Rename run_analsis to run_analysis and move -nt to base args

docs/CHANGELOG.rst

@@ -2,10 +2,12 @@
 Changelog
 =========
 
+* Rename run_analsis to run_analysis
+* Move `-nt` to base args (Fixes #109)
 * set `long-description` to single file
 * remove Py3.8
 * Fixing codecov upload
-* Translate ```setup.py`` into ``pyproject.toml``
+* Translate ``setup.py`` into ``pyproject.toml``
 
 v0.1.24 (2023-01-27)
 ------------------------------------------

src/mdacli/cli.py

@@ -19,7 +19,7 @@
 from .libcli import (
     find_cls_members,
     init_base_argparse,
-    run_analsis,
+    run_analysis,
     setup_clients,
     split_argparse_into_groups,
     )
@@ -130,12 +130,12 @@ def cli(name,
             arg_grouped_dict.setdefault("Output Parameters", {})
 
             with threadpool_limits(limits=args.num_threads):
-                run_analsis(analysis_callable,
-                            arg_grouped_dict["Mandatory Parameters"],
-                            arg_grouped_dict["Optional Parameters"],
-                            arg_grouped_dict["Reference Universe Parameters"],
-                            arg_grouped_dict["Analysis Run Parameters"],
-                            arg_grouped_dict["Output Parameters"])
+                run_analysis(analysis_callable,
+                             arg_grouped_dict["Mandatory Parameters"],
+                             arg_grouped_dict["Optional Parameters"],
+                             arg_grouped_dict["Reference Universe Parameters"],
+                             arg_grouped_dict["Analysis Run Parameters"],
+                             arg_grouped_dict["Output Parameters"])
         except Exception as e:
             if args.debug:
                 traceback.print_exc()

src/mdacli/libcli.py

@@ -203,13 +203,6 @@ def add_run_group(analysis_class_parser):
         help="step or time step for evaluation (default: %(default)s)"
         )
 
-    run_group.add_argument(
-        "-nt",
-        dest="num_threads",
-        type=int,
-        default=0,
-        help="Total number of threads to start (0 is guess)")
-
     run_group.add_argument(
         "-v",
         dest="verbose",
@@ -375,8 +368,8 @@ def create_cli(sub_parser, interface_name, parameters):
         formatter_class=argparse.RawDescriptionHelpFormatter,
         )
 
-    # Add run_analsis function as the default func parameter.
-    # this is possible because the run_analsis function is equal to all
+    # Add run_analysis function as the default func parameter.
+    # this is possible because the run_analysis function is equal to all
     # Analysis Classes
     analysis_class_parser.set_defaults(
         analysis_callable=parameters["callable"])
@@ -550,12 +543,12 @@ def create_universe(topology,
     return universe
 
 
-def run_analsis(analysis_callable,
-                mandatory_analysis_parameters,
-                optional_analysis_parameters=None,
-                reference_universe_parameters=None,
-                run_parameters=None,
-                output_parameters=None):
+def run_analysis(analysis_callable,
+                 mandatory_analysis_parameters,
+                 optional_analysis_parameters=None,
+                 reference_universe_parameters=None,
+                 run_parameters=None,
+                 output_parameters=None):
     """Perform main client logic.
 
     Parameters
@@ -786,6 +779,13 @@ def init_base_argparse(name, version, description):
         help="Run with debug options.",
         )
 
+    ap.add_argument(
+        "-nt",
+        dest="num_threads",
+        type=int,
+        default=0,
+        help="Total number of threads to start (0 is guess)")
+
     ap.add_argument('--logfile',
                     dest='logfile',
                     action='store',

tests/test_cli.py

@@ -10,6 +10,7 @@
 import subprocess
 
 import pytest
+from MDAnalysisTests.datafiles import TPR, XTC
 
 
 def test_required_args():
@@ -34,3 +35,9 @@ def test_extra_options(args):
 def test_case_insensitive(args):
     """Test for beeing case insensitive."""
     subprocess.check_call(['mda', args, "-h"])
+
+
+def test_running_analysis():
+    """Test running a complete analysis."""
+    subprocess.check_call(
+        ['mda', "rmsf", "-s", TPR, "-f", XTC, "-atomgroup", "all"])

tests/test_libcli.py

@@ -39,7 +39,7 @@
     find_classes_in_modules,
     find_cls_members,
     init_base_argparse,
-    run_analsis,
+    run_analysis,
     setup_clients,
     split_argparse_into_groups,
     )
@@ -478,7 +478,7 @@ def test_multi_atomgroup_None(self, universe):
         assert analysis_parameters["p0"] is None
 
 
-class Test_run_analsis:
+class Test_run_analysis:
     """Test class for analyze_data."""
 
     @pytest.fixture()
@@ -506,7 +506,7 @@ def test_default(self,
                      tmpdir):
         """Test with default arguments."""
         with tmpdir.as_cwd():
-            run_analsis(
+            run_analysis(
                 analysis_callable=InterRDF,
                 reference_universe_parameters=reference_universe_parameters,
                 mandatory_analysis_parameters=mandatory_parameters)
@@ -518,7 +518,7 @@ def test_optional_paramaters(self,
         """Test with optional parameters given."""
         opt_params = {"nbins": 100}
         with tmpdir.as_cwd():
-            a = run_analsis(
+            a = run_analysis(
                 analysis_callable=InterRDF,
                 reference_universe_parameters=reference_universe_parameters,
                 mandatory_analysis_parameters=mandatory_parameters,
@@ -535,7 +535,7 @@ def test_verbose(self,
         run_parameters = {"verbose": True}
         caplog.set_level(logging.INFO)
         with tmpdir.as_cwd():
-            run_analsis(
+            run_analysis(
                 analysis_callable=InterRDF,
                 reference_universe_parameters=reference_universe_parameters,
                 mandatory_analysis_parameters=mandatory_parameters,
@@ -552,7 +552,7 @@ def test_custom_output(self,
 
         with tmpdir.as_cwd():
             os.mkdir("foo")
-            run_analsis(
+            run_analysis(
                 analysis_callable=InterRDF,
                 reference_universe_parameters=reference_universe_parameters,
                 mandatory_analysis_parameters=mandatory_parameters,
@@ -569,7 +569,7 @@ def test_output_directory(self,
         output_parameters = {"output_directory": "foo"}
         with tmpdir.as_cwd():
             os.mkdir("foo")
-            run_analsis(
+            run_analysis(
                 analysis_callable=InterRDF,
                 reference_universe_parameters=reference_universe_parameters,
                 mandatory_analysis_parameters=mandatory_parameters,
@@ -585,7 +585,7 @@ def test_output_prefix(self,
         output_parameters = {"output_prefix": "foo"}
         with tmpdir.as_cwd():
             os.mkdir("foo")
-            run_analsis(
+            run_analysis(
                 analysis_callable=InterRDF,
                 reference_universe_parameters=reference_universe_parameters,
                 mandatory_analysis_parameters=mandatory_parameters,