Keep empty answers in the final individual outputs.

copienator/annotation_modifications.py

@@ -155,7 +155,7 @@ def output_removals(directory: Path) -> tuple[str, ...]:
     info = read_json(directory / "info.json") if (directory / "info.json").exists() else {}
     return ("Concat.jpg", "Concat_F.jpg", "Concat_F.pdf", "touched.json", "answer_labels.json",
             *(f"{label}.jpg" for label, entry in info.items()
-              if entry.get("not_empty") and Path(label).name == label))
+              if Path(label).name == label))
 
 
 def rebuild(root: Path, mode: str, directory: Path, staging: Path, meta: dict,
@@ -169,7 +169,15 @@ def rebuild(root: Path, mode: str, directory: Path, staging: Path, meta: dict,
 
     headers, bodies, changed = edited_bodies(directory, meta, instructions)
     info = deepcopy(meta["info"])
-    filtered = set(meta["filtered"]) | changed
+    for label, entry in info.items():
+        # Retained empty scans are images, not evidence of a non-empty answer.
+        entry["not_empty"] = label in bodies and (entry["not_empty"] or label in changed)
+        if label in changed:
+            entry["present"] = label in bodies
+        entry["score"] = scores.get(label, entry["score"])
+    filtered = (set(meta["filtered"]) | changed) & {
+        label for label, entry in info.items() if entry["not_empty"]
+    }
     all_labels = utils.read_all_labels(root)
     images, groups = [], []
     seen_contexts = set()
@@ -187,15 +195,13 @@ def rebuild(root: Path, mode: str, directory: Path, staging: Path, meta: dict,
                                         fill="black", font_size=30)
         image = stack([header, body])
         image.save(staging / f"{label}.jpg")
-        images.append(image)
+        if info[label]["not_empty"]:
+            images.append(image)
         if label in filtered:
             extras = get_extra_pdfs_as_images(root, label, annotating, all_labels,
                                             seen_contexts=seen_contexts) if mode == "BGnot" else []
             groups.append([*extras, image])
     for label, entry in info.items():
-        entry["not_empty"] = label in bodies
-        if label in changed and label in bodies:
-            entry["present"] = True
         entry["touched"] = mode == "BGnot" and label in bodies and label in filtered
         entry["score"] = scores.get(label, entry["score"])
     atomic_write_json(staging / "info.json", info)

copienator/commands/annotating.py

@@ -550,8 +550,7 @@ def process_student(student_id, labels_data, root_dir, all_labels, overwrite):
                 canvas.paste(image, (0, current_y))
                 current_y += image.height
             canvas.save(staging / "Concat.jpg")
-        elif labels_data:
-            problems = True
+        # An all-empty copy still has valid individual return images.
     return "partial" if problems else "success"
 
 

copienator/commands/reading_annotations.py

@@ -157,10 +157,14 @@ def apply_actions_and_regenerate(
     """Apply annotations and atomically merge the regenerated student files."""
     output_dir = workspace.annotation_dir("checks") / f"Copie{student_id}"
     bnote_path = output_dir / "bnote.json"
-    if not bnote_path.is_file():
+    only_empty = bool(data[student_id]) and all(
+        content["result"].get("error") == "empty-answer"
+        for content in data[student_id].values()
+    )
+    if not bnote_path.is_file() and not only_empty:
         print(f"  Missing {bnote_path}")
         return ExitCode.PARTIAL
-    bnote_data = read_json(bnote_path)
+    bnote_data = read_json(bnote_path) if bnote_path.is_file() else {"images": []}
     if not isinstance(bnote_data, dict):
         raise TypeError(f"Expected a JSON object in {bnote_path}")
 
@@ -180,7 +184,14 @@ def apply_actions_and_regenerate(
     filtered: list[Image.Image] = []
     incomplete = False
 
