Standardisation 3

Readme.org

@@ -171,6 +171,8 @@ scripts migrés vers cette convention sont actuellement :
 
 - =copies_tools.py=, =grouping.py= et =verify_groups.py= ;
 - =post-correction.py= et =resolve_manual.py= ;
+- =annotating.py=, =annotating_with_checks.py= et
+  =annotating_by_label.py= ;
 - =export.py=, =import.py= et =giving_names.py=.
 
 ** Correction d'un paquet de copies
@@ -355,6 +357,11 @@ OU
     Ajoute les annotations Gemini, et des checkboxes à cocher.
     Enregistrées dans le dossier =Bnot=,
     =--overwrite=
+
+    Une seule copie peut être ciblée avec, par exemple,
+    =python annotating_with_checks.py Interro/Copies/Copie01.pdf=.
+    Le mode =--refaire= exige un fichier =refaire.json= et écrit dans
+    =BRnot=.
 OU
  2. =python annotating_by_label.py Interro= dans =BGnot=
 
@@ -364,6 +371,12 @@ OU
 
     _Needs_ : label_groups file (made automatically by this function),
     qui dit quelles questions regrouper.
+
+Dans ces trois modes, les métadonnées JSON sont écrites atomiquement.
+Lors d'une régénération, les nouvelles sorties sont préparées dans un
+dossier temporaire voisin. Une erreur de rendu conserve donc la sortie
+précédente ; pour =BGnot --overwrite=, le dossier complet n'est remplacé
+que si tous les groupes ont été produits.
  3. =python export.py Interro= (gestion perso)
     Cela déplace les groupes dans le dossier configuré par =EXPORT_DIR=
     (par défaut =Export=).

annotating.py

@@ -1,140 +1,52 @@
-import sys
+from __future__ import annotations
+
+import argparse
+import io
 import os
-import json
-import glob
-from pathlib import Path
+import re
 import subprocess
-from PIL import Image
+import tempfile
+from collections.abc import Sequence
+from pathlib import Path
+
+import matplotlib
+import matplotlib.colors as mcolors
+import PIL.ImageOps
+
+matplotlib.use("Agg")
+
+from matplotlib import pyplot as plt
+from pdf2image import convert_from_path
+from PIL import Image, ImageDraw, ImageFont
+
+import utils
+from config import LATEX_ANOT_AFTER, LATEX_ANOT_BEFORE
+from copienator import (
+    EvaluationWorkspace,
+    ExitCode,
+    atomic_write_json,
+    evaluation_parser,
+    execute,
+    workspace_from_args,
+)
+from copienator.annotation_data import load_annotation_data
+from copienator.filesystem import staged_directory
+from utils import natural_key
 
 MARGIN_LEFT = 300
 ANNOT_WIDTH = 600
 
-# Results is : Copie id -> label -> {pdf_path, gemini_result, coordinates}
-# Coordinates are the real coordinates (hmin, hmax) of the image in the Group
-# The gemini_result coordinates should be un-normalized !
-def make_dictionary(root_dir, refaire=False, refaire_list=[]):
-    correction_path = os.path.join(root_dir, "correction.json")
 
-    # Load correction data
-    try:
-        with open(correction_path, 'r', encoding='utf-8') as f:
-            corrections = json.load(f)
-    except FileNotFoundError:
-        print(f"Error: {correction_path} not found.")
-        sys.exit(1)
 
-    # Dictionary: keys are IDs
-    result_data = {}
+def make_dictionary(root_dir, refaire=False, refaire_list=None):
+    """Compatibility wrapper used by the annotation-reading scripts."""
+    workspace = EvaluationWorkspace(Path(root_dir))
+    loaded = load_annotation_data(
+        workspace,
+        refaire_list=(refaire_list or []) if refaire else None,
+    )
+    return loaded.data
 
-    # Iterate through labels and items in correction.json
-    for label, items in corrections.items():
-        items = sum(items, []) # Flatten
-        for item in items:
-            # print(item)
-            student_id = item['id']
-            result_obj = item['result']
-
-            if result_obj.get("suffix") == "_old":
-                continue
-
-            # Find coordinates
-            coordinates = None
-            height,width= None, None
-            label_dir = Path(root_dir) / "Par label" / label
-
-            # Search all json files in Dir/label
-            json_files = glob.glob(os.path.join(label_dir, "*.json"))
-            for jf in json_files:
-                try:
-                    with open(jf, 'r', encoding='utf-8') as f:
-                        coord_list = json.load(f)
-                        # Format: [["id", x, y, width_r, "label"], ...]
-                        for entry in coord_list:
-                            if entry[0] == student_id:
-                                coordinates = (entry[1], entry[2])
-                                img_path = os.path.splitext(jf)[0] + ".jpg"
-                                with Image.open(img_path) as img:
-                                    width, height = img.size
-                                break
-                except json.JSONDecodeError:
-                    continue
-                if coordinates:
-                    break
-
-            suffix = result_obj.get("suffix", "")
-            if suffix == "_new":
-                pdf_path = Path(root_dir) / "Copies" / f"Copie{student_id}" / f"{label}_new.pdf"
-            else:
-                pdf_path = Path(root_dir) / "Copies" / f"Copie{student_id}" / f"{label}.pdf"
-            # Initialize dictionary structure for this ID if missing
-            if student_id not in result_data:
-                result_data[student_id] = {}
-
-            fb = result_obj.get("feedback", [])
-            for i in range(len(fb)):
-                el = fb[i]
-                if height == None or width == None:
-                    print("?? height or width is None, for ", student_id, label)
-                if "box_2d" in el and el["box_2d"]:
-                    el["box_2d"][0] = (el["box_2d"][0] * height)//1000
-                    el["box_2d"][2] = (el["box_2d"][2] * height)//1000
-                    el["box_2d"][1] = (el["box_2d"][1] * width)//1000
-                    el["box_2d"][3] = (el["box_2d"][3] * width)//1000
-
-            # Populate the object
-            result_data[student_id][label] = {
-                "pdf_path": pdf_path,
-                "result": result_obj,
-                "coordinates": coordinates
-            }
-
-    if refaire:
-        for copie_name, labels_to_redo in refaire_list:
-            sid = copie_name.replace("Copie", "") # Extract "01" from "Copie01"
-            if sid in result_data:
-                # Si des labels à refaire ne sont pas présent dans la correction
-                # On ajoute des dummies
-                if labels_to_redo: # Si la liste est non vide
-                    for lbl in labels_to_redo:
-                        pdf_path = Path(root_dir) / "Copies" / f"Copie{sid}" / f"{lbl}.pdf"
-                        if not Path(pdf_path).exists():
-                            pdf_path_new = Path(root_dir) / "Copies" / f"Copie{sid}" / f"{lbl}_new.pdf"
-                            if pdf_path_new.exists():
-                                pdf_path = pdf_path_new
-                            else:
-                                print("Debug : asked to refaire", sid, lbl, "but pdf absent")
-                                continue
-                        # result_data[sid][lbl] = {
-                        #     "pdf_path": pdf_path,
-                        #     "result": {
-                        #         "score": 0.0,
-                        #         "feedback": [],
-                        #         "error": "non traité"
-                        #     },
-                        #     "coordinates": (0,0)
-                        # }
-            else: # Ce student id n'a jamais été corrigé
-                result_data[sid] = {}
-                for lbl in labels_to_redo:
-                    pdf_path = Path(root_dir) / "Copies" / f"Copie{sid}" / f"{lbl}.pdf"
-                    if not pdf_path.exists():
-                        pdf_path_new = Path(root_dir) / "Copies" / f"Copie{sid}" / f"{lbl}_new.pdf"
-                        if pdf_path_new.exists():
-                            pdf_path = pdf_path_new
-                        else:
-                            print("Debug : asked to refaire", sid, lbl, "but pdf absent")
-                            continue
-                    result_data[sid][lbl] = {
-                        "pdf_path": pdf_path,
-                        "result": {
-                            "score": 0.0,
-                            "feedback": [],
-                            "error": "non traité"
-                        },
-                        "coordinates": (0,0)
-                    }
-
-    return result_data
 
 def make_base_image(pdf_path):
     pages = convert_from_path(pdf_path)
@@ -152,20 +64,6 @@ def make_base_image(pdf_path):
         current_y += page.height
     return (base_img, total_h, max_w)
 
-import io
-import shutil
-from pdf2image import convert_from_path
-from PIL import Image, ImageDraw, ImageFont
-import matplotlib
-matplotlib.use('Agg')  # Force headless rendering
-import matplotlib.pyplot as plt
-
-# plt.rcParams.update({ "text.usetex": True,
-                     # "text.latex.preamble": r"\usepackage{bbold}"})
-
-import re
-import textwrap
-
 def normalize_mathtext(text):
     """
     Replaces LaTeX shortcuts not supported by Matplotlib's mathtext parser.
@@ -274,16 +172,6 @@ def render_latex_text(text, width_px, bg_color=(255, 255, 255, 255), max_lines=N
     final_img.alpha_composite(img)
     return final_img
 
-import os
-import tempfile
-import subprocess
-import PIL.ImageOps
-
-
-from config import LATEX_ANOT_AFTER, LATEX_ANOT_BEFORE
-from string import Template
-
-
 def render_real_latex_text(text, width_px, bg_color=(255, 255, 255, 255), max_lines=None, fontsize=19):
     dpi = 100
     width_in = width_px / dpi
@@ -303,11 +191,12 @@ def render_real_latex_text(text, width_px, bg_color=(255, 255, 255, 255), max_li
             f.write(latex_template)
 
