fix: fit to new rpPathway specs

brsynth · Oct 23, 2023 · d69377d · d69377d
1 parent ceb0a57
commit d69377d
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Showing 7 changed files with 8 additions and 8 deletions.
diff --git a/rptools/rpfba/README.md b/rptools/rpfba/README.md
@@ -42,7 +42,7 @@ Please see `rptool` documentation.
 from rptools.rplibs import rpPathway
 from rptools.rpfba import runFBA
 
-pathway = rpPathway.from_rpSBML(infile='tests/rpfba/data/sets/measured_3/B.xml')
+pathway = rpPathway(infile='tests/rpfba/data/sets/measured_3/B.xml')
 
 results = runFBA(
     pathway=pathway,

diff --git a/rptools/rplibs/stats.py b/rptools/rplibs/stats.py
@@ -79,7 +79,7 @@ def entry_point():
 
     # Build the list of pathways to rank
     pathways = [
-        rpPathway.from_rpSBML(
+        rpPathway(
             infile=pathway_filename,
             logger=logger
         ) for pathway_filename in args.pathways

diff --git a/rptools/rprank/README.md b/rptools/rprank/README.md
@@ -22,7 +22,7 @@ Please see `rptool` documentation.
 from rptools.rpscore import predict_score
 from rptools.rplibs import rpPathway
 
-pathway = rpPathway.from_rpSBML(
+pathway = rpPathway(
     infile='tests/rpscore/data/pathway.xml'
 )
 

diff --git a/rptools/rprank/__main__.py b/rptools/rprank/__main__.py
@@ -31,7 +31,7 @@ def entry_point():
     # Build the list of pathways to rank (with their filename)
     pathways = {}
     for pathway_fname in args.pathways:
-        pathway = rpPathway.from_rpSBML(
+        pathway = rpPathway(
             infile=pathway_fname,
             logger=logger
         )

diff --git a/rptools/rpscore/README.md b/rptools/rpscore/README.md
@@ -27,7 +27,7 @@ Please see `rptool` documentation.
 from rptools.rpscore import predict_score
 from rptools.rplibs import rpPathway
 
-pathway = rpPathway.from_rpSBML(
+pathway = rpPathway(
     infile='tests/rpscore/data/pathway.xml'
 )
 

diff --git a/rptools/rpscore/__main__.py b/rptools/rpscore/__main__.py
@@ -36,13 +36,13 @@ def entry_point():
     # pathways = []
     # for pathway in args.pathways:
     #     pathways.append(
-    #         rpPathway.from_rpSBML(
+    #         rpPathway(
     #             infile=pathway,
     #             logger=logger
     #         )
     #     )
 
-    pathway = rpPathway.from_rpSBML(
+    pathway = rpPathway(
         infile=args.infile,
         logger=logger
     )

diff --git a/rptools/rpthermo/__main__.py b/rptools/rpthermo/__main__.py
@@ -36,7 +36,7 @@ def _cli():
     )
 
     ## READ PATHWAY FROM FILE
-    pathway = rpPathway.from_rpSBML(
+    pathway = rpPathway(
       infile=args.infile,
       logger=logger
     )