-    for image_info in bnote_data.get("images", []):
+    review_images = list(bnote_data.get("images", []))
+    reviewed_labels = {str(item.get("label", "")) for item in review_images if isinstance(item, dict)}
+    # Empty answers are omitted from the review sheet, but still need return images.
+    review_images.extend(
+        {"label": label} for label, content in labels_data.items()
+        if label not in reviewed_labels and content["result"].get("error") == "empty-answer"
+    )
+    for image_info in review_images:
         if not isinstance(image_info, dict):
             incomplete = True
             continue
@@ -191,11 +202,10 @@ def apply_actions_and_regenerate(
         content = labels_data[label]
         result = content["result"]
         scores[label] = str(result.get("score", 0))
-        if result.get("error") == "empty-answer":
-            continue
+        is_empty = result.get("error") == "empty-answer"
 
         sub_note = None
-        if notes_layer is not None:
+        if notes_layer is not None and "hmin" in image_info:
             hmin = int(image_info.get("hmin", 0))
             hmax = int(image_info.get("hmax", 0))
             sub_note = notes_layer.crop((0, hmin, notes_layer.width, hmax))
@@ -213,6 +223,7 @@ def apply_actions_and_regenerate(
             result,
             content["coordinates"][0],
             with_error=False,
+            with_empty=True,
         )
         if final_image is None:
             incomplete = True
@@ -230,6 +241,8 @@ def apply_actions_and_regenerate(
 
         dirty_images[label] = final_image
         header_heights[label] = new_header_height
+        if is_empty:
+            continue
         answer_labels.append(label)
         concatenated.append(final_image)
         if float(scores[label]) != 4.0 or result.get("feedback", []):
@@ -302,13 +315,15 @@ def run(
     status = ExitCode.PARTIAL if loaded.warnings else ExitCode.SUCCESS
     for student_id in sorted(loaded.data, key=utils.natural_key):
         output_dir = workspace.annotation_dir("checks") / f"Copie{student_id}"
-        if not output_dir.is_dir():
+        only_empty = all(content["result"].get("error") == "empty-answer"
+                         for content in loaded.data[student_id].values())
+        if not output_dir.is_dir() and not only_empty:
             print(f"Warning: missing annotation directory {output_dir}")
             status = ExitCode.PARTIAL
             continue
         print(f"Processing annotations for: {student_id}")
-        actions, notes = detect_checks_and_notes(output_dir)
-        if notes is None and not actions and not update_score:
+        actions, notes = ([], None) if only_empty else detect_checks_and_notes(output_dir)
+        if notes is None and not actions and not update_score and not only_empty:
             print("  No readable annotation input found.")
             status = ExitCode.PARTIAL
             continue

copienator/commands/reading_grouped_annotations.py

@@ -292,8 +292,7 @@ def apply_actions_and_regenerate_grouped(
             result["score"] = old_scores[label]
         scores[label] = str(result.get("score", 0))
         touched[label] = False
-        if result.get("error") == "empty-answer":
-            continue
+        is_empty = result.get("error") == "empty-answer"
         saved_image = output_dir / f"{label}.jpg"
         baseline_entry = (previous_baseline or {}).get("images", {}).get(label)
         if selected_labels and label not in selected_labels and (saved_image.is_file() or baseline_entry):
@@ -319,6 +318,8 @@ def apply_actions_and_regenerate_grouped(
                 )
             dirty_images[label] = final_image
             scores[label] = str(old_scores.get(label, scores[label]))
+            if is_empty:
+                continue
             concat_images.append(final_image)
             answer_labels.append(label)
             filtered_labels.append(label)
@@ -344,6 +345,7 @@ def apply_actions_and_regenerate_grouped(
             result,
             content["coordinates"][0],
             with_error=False,
+            with_empty=True,
         )
         if final_image is None:
             incomplete = True
@@ -368,6 +370,8 @@ def apply_actions_and_regenerate_grouped(
         # Persist every final block, including unchanged answers, for returns.
         dirty_images[label] = final_image
         header_heights[label] = new_header_height
+        if is_empty:
+            continue
         answer_labels.append(label)
         concat_images.append(final_image)
 

copienator/return_answers.py

@@ -84,7 +84,7 @@ def publish_answer_returns(
         raise ValueError(f"Expected a real answer directory: {answers_dir}")
     if configuration.RETURN_ANSWERS_ENABLED:
         options = load_return_answer_options(root)
-        labels = [label for label, entry in info.items() if entry["present"] and entry["not_empty"]]
+        labels = [label for label, entry in info.items() if entry["present"]]
 