         # Compile to PDF
-        result = subprocess.run(
+        subprocess.run(
             ['pdflatex', '-interaction=nonstopmode', 'text.tex'],
             cwd=temp_dir,
             stdout=subprocess.DEVNULL,
-            stderr=subprocess.DEVNULL
+            stderr=subprocess.DEVNULL,
+            check=False,
         )
 
         if not os.path.exists(pdf_path):
@@ -336,12 +225,6 @@ def render_real_latex_text(text, width_px, bg_color=(255, 255, 255, 255), max_li
 
     return final_img
 
-import io
-from PIL import Image
-import matplotlib.pyplot as plt
-import matplotlib.colors as mcolors
-from highlight_text import ax_text
-
 def color(score):
     t = max(0.0, min(1.0, float(score) / 4.0))
     t = t*1.5 - 0.25
@@ -350,8 +233,6 @@ def color(score):
     green = 150 * t
     return mcolors.to_hex((red/255, green/255, 0))
 
-from PIL import Image, ImageDraw, ImageFont
-
 def render_score_text(label, score, error, width_px, fontsize=30,
                       bg_color=(255, 255, 255, 255),
                       with_error=True, id=None):
@@ -380,7 +261,7 @@ def render_score_text(label, score, error, width_px, fontsize=30,
     try:
         font_regular = ImageFont.truetype("DejaVuSans.ttf", fontsize)
         font_bold = ImageFont.truetype("DejaVuSans-Bold.ttf", fontsize)
-    except IOError:
+    except OSError:
         # Fallback for systems without specific TTFs readily available
         print("here")
         try:
@@ -429,7 +310,6 @@ def compose_label_image(base_img, label, result, hmin,
     if base_img.width < TARGET_MIN_WIDTH:
         total_missing = TARGET_MIN_WIDTH - base_img.width
         left_pad = min(total_missing, MARGIN_LEFT)
-        right_pad = total_missing - left_pad
 
         new_base = Image.new("RGB", (TARGET_MIN_WIDTH, base_img.height), "white")
         new_base.paste(base_img, (left_pad, 0))
@@ -549,100 +429,118 @@ def compose_label_image(base_img, label, result, hmin,
 
     return final_img, header_height
 
-from utils import natural_key
-import concurrent.futures
-
 def process_student(student_id, labels_data, root_dir, all_labels, overwrite):
     """Helper function to process a single student."""
 
     # Prepare output directory: Dir/Anot_CopieID
-    output_dir = os.path.join(root_dir, "Anot", f"Copie{student_id}")
+    output_dir = Path(root_dir) / "Anot" / f"Copie{student_id}"
 
     # Check if already processed (Concat.jpg exists)
-    concat_path = os.path.join(output_dir, "Concat.jpg")
-    if os.path.exists(concat_path) and not overwrite:
+    concat_path = output_dir / "Concat.jpg"
+    if concat_path.exists() and not overwrite:
         print(f"Skipping Copie {student_id} (Concat.jpg exists)")
-        return
+        return "skipped"
 
     print("Processing :", student_id)
-
-    # Clean folder if re-processing
-    if os.path.exists(output_dir):
-        shutil.rmtree(output_dir)
-    os.makedirs(output_dir)
-
+    problems = False
+    with staged_directory(output_dir) as staging:
         d_notes = dict.fromkeys(all_labels, "")
         label_images = []
-
-    # !! Trier par l'ordre des labels plutôt
-    sorted_labels = sorted(list(labels_data.items()), key=natural_key)
+        sorted_labels = sorted(labels_data.items(), key=lambda item: natural_key(item[0]))
 
         for label, content in sorted_labels:
-        # 1. Find PDF path
-        copie_folder = f"Copie{student_id}"
             pdf_full_path = content.get('pdf_path')
-
-        if not pdf_full_path or not os.path.exists(pdf_full_path):
+            if not pdf_full_path or not Path(pdf_full_path).exists():
                 print(f"File not found: {pdf_full_path}")
+                problems = True
                 continue
-
-        # 2. Convert PDF to Image
             try:
-            (base_img, _, _) = make_base_image(pdf_full_path)
-        except Exception as e:
-            print(f"Error converting {pdf_full_path}: {e}")
+                base_img, _, _ = make_base_image(pdf_full_path)
+            except Exception as exc:  # noqa: BLE001 - PDF/LaTeX backends vary
+                print(f"Error converting {pdf_full_path}: {exc}")
+                problems = True
                 continue
 
             result = content.get('result', {})
-        coordinates = content.get('coordinates', (0, 0))  # (hmin, hmax)
-        score = result.get('score', 0)
-        d_notes[label] = str(score)
-
-        final_img, _ = compose_label_image(base_img, label, result, coordinates[0],
+            coordinates = content.get('coordinates', (0, 0))
+            d_notes[label] = str(result.get('score', 0))
+            final_img, _ = compose_label_image(
+                base_img,
+                label,
+                result,
+                coordinates[0],
                 with_empty=True,
-                                           render_fn=render_real_latex_text)
-        # 7. Save Image
-        save_path = os.path.join(output_dir, f"{label}.jpg")
-        final_img.save(save_path)
+                render_fn=render_real_latex_text,
+            )
+            final_img.save(staging / f"{label}.jpg")
             if result.get('error', "") != "empty-answer":
                 label_images.append(final_img)
 
-    # Save scores
-    with open(os.path.join(output_dir, "score.json"), "w") as f:
-        json.dump(d_notes, f, indent=4)
-
-    # Concatenate
+        atomic_write_json(staging / "score.json", d_notes)
         if label_images:
-        max_w = max(i.width for i in label_images)
-        total_h = sum(i.height for i in label_images)
+            max_w = max(image.width for image in label_images)
+            total_h = sum(image.height for image in label_images)
             canvas = Image.new('RGB', (max_w, total_h))
-        cy = 0
-        for img in label_images:
-            canvas.paste(img, (0, cy))
-            cy += img.height
-        canvas.save(concat_path)
+            current_y = 0
+            for image in label_images:
+                canvas.paste(image, (0, current_y))
+                current_y += image.height
+            canvas.save(staging / "Concat.jpg")
+        elif labels_data:
+            problems = True
+    return "partial" if problems else "success"
 
 
 def process_correction(root_dir, data, all_labels, overwrite=False):
     # Ne pas thread cette application
     #  1. Il faut protéger les appels à matplotlib
     #  2. tu vas perdre les erreurs
-    for student_id, labels in sorted(data.items()):
+    statuses = [
         process_student(student_id, labels, root_dir, all_labels, overwrite)
+        for student_id, labels in sorted(data.items())
+    ]
+    return ExitCode.PARTIAL if "partial" in statuses else ExitCode.SUCCESS
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = evaluation_parser("Generate simple annotated copies.")
+    parser.add_argument(
+        "--overwrite",
+        action="store_true",
+        help="Replace existing student output directories",
+    )
+    return parser
+
+
+def run(workspace: EvaluationWorkspace, *, overwrite: bool = False) -> ExitCode:
+    workspace.require_files("labels", "correction.json")
+    workspace.require_directories("Copies", "Par label")
+    labels = utils.read_all_labels(workspace.root)
+    loaded = load_annotation_data(workspace)
+    for warning in loaded.warnings:
+        print(f"Warning: {warning}")
+    if not loaded.data:
+        print("Warning: no annotation data was found.")
+        return ExitCode.PARTIAL
+    result = process_correction(
+        workspace.root,
+        loaded.data,
+        labels,
+        overwrite=overwrite,
+    )
+    if loaded.warnings and result == ExitCode.SUCCESS:
+        return ExitCode.PARTIAL
+    return result
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    parser = build_parser()
+    return execute(
+        parser,
+        argv,
+        lambda args: run(workspace_from_args(args), overwrite=args.overwrite),
+    )
 
-import argparse
-import utils
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Annotate copies")
-    parser.add_argument("root_dir", help="Directory containing the copies")
-    parser.add_argument("--overwrite", action="store_true", help="Reprocess even if Concat.jpg exists")
-
-    args = parser.parse_args()
-    root_dir = args.root_dir
-    labels = utils.read_all_labels(root_dir)
-    results = make_dictionary(root_dir)
-    # Results is : Copie id -> label -> {pdf_path, gemini_result, coordinates}
-    # Coordinates are the real coordinates (hmin, hmax) of the image in the Group
-    # print(results,"\n\n\n")
-    process_correction(root_dir, results, labels,overwrite=args.overwrite)
+    raise SystemExit(main())

annotating_by_label.py

@@ -1,256 +1,323 @@
-import sys
-import os
-import json
-import utils
-import shutil
+from __future__ import annotations
+
 import argparse
 import concurrent.futures
+import os
+from collections.abc import Sequence
+from pathlib import Path
+from typing import Any
+
 from PIL import Image, ImageDraw
 from reportlab.pdfgen import canvas
 
 import annotating
 import annotating_with_checks
-
+import utils
+from copienator import (
+    CliError,
+    EvaluationWorkspace,
+    ExitCode,
+    atomic_write_json,
+    atomic_write_text,
+    evaluation_parser,
+    execute,
+    read_json,
+    workspace_from_args,
+)
+from copienator.annotation_data import load_annotation_data
+from copienator.filesystem import staged_directory
 from utils import natural_key
 
-MAX_HEIGHT_PX = 25000 # Can be increased by 10%.
+MAX_HEIGHT_PX = 25000
+
 
 def render_item(item):
     student_id, label, content = item
-    pdf_path = content['pdf_path']
-    if not os.path.exists(pdf_path):
-        print("no pdf path for ", pdf_path)
+    pdf_path = Path(content["pdf_path"])
+    if not pdf_path.exists():
+        print(f"Warning: answer PDF not found: {pdf_path}")
         return None
-
-    base_img, _, _ = annotating.make_base_image(pdf_path)
-    cb_renderer = annotating_with_checks.CheckboxRenderer(label)
-
-    final_img, header_h = annotating.compose_label_image(
-        base_img, label, content['result'], content['coordinates'][0],
-        draw_callback=cb_renderer.callback,
+    base_image, _, _ = annotating.make_base_image(pdf_path)
+    checkbox_renderer = annotating_with_checks.CheckboxRenderer(label)
+    final_image, header_height = annotating.compose_label_image(
+        base_image,
+        label,
+        content["result"],
+        content["coordinates"][0],
+        draw_callback=checkbox_renderer.callback,
         more_right=True,
-        with_id=student_id
+        with_id=student_id,
     )
-    if final_img is None:
+    if final_image is None:
         return None
+    return (
+        student_id,
+        label,
+        final_image,
+        header_height,
+        checkbox_renderer.checkboxes,
+    )
 
