From bc162d065c9a09b0e9a026444fb52b530d509c8f Mon Sep 17 00:00:00 2001 From: Sven Thiele <sthiele78@gmail.com> Date: Tue, 23 Feb 2016 11:31:40 +0100 Subject: [PATCH] prepare next release follow Clemence's suggestions regarding the flags for darftnet/seeds/targets --- CHANGES.txt | 3 ++- README.rst | 16 +++++++++------- meneco.py | 12 ++++++------ setup.py | 2 +- 4 files changed, 18 insertions(+), 15 deletions(-) diff --git a/CHANGES.txt b/CHANGES.txt index eb5370a..ce80ffc 100644 --- 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 index 12a5ae9..815cc53 100644 --- 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 index add55c8..c19f0dc 100644 --- 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 index 3d52016..48dbc1a 100644 --- 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 '