From 0443e4a00c3aba46d20bb494ee84e17cf8e4c778 Mon Sep 17 00:00:00 2001
From: Marieke Westendorp <ma3ke.cyber@gmail.com>
Date: Thu, 30 May 2024 11:29:00 +0200
Subject: [PATCH 1/2] pack: Implement an implied default compartment if the
 field is unset

Closes #26
---
 src/bentopy/pack/config.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/bentopy/pack/config.py b/src/bentopy/pack/config.py
index b74aaac..a5c6ff9 100644
--- a/src/bentopy/pack/config.py
+++ b/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"),
             )

From 4673fca3bf970a572a1ccb286134f7968099761b Mon Sep 17 00:00:00 2001
From: Marieke Westendorp <ma3ke.cyber@gmail.com>
Date: Thu, 30 May 2024 11:35:15 +0200
Subject: [PATCH 2/2] Update README to mention the implied default compartment

Describes the change proposed in #26.
---
 README.md | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/README.md b/README.md
index 3fdc450..d0332dc 100644
--- a/README.md
+++ b/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