chore: version 8.4.1

SysBioChalmers · Jul 20, 2020 · 72c4d3b · 72c4d3b
1 parent 66a7b97
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Showing 5 changed files with 17 additions and 3 deletions.
diff --git a/ModelFiles/mat/yeastGEM.mat b/ModelFiles/mat/yeastGEM.mat
diff --git a/ModelFiles/xlsx/yeastGEM.xlsx b/ModelFiles/xlsx/yeastGEM.xlsx
diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false">
-  <model metaid="yeastGEM.xml" id="M_yeastGEM_v8__46__4__46__0" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
+  <model metaid="yeastGEM.xml" id="M_yeastGEM_v8__46__4__46__1" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

diff --git a/history.md b/history.md
@@ -1,5 +1,19 @@
 # History
 
+### yeast 8.4.1:
+* Features:
+  * Switched to `pip-tools` for managing python dependencies, distinguishing between user requirements `/requirements/requirements.txt` and developer requirements `/requirements/dev-requirements.txt` (PR #235).
+* Fixes:
+  * Closes #201: Changed generic protein name to avoid confusion (PR #237).
+  * Closes #205: Finished correcting reactions' stoichiometry based on KEGG data (PR #237).
+  * Closes #215: Corrected wrong gene rule in reaction (PR #237).
+  * Closes #225: Moved MNX rxn ids from notes to the proper annotation field (PR #226).
+* Documentation:
+  * Closes #223: Clarified releasing steps, including authorship criteria for Zenodo releases, in contributing guidelines (PR #233).
+  * Closes #227: Removed authorships/dates from all scripts, as it is redundant information (PR #230).
+  * Added admin guidelines for managing python dependencies (PR #235).
+  * Included links for model visualization in README file (PR #240).
+
 ### yeast 8.4.0:
 * Features:
   * New functions `mapKEGGID.m ` and `mapMNXMID.m` for adding ids in model. Used them to add missing KEGG and MetaNetX ids for both metabolites and reactions (PR #220).
@@ -195,5 +209,5 @@ First version of the yeast8 model, to separate it from previous versions:
   * NGAM rxn introduced
   * GAM in biomass pseudo-rxn fixed and refitted to chemostat data
 
-  ### yeast 7.6.0:
+### yeast 7.6.0:
 First release of the yeast model in GitHub, identical to the last model available at https://sourceforge.net/projects/yeast/
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-8.4.0
+8.4.1