Implement an implied default compartment when compartment definitions are omitted

README.md

@@ -225,6 +225,30 @@ at 50 nm.
 
 </details>
 
+<details>
+<summary>Implied default compartment.</summary>
+
+If you omit the `"compartments"` field from the `"space"` section, and don't
+set the `"compartments"` field in any of the segments in the `"segments"`
+section, a single default compartment is implied.
+This compartment is set up like this.
+
+```json
+		{
+			"id": "main",
+			"shape": "cuboid"
+		}
+```
+
+Each segment, when the compartment is implied, is assigned to that `"main"`
+compartment.
+
+Note that when the `"compartments"` field on any segment is not set, its
+compartment id will be set to `"main"`, even when a compartment is defined in
+the `"space"` section.
+
+</details>
+
 #### Output
 
 In **output**, we set a **title** and **dir**ectory to write the placement list

src/bentopy/pack/config.py

@@ -4,6 +4,8 @@
 from .segment import Segment
 from .space import Space
 
+DEFAULT_COMPARTMENT_ID = "main"
+
 
 class Configuration:
     def __init__(
@@ -16,20 +18,31 @@ def __init__(
     ):
         config = json.loads(json_src)
         space = config["space"]
+        compartments = space.get("compartments")
         self.space = Space(
             space["size"],
             space["resolution"],
-            space["compartments"],
+            compartments or [{"id": DEFAULT_COMPARTMENT_ID, "shape": "cuboid"}],
             space.get("constraint"),
         )
         segments = config["segments"]
+        # Verify that if `output.compartments` is unset, the `compartments`
+        # field is unset for every segment, as well.
+        if compartments is None:
+            assert all(s.get("compartments") is None for s in segments), """
+            If no `compartments` are defined in the `space` section,
+            compartment selections in segment definitions are not allowed.
+            When no compartments are defined in the `space` section, a single
+            default compartment is implied. To set each segment's compartment
+            to the implied default compartment, remove the `compartments`
+            field from all segment definitions."""
         self.segments = [
             Segment(
                 s["name"],
                 s["number"],
                 s["path"],
                 self.space.resolution,
-                s["compartments"],
+                s.get("compartments") or [DEFAULT_COMPARTMENT_ID],
                 s.get("rotation_axes"),
                 s.get("center"),
             )