
+This can easily be done by specifying the ``--unrestricted-exchange`` option
 which removes all limits on the exchange reactions during the check.
 
 There are some additional gap checking methods that can be enabled with the

psamm/commands/gapcheck.py

@@ -41,7 +41,7 @@ def init_parser(cls, parser):
             '--no-implicit-sinks', action='store_true',
             help='Do not include implicit sinks when gap-filling')
         parser.add_argument(
-            '--unrestricted-medium', action='store_true',
+            '--unrestricted-exchange', action='store_true',
             help='Remove all limits on exchange reactions while gap checking')
         parser.add_argument(
             '--exclude-extracellular', action='store_true',
@@ -67,7 +67,7 @@ def run(self):
 
         implicit_sinks = not self._args.no_implicit_sinks
 
-        if self._args.unrestricted_medium:
+        if self._args.unrestricted_exchange:
             # Allow all exchange reactions with no flux limits
             for reaction in self._mm.reactions:
                 if self._mm.is_exchange(reaction):

psamm/tests/test_command.py

@@ -383,9 +383,9 @@ def test_run_gapcheck_prodcheck_without_extracellular(self):
         self.run_solver_command(
             GapCheckCommand, ['--method=prodcheck', '--exclude-extracellular'])
 
-    def test_run_gapcheck_prodcheck_with_unrestricted_medium(self):
+    def test_run_gapcheck_prodcheck_with_unrestricted_exchange(self):
         self.run_solver_command(
-            GapCheckCommand, ['--method=prodcheck', '--unrestricted-medium'])
+            GapCheckCommand, ['--method=prodcheck', '--unrestricted-exchange'])
 
     def test_run_gapcheck_sinkcheck(self):
         self.run_solver_command(

setup.py

@@ -24,7 +24,7 @@
 
 setup(
     name='psamm',
-    version='0.27',
+    version='0.28',
     description='PSAMM metabolic modeling tools',
     maintainer='Jon Lund Steffensen',
     maintainer_email='jon_steffensen@uri.edu',