Fix grading to match assignment, add deployment guide, cleanup

- Fix grade_answers.py to match answer_assignment.py fields
  - Remove q3b_blast_tree_agree, q3c_socal_species questions
  - Rename q3d_confidence to q3b_confidence
  - Update total points: 40 → 36
- Add docs/instructor_deployment.md (Classroom + Codespaces setup)
- Remove lab_quiz.py references from README (quiz removed)
- Delete duplicate answer_key_template.json
- Update README date to November 29, 2025

Author: cosmelab

.github/grading/answer_key_template.json

@@ -19,7 +19,7 @@ def __init__(self, answers_path: str, answer_key_path: str):
         self.answers_path = Path(answers_path)
         self.answer_key_path = Path(answer_key_path)
         self.earned_points = 0
-        self.total_points = 40  # Part 2 (20) + Part 3 (20)
+        self.total_points = 36  # Species table (20) + Q1 (5) + Q2 (7) + Q3 (4)
         self.feedback = []
 
     def load_json(self, path: Path) -> Dict:
@@ -175,9 +175,9 @@ def grade_question2(self, student: Dict, key: Dict) -> int:
         return points
 
     def grade_question3(self, student: Dict, key: Dict) -> int:
-        """Grade Question 3 - Species Identification (8 points)."""
+        """Grade Question 3 - Species Identification (4 points)."""
         points = 0
-        max_points = 8
+        max_points = 4
 
         # Q3a: Species list (2 points)
         student_ans = student.get('q3a_species_list', '').lower()
@@ -192,35 +192,15 @@ def grade_question3(self, student: Dict, key: Dict) -> int:
                 f"❌ Q3(a): Missing species. Expected: {', '.join(key['q3a_species_list'])}"
             )
 
-        # Q3b: BLAST-tree agreement (2 points)
-        student_ans = student.get('q3b_blast_tree_agree', '').lower()
-        expected_ans = key['q3b_blast_tree_agree']
-
-        if student_ans == expected_ans:
-            points += 2
-            self.feedback.append("✓ Q3(b): Correct BLAST-tree comparison")
-        else:
-            self.feedback.append("❌ Q3(b): Incorrect BLAST-tree comparison")
-
-        # Q3c: SoCal occurrence (2 points)
-        student_ans = student.get('q3c_socal_species', '').lower()
-        expected_ans = key['q3c_socal_species']
-
-        if student_ans == expected_ans:
-            points += 2
-            self.feedback.append("✓ Q3(c): Correct geographic assessment")
-        else:
-            self.feedback.append("❌ Q3(c): Incorrect geographic assessment")
-
-        # Q3d: Confidence (2 points)
-        student_ans = student.get('q3d_confidence', '')
-        acceptable = key['q3d_confidence_acceptable']
+        # Q3b: Confidence (2 points)
+        student_ans = student.get('q3b_confidence', '')
+        acceptable = key['q3b_confidence_acceptable']
 
         if any(acc in student_ans for acc in acceptable):
             points += 2
-            self.feedback.append("✓ Q3(d): Appropriate confidence level")
+            self.feedback.append("✓ Q3(b): Appropriate confidence level")
         else:
-            self.feedback.append("⚠️  Q3(d): Confidence level should be 'Very confident' or 'Confident'")
+            self.feedback.append("⚠️  Q3(b): Confidence level should be 'Very confident' or 'Confident'")
 
         self.feedback.append(f"✓ Question 3: {points}/{max_points} points\n")
         return points

.github/grading/grade_answers.py

@@ -52,13 +52,10 @@ See **[start_here.md](start_here.md)** for the complete beginner's guide.
 # STEP 2: Analyze the class mosquito sequences (5 min)
 ./run-analysis-cs.sh
 
-# STEP 3: Take the lab quiz (OPTIONAL but recommended)
-python3 lab_quiz.py
-
-# STEP 4: Answer questions interactively (10 min)
+# STEP 3: Answer questions interactively (10 min)
 python3 answer_assignment.py
 
-# STEP 5: Submit to GitHub (auto-graded!)
+# STEP 4: Submit to GitHub (auto-graded!)
 git add answers.json results/
 git commit -m "Complete assignment"
 git push origin main
@@ -75,13 +72,10 @@ git push origin main
 # STEP 2: Analyze the class mosquito sequences (5 min)
 ./run-analysis.sh
 
-# STEP 3: Take the lab quiz (OPTIONAL but recommended)
-python3 lab_quiz.py
-
-# STEP 4: Answer questions interactively (10 min)
+# STEP 3: Answer questions interactively (10 min)
 python3 answer_assignment.py
 
-# STEP 5: Submit to GitHub (auto-graded!)
+# STEP 4: Submit to GitHub (auto-graded!)
 git add answers.json results/
 git commit -m "Complete assignment"
 git push origin main
@@ -261,7 +255,6 @@ dna-barcoding-analysis/
 ├── tutorial-cs.sh                # Learn with test data (Codespaces)
 ├── run-analysis.sh               # Analyze YOUR data (Docker)
 ├── run-analysis-cs.sh            # Analyze YOUR data (Codespaces)
-├── lab_quiz.py                   # Interactive quiz (learning tool)
 │
 ├── data/
 │   ├── student_sequences/        # PUT YOUR .ab1 FILES HERE
@@ -460,7 +453,6 @@ docker run hello-world
 | **Tree Layouts** | 4 visualizations (rectangular, circular, unrooted, radial) |
 | **HTML Reports** | 6 interactive dashboards + student reports |
 | **Container Size** | ~2.5GB (includes all tools) |
-| **Quiz Questions** | 13 multiple-choice (learning tool) |
 
 ---
 
@@ -617,7 +609,7 @@ You are free to:
 
 ---
 
-**Last Updated**: November 27, 2025
+**Last Updated**: November 29, 2025
 **Status**: Production Ready — Student Tested
 **Container**: `cosmelab/dna-barcoding-analysis:latest` (multi-arch: amd64 + arm64)
 **GitHub Classroom**: Template Ready