Fix parsing of $not expression on command line

signac/filterparse.py

@@ -195,6 +195,8 @@
 
 def _add_prefix(filter):
     """Add prefix "sp." to a (possibly nested) filter."""
+
+    # Logical operators ($and, $or, $not) should not be prefixed, but their values should.
     for key, value in filter.items():
         if key in ("$and", "$or"):
             if isinstance(value, list) or isinstance(value, tuple):
@@ -203,6 +205,8 @@
                 raise ValueError(
                     "The argument to a logical operator must be a list or a tuple!"
                 )
+        elif key == "$not":
+            yield key, dict(_add_prefix(value))
         elif "." in key and key.split(".", 1)[0] in ("sp", "doc"):
             yield key, value
         elif key in ("sp", "doc"):

tests/test_find_command_line_interface.py

@@ -11,6 +11,7 @@
 
 from signac.filterparse import parse_filter_arg, parse_simple
 
+# also used in test_shell
 FILTERS = [
     {"a": 0},
     {"a.b": 0},
@@ -70,6 +71,8 @@ def _parse(args):
 
     def test_interpret_json(self):
         def _assert_equal(q):
+            # TODO: full code path not tested with this test.
+            # _assert_equal and _find_expression, are not tested
             assert q == self._parse([json.dumps(q)])
 
         for f in FILTERS:

tests/test_shell.py

@@ -9,6 +9,7 @@
 from tempfile import TemporaryDirectory
 
 import pytest
+from test_find_command_line_interface import FILTERS
 from test_project import WINDOWS, _initialize_v1_project, skip_windows_without_symlinks
 
 import signac
@@ -280,6 +281,12 @@ def test_find(self):
                 == [job.id for job in project.find_jobs({"doc.b": i})][0]
             )
 
+        # ensure that there are no errors due to adding sp and doc prefixes
+        # by testing on all the example complex expressions
+        for f in FILTERS:
+            command = "python -m signac find ".split() + [json.dumps(f)]
+            self.call(command).strip()
+
     def test_diff(self):
         self.call("python -m signac init".split())
         project = signac.Project()