updated/fixed gmxfatal message matching

- can now recognize newer gromacs messages
- added quick tests for the three fail modes of GromacsCommand

gromacs/core.py

@@ -435,12 +435,13 @@ class GromacsCommand(Command):
     command_name = None
     driver = None
     doc_pattern = r""".*?(?P<DOCS>DESCRIPTION.*)"""
-    gmxfatal_pattern = r"""----+\n                  # ---- decorator line
-            \s*Program\s+(?P<program_name>\w+),     #  Program name,
-              \s+VERSION\s+(?P<version>[\w.]+)\s*\n #    VERSION 4.0.5
-            (?P<message>.*?)\n                      # full message, multiple lines
-            \s*                                     # empty line (?)
-            ----+\n                                 # ---- decorator line
+    # gmxfatal_pattern is used with re.X | re.DOTALL so no need to match \n
+    gmxfatal_pattern = r"""----+\s*                       # ---- decorator line
+            \s*Program:?\s+(?P<program_name>[^,]+),\s*    # Program[:] gmx grompp
+            \s+(VERSION|version)\s+(?P<version>[^\s]+)\s* # VERSION 4.0.5, version 2023.1-macports
+            (?P<message>.*?)                              # full message, multiple lines
+            \s*                                           # empty line (?)
+            ----+                                         # ---- decorator line
             """
     # matches gmx_fatal() output
     # -------------------------------------------------------

tests/test_core.py

@@ -81,3 +81,25 @@ def test_help_long(self, command, capsys):
         captured = capsys.readouterr()
         assert command.command_name in captured.out
         assert gromacs.core.Command.__call__.__doc__ in captured.out
+
+
+class TestGromacsCommand:
+    def test_check_failure_raise(self):
+        assert gromacs.grompp.failuremode == "raise"
+        with pytest.raises(gromacs.GromacsError,
+                           match="Gromacs tool failed.*\nCommand invocation:.*grompp"):
+            gromacs.grompp()
+
+    def test_check_failure_warn(self):
+        grompp = gromacs.tools.Grompp(failure="warn")
+        assert grompp.failuremode == "warn"
+        with pytest.warns(gromacs.GromacsFailureWarning,
+                           match="Error code"):
+            rc, stout, stderr = grompp()
+        assert rc == 1
+
+    def test_check_failure_none(self):
+        grompp = gromacs.tools.Grompp(failure=None)
+        assert grompp.failuremode == None
+        rc, stout, stderr = grompp()
+        assert rc == 1