fixed off-by-one error in signal writing

segrelab · Oct 26, 2021 · 6659ed4 · 6659ed4
1 parent b59945e
commit 6659ed4
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/cometspy/comets.py b/cometspy/comets.py
@@ -21,8 +21,9 @@
 __copyright__ = "Copyright 2019, The COMETS Consortium"
 __credits__ = ["Djordje Bajic", "Jean Vila", "Jeremy Chacon"]
 __license__ = "MIT"
-__version__ = "0.4.14"
-__comets_compatibility__ = "2.10.2" # version of comets this was tested with
+__version__ = "0.4.15"
+__comets_compatibility__ = "2.10.2" # version of comets this was tested with (except signaling)
+__comets_compatibility_signaling__ = "2.10.7" # version signaling was tested with
 
 __maintainer__ = "Djordje Bajic"
 __email__ = "djordje.bajic@yale.edu"

diff --git a/cometspy/model.py b/cometspy/model.py
@@ -971,8 +971,7 @@ def write_comets_model(self, working_dir : str = None):
                     curr_col_names = col_names + [str(i) for i in range(n_parms)]
                     temp_df = pd.DataFrame(columns=curr_col_names)
                     if row.loc['REACTION_NUMBER'] != 'death':
-                        # this is to deal with the off-by-one difference between the pandas table and java
-                        row.loc['REACTION_NUMBER'] = str(int(row.loc['REACTION_NUMBER']) - 1)
+                        row.loc['REACTION_NUMBER'] = str(int(row.loc['REACTION_NUMBER']))
                     temp_df.loc[0, 'REACTION_NUMBER'] = row.loc['REACTION_NUMBER']
                     temp_df.loc[0, 'EXCH_IND'] = row.loc['EXCH_IND']
                     temp_df.loc[0, 'BOUND'] = row.loc['BOUND']

diff --git a/dist/cometspy-0.4.15.tar.gz b/dist/cometspy-0.4.15.tar.gz
diff --git a/setup.py b/setup.py
@@ -4,13 +4,13 @@
 setup(
     name='cometspy',
     packages=['cometspy'],
-    version='0.4.14',
+    version='0.4.15',
     license='GPL',
     description='The Python interface to COMETS',
     author='The COMETSPy Core Team',
     author_email='djordje.bajic@yale.edu',
     url='https://github.com/segrelab/cometspy',
-    download_url='https://github.com/segrelab/cometspy/archive/v0.4.14.tar.gz',  # New releases here!! 
+    download_url='https://github.com/segrelab/cometspy/archive/v0.4.15.tar.gz',  # New releases here!! 
     keywords=['metabolism', 'dynamic', 'flux', 'balance', 'analysis', 'spatial', 'evolution'],
     install_requires=[
         # I get to this in a second