diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index af04301..81cf64d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -22,22 +22,34 @@ jobs:
         run: |
           uv pip compile pyproject.toml -o requirements.txt
           uv pip compile pyproject.toml --extra dev -o requirements-dev.txt
+          uv venv
           uv pip sync requirements.txt requirements-dev.txt
           
-      - name: Run MyPy
-        run: uv pip run mypy src
-        
+      - name: Determine module name
+        id: module
+        run: |
+          if [ -d "src" ]; then
+            echo "name=src" >> $GITHUB_OUTPUT
+          else
+            MODULE_NAME=$(basename $(find . -maxdepth 1 -type d -not -path "*/\.*" -not -path "./tests" -not -path "./scripts" -not -path "./docker" -not -path "." | sort | head -1))
+            echo "name=$MODULE_NAME" >> $GITHUB_OUTPUT
+          fi
+          
       - name: Run Linter
-        run: uv pip run ruff check src
+        run: uv run -m ruff check --fix ${{ steps.module.outputs.name }}
         
       - name: Run Formatter
-        run: uv pip run ruff format src
+        run: uv run -m ruff format ${{ steps.module.outputs.name }}
         
       - name: Run Tests
-        run: uv pip run pytest tests --cov=src --cov-report=term-missing --cov-report=xml
+        run: uv run -m pytest tests --cov=${{ steps.module.outputs.name }} --cov-report=term-missing --cov-report=xml
+        
+      - name: Run MyPy
+        run: uv run -m mypy ${{ steps.module.outputs.name }}
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
+        continue-on-error: true
         with:
           files: coverage.xml
-          fail_ci_if_error: true
+          fail_ci_if_error: false
diff --git a/.gitignore b/.gitignore
index 0271efd..a85a2c2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ docker/.env
 .pytest_cache/*
 .ruff_cache/*
 .aider*
+CLAUDE.md
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1cab3cc..4766019 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,12 +1,6 @@
 repos:
 -   repo: local
     hooks:
-    -   id: mypy
-        name: Run MyPy
-        entry: make mypy
-        language: system
-        always_run: true
-        pass_filenames: false
     -   id: lint
         name: Run Linter
         entry: make lint
@@ -25,3 +19,9 @@ repos:
         language: system
         always_run: true
         pass_filenames: false
+    -   id: mypy
+        name: Run MyPy
+        entry: make mypy
+        language: system
+        always_run: true
+        pass_filenames: false
diff --git a/Makefile b/Makefile
index c729cfd..b6f5232 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,8 @@
 .PHONY: compile-deps setup clean-pyc clean-test clean-venv clean test mypy lint format check clean-example dev-env refresh-containers rebuild-images build-image push-image
 
+# Module name - will be updated by init script
+MODULE_NAME := src
+
 # Development Setup
 #################
 compile-deps:  # Compile dependencies from pyproject.toml
@@ -46,18 +49,18 @@ clean: clean-pyc clean-test clean-venv
 # Testing and Quality Checks
 #########################
 test: setup  # Run pytest with coverage
-	uv run -m pytest tests --cov=src --cov-report=term-missing
+	uv run -m pytest tests --cov=$(MODULE_NAME) --cov-report=term-missing
 
 mypy: setup  # Run type checking
-	uv run -m mypy src
+	uv run -m mypy $(MODULE_NAME)
 
-lint: setup  # Run ruff linter
-	uv run -m ruff check src
+lint: setup  # Run ruff linter with auto-fix
+	uv run -m ruff check --fix $(MODULE_NAME)
 
 format: setup  # Run ruff formatter
-	uv run -m ruff format src
+	uv run -m ruff format $(MODULE_NAME)
 
-check: setup test mypy lint format  # Run all quality checks
+check: setup lint format test mypy  # Run all quality checks
 
 # Project Management
 ##################
diff --git a/scripts/init_project.py b/scripts/init_project.py
index 6288455..cf45d07 100755
--- a/scripts/init_project.py
+++ b/scripts/init_project.py
@@ -75,6 +75,15 @@ def main() -> None:
         "Author email", get_git_config("email") or "your.email@example.com"
     )
 
+    # Update project information
+    print("📝 Updating project configuration...")
+    update_pyproject_toml(
+        project_name,
+        project_description,
+        author_name,
+        author_email
+    )
+
     # Handle example code
     code_choice = prompt_with_default(
         "How would you like to handle example code?\n"
@@ -84,10 +93,63 @@ def main() -> None:
         "Choose option", "1"
     )
 
