From 96f04553992f4c0ad6596980039abd0180b7af46 Mon Sep 17 00:00:00 2001 From: Chris Powers Date: Tue, 10 May 2022 18:02:40 -0400 Subject: [PATCH 1/2] bugfix for generate model and formatting --- docs/tutorial/generating_models.rst | 4 ++-- psamm/generate_model.py | 3 +-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/tutorial/generating_models.rst b/docs/tutorial/generating_models.rst index 1bd954fb..9e406139 100644 --- a/docs/tutorial/generating_models.rst +++ b/docs/tutorial/generating_models.rst @@ -47,7 +47,7 @@ organism of interest within the class Mollicutes. Basic use of the ``generate-database`` command -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +---------------------------------------------- As noted above, the `generate-database` command uses an annotation file to query the KEGG database and download reaction data. You will need an @@ -129,7 +129,7 @@ column in the table specified with `--annotations` Basic use of the ``generate-transporters`` command -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-------------------------------------------------- In addition to the database of metabolic reactions, another important component of metabolic models is the presence of transporters. These diff --git a/psamm/generate_model.py b/psamm/generate_model.py index 2c6afd88..52cdb986 100644 --- a/psamm/generate_model.py +++ b/psamm/generate_model.py @@ -921,8 +921,7 @@ def init_parser(cls, parser): def run(self): """Entry point for the database generation script""" # check if required packages are installed - if 'Bio.KEGG.Enzyme' not in sys.modules or \ - 'Bio.KEGG.REST' not in sys.modules: + if 'Bio.KEGG.REST' not in sys.modules: quit('No biopython package found. ' 'Please run ''') if "libchebipy._chebi_entity" not in sys.modules: From f63e796448101e110e3d632cfe5790b8cf8e9566 Mon Sep 17 00:00:00 2001 From: Ying Zhang Date: Thu, 12 May 2022 16:34:05 -0400 Subject: [PATCH 2/2] bump setup.py to v1.2.1, updated NEWS.md --- NEWS.md | 5 +++++ setup.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index e797f375..0a4c0de1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +v1.2.1 (2022-05-12) +------------------ +- fix bug in `generate-database` +- revise formatting of doc + v1.2 (2022-05-10) ------------------ diff --git a/setup.py b/setup.py index 003c71ce..629819e1 100755 --- a/setup.py +++ b/setup.py @@ -51,7 +51,7 @@ setup( name='psamm', - version='1.2', + version='1.2.1', description='PSAMM metabolic modeling tools', maintainer='Jon Lund Steffensen', maintainer_email='jon_steffensen@uri.edu',