Fix doesn't loop over single frames (#99)

MDAnalysis · Apr 22, 2022 · 8a844fa · 8a844fa
1 parent cd90206
commit 8a844fa
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -2,6 +2,7 @@
 Changelog
 =========
 
+* Allow None as start/stop values (need for 1 frame trajectories)
 
 v0.1.20 (2022-04-13)
 ------------------------------------------

diff --git a/src/mdacli/libcli.py b/src/mdacli/libcli.py
@@ -183,15 +183,15 @@ def add_run_group(analysis_class_parser):
         "-b",
         dest="start",
         type=str,
-        default="0",
+        default=None,
         help="start frame or time for evaluation (default: %(default)s)"
         )
 
     run_group.add_argument(
         "-e",
         dest="stop",
         type=str,
-        default="-1",
+        default=None,
         help="end frame or time for evaluation (default: %(default)s)"
         )
 
@@ -602,7 +602,8 @@ def run_analsis(analysis_callable,
 
     # Run the analysis
     for key, value in run_parameters.items():
-        run_parameters[key] = convert_str_time(value, universe.trajectory.dt)
+        run_parameters[key] = \
+            convert_str_time(value, universe.trajectory.dt) if value else value
 
     ac.run(verbose=verbose, **run_parameters)
 

diff --git a/tests/test_libcli.py b/tests/test_libcli.py
@@ -161,7 +161,7 @@ def test_split_argparse_into_groups():
 
 @pytest.mark.parametrize(
     'dest, default',
-    [("start", "0"), ("stop", "-1"), ("step", "1"), ("verbose", False)])
+    [("start", None), ("stop", None), ("step", "1"), ("verbose", False)])
 def test_add_run_group_args(dest, default):
     """Test for added run arguments."""
     parser = argparse.ArgumentParser()