prepare next release follow Clemence's suggestions regarding the flag…

…s for darftnet/seeds/targets
bioasp · Feb 23, 2016 · bc162d0 · bc162d0
1 parent a454ba9
commit bc162d0
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Showing 4 changed files with 18 additions and 15 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,6 +1,7 @@
 1.5.0
 -----
-make repairnet optional if repairnet is not set meneco does only producibility checking
+Make repairnet optional.
+If no repairnet is set meneco only performs a producibility check.
 
 1.4.3
 -----

diff --git a/README.rst b/README.rst
@@ -16,20 +16,22 @@ Usage
 
 Typical usage is::
 
-	$ meneco.py draftnetwork.sbml seeds.sbml targets.sbml -r repairnetwork.sbml 
+	$ meneco.py -d draftnetwork.sbml -s seeds.sbml -t targets.sbml -r repairnetwork.sbml 
 
 For more options you can ask for help as follows::
 
         $meneco.py --h
-        usage: meneco.py [-h] [-r REPAIRNET] [--enumerate] draftnet seeds targets
-
-        positional arguments:
-          draftnet              metabolic network in SBML format
-          seeds                 seeds in SBML format
-          targets               targets in SBML format
+        usage: meneco.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
+                         [--enumerate]
 
         optional arguments:
           -h, --help            show this help message and exit
+          -d DRAFTNET, --draftnet DRAFTNET
+                                metabolic network in SBML format
+          -s SEEDS, --seeds SEEDS
+                                seeds in SBML format
+          -t TARGETS, --targets TARGETS
+                                targets in SBML format
           -r REPAIRNET, --repairnet REPAIRNET
                                 perform network completion using REPAIRNET a metabolic
                                 network in SBML format

diff --git a/meneco.py b/meneco.py
@@ -26,12 +26,12 @@
 
     parser = argparse.ArgumentParser()
 
-    parser.add_argument('draftnet',
-                        help='metabolic network in SBML format')
-    parser.add_argument('seeds',
-                        help='seeds in SBML format')
-    parser.add_argument('targets',
-                        help='targets in SBML format')
+    parser.add_argument("-d", "--draftnet",
+                        help='metabolic network in SBML format', required=True)
+    parser.add_argument("-s", "--seeds",
+                        help='seeds in SBML format', required=True)
+    parser.add_argument("-t", "--targets",
+                        help='targets in SBML format', required=True)
 
     parser.add_argument('-r', '--repairnet',
                         help='perform network completion using REPAIRNET '

diff --git a/setup.py b/setup.py
@@ -19,7 +19,7 @@
 
 setup(
   name             = 'meneco',
-  version          = '1.5.0a',
+  version          = '1.5.0',
   url              = 'http://bioasp.github.io/meneco/',
   license          = 'GPLv3+',
   description      = 'Metabolic Network Completion. Compute minimal completions '