-    return (student_id, label, final_img, header_h, cb_renderer.checkboxes)
 
-def save_batch(batch, prefix, group_id, root_dir, overwrite):
-    output_dir = os.path.join(root_dir, "BGnot", f"{prefix} G{group_id}")
-
-    if os.path.exists(output_dir):
-        if not overwrite:
-            print(f"Skipping {output_dir}: Output already exists.")
-            return
-        shutil.rmtree(output_dir)
-
-    print(f"Generating Group PDF: {prefix} G{group_id} ({len(batch)} elements)")
-    os.makedirs(output_dir)
-
-    max_w = max(item[2].width for item in batch)
-    total_h = sum(item[2].height for item in batch)
-    concat_img = Image.new("RGB", (max_w, total_h), "white")
-    draw = ImageDraw.Draw(concat_img)
-
-    final_json_map = []
-    bnote_entries = []
+def save_batch(batch, prefix, group_id, output_root: Path) -> None:
+    output_dir = output_root / f"{prefix} G{group_id}"
+    print(f"Generating group PDF: {prefix} G{group_id} ({len(batch)} elements)")
+    max_width = max(item[2].width for item in batch)
+    total_height = sum(item[2].height for item in batch)
+    concatenated = Image.new("RGB", (max_width, total_height), "white")
+    draw = ImageDraw.Draw(concatenated)
+    checkbox_map: list[dict[str, Any]] = []
+    bnote_entries: list[dict[str, Any]] = []
     current_y = 0
-    last_sid = None
+    previous_student = None
 
-    for sid, label, img, header_h, boxes in batch:
-        concat_img.paste(img, (0, current_y))
-
-        if sid != last_sid:
-            draw.rectangle([0, current_y, max_w, current_y + 4], fill="purple")
-        last_sid = sid
-
-        bnote_entries.append({
-            "id": sid,
+    for student_id, label, image, header_height, checkboxes in batch:
+        concatenated.paste(image, (0, current_y))
+        if student_id != previous_student:
+            draw.rectangle([0, current_y, max_width, current_y + 4], fill="purple")
+        previous_student = student_id
+        bnote_entries.append(
+            {
+                "id": student_id,
                 "label": label,
-            "header_height": header_h,
+                "header_height": header_height,
                 "hmin": current_y,
-            "hmax": current_y + img.height
-        })
+                "hmax": current_y + image.height,
+            }
+        )
+        for item in checkboxes:
+            box = item.get("final_box") or item.get("rel_box")
+            item["global_box"] = [
+                box[0],
+                box[1] + current_y,
+                box[2],
+                box[3] + current_y,
+            ]
+            item["student_id"] = student_id
+            checkbox_map.append(item)
+        current_y += image.height
 
-        for item in boxes:
-            b = item.get('final_box') or item.get('rel_box')
-            item['global_box'] = [b[0], b[1] + current_y, b[2], b[3] + current_y]
-            item['student_id'] = sid  # Required to map checkbox to the correct student
-            final_json_map.append(item)
+    with staged_directory(output_dir) as staging:
+        atomic_write_json(
+            staging / "bnote.json",
+            {"width": max_width, "height": total_height, "images": bnote_entries},
+        )
+        atomic_write_json(staging / "checkboxes.json", checkbox_map)
+        reference = staging / "Reference.jpg"
+        concatenated.save(reference, quality=90)
+        pdf_path = staging / "Concat.pdf"
+        pdf_canvas = canvas.Canvas(str(pdf_path), pagesize=(max_width, total_height))
+        pdf_canvas.drawImage(
+            str(reference),
+            0,
+            0,
+            width=max_width,
+            height=total_height,
+        )
+        pdf_canvas.save()
 
-        current_y += img.height
 
-    with open(os.path.join(output_dir, "bnote.json"), "w") as f:
-        json.dump({"width": max_w, "height": total_h, "images": bnote_entries}, f, indent=2)
+def _initial_label_groups(labels: list[str]) -> str:
+    groups: dict[str, list[str]] = {}
+    for label in labels:
+        key = label.split(" : ")[0] if " : " in label else label
+        groups.setdefault(key, []).append(label)
+    return "".join(",".join(items) + "\n" for items in groups.values())
 
-    with open(os.path.join(output_dir, "checkboxes.json"), "w") as f:
-        json.dump(final_json_map, f, indent=2)
 
-    temp_img_path = os.path.join(output_dir, "Reference.jpg")
-    concat_img.save(temp_img_path, quality=90)
-
-    pdf_path = os.path.join(output_dir, "Concat.pdf")
-    w, h = concat_img.size
-    c = canvas.Canvas(pdf_path, pagesize=(w, h))
-    c.drawImage(temp_img_path, 0, 0, width=w, height=h)
-    c.save()
-
-def main():
-    parser = argparse.ArgumentParser(description="Generate annotated PDFs grouped by labels.")
-    parser.add_argument("input_path", help="Directory containing Bnot structure")
-    parser.add_argument("--overwrite", action="store_true", help="Overwrite existing output files")
-    args = parser.parse_args()
-
-    root_dir = args.input_path
-    validated_labels = utils.read_all_labels(root_dir)
-    results = annotating.make_dictionary(root_dir)
-    label_groups = os.path.join(root_dir, "label_groups")
-    all_labels = os.path.join(root_dir, "labels")
-
-    if not os.path.exists(label_groups):
-        print(f"Warning: Labels file '{label_groups}' not found, making it out of '{all_labels}'")
-        if not os.path.exists(all_labels):
-            print(f"Error: {all_labels} not found.")
-            sys.exit(1)
-
-        lines = validated_labels
-
-        groups = {}
-        for line in lines:
-            # Key is the part before the colon, or the whole line if no colon
-            key = line.split(' : ')[0] if ' : ' in line else line
-            groups.setdefault(key, []).append(line)
-
-        with open(label_groups, 'w') as f:
-            for items in groups.values():
-                f.write(",".join(items) + "\n")
+def _load_label_groups(workspace: EvaluationWorkspace, labels: list[str]) -> list[list[str]]:
+    label_groups = workspace.root / "label_groups"
+    if not label_groups.exists():
+        atomic_write_text(label_groups, _initial_label_groups(labels))
+        print(f"Created {label_groups}; review the groups before continuing.")
         utils.edit_file_and_enter(label_groups)
+    known_labels = set(labels)
+    groups: list[list[str]] = []
+    unknown: set[str] = set()
+    for line in label_groups.read_text(encoding="utf-8").splitlines():
+        group = [label.strip() for label in line.split(",") if label.strip()]
+        unknown.update(label for label in group if label not in known_labels)
+        if group:
+            groups.append(group)
+    if unknown:
+        raise CliError(
+            "label_groups contains unknown labels: " + ", ".join(sorted(unknown))
+        )
+    return groups
 
-    with open(label_groups, "r") as f:
-        lines = [line.strip() for line in f if line.strip()]
 
-    bgnot_dir = os.path.join(root_dir, "BGnot")
-    if args.overwrite and os.path.exists(bgnot_dir):
-        shutil.rmtree(bgnot_dir)
-    os.makedirs(bgnot_dir, exist_ok=True)
-
-    used_prefixes = set()
-
-    previous_prefix = None
-    for line in lines:
-        labels = [l.strip() for l in line.split(',') if l.strip()]
-        safe_labels = [l.replace(":", "").strip() for l in line.split(',') if l.strip()]
-        if not labels:
-            continue
-
-        base_prefix = os.path.commonprefix(safe_labels).strip()
-
-        if base_prefix and previous_prefix is not None:
-            if natural_key(base_prefix) < natural_key(previous_prefix):
-                base_prefix_maybe = f"{safe_labels[0]}+"
-                if natural_key(base_prefix_maybe) > natural_key(previous_prefix):
-                    base_prefix = base_prefix_maybe
-
-        if not base_prefix:
-            base_prefix = "Group"
-
-        unique_prefix = base_prefix
-        if unique_prefix[-1] == "i":
-            unique_prefix = unique_prefix[:-1]
+def _unique_prefixes(groups: list[list[str]]) -> list[tuple[str, list[str]]]:
+    used: set[str] = set()
+    result: list[tuple[str, list[str]]] = []
+    previous: str | None = None
+    for labels in groups:
+        safe_labels = [label.replace(":", "").strip() for label in labels]
+        base = os.path.commonprefix(safe_labels).strip() or "Group"
+        if base and previous is not None and natural_key(base) < natural_key(previous):
+            candidate = f"{safe_labels[0]}+"
+            if natural_key(candidate) > natural_key(previous):
+                base = candidate
+        prefix = base.removesuffix("i")
         counter = 2
-        while unique_prefix in used_prefixes:
-            unique_prefix = f"{base_prefix}-{counter}"
+        while prefix in used:
+            prefix = f"{base}-{counter}"
             counter += 1
-        if counter == 2 and previous_prefix and previous_prefix in unique_prefix:
-            unique_prefix = f"{previous_prefix}-{counter}"
+        if counter == 2 and previous and previous in prefix:
+            prefix = f"{previous}-{counter}"
         elif counter == 2:
-            previous_prefix = unique_prefix
-
-        used_prefixes.add(unique_prefix)
-
-        existing_items = set()
-        max_existing_group = 0
+            previous = prefix
+        used.add(prefix)
+        result.append((prefix, labels))
+    return result
 
