Merge branch 'main' into logger-level

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.28
+current_version = 0.1.29
 commit = True
 message = 
 	[SKIP] version bump {current_version} -> {new_version}

docs/CHANGELOG.rst

@@ -5,6 +5,11 @@ Changelog
 * Replace Boolean ``debug`` option in  ``setup_logging`` by more flexible integer
   ``level`` parameter.
 
+v0.1.29 (2024-03-21)
+------------------------------------------
+
+* Change handling of lowercase module names
+
 v0.1.28 (2023-09-29)
 ------------------------------------------
 

docs/rst/conf.py

@@ -62,7 +62,7 @@
 year = '2021'
 author = 'Philip Loche, Joao MC Teixeira and Oliver Beckstein'
 copyright = '{0}, {1}'.format(year, author)
-version = release = '0.1.28'
+version = release = '0.1.29'
 
 pygments_style = 'trac'
 templates_path = ['_templates']

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mdacli"
-version = "0.1.28"
+version = "0.1.29"
 description = "A command line client for MDAnalysis Analysis classes."
 authors = [
     {name = "MDAnalysis Development Team and contributors", email = "mdanalysis@numfocus.org"},

src/mdacli/__init__.py

@@ -11,5 +11,5 @@
 
 
 __all__ = ["cli"]
-__version__ = '0.1.28'
+__version__ = '0.1.29'
 __authors__ = 'MDAnalysis Development Team and contributors'

src/mdacli/__main__.py

@@ -10,8 +10,9 @@
 A command line interface (CLI) to the analysis modules of MDAnalysis.
 
 The modules are all structured as part of a single mdacli wrapper, and invoked
-with commands like `mda RMSD`. This command uses the class
-:class:`MDAnalysis.analysis.rms.RMSD` for calculating the RMSD.
+with commands like `mda RMSD` (The lowercase `mda rmsd` is also supported).
+This command uses the class :class:`MDAnalysis.analysis.rms.RMSD` for
+calculating the RMSD.
 Documentation for each module can be found at the respective sections on the
 `MDAnalysis Documentation`_, as well as
 `mda command -h`.

src/mdacli/cli.py

@@ -124,7 +124,7 @@ def cli(name,
 
             # Get the correct ArgumentParser instance from all subparsers
             # `[0]` selects the first subparser where our analysises live in.
-            _key = analysis_callable.__name__.lower()
+            _key = analysis_callable.__name__
             ap_sup = ap._subparsers._group_actions[0].choices[_key]
             arg_grouped_dict = split_argparse_into_groups(ap_sup, args)
 

tests/test_cli.py

@@ -37,6 +37,13 @@ def test_case_insensitive(args):
     subprocess.check_call(["mda", args, "-h"])
 
 
+@pytest.mark.parametrize('args', ("RMSF", "rmsf"))
+def test_case_insensitive_with_flags(args):
+    """Test for module name being case insensitive with additional flags."""
+    # Check if it still works if the module name is not the second argument
+    subprocess.check_call(['mda', '--debug', args, "-h"])
+
+
 def test_running_analysis(tmpdir):
     """Test running a complete analysis."""
     with tmpdir.as_cwd():