Fix unit tests

src/annotate_sbml.py

@@ -1,3 +1,4 @@
+import os
 import sys
 import argparse
 import traceback
@@ -24,12 +25,18 @@ def main():
         raise FileNotFoundError(f'Annotations file [{f_ann}] does not exist.')
     try:
         if not f_out.exists() or args.force:
-            sbml_file = f_in
-            annotations_file = f_ann
-            out_file = f_out
+
+            # Check if output folder exists, otherwise create it
+            out_dir = os.path.dirname(f_out)
+            if not os.path.exists(out_dir):
+                os.makedirs(out_dir)
+
+            # Annotate SBML file
             annotator = PbkModelAnnotator()
-            document = annotator.annotate(sbml_file, annotations_file, logger)
-            ls.writeSBML(document, str(out_file))
+            document = annotator.annotate(f_in, f_ann, logger)
+
+            # Write SBML
+            ls.writeSBML(document, str(f_out))
         else:
             print(f'[{f_out}] already exists, use -f to force conversion')
     except Exception as e:

src/ant2sbml.py

@@ -8,7 +8,7 @@
 def main():
     parser = argparse.ArgumentParser(description="Convert Antimony file to SBML")
     parser.add_argument("ant_file", help="Full path to Antimony file")
-    parser.add_argument("out_file", help="Output file")
+    parser.add_argument("-o", "--output", type=str, help="Output file (optional)")
     parser.add_argument("-f", "--force", action="store_true", help="Overwrite existing")
     args = parser.parse_args()
     f_in = Path(args.ant_file)
@@ -22,7 +22,7 @@ def main():
         sys.exit(1)
 
     # Get output file from command line args, otherwise derive from antimony file
-    f_out = Path(args.out_file) if args.out_file is not None else Path(args.ant_file).with_suffix('.sbml')
+    f_out = Path(args.output) if args.output is not None else Path(args.ant_file).with_suffix('.sbml')
 
     # Check if output folder exists, otherwise create it
     out_dir = os.path.dirname(f_out)

src/validate_sbml.py

@@ -1,5 +1,6 @@
 import argparse
 import logging
+import os
 import sys
 from pathlib import Path
 from sbmlpbkutils import PbkModelValidator
@@ -26,7 +27,16 @@ def main():
     f_in = Path(args.f_in)
     if not f_in.is_file():
         raise FileNotFoundError(f'File {f_in} does not exist.')
-    logger = get_logger(__name__) if args.log_file is None else create_file_logger(Path(args.log_file))
+    if args.log_file is not None:
+        # Check if output folder exists, otherwise create it
+        out_dir = os.path.dirname(args.log_file)
+        if not os.path.exists(out_dir):
+            os.makedirs(out_dir)
+
+        # Create file logger
+        logger = create_file_logger(Path(args.log_file))
+    else:
+        logger = get_logger(__name__)
 
     validator = PbkModelValidator()
     validator.validate(f_in, logger)

tests/test_annotate_sbml.py

@@ -6,7 +6,7 @@
 
 class TestAnnotateSbml(TestBase):
 
-    @patch('sys.argv', ['ant2sbml.py', './tests/models/simple.sbml', './tests/models/simple.annotations.csv', './tests/output/simple.annotated.sbml'])
+    @patch('sys.argv', ['ant2sbml.py', './tests/models/simple.sbml', './tests/models/simple.annotations.csv', './tests/output/simple.annotated.sbml', '-f'])
     def test_simple(self):
         src.annotate_sbml.main()
         path = pl.Path('./tests/output/simple.annotated.sbml')

tests/test_ant2sbml.py

@@ -6,7 +6,7 @@
 
 class TestAnt2Sbml(TestBase):
 
-    @patch('sys.argv', ['ant2sbml.py', './tests/models/simple.ant', './tests/output/simple.sbml'])
+    @patch('sys.argv', ['ant2sbml.py', './tests/models/simple.ant', '-o', './tests/output/simple.sbml', '-f'])
     def test_simple(self):
         src.ant2sbml.main()
         path = pl.Path('./tests/output/simple.sbml')