 
-        if not args.overwrite and os.path.exists(bgnot_dir):
-            for d in os.listdir(bgnot_dir):
-                if d.startswith(f"{unique_prefix} G"):
+def _existing_group_state(
+    output_root: Path,
+    prefix: str,
+) -> tuple[set[tuple[str, str]], int]:
+    existing_items: set[tuple[str, str]] = set()
+    maximum_group = 0
+    if not output_root.is_dir():
+        return existing_items, maximum_group
+    for directory in output_root.iterdir():
+        if not directory.is_dir() or not directory.name.startswith(f"{prefix} G"):
+            continue
         try:
-                        g_id = int(d.split(' G')[-1])
-                        max_existing_group = max(max_existing_group, g_id)
+            maximum_group = max(maximum_group, int(directory.name.split(" G")[-1]))
         except ValueError:
+            continue
+        metadata = directory / "bnote.json"
+        if not metadata.exists():
+            continue
+        loaded = read_json(metadata)
+        if not isinstance(loaded, dict):
+            raise TypeError(f"Expected a JSON object in {metadata}")
+        for image in loaded.get("images", []):
+            existing_items.add((str(image["id"]), str(image["label"])))
+    return existing_items, maximum_group
+
+
+def split_batches(rendered):
+    def split(maximum_height: float):
+        batches = []
+        current = []
+        current_height = 0
+        previous_student = None
+        for item in rendered:
+            student_id = item[0]
+            image_height = item[2].height
+            if (
+                current
+                and current_height + image_height > maximum_height
+                and student_id != previous_student
+            ):
+                batches.append(current)
+                current = []
+                current_height = 0
+            current.append(item)
+            current_height += image_height
+            previous_student = student_id
+        if current:
+            batches.append(current)
+        return batches
+
+    strict = split(MAX_HEIGHT_PX)
+    relaxed = split(1.1 * MAX_HEIGHT_PX)
+    return relaxed if len(relaxed) < len(strict) else strict
+
+
+def _generate_groups(
+    output_root: Path,
+    data,
+    groups: list[list[str]],
+    *,
+    resume: bool,
+) -> tuple[int, bool]:
+    generated = 0
+    problems = False
+    for prefix, labels in _unique_prefixes(groups):
+        existing_items, maximum_group = (
+            _existing_group_state(output_root, prefix) if resume else (set(), 0)
+        )
+        items = [
+            (student_id, label, student_labels[label])
+            for student_id, student_labels in data.items()
+            for label in labels
+            if label in student_labels and (student_id, label) not in existing_items
+        ]
+        if not items:
+            continue
+        items.sort(key=lambda item: (natural_key(item[0]), natural_key(item[1])))
+        with concurrent.futures.ThreadPoolExecutor(max_workers=2) as executor:
+            rendered = list(executor.map(render_item, items))
+        if any(item is None for item in rendered):
+            problems = True
+        successful = [item for item in rendered if item is not None]
+        for index, batch in enumerate(split_batches(successful), start=1):
+            save_batch(batch, prefix, maximum_group + index, output_root)
+            generated += 1
+    return generated, problems
+
+
+def run(workspace: EvaluationWorkspace, *, overwrite: bool = False) -> ExitCode:
+    workspace.require_files("labels", "correction.json")
+    workspace.require_directories("Copies", "Par label")
+    labels = utils.read_all_labels(workspace.root)
+    groups = _load_label_groups(workspace, labels)
+    loaded = load_annotation_data(workspace)
+    for warning in loaded.warnings:
+        print(f"Warning: {warning}")
+    if not loaded.data:
+        print("Warning: no annotation data was found.")
+        return ExitCode.PARTIAL
+
+    output_root = workspace.annotation_dir("grouped")
+    if overwrite:
+        class IncompleteGroupedOutput(Exception):
             pass
 
-                    bnote_path = os.path.join(bgnot_dir, d, "bnote.json")
-                    if os.path.exists(bnote_path):
-                        with open(bnote_path, "r") as bf:
-                            bdata = json.load(bf)
-                            for img in bdata.get("images", []):
-                                existing_items.add((img["id"], img["label"]))
+        try:
+            with staged_directory(output_root) as staging:
+                generated, problems = _generate_groups(
+                    staging,
+                    loaded.data,
+                    groups,
+                    resume=False,
+                )
+                if generated == 0 or problems or loaded.warnings:
+                    raise IncompleteGroupedOutput
+        except IncompleteGroupedOutput:
+            print("Warning: grouped overwrite was incomplete; previous BGnot was preserved.")
+            return ExitCode.PARTIAL
+    else:
+        output_root.mkdir(parents=True, exist_ok=True)
+        generated, problems = _generate_groups(
+            output_root,
+            loaded.data,
+            groups,
+            resume=True,
+        )
+        if problems:
+            return ExitCode.PARTIAL
+        if generated == 0:
+            print("No new grouped annotations were required.")
+    return ExitCode.PARTIAL if loaded.warnings else ExitCode.SUCCESS
 
-        items_to_render = []
-        for sid, lbls in results.items():
-            for lbl in labels:
-                if lbl in lbls:
-                    # Only add if it hasn't been generated yet
-                    if (sid, lbl) not in existing_items:
-                        items_to_render.append((sid, lbl, lbls[lbl]))
-        if not items_to_render:
-            continue
 
-        # Sort structurally: by student id and label
-        items_to_render.sort(key=lambda x: (natural_key(x[0]), natural_key(x[1])))
-        # Render images in parallel using the pre-existing lock & render function
-        with concurrent.futures.ThreadPoolExecutor(max_workers=2) as executor:
-            rendered = list(executor.map(render_item, items_to_render))
+def build_parser() -> argparse.ArgumentParser:
+    parser = evaluation_parser("Generate annotated PDFs grouped by labels.")
+    parser.add_argument("--overwrite", action="store_true", help="Replace BGnot safely")
+    return parser
 
-        rendered = [r for r in rendered if r is not None]
-        if not rendered:
-            continue
 
-        # Split into constrained height batches
-        batches = []
-        current_batch = []
-        current_h = 0
-        for r in rendered:
-            sid = r[0]
-            img_h = r[2].height
-            # Split if we exceed max height AND we are on a new student
-            if current_batch and current_h + img_h > MAX_HEIGHT_PX and sid != last_sid:
-                batches.append(current_batch)
-                current_batch = []
-                current_h = 0
-            current_batch.append(r)
-            current_h += img_h
-            last_sid = sid
-        if current_batch:
-            batches.append(current_batch)
+def main(argv: Sequence[str] | None = None) -> int:
+    parser = build_parser()
+    return execute(
+        parser,
+        argv,
+        lambda args: run(workspace_from_args(args), overwrite=args.overwrite),
+    )
 
-        batches2 = []
-        current_batch2 = []
-        current_h2 = 0
-        last_sid2 = None
-        for r in rendered:
-            sid = r[0]
-            img_h = r[2].height
-            # Split if we exceed max height AND we are on a new student
-            if current_batch2 and current_h2 + img_h > 1.1 *MAX_HEIGHT_PX \
-               and sid != last_sid2:
-                batches2.append(current_batch2)
-                current_batch2 = []
-                current_h2 = 0
-            current_batch2.append(r)
-            current_h2 += img_h
-            last_sid2 = sid
-        if current_batch2:
-            batches2.append(current_batch2)
-
-        if len(batches2) < len(batches):
-            batches = batches2
-
-        for i, batch in enumerate(batches, 1):
-            save_batch(batch, unique_prefix, max_existing_group + i, root_dir, args.overwrite)
 
 if __name__ == "__main__":
-    main()
+    raise SystemExit(main())

annotating_with_checks.py

@@ -1,283 +1,330 @@
-import sys
-import os
-import json
-import shutil
+from __future__ import annotations
+
+import argparse
 import concurrent.futures
-import threading
-import img2pdf
+import re
+from collections.abc import Sequence
+from pathlib import Path
+from typing import Any
+
+import matplotlib
+
+matplotlib.use("Agg")
+
+from PIL import Image, ImageFont
 from reportlab.pdfgen import canvas
 
-# Fix for Matplotlib in threads: Set backend to non-interactive 'Agg'
-import matplotlib
-matplotlib.use('Agg')
-
-from PIL import Image, ImageDraw, ImageFont
 import annotating
 import utils
-from annotating import MARGIN_LEFT, ANNOT_WIDTH
+from copienator import (
+    CliError,
+    EvaluationWorkspace,
+    ExitCode,
+    atomic_write_json,
+    execute,
+    read_json,
+    target_parser,
+    workspace_from_target,
+)
+from copienator.annotation_data import load_annotation_data
+from copienator.filesystem import staged_directory
+from utils import natural_key
 
-# Global lock for Matplotlib/Latex rendering to prevent race conditions
-LATEX_LOCK = threading.Lock()
-DPI = 100
 BOX_SIZE = 30
 SCORE_BOX_SIZE = 40
-SCORES = [x * 0.5 for x in range(10)]  # 0.0 to 4.5
+SCORES = [value * 0.5 for value in range(10)]
+EXPECTED_OUTPUTS = ("bnote.json", "checkboxes.json", "Reference.jpg", "Concat.pdf")
 
 try:
     CHECKBOX_FONT = ImageFont.truetype("DejaVuSans.ttf", 20)
-except IOError:
+except OSError:
     try:
         CHECKBOX_FONT = ImageFont.truetype("arial.ttf", 20)
-    except IOError:
+    except OSError:
         CHECKBOX_FONT = ImageFont.load_default()
 
