Merge branch 'release'

zhanglab · Apr 18, 2017 · 84e77e1 · 84e77e1
2 parents 319507d + 39502e2
commit 84e77e1
Show file tree

Hide file tree

Showing 44 changed files with 3,467 additions and 2,432 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,25 @@
 
+v0.29 (2017-04-18)
+------------------
+
+- [The tutorial](https://psamm.readthedocs.io/en/stable/tutorial.html) in the
+  PSAMM documentation has been updated and expanded to include additional
+  information on using PSAMM for model curation and constraint-based analyses.
+- The experimental command `psamm-sbml-model` was added which makes it possible
+  to run any command from `psamm-model` (e.g. `fba`, `robustness`, etc.)
+  directly on an SBML file. For now this only supports SBML level 3 files with
+  FBC. This provides a quick way of running basic analyses on SBML files. We
+  still recommend importing the SBML file to YAML format with `psamm-import`
+  for anyone wishing to make changes to a model.
+- Fixes access to charge parameter parsed from SBML files. The charge is now
+  correctly imported with `psamm-import`.
+- Fixes import of compartments from SBML files. The empty boundary compartments
+  are now no longer included in the import.
+- Fixes bug in writing the reaction flux limits sheet of the `excelexport`
+  command.
+- The `console` command was changed to only provide the `model` variable since
+  the metabolic model can easily be created.
+
 v0.28 (2017-03-03)
 ------------------
 

diff --git a/docs/api/gapfilling.rst b/docs/api/gapfilling.rst
@@ -0,0 +1,6 @@
+
+``psamm.gapfilling`` -- Gap-filling functions
+=============================================
+
+.. automodule:: psamm.gapfilling
+   :members:
diff --git a/docs/commands.rst b/docs/commands.rst
@@ -460,7 +460,9 @@ minimal solution.
 SBML Export (``sbmlexport``)
 ----------------------------
 
-Exports the model to the SBML file format.
+Exports the model to the SBML file format. This command exports the model as
+an `SBML level 3`_ file with flux bounds, objective and gene information
+encoded with `Flux Balance Constraints version 2`_.
 
 .. code-block:: shell
 
@@ -470,6 +472,9 @@ If the file name is omitted, the file contents will be output directly to the
 screen. Using the ``--pretty`` option makes the output formatted for
 readability.
 
+.. _`SBML level 3`: http://sbml.org/Documents/Specifications
+.. _`Flux Balance Constraints version 2`: http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc
+
 Excel Export (``excelexport``)
 ------------------------------
 

diff --git a/docs/references.rst b/docs/references.rst
@@ -36,3 +36,11 @@ References
 .. [Vlassis14] Vlassis N, Pacheco MP, Sauter T. Fast Reconstruction of Compact
     Context-Specific Metabolic Network Models. PLoS Comput Biol. 2014;10:
     e1003424. :doi:`10.1371/journal.pcbi.1003424`.
+.. [Orth13] Orth JD, Palsson BØ, Fleming RMT. Reconstruction and Use of Microbial
+    Metabolic Networks: the Core Escherichia coli Metabolic Model as an
+    Educational Guide. EcoSal Plus. asm Pub2Web; 2013;1.
+    :doi:`10.1128/ecosalplus.10.2.1`.
+.. [Orth11] Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, et al. A
+    comprehensive genome-scale reconstruction of Escherichia coli
+    metabolism--2011. Mol Syst Biol. EMBO Press; 2011;7: 535.
+    :doi:`10.1038/msb.2011.65`.