         # Import the rendering backend only when individual images are requested.
         from copienator.commands.annotating import make_base_image

docs/final_output.md

@@ -39,7 +39,7 @@ answer JPEGs.
 | `Student Name.pdf` | `Concat_F.pdf` | Filtered, paginated correction with context, questions and solutions. |
 | `score.json` | `score.json` | Per-question scores, including questions omitted from the filtered PDF. |
 | `info.json` | `info.json` | Answer presence, empty-answer classification, PDF membership and score. |
-| `answers/*.jpg` | Final per-label JPEGs selected by `info.json` | One annotated non-empty answer, with optional supplementary material. |
+| `answers/*.jpg` | Final per-label JPEGs selected by `info.json` | One annotated answer, including empty scans, with optional supplementary material. |
 
 ## Enabling or disabling outputs
 
@@ -69,9 +69,9 @@ and preserves return PDFs when present.
 ## Individual answer JPEGs
 
 With `RETURN_ANSWERS_ENABLED = True`, `giving-names` generates an `answers/`
-subdirectory inside each student's return folder. It includes **every non-empty
-compiled answer**, even a perfect answer omitted from the filtered PDF. Labels
-marked `empty-answer` and labels without an answer are excluded. Every JPEG
+subdirectory inside each student's return folder. It includes **every present
+compiled answer**, even a perfect answer omitted from the filtered PDF. Scans
+marked `empty-answer` are included; labels without an answer are excluded. Every JPEG
 contains the final annotated student answer, including retained feedback and
 extracted handwriting.
 