+
 def draw_checkbox(draw, x, y, size=BOX_SIZE, label=None, fill="white"):
     if label:
-        draw.text((x - BOX_SIZE-5, y + 2), str(label), fill="black", font=CHECKBOX_FONT)
+        draw.text((x - BOX_SIZE - 5, y + 2), str(label), fill="black", font=CHECKBOX_FONT)
     draw.rectangle([x, y, x + size, y + size], fill=fill, outline="black", width=2)
-
     return [x, y, x + size, y + size]
 
-def safe_render_latex(*args, **kwargs):
-    """Thread-safe wrapper for latex rendering."""
-    # with LATEX_LOCK:
-    #     return annotating.render_latex_text(*args, **kwargs)
-    return annotating.render_real_latex_text(*args, **kwargs)
 
 class CheckboxRenderer:
     def __init__(self, label_name):
         self.label = label_name
-        self.checkboxes = [] # List of {type, box, etc.}
+        self.checkboxes = []
 
     def callback(self, kind, draw, pos, meta):
-        """
-        Called by compose_label_image during rendering.
-        pos contains {x, y, w, h} or {box}.
-        meta contains {data, index, etc.}
-        """
         if kind == "header_item":
-            # meta['data'] is either result object (for score) or feedback object
             if meta.get("type") == "score":
-                # Draw score boxes
-                start_x = pos['w'] + 20
-                for val in SCORES:
-                    box = draw_checkbox(draw, start_x, pos['y'] + 25,
-                                        SCORE_BOX_SIZE, str(val))
-                    self.checkboxes.append({
-                        "type": "score", "label": self.label, "value": val,
-                        "rel_box": box # Will be adjusted for global Y later
-                    })
-                    start_x += SCORE_BOX_SIZE + 45
-
-                start_x += SCORE_BOX_SIZE + 60
-                box = draw_checkbox(draw, start_x, pos['y'] + 25, SCORE_BOX_SIZE, "clr")
-                self.checkboxes.append({
-                    "type": "clear_all", "label": self.label,
-                    "rel_box": box
-                })
-
-            elif meta.get("type") == "global_fb":
-                # Draw delete box for global feedback
-                bx = pos['w'] - BOX_SIZE - 5
-                by = pos['y'] + 5
-                box = draw_checkbox(draw, bx, by, BOX_SIZE)
-                self.checkboxes.append({
-                    "type": "del_global", "label": self.label, "index": meta["index"],
-                    "rel_box": box, "text_preview": meta["data"]["text"][:20]
-                })
-
-        elif kind == "local_rect":
-            # Delete rect checkbox
-            b = pos['box'] # [xmin, ymin, xmax, ymax]
-            box = draw_checkbox(draw, b[2] - BOX_SIZE, b[1], BOX_SIZE)
-            self.checkboxes.append({
-                "type": "del_local_rect", "label": self.label, "index": meta["index"],
-                "final_box": box, "text_preview": meta["data"]["text"][:20]
-            })
-
-        elif kind == "local_text":
-             # Delete whole local feedback checkbox
-             bx = pos['x'] + pos['w'] - BOX_SIZE
-             by = pos['y']
-             box = draw_checkbox(draw, bx, by, BOX_SIZE)
-             self.checkboxes.append({
-                "type": "del_local", "label": self.label, "index": meta["index"],
-                "final_box": box, "text_preview": meta["data"]["text"][:20]
-             })
-
-from utils import natural_key
-
-def process_student(args):
-    """Thread worker: Processes one student."""
-    root_dir, student_id, labels, overwrite, sub_folder = args
-
-    output_dir = os.path.join(root_dir, sub_folder, f"Copie{student_id}")
-
-    if os.path.exists(output_dir):
-        if not overwrite:
-            print(f"Skipping {student_id}: Output already exists.")
-            return
-        shutil.rmtree(output_dir)
-
-    print(f"Generating Checkable PDF for: {student_id}")
-    os.makedirs(output_dir)
-
-    label_images = []
-    # ... (rest of the function remains exactly the same)
-    all_checkboxes = []
-    bnote_entries = [] # For bnote.json
-
-    sorted_labels = sorted(labels.items(), key=lambda x: natural_key(x[0]))
-
-    for label, content in sorted_labels:
-        pdf_path = content['pdf_path']
-        if not os.path.exists(pdf_path): continue
-
-        base_img, _, _ = annotating.make_base_image(pdf_path)
-
-        # Initialize the hook
-        cb_renderer = CheckboxRenderer(label)
-
-        # Render using the shared engine
-        final_img, header_h = annotating.compose_label_image(
-            base_img, label, content['result'], content['coordinates'][0],
-            draw_callback=cb_renderer.callback
+                start_x = pos["w"] + 20
+                for value in SCORES:
+                    box = draw_checkbox(
+                        draw,
+                        start_x,
+                        pos["y"] + 25,
+                        SCORE_BOX_SIZE,
+                        str(value),
+                    )
+                    self.checkboxes.append(
+                        {
+                            "type": "score",
+                            "label": self.label,
+                            "value": value,
+                            "rel_box": box,
+                        }
+                    )
+                    start_x += SCORE_BOX_SIZE + 45
+                start_x += SCORE_BOX_SIZE + 60
+                box = draw_checkbox(
+                    draw,
+                    start_x,
+                    pos["y"] + 25,
+                    SCORE_BOX_SIZE,
+                    "clr",
+                )
+                self.checkboxes.append(
+                    {"type": "clear_all", "label": self.label, "rel_box": box}
+                )
+            elif meta.get("type") == "global_fb":
+                box = draw_checkbox(
+                    draw,
+                    pos["w"] - BOX_SIZE - 5,
+                    pos["y"] + 5,
+                    BOX_SIZE,
+                )
+                self.checkboxes.append(
+                    {
+                        "type": "del_global",
+                        "label": self.label,
+                        "index": meta["index"],
+                        "rel_box": box,
+                        "text_preview": meta["data"]["text"][:20],
+                    }
+                )
+        elif kind == "local_rect":
+            rectangle = pos["box"]
+            box = draw_checkbox(
+                draw,
+                rectangle[2] - BOX_SIZE,
+                rectangle[1],
+                BOX_SIZE,
+            )
+            self.checkboxes.append(
+                {
+                    "type": "del_local_rect",
+                    "label": self.label,
+                    "index": meta["index"],
+                    "final_box": box,
+                    "text_preview": meta["data"]["text"][:20],
+                }
+            )
+        elif kind == "local_text":
+            box = draw_checkbox(
+                draw,
+                pos["x"] + pos["w"] - BOX_SIZE,
+                pos["y"],
+                BOX_SIZE,
+            )
+            self.checkboxes.append(
+                {
+                    "type": "del_local",
+                    "label": self.label,
+                    "index": meta["index"],
+                    "final_box": box,
+                    "text_preview": meta["data"]["text"][:20],
+                }
             )
-        if final_img == None:
-                continue
 
-        label_images.append(final_img)
-        all_checkboxes.append(cb_renderer.checkboxes)
-        bnote_entries.append({
+
+def _output_complete(output_dir: Path) -> bool:
+    return all((output_dir / name).is_file() for name in EXPECTED_OUTPUTS)
+
+
+def _render_student(
+    workspace: EvaluationWorkspace,
+    student_id: str,
+    labels: dict[str, dict[str, Any]],
+    *,
+    overwrite: bool,
+    output_mode: str,
+) -> str:
+    output_dir = workspace.annotation_dir(output_mode) / f"Copie{student_id}"
+    if _output_complete(output_dir) and not overwrite:
+        print(f"Skipping {student_id}: output is complete.")
+        return "skipped"
+
+    print(f"Generating checkable PDF for: {student_id}")
+    label_images: list[Image.Image] = []
+    checkbox_groups: list[list[dict[str, Any]]] = []
+    bnote_entries: list[dict[str, Any]] = []
+    problems = False
+
+    for label, content in sorted(labels.items(), key=lambda item: natural_key(item[0])):
+        pdf_path = Path(content["pdf_path"])
+        if not pdf_path.exists():
+            print(f"Warning: answer PDF not found: {pdf_path}")
+            problems = True
+            continue
+        base_image, _, _ = annotating.make_base_image(pdf_path)
+        checkbox_renderer = CheckboxRenderer(label)
+        final_image, header_height = annotating.compose_label_image(
+            base_image,
+            label,
+            content["result"],
+            content["coordinates"][0],
+            draw_callback=checkbox_renderer.callback,
+        )
+        if final_image is None:
+            continue
+        label_images.append(final_image)
+        checkbox_groups.append(checkbox_renderer.checkboxes)
+        bnote_entries.append(
+            {
                 "id": student_id,
                 "label": label,
-            "header_height": header_h,
-            # hmin/hmax will be filled during concatenation
-            "img_h": final_img.height
-        })
-
-    if not label_images: return
-
-    # Concatenate
-    max_w = max(i.width for i in label_images)
-    total_h = sum(i.height for i in label_images)
-    concat_img = Image.new("RGB", (max_w, total_h), "white")
-
-    final_json_map = []
-    current_y = 0
-
-    for idx, (img, boxes) in enumerate(zip(label_images, all_checkboxes)):
-        concat_img.paste(img, (0, current_y))
-
-        bnote_entries[idx]["hmin"] = current_y
-        bnote_entries[idx]["hmax"] = current_y + img.height
-        del bnote_entries[idx]["img_h"] # Clean up temp data
-
-        # Adjust coordinates for concatenated image
-        for item in boxes:
-            # item might have 'rel_box' (header) or 'final_box' (local)
-            # Both were relative to the label image. We just add current_y.
-            b = item.get('final_box') or item.get('rel_box')
-            item['global_box'] = [b[0], b[1] + current_y, b[2], b[3] + current_y]
-            final_json_map.append(item)
-
-        current_y += img.height
-
-    bnote_data = {
-        "width": max_w,
-        "height": total_h,
-        "images": bnote_entries
+                "header_height": header_height,
+                "img_h": final_image.height,
             }
-    with open(os.path.join(output_dir, "bnote.json"), "w") as f:
-        json.dump(bnote_data, f, indent=2)
+        )
 
