Add test for cli

molSimplify/__main__.py

@@ -166,7 +166,7 @@ def main(args=None):
             parser = argparse.ArgumentParser(description=DescString_basic,
                                              formatter_class=argparse.RawDescriptionHelpFormatter)
             parseinputs_basic(parser)
-        exit()
+        return
     # ## run with gui ###
     elif gui and len(args) == 0:
         print('molSimplify is starting!')

tests/test_cli.py

@@ -0,0 +1,22 @@
+import pytest
+from molSimplify.__main__ import main
+
+
+def test_main_empty(tmpdir, resource_path_root):
+    main(args=[f"-rundir {tmpdir}"])
+    with open(tmpdir / "fe_oct_2_water_6_s_5" /
+              "fe_oct_2_water_6_s_5_conf_1" /
+              "fe_oct_2_water_6_s_5_conf_1.report", "r") as fin:
+        lines = fin.readlines()
+    with open(resource_path_root / "refs" / "test_cli" /
+              "fe_oct_2_water_6_s_5_conf_1.report", "r") as fin:
+        lines_ref = fin.readlines()
+    assert lines == lines_ref
+
+
+@pytest.mark.skip("Test for help not working yet.")
+def test_help(capsys):
+    main(args=["--help",])
+    captured = capsys.readouterr()
+    print(captured.out)
+    assert "Welcome to molSimplify. Only basic usage is described here." in captured.out

tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.molinp

@@ -0,0 +1,22 @@
+# Input file generated from molSimplify at 11/10/2023 22:28
+-checkdirb True
+-core Fe
+-oxstate 2
+-coord 6
+-geometry oct
+-lig water
+-ligocc 6
+-spin 5
+-keepHs auto
+-rundir /private/var/folders/l6/1j71dcgj4j7c_vc466yjsq3r0000gn/T/pytest-of-ralf/pytest-5/test_main0
+-ffoption N
+-nconfs 1
+-charge 2
+-calccharge True
+-distort 0
+-qccode terachem
+-runtyp energy
+-method b3lyp
+-basis lacvps_ecp
+-jsched sge
+-bcharge 0

tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.report

@@ -0,0 +1,26 @@
+Bad structure?, False
+Min_dist (A), 1000
+Was ANN used?, True
+geo_label, 1
+geo_prob, 0.830863893032074
+geo_LSE, 0.056454913968045105
+geo_label_trust, very high
+sc_label, 1
+sc_prob, 0.7422247529029846
+sc_LSE, 0.0010312223992481981
+sc_label_trust, very high
+split, -24.547232997490973
+split_dist, 3.5700187674544474e-15
+This spin, 5
+ANN_ground_state, 5
+homo, -14.943396781167465
+gap, 4.31362875686047
+homo_dist, 0.17068386
+gap_dist, 0.0
+ANN_bondl, [2.1664019408351636, 2.1664019408351636, 2.1664019408351636, 2.1664019408351636, 2.134863201844001, 2.1218319126203653]
+homo_trust, high
+gap_trust, high
+split_trust, high
+Was Catalytic ANN used?, False
+Catalytic ANN reason, False
+ML-bl (database, A), 2.12

tests/testresources/refs/test_cli/fe_oct_2_water_6_s_5_conf_1.xyz

@@ -0,0 +1,21 @@
+19
+11/10/2023 22:23, XYZ structure generated by mol3D Class, molSimplify
+Fe 	0.000000	0.000000	0.000000
+O 	0.000000	2.120000	0.000000
+H 	0.685027	2.726198	-0.379294
+H 	-0.685027	2.726184	0.379294
+O 	2.120000	0.000000	0.000000
+H 	2.726198	-0.671373	-0.402970
+H 	2.726184	0.671373	0.402970
+O 	0.000000	-2.120000	0.000000
+H 	-0.656900	-2.726198	-0.426155
+H 	0.656900	-2.726184	0.426155
+O 	-2.120000	0.000000	0.000000
+H 	-2.726198	0.641627	-0.448821
+H 	-2.726184	-0.641627	0.448821
+O 	0.000000	0.000000	2.120000
+H 	-0.470940	0.625573	2.726198
+H 	0.470940	-0.625573	2.726184
+O 	0.000000	0.000000	-2.120000
+H 	0.492486	0.608756	-2.726198
+H 	-0.492486	-0.608756	-2.726184