@@ -92,7 +92,7 @@ Filenames use natural label order, a three-digit minimum sequence number, and a
 sanitized label (`001 - Ex 1.jpg`). Numbering prevents filename collisions when
 labels differ only by characters forbidden in filenames. JSON keys retain exact
 labels. The managed `answers/` directory is replaced on successful generation,
-so removed/empty answers do not leave stale images; failures preserve the previous
+so removed answers do not leave stale images; failures preserve the previous
 directory. Disabling the option clears this directory on the next `giving-names`
 run. Separate storage keeps these images out of the personal final-mark stamping
 step, which reads only JPEGs directly inside the student's folder.
@@ -116,11 +116,13 @@ Every label in `score.json` has an object containing exactly four fields:
 ```
 
 - `present`: an answer entry exists for this student and label in the compilation
-  data. A supplied answer judged empty still has `present: true`.
+  data. A supplied answer judged empty still has `present: true`. A body removed by
+  manual annotation edits has `present: false`.
 - `not_empty`: the answer was not marked `empty-answer` and was successfully
   compiled. Absent answers have `not_empty: false`. When individual export is
-  enabled, a JPEG is generated if and only if both `present` and `not_empty` are
-  true. These fields describe the answer regardless of export settings.
+  enabled, every `present` answer gets a JPEG, including those with `not_empty: false`.
+  Image retention alone does not change the empty classification. These fields
+  describe the answer regardless of export settings.
 - `touched`: the answer appears in the compiled filtered `Concat_F.pdf`, using
   the actual selection including handwriting and selective redo preservation.
   It is not a flag for human edits. Empty and absent answers have `false`.
@@ -151,7 +153,8 @@ The result is one RGB image of variable height, with no page breaks. It contains
 all successfully compiled answer blocks, including answers scored 4 with no
 remaining feedback. “Full” refers to those answer blocks, not the original scan
 pages or every question in the statement. Missing/unrenderable answers cannot
-be included, and the renderer normally suppresses `empty-answer` results.
+be included. Empty-answer scans are retained individually but excluded from
+the combined and filtered documents.
 The grouped compiler refuses to publish a new set when compilation is incomplete.
 
 The JPEG does not prepend the question, context or model solution PDFs.

tests/test_annotation_modifications.py

@@ -115,6 +115,29 @@ class ModificationTests(unittest.TestCase):
         self.assertFalse((self.output / "Empty.jpg").exists())
         self.assertFalse(read_json(self.output / "info.json")["Empty"]["not_empty"])
 
+    def test_retained_empty_scan_stays_empty_after_unrelated_edits_and_can_be_replaced(self):
+        self.images["Empty"] = Image.new("RGB", (100, 60), "white")
+        self.heights["Empty"] = 10
+        self.info["Empty"]["present"] = True
+        self.seed()
+        self.apply("Copie43 Ex 1 -> Ex 2|")
+        info = read_json(self.output / "info.json")
+        self.assertTrue((self.output / "Empty.jpg").is_file())
+        self.assertEqual(info["Empty"], self.info["Empty"])
+        with Image.open(self.output / "Concat.jpg") as image:
+            self.assertEqual(image.height, 120 + 180 + 40)
+        self.apply("Copie43 Ex 1 -> Empty")
+        self.assertTrue(read_json(self.output / "info.json")["Empty"]["not_empty"])
+        self.apply()
+        self.assertEqual(read_json(self.output / "info.json")["Empty"], self.info["Empty"])
+
+    def test_removed_body_is_absent_and_not_exported_as_an_empty_scan(self):
+        self.apply("Copie43 Ex 1 x> Ex 2")
+        info = read_json(self.output / "info.json")["Ex 1"]
+        self.assertFalse(info["present"])
+        self.assertFalse(info["not_empty"])
+        self.assertFalse((self.output / "Ex 1.jpg").exists())
+
     def test_invalid_file_does_not_apply_valid_first_instruction(self):
         before = {p.name: p.read_bytes() for p in self.output.iterdir() if p.is_file()}
         with self.assertRaises(CliError):

tests/test_answer_returns.py

@@ -57,8 +57,8 @@ class AnswerReturnTests(unittest.TestCase):
             ), patch.object(annotating, "make_base_image", side_effect=self.supplement):
                 publish_answer_returns(self.root, self.source, self.destination)
                 files = sorted((self.destination / "answers").glob("*.jpg"))
-                self.assertEqual([p.name for p in files], ["Ex 1.jpg", "Ex 2.jpg"])
-                with Image.open(files[0]) as image:
+                self.assertEqual([p.name for p in files], ["Empty.jpg", "Ex 1.jpg", "Ex 2.jpg"])
+                with Image.open(self.destination / "answers" / "Ex 1.jpg") as image:
                     self.assertEqual(image.size, (100, 30 + 20 * sum((context, question, solution))))
                     colors = []
                     if context:
@@ -212,7 +212,7 @@ class AnswerReturnTests(unittest.TestCase):
         )
         self.assertEqual(
             sorted(path.name for path in answers.iterdir()),
-            ["Ex 1.jpg", "Ex 2.jpg"],
+            ["Empty.jpg", "Ex 1.jpg", "Ex 2.jpg"],
         )
 
 
@@ -304,7 +304,7 @@ class CompiledMembershipTests(unittest.TestCase):
                 self.assertEqual(info["Empty"], {"present": True, "not_empty": False, "touched": False, "score": "0"})
                 self.assertEqual(info["Absent"], {"present": False, "not_empty": False, "touched": False, "score": ""})
                 self.assertEqual(info["Perfect"], {"present": True, "not_empty": True, "touched": False, "score": "4"})
-                self.assertNotIn("Empty", rendered)
+                self.assertIn("Empty", rendered)
                 for label in rendered:
                     self.assertTrue((output / f"{label}.jpg").is_file())
                 # Selective redo keeps unselected saved answers in the PDF,
@@ -316,6 +316,76 @@ class CompiledMembershipTests(unittest.TestCase):
                 self.assertTrue(read_json(output / "info.json")["Perfect"]["touched"])