-    with open(os.path.join(output_dir, "checkboxes.json"), "w") as f:
-        json.dump(final_json_map, f, indent=2)
+    if not label_images:
+        print(f"Warning: no annotations could be rendered for Copie{student_id}")
+        return "partial"
 
-    temp_img_path = os.path.join(output_dir, "Reference.jpg") # Can't use png here
-    concat_img.save(temp_img_path, quality=90)
+    max_width = max(image.width for image in label_images)
+    total_height = sum(image.height for image in label_images)
+    concatenated = Image.new("RGB", (max_width, total_height), "white")
+    checkbox_map: list[dict[str, Any]] = []
+    current_y = 0
+    for index, (image, checkboxes) in enumerate(
+        zip(label_images, checkbox_groups, strict=True)
+    ):
+        concatenated.paste(image, (0, current_y))
+        bnote_entries[index]["hmin"] = current_y
+        bnote_entries[index]["hmax"] = current_y + image.height
+        del bnote_entries[index]["img_h"]
+        for item in checkboxes:
+            box = item.get("final_box") or item.get("rel_box")
+            item["global_box"] = [
+                box[0],
+                box[1] + current_y,
+                box[2],
+                box[3] + current_y,
+            ]
+            checkbox_map.append(item)
+        current_y += image.height
 
-    pdf_path = os.path.join(output_dir, "Concat.pdf")
-    w, h = concat_img.size
-    c = canvas.Canvas(pdf_path, pagesize=(w, h))
-    c.drawImage(temp_img_path, 0, 0, width=w, height=h)
-    c.save()
+    with staged_directory(output_dir) as staging:
+        atomic_write_json(
+            staging / "bnote.json",
+            {"width": max_width, "height": total_height, "images": bnote_entries},
+        )
+        atomic_write_json(staging / "checkboxes.json", checkbox_map)
+        reference = staging / "Reference.jpg"
+        concatenated.save(reference, quality=90)
+        pdf_path = staging / "Concat.pdf"
+        pdf_canvas = canvas.Canvas(str(pdf_path), pagesize=(max_width, total_height))
+        pdf_canvas.drawImage(
+            str(reference),
+            0,
+            0,
+            width=max_width,
+            height=total_height,
+        )
+        pdf_canvas.save()
+    return "partial" if problems else "success"
+
+
+def _copy_id_from_target(workspace: EvaluationWorkspace, target: Path) -> str | None:
+    if target == workspace.root:
+        return None
+    match = re.search(r"Copie(\d+)", target.name)
+    if match is None:
+        raise CliError(f"Could not extract a copy id from target: {target}")
+    return match.group(1)
+
+
+def _load_refaire(workspace: EvaluationWorkspace):
+    workspace.require_files("refaire.json")
+    loaded = read_json(workspace.refaire_file)
+    if not isinstance(loaded, list):
+        raise CliError("refaire.json must contain a JSON array")
+    return loaded
+
+
+def run(
+    workspace: EvaluationWorkspace,
+    target: Path,
+    *,
+    overwrite: bool = False,
+    refaire: bool = False,
+) -> ExitCode:
+    workspace.require_files("labels", "correction.json")
+    workspace.require_directories("Copies", "Par label")
+    utils.read_all_labels(workspace.root)
+    copy_id = _copy_id_from_target(workspace, target)
+    refaire_list = _load_refaire(workspace) if refaire else None
+    loaded = load_annotation_data(
+        workspace,
+        refaire_list=refaire_list,
+        copy_id=None if refaire else copy_id,
+    )
+    for warning in loaded.warnings:
+        print(f"Warning: {warning}")
+    if not loaded.data:
+        print("Warning: no annotation data was found.")
+        return ExitCode.PARTIAL
+
+    output_mode = "refaire" if refaire else "checks"
+    tasks = sorted(loaded.data.items(), key=lambda item: natural_key(item[0]))
+    statuses: list[str] = []
+    with concurrent.futures.ThreadPoolExecutor(max_workers=2) as executor:
+        futures = [
+            executor.submit(
+                _render_student,
+                workspace,
+                student_id,
+                labels,
+                overwrite=overwrite,
+                output_mode=output_mode,
+            )
+            for student_id, labels in tasks
+        ]
+        for future in futures:
+            statuses.append(future.result())
+    if loaded.warnings or "partial" in statuses:
+        return ExitCode.PARTIAL
+    return ExitCode.SUCCESS
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = target_parser("Generate annotated PDFs with checkboxes.")
+    parser.add_argument("--overwrite", action="store_true", help="Replace existing outputs")
+    parser.add_argument(
+        "--refaire",
+        action="store_true",
+        help="Process only entries from refaire.json",
+    )
+    return parser
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    parser = build_parser()
+
+    def handler(args: argparse.Namespace) -> ExitCode:
+        workspace, target = workspace_from_target(args)
+        return run(
+            workspace,
+            target,
+            overwrite=args.overwrite,
+            refaire=args.refaire,
+        )
+
+    return execute(parser, argv, handler)
 
-import argparse # Added
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Generate annotated PDFs.")
-    parser.add_argument("input_path", help="Directory or specific file path")
-    parser.add_argument("--overwrite", action="store_true", help="Overwrite existing output files")
-    parser.add_argument("--refaire", action="store_true", help="Process only copies/labels defined in refaire.json") # ADD THIS LINE
-
-
-    args = parser.parse_args()
-
-    input_path = args.input_path
-    overwrite = args.overwrite # Capture flag
-    target_id = None
-
-    # Detect if input is a specific file
-    if os.path.isfile(input_path):
-        root_dir = os.path.dirname(input_path) or "."
-        # Extract ID from filename (e.g., Copie40.pdf -> 40)
-        match = re.search(r'Copie(\d+)', os.path.basename(input_path))
-        if match:
-            target_id = match.group(1)
-        else:
-            print("Error: Could not extract student ID from filename.")
-            sys.exit(1)
-    else:
-        root_dir = input_path
-
-    if os.path.exists(os.path.join(root_dir, "labels")):
-        utils.read_all_labels(root_dir)
-
-    if not args.refaire:
-        results = annotating.make_dictionary(root_dir)
-
-    if args.refaire:
-        refaire_path = os.path.join(root_dir, "refaire.json")
-        if os.path.exists(refaire_path):
-            with open(refaire_path, "r", encoding="utf-8") as f:
-                refaire_list = json.load(f)
-            results = annotating.make_dictionary(root_dir,
-                                                 refaire=True,refaire_list=refaire_list)
-
-            filtered_results = {}
-            for copie_name, labels_to_redo in refaire_list:
-                sid = copie_name.replace("Copie", "") # Extract "01" from "Copie01"
-                if sid in results:
-                    if not labels_to_redo:
-                        # Empty list: keep all labels for this Copie
-                        filtered_results[sid] = results[sid]
-                    else:
-                        # Keep only the requested labels
-                        filtered_results[sid] = {
-                            lbl: data for lbl, data in results[sid].items()
-                            if lbl in labels_to_redo
-                        }
-            results = filtered_results
-        else:
-            print(f"Warning: --refaire flag used, but {refaire_path} not found.")
-    elif target_id:
-        if target_id in results:
-            results = {target_id: results[target_id]}
-        else:
-            print(f"Student ID {target_id} not found in directory scan.")
-            results = {}
-
-    sub_folder = "BRnot" if args.refaire else "Bnot"
-
-    tasks = sorted([(root_dir, sid, lbls, overwrite, sub_folder)
-                    for sid, lbls in results.items()])
-
-    with concurrent.futures.ThreadPoolExecutor(max_workers=2) as executor:
-        results = executor.map(process_student, tasks)
-        try:
-            for _ in results:
-                pass
-        except Exception:
-            import traceback
-            traceback.print_exc()
+    raise SystemExit(main())

copienator/__init__.py

@@ -7,7 +7,9 @@ from .cli import (
     evaluation_workspace,
     execute,
     standard_parser,
+    target_parser,
     workspace_from_args,
+    workspace_from_target,
 )
 from .json_io import (
     JsonLockTimeout,
@@ -37,5 +39,7 @@ __all__ = [
     "execute",
     "read_json",
     "standard_parser",
+    "target_parser",
     "workspace_from_args",
+    "workspace_from_target",
 ]