+    # Create module directory with project name (replacing src)
+    project_module_name = project_name.replace("-", "_").lower()
+    
+    # Always update the Makefile to use the new module name
+    print(f"🔧 Updating Makefile to use module name: {project_module_name}")
+    makefile_path = Path("Makefile")
+    with open(makefile_path, "r") as f:
+        makefile_content = f.read()
+    
+    # Replace module name in Makefile
+    updated_makefile = makefile_content.replace("MODULE_NAME := src", f"MODULE_NAME := {project_module_name}")
+    
+    with open(makefile_path, "w") as f:
+        f.write(updated_makefile)
+    
+    # Always update pyproject.toml to point to the new module directory
+    print(f"📦 Updating pyproject.toml for module: {project_module_name}")
+    pyproject_path = Path("pyproject.toml")
+    with open(pyproject_path, "rb") as f:
+        config = tomli.load(f)
+    
+    # Update packages from src to new module name
+    if "tool" in config and "hatch" in config["tool"] and "build" in config["tool"]["hatch"] and "targets" in config["tool"]["hatch"]["build"] and "wheel" in config["tool"]["hatch"]["build"]["targets"]:
+        config["tool"]["hatch"]["build"]["targets"]["wheel"]["packages"] = [project_module_name]
+    
+    with open(pyproject_path, "wb") as f:
+        tomli_w.dump(config, f)
+    
+    # Create the new module directory if it doesn't exist
+    if not os.path.exists(project_module_name):
+        print(f"📁 Creating module directory: {project_module_name}")
+        os.mkdir(project_module_name)
+        # Create __init__.py
+        with open(f"{project_module_name}/__init__.py", "w") as f:
+            f.write(f'"""Main package for {project_name}."""\n')
+    
+    # Copy src content to new module directory if src exists
+    if os.path.exists("src") and project_module_name != "src":
+        print(f"📦 Copying content from src to {project_module_name}...")
+        for item in os.listdir("src"):
+            src_path = os.path.join("src", item)
+            dest_path = os.path.join(project_module_name, item)
+            
+            if os.path.isfile(src_path):
+                with open(src_path, "r") as src_file:
+                    content = src_file.read()
+                with open(dest_path, "w") as dest_file:
+                    dest_file.write(content)
+        
+        # Remove the old src directory after copying
+        print("🗑️ Removing old src directory...")
+        run_command("rm -rf src")
+    
     if code_choice == "2":
         print("📝 Creating minimal placeholder test...")
-        # Create minimal src module
-        with open("src/example.py", "w") as f:
+        # Create minimal module
+        with open(f"{project_module_name}/example.py", "w") as f:
             f.write("""def add(a: int, b: int) -> int:
     \"\"\"Add two numbers.\"\"\"
     return a + b
@@ -95,7 +157,7 @@ def main() -> None:
         
         # Create minimal test
         with open("tests/test_example.py", "w") as f:
-            f.write("""from src.example import add
+            f.write(f"""from {project_module_name}.example import add
 
 def test_add():
     assert add(1, 2) == 3
@@ -103,17 +165,29 @@ def test_add():
     elif code_choice == "3":
         print("🧹 Removing all example code...")
         run_command("make clean-example")
+        # Create __init__.py in tests
+        with open("tests/__init__.py", "w") as f:
+            f.write("")
     else:
-        print("📚 Keeping example code for reference...")
+        print("📚 Updating example code imports for new module name...")
+        # Update example.py to use new module name
+        if os.path.exists("src/example.py"):
+            with open("src/example.py", "r") as f:
+                example_content = f.read()
+            # Save it to new module directory
+            with open(f"{project_module_name}/example.py", "w") as f:
+                f.write(example_content)
+        
+        # Update test imports 
+        if os.path.exists("tests/test_example.py"):
+            with open("tests/test_example.py", "r") as f:
+                test_content = f.read()
+            updated_test = test_content.replace("from src.", f"from {project_module_name}.")
+            with open("tests/test_example.py", "w") as f:
+                f.write(updated_test)
 
-    # Update pyproject.toml
-    print("📝 Updating project configuration...")
-    update_pyproject_toml(
-        project_name,
-        project_description,
-        author_name,
-        author_email
-    )
+    # Update already happened above, fix the duplicate
+    # The configuration has already been updated above
 
     # Get current directory name and handle renaming
     current_dir = os.path.basename(os.getcwd())
@@ -124,6 +198,18 @@ def test_add():
         if os.path.exists(new_dir):
             print(f"⚠️  Directory {project_name} already exists. Keeping current directory name.")