                 self.assertFalse(read_json(output / "info.json")["Empty"]["not_empty"])
 
+    def test_real_empty_pdf_is_published_in_all_annotation_modes(self):
+        import fitz
+        from copienator.commands import reading_annotations as standard
+        for mode in ("Anot", "Bnot", "BGnot"):
+            with self.subTest(mode=mode), tempfile.TemporaryDirectory() as directory:
+                root = Path(directory)
+                workspace = EvaluationWorkspace(root)
+                (root / "labels").write_text("Empty\nAbsent\n")
+                pdf = root / "answer.pdf"
+                with fitz.open() as document:
+                    page = document.new_page(width=200, height=60)
+                    page.insert_text((10, 30), "Copied question only")
+                    document.save(pdf)
+                data = {"01": {"Empty": {"pdf_path": pdf, "coordinates": (0, 0),
+                    "result": {"score": 0, "error": "empty-answer", "feedback": []}}}}
+                if mode == "Anot":
+                    status = annotating.process_student("01", data["01"], root, ["Empty", "Absent"], True)
+                    self.assertEqual(status, "success")
+                elif mode == "Bnot":
+                    status = standard.apply_actions_and_regenerate(
+                        workspace, data, "01", [], None, ["Empty", "Absent"])
+                    self.assertEqual(status, 0)
+                else:
+                    status, _ = reader.apply_actions_and_regenerate_grouped(
+                        workspace, data, "01", [], {}, ["Empty", "Absent"])
+                    self.assertEqual(status, 0)
+                output = root / mode / "Copie01"
+                destination = root / "return"
+                destination.mkdir()
+                with patch.multiple(configuration, RETURN_ANSWERS_ENABLED=True,
+                                    RETURN_ANSWERS_CONTEXT=False, RETURN_ANSWERS_QUESTION=False,
+                                    RETURN_ANSWERS_SOLUTION=False):
+                    publish_answer_returns(root, output, destination)
+                self.assertEqual([p.name for p in (destination / "answers").iterdir()], ["Empty.jpg"])
+                with Image.open(destination / "answers" / "Empty.jpg") as image:
+                    self.assertGreater(image.height, 0)
+                    self.assertLess(image.convert("L").getextrema()[0], 100)
+                self.assertFalse(read_json(destination / "info.json")["Empty"]["not_empty"])
+                self.assertFalse((output / "Concat.jpg").exists())
+                self.assertFalse((output / "Concat_F.pdf").exists())
+
+    def test_bnot_recovers_empty_scans_missing_from_review_layout(self):
+        from copienator.commands import reading_annotations as standard
+        for only_empty in (False, True):
+            with self.subTest(only_empty=only_empty), tempfile.TemporaryDirectory() as directory:
+                workspace = EvaluationWorkspace(Path(directory))
+                output = workspace.root / "Bnot" / "Copie01"
+                output.mkdir(parents=True)
+                answer = workspace.root / "answer.pdf"
+                answer.touch()
+                labels = {"Empty": {"pdf_path": answer, "coordinates": (0, 0),
+                                    "result": {"score": 0, "error": "empty-answer"}}}
+                if not only_empty:
+                    labels["Full"] = {"pdf_path": answer, "coordinates": (0, 0),
+                                      "result": {"score": 4}}
+                    atomic_write_json(output / "bnote.json", {"images": [
+                        {"label": "Full", "hmin": 0, "hmax": 50, "header_height": 0}]})
+                with patch.object(annotating, "make_base_image", return_value=(None, 0, 0)), patch.object(
+                    annotating, "compose_label_image", return_value=(Image.new("RGB", (100, 50)), 0)
+                ) as render:
+                    status = standard.apply_actions_and_regenerate(
+                        workspace, {"01": labels}, "01", [], None, [*labels, "Absent"])
+                self.assertEqual(status, 0)
+                self.assertTrue(all(call.kwargs["with_empty"] for call in render.call_args_list))
+                self.assertTrue((output / "Empty.jpg").is_file())
+                self.assertFalse((output / "Absent.jpg").exists())
+                self.assertFalse(read_json(output / "info.json")["Empty"]["not_empty"])
+                self.assertEqual((output / "Concat.jpg").exists(), not only_empty)
+                self.assertFalse((output / "Concat_F.jpg").exists())
+
     def test_all_empty_removes_stale_concat_and_records_false(self):
         with tempfile.TemporaryDirectory() as directory:
             workspace = EvaluationWorkspace(Path(directory))
@@ -325,10 +395,17 @@ class CompiledMembershipTests(unittest.TestCase):
                 (output / name).write_bytes(b"stale")
             atomic_write_json(output / "touched.json", {"Empty": True})
             atomic_write_json(output / "answer_labels.json", ["Empty"])
-            status, _ = reader.apply_actions_and_regenerate_grouped(
-                workspace, {"01": {"Empty": {"result": {"score": 0, "error": "empty-answer"}}}},
-                "01", [], {}, ["Empty"]
-            )
+            answer = workspace.root / "answer.pdf"
+            answer.touch()
+            with patch.object(annotating, "make_base_image", return_value=(Image.new("RGB", (100, 50)), 0, 0)), patch.object(
+                annotating, "compose_label_image", return_value=(Image.new("RGB", (100, 50)), 0)
+            ):
+                status, _ = reader.apply_actions_and_regenerate_grouped(
+                    workspace, {"01": {"Empty": {"result": {"score": 0, "error": "empty-answer"},
+                        "pdf_path": answer, "coordinates": (0, 0)}}},
+                    "01", [], {}, ["Empty"]
+                )
+            self.assertTrue((output / "Empty.jpg").is_file())
             self.assertEqual(status, 0)
             self.assertEqual(read_json(output / "info.json"), {
                 "Empty": {"present": True, "not_empty": False, "touched": False, "score": "0"}