copienator/annotation_data.py

@@ -0,0 +1,201 @@
+from __future__ import annotations
+
+import copy
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+from PIL import Image
+
+from .json_io import read_json
+from .workspace import EvaluationWorkspace
+
+AnnotationData = dict[str, dict[str, dict[str, Any]]]
+RefaireList = list[list[Any]]
+
+
+@dataclass(frozen=True, slots=True)
+class GroupCoordinates:
+    minimum: int
+    maximum: int
+    width: int
+    height: int
+
+
+@dataclass(slots=True)
+class AnnotationLoadResult:
+    data: AnnotationData
+    warnings: list[str]
+
+
+def _coordinate_index(
+    workspace: EvaluationWorkspace,
+) -> tuple[dict[tuple[str, str], GroupCoordinates], list[str]]:
+    index: dict[tuple[str, str], GroupCoordinates] = {}
+    warnings: list[str] = []
+    if not workspace.groups_dir.is_dir():
+        return index, [f"Group directory not found: {workspace.groups_dir}"]
+
+    for metadata_path in sorted(workspace.groups_dir.glob("*/Group_*.json")):
+        image_path = metadata_path.with_suffix(".jpg")
+        try:
+            entries = read_json(metadata_path)
+            if not isinstance(entries, list):
+                raise TypeError("expected a JSON array")
+            with Image.open(image_path) as image:
+                width, height = image.size
+            for entry in entries:
+                copy_id = str(entry[0])
+                minimum = int(entry[1])
+                maximum = int(entry[2])
+                label = str(entry[4])
+                index.setdefault(
+                    (label, copy_id),
+                    GroupCoordinates(minimum, maximum, width, height),
+                )
+        except (IndexError, OSError, TypeError, ValueError) as exc:
+            warnings.append(f"Could not read group metadata {metadata_path}: {exc}")
+    return index, warnings
+
+
+def _scaled_result(result: dict[str, Any], coordinates: GroupCoordinates | None):
+    scaled = copy.deepcopy(result)
+    if coordinates is None:
+        return scaled
+    for feedback in scaled.get("feedback", []):
+        box = feedback.get("box_2d")
+        if not box or len(box) != 4:
+            continue
+        box[0] = int(box[0] * coordinates.height) // 1000
+        box[2] = int(box[2] * coordinates.height) // 1000
+        box[1] = int(box[1] * coordinates.width) // 1000
+        box[3] = int(box[3] * coordinates.width) // 1000
+    return scaled
+
+
+def _answer_pdf(
+    workspace: EvaluationWorkspace,
+    copy_id: str,
+    label: str,
+    suffix: str = "",
+) -> Path:
+    copy_dir = workspace.copies_dir / f"Copie{copy_id}"
+    preferred = copy_dir / f"{label}{suffix}.pdf"
+    if preferred.exists():
+        return preferred
+    for candidate in (
+        copy_dir / f"{label}.pdf",
+        copy_dir / f"{label}_new.pdf",
+    ):
+        if candidate.exists():
+            return candidate
+    return preferred
+
+
+def _dummy_entry(
+    workspace: EvaluationWorkspace,
+    copy_id: str,
+    label: str,
+) -> dict[str, Any]:
+    return {
+        "pdf_path": _answer_pdf(workspace, copy_id, label),
+        "result": {
+            "score": 0.0,
+            "feedback": [],
+            "error": "non traité",
+        },
+        "coordinates": (0, 0),
+        "issues": ["No correction result was available for this answer."],
+    }
+
+
+def _apply_refaire_filter(
+    workspace: EvaluationWorkspace,
+    data: AnnotationData,
+    refaire_list: RefaireList,
+    warnings: list[str],
+) -> AnnotationData:
+    filtered: AnnotationData = {}
+    for raw_entry in refaire_list:
+        if not isinstance(raw_entry, list) or len(raw_entry) != 2:
+            warnings.append(f"Ignoring malformed refaire entry: {raw_entry!r}")
+            continue
+        copy_name, requested_labels = raw_entry
+        copy_id = str(copy_name).removeprefix("Copie")
+        available = data.get(copy_id, {})
+        if not requested_labels:
+            filtered[copy_id] = dict(available)
+            continue
+        selected: dict[str, dict[str, Any]] = {}
+        for raw_label in requested_labels:
+            label = str(raw_label)
+            selected[label] = (
+                available[label]
+                if label in available
+                else _dummy_entry(workspace, copy_id, label)
+            )
+        filtered[copy_id] = selected
+    return filtered
+
+
+def load_annotation_data(
+    workspace: EvaluationWorkspace,
+    *,
+    refaire_list: RefaireList | None = None,
+    copy_id: str | None = None,
+) -> AnnotationLoadResult:
+    workspace.require_files("correction.json")
+    corrections = read_json(workspace.correction_file)
+    if not isinstance(corrections, dict):
+        raise TypeError("correction.json must contain a JSON object")
+
+    coordinate_index, warnings = _coordinate_index(workspace)
+    data: AnnotationData = {}
+    for label, raw_batches in corrections.items():
+        if not isinstance(raw_batches, list):
+            warnings.append(f"Ignoring malformed correction batches for {label!r}")
+            continue
+        for raw_batch in raw_batches:
+            if not isinstance(raw_batch, list):
+                warnings.append(f"Ignoring malformed correction batch for {label!r}")
+                continue
+            for item in raw_batch:
+                if not isinstance(item, dict) or not isinstance(item.get("result"), dict):
+                    warnings.append(f"Ignoring malformed correction item for {label!r}")
+                    continue
+                student_id = str(item.get("id", ""))
+                if not student_id:
+                    warnings.append(f"Ignoring correction item without an id for {label!r}")
+                    continue
+                result = item["result"]
+                suffix = str(result.get("suffix", ""))
+                if suffix == "_old":
+                    continue
+                coordinates = coordinate_index.get((str(label), student_id))
+                issues: list[str] = []
+                if coordinates is None:
+                    issues.append("Group coordinates were not found.")
+                pdf_path = _answer_pdf(workspace, student_id, str(label), suffix)
+                if not pdf_path.exists():
+                    issues.append(f"Answer PDF not found: {pdf_path}")
+                data.setdefault(student_id, {})[str(label)] = {
+                    "pdf_path": pdf_path,
+                    "result": _scaled_result(result, coordinates),
+                    "coordinates": (
+                        (coordinates.minimum, coordinates.maximum)
+                        if coordinates is not None
+                        else (0, 0)
+                    ),
+                    "issues": issues,
+                }
+                warnings.extend(
+                    f"Copie{student_id} {label}: {issue}" for issue in issues
+                )
+
+    if refaire_list is not None:
+        data = _apply_refaire_filter(workspace, data, refaire_list, warnings)
+    if copy_id is not None:
+        data = {copy_id: data[copy_id]} if copy_id in data else {}
+        if not data:
+            warnings.append(f"Copy id {copy_id} was not found in correction.json")
+    return AnnotationLoadResult(data, warnings)

copienator/cli.py

@@ -50,6 +50,16 @@ def evaluation_parser(description: str) -> argparse.ArgumentParser:
     return parser
 
 
+def target_parser(description: str) -> argparse.ArgumentParser:
+    parser = standard_parser(description)
+    parser.add_argument(
+        "target",
+        type=Path,
+        help="Evaluation directory or nested file to process",
+    )
+    return parser
+
+
 def evaluation_workspace(
     path: str | Path,
     *,
@@ -77,6 +87,21 @@ def workspace_from_args(
     return evaluation_workspace(args.evaluation, repository=repository)
 
 
+def workspace_from_target(
+    args: argparse.Namespace,
+    *,
+    repository: str | Path | None = None,
+) -> tuple[EvaluationWorkspace, Path]:
+    target = Path(args.target).expanduser().resolve()
+    if not target.exists():
+        raise CliError(f"Target does not exist: {target}", ExitCode.INVALID_WORKSPACE)
+    repository_path = Path(repository) if repository is not None else None
+    if target.is_dir() and EvaluationWorkspace.looks_like_evaluation(target):
+        return EvaluationWorkspace(target, repository_path), target
+    workspace = EvaluationWorkspace.discover(target, repository=repository_path)
+    return workspace, target
+
+
 def execute(
     parser: argparse.ArgumentParser,
     argv: Sequence[str] | None,

copienator/filesystem.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+import shutil
+import uuid
+from contextlib import contextmanager
+from pathlib import Path
+
+
+def _remove_path(path: Path) -> None:
+    if path.is_symlink() or path.is_file():
+        path.unlink()
+    elif path.exists():
+        shutil.rmtree(path)
+
+
+@contextmanager
+def staged_directory(destination: str | Path):
+    """Build a directory beside its destination and replace on success."""
+    target = Path(destination)
+    target.parent.mkdir(parents=True, exist_ok=True)
+    token = uuid.uuid4().hex
+    staging = target.with_name(f".{target.name}.{token}.tmp")
+    backup = target.with_name(f".{target.name}.{token}.backup")
+    staging.mkdir()
+    committed = False
+    try:
+        yield staging
+        if target.exists():
+            target.replace(backup)
+        try:
+            staging.replace(target)
+            committed = True
+        except Exception:
+            if backup.exists() and not target.exists():
+                backup.replace(target)
+            raise
+        if backup.exists():
+            _remove_path(backup)
+    finally:
+        if staging.exists():
+            _remove_path(staging)
+        if not committed and backup.exists() and not target.exists():
+            backup.replace(target)

tests/test_gui_core.py

@@ -13,6 +13,7 @@ from contextlib import redirect_stderr
 from pathlib import Path
 from unittest.mock import patch
 
+from PIL import Image
 from pypdf import PdfReader, PdfWriter
 
 from copienator import (
@@ -22,7 +23,10 @@ from copienator import (
     atomic_update_json,
     atomic_write_json,
     read_json,
+    workspace_from_target,
 )
+from copienator.annotation_data import AnnotationLoadResult, load_annotation_data
+from copienator.filesystem import staged_directory
 from copienator_gui.app import process_status
 from copienator_gui.diagnostics import collect_diagnostics
 from copienator_gui.runner import ProcessRunner
@@ -156,10 +160,95 @@ class AtomicJsonTests(unittest.TestCase):
             self.assertEqual(persisted["steps"]["labels"]["status"], "success")
 
 
+class AnnotationDataTests(unittest.TestCase):
+    def test_loader_indexes_coordinates_without_mutating_correction(self) -> None:
+        with tempfile.TemporaryDirectory() as directory:
+            evaluation = Path(directory) / "Exam"
+            copy_dir = evaluation / "Copies" / "Copie01"
+            group_dir = evaluation / "Par label" / "Ex 1"
+            copy_dir.mkdir(parents=True)
+            group_dir.mkdir(parents=True)
+            (copy_dir / "Ex 1_new.pdf").write_bytes(b"pdf")
+            correction = {
+                "Ex 1": [
+                    [
+                        {
+                            "id": "01",
+                            "result": {
+                                "suffix": "_new",
+                                "feedback": [{"text": "x", "box_2d": [100, 200, 300, 400]}],
+                            },
+                        }
+                    ]
+                ]
+            }
+            atomic_write_json(evaluation / "correction.json", correction)
+            atomic_write_json(
+                group_dir / "Group_1.json",
+                [["01", 10, 90, 1.0, "Ex 1"]],
+            )
+            Image.new("RGB", (100, 200), "white").save(group_dir / "Group_1.jpg")
+
+            loaded = load_annotation_data(EvaluationWorkspace(evaluation))
+            item = loaded.data["01"]["Ex 1"]
+            self.assertEqual(item["pdf_path"], copy_dir / "Ex 1_new.pdf")
+            self.assertEqual(item["coordinates"], (10, 90))
+            self.assertEqual(item["result"]["feedback"][0]["box_2d"], [20, 20, 60, 40])
+            self.assertEqual(read_json(evaluation / "correction.json"), correction)
+            self.assertEqual(loaded.warnings, [])
+
+    def test_refaire_filter_adds_a_missing_correction_entry(self) -> None:
+        with tempfile.TemporaryDirectory() as directory:
+            evaluation = Path(directory) / "Exam"
+            copy_dir = evaluation / "Copies" / "Copie01"
+            copy_dir.mkdir(parents=True)
+            (evaluation / "Par label").mkdir()
+            (copy_dir / "Ex 2.pdf").write_bytes(b"pdf")
+            atomic_write_json(evaluation / "correction.json", {})
+
+            loaded = load_annotation_data(
+                EvaluationWorkspace(evaluation),
+                refaire_list=[["Copie01", ["Ex 2"]]],
+            )
+            item = loaded.data["01"]["Ex 2"]
+            self.assertEqual(item["pdf_path"], copy_dir / "Ex 2.pdf")
+            self.assertEqual(item["result"]["error"], "non traité")
+
+    def test_staged_directory_preserves_then_replaces_destination(self) -> None:
+        with tempfile.TemporaryDirectory() as directory:
+            destination = Path(directory) / "output"
+            destination.mkdir()
+            (destination / "state.txt").write_text("old", encoding="utf-8")
+
+            with self.assertRaises(RuntimeError), staged_directory(
+                destination
+            ) as staging:
+                (staging / "state.txt").write_text("broken", encoding="utf-8")
+                raise RuntimeError("rendering failed")
+            self.assertEqual(
+                (destination / "state.txt").read_text(encoding="utf-8"), "old"
+            )
+
+            with staged_directory(destination) as staging:
+                (staging / "state.txt").write_text("new", encoding="utf-8")
+            self.assertEqual(
+                (destination / "state.txt").read_text(encoding="utf-8"), "new"
+            )
+            leftovers = [path for path in destination.parent.iterdir() if path.name.startswith(".output.")]
+            self.assertEqual(leftovers, [])
+
+
 class StandardCliTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls) -> None:
         cls.modules = {
+            "annotating": load_script_module("annotating.py", "annotating"),
+            "annotating_with_checks": load_script_module(
+                "annotating_with_checks.py", "annotating_with_checks"
+            ),
+            "annotating_by_label": load_script_module(
+                "annotating_by_label.py", "annotating_by_label"
+            ),
             "copies_tools": load_script_module(
                 "copies_tools.py", "copienator_copies_tools_test"
             ),
@@ -192,6 +281,9 @@ class StandardCliTests(unittest.TestCase):
                 "resolve_manual": [missing],
                 "verify_groups": [missing],
                 "copies_tools": ["rotate", missing],
+                "annotating": [missing],
+                "annotating_with_checks": [missing],
+                "annotating_by_label": [missing],
             }
             for name, arguments in invocations.items():
                 with self.subTest(script=name), redirect_stderr(io.StringIO()):
@@ -259,6 +351,21 @@ class StandardCliTests(unittest.TestCase):
                 "default",
                 {"target": evaluation},
             ),
+            "annotating": (
+                "annotation",
+                "simple",
+                {"target": evaluation, "overwrite": True},
+            ),
+            "annotating_with_checks": (
+                "annotation",
+                "checks",
+                {"target": evaluation, "overwrite": True, "refaire": True},
+            ),
+            "annotating_by_label": (
+                "annotation",
+                "grouped",
+                {"target": evaluation, "overwrite": True},
+            ),
         }
         for module_name, (step_id, variant_id, values) in cases.items():
             step = steps[step_id]
@@ -266,7 +373,8 @@ class StandardCliTests(unittest.TestCase):
             command = build_command(REPOSITORY, step, variant, values, evaluation)
             with self.subTest(script=module_name):
                 parsed = self.modules[module_name].build_parser().parse_args(command[3:])
-                self.assertEqual(str(parsed.evaluation), evaluation)
+                parsed_path = getattr(parsed, "evaluation", None) or parsed.target
+                self.assertEqual(str(parsed_path), evaluation)
 
         for step_id in ("rotate", "rename"):
             step = steps[step_id]
@@ -458,6 +566,104 @@ class StandardCliTests(unittest.TestCase):
             )
             self.assertEqual(module.main([str(evaluation)]), 0)
 
+    def test_checked_annotation_discovers_workspace_from_copy_pdf(self) -> None:
+        module = self.modules["annotating_with_checks"]
+        with tempfile.TemporaryDirectory() as directory:
+            evaluation = Path(directory) / "Exam"
+            copy_pdf = evaluation / "Copies" / "Copie40.pdf"
+            copy_pdf.parent.mkdir(parents=True)
+            copy_pdf.write_bytes(b"pdf")
+            args = module.build_parser().parse_args([str(copy_pdf)])
+            workspace, target = workspace_from_target(args)
+            self.assertEqual(workspace.root, evaluation)
+            self.assertEqual(target, copy_pdf)
+            self.assertEqual(module._copy_id_from_target(workspace, target), "40")
+
+    def test_checked_refaire_requires_refaire_file(self) -> None:
+        module = self.modules["annotating_with_checks"]
+        with tempfile.TemporaryDirectory() as directory:
+            evaluation = Path(directory) / "Exam"
+            (evaluation / "Copies").mkdir(parents=True)
+            (evaluation / "Par label").mkdir()
+            (evaluation / "labels").write_text("Ex 1\n", encoding="utf-8")
+            atomic_write_json(evaluation / "correction.json", {})
+            with redirect_stderr(io.StringIO()):
+                self.assertEqual(module.main([str(evaluation), "--refaire"]), 3)
+
+    def test_checked_render_failure_preserves_previous_student_output(self) -> None:
+        module = self.modules["annotating_with_checks"]
+        with tempfile.TemporaryDirectory() as directory:
+            evaluation = Path(directory) / "Exam"
+            copy_dir = evaluation / "Copies" / "Copie01"
+            copy_dir.mkdir(parents=True)
+            (evaluation / "Par label").mkdir()
+            (evaluation / "labels").write_text("Ex 1\n", encoding="utf-8")
+            atomic_write_json(evaluation / "correction.json", {})
+            answer = copy_dir / "Ex 1.pdf"
+            answer.write_bytes(b"pdf")
+            previous = evaluation / "Bnot" / "Copie01"
+            previous.mkdir(parents=True)
+            (previous / "sentinel.txt").write_text("old", encoding="utf-8")
+            loaded = AnnotationLoadResult(
+                {
+                    "01": {
+                        "Ex 1": {
+                            "pdf_path": answer,
+                            "result": {"feedback": [], "score": 1},
+                            "coordinates": (0, 0),
+                        }
+                    }
+                },
+                [],
+            )
+            with patch.object(
+                module, "load_annotation_data", return_value=loaded
+            ), patch.object(
+                self.modules["annotating"],
+                "make_base_image",
+                side_effect=RuntimeError("render failed"),
+            ), redirect_stderr(io.StringIO()):
+                self.assertEqual(module.main([str(evaluation), "--overwrite"]), 1)
+            self.assertEqual(
+                (previous / "sentinel.txt").read_text(encoding="utf-8"), "old"
+            )
+
+    def test_grouped_overwrite_preserves_previous_output_when_incomplete(self) -> None:
+        module = self.modules["annotating_by_label"]
+        with tempfile.TemporaryDirectory() as directory:
+            evaluation = Path(directory) / "Exam"
+            (evaluation / "Copies").mkdir(parents=True)
+            (evaluation / "Par label").mkdir()
+            (evaluation / "labels").write_text("Ex 1\n", encoding="utf-8")
+            (evaluation / "label_groups").write_text("Ex 1\n", encoding="utf-8")
+            atomic_write_json(evaluation / "correction.json", {})
+            previous = evaluation / "BGnot"
+            previous.mkdir()
+            (previous / "sentinel.txt").write_text("old", encoding="utf-8")
+            loaded = AnnotationLoadResult(
+                {"01": {"Ex 1": {"pdf_path": Path("missing")}}},
+                [],
+            )
+            with patch.object(
+                module, "load_annotation_data", return_value=loaded
+            ), patch.object(module, "_generate_groups", return_value=(1, True)):
+                self.assertEqual(module.main([str(evaluation), "--overwrite"]), 4)
+            self.assertEqual(
+                (previous / "sentinel.txt").read_text(encoding="utf-8"), "old"
+            )
+
+    def test_grouped_batching_does_not_split_one_student(self) -> None:
+        module = self.modules["annotating_by_label"]
+        image = Image.new("RGB", (10, 60), "white")
+        rendered = [
+            ("01", "Ex 1", image, 0, []),
+            ("01", "Ex 2", image, 0, []),
+            ("02", "Ex 1", image, 0, []),
+        ]
+        with patch.object(module, "MAX_HEIGHT_PX", 100):
+            batches = module.split_batches(rendered)
+        self.assertEqual([len(batch) for batch in batches], [2, 1])
+
 
 class WorkflowTests(unittest.TestCase):
     def setUp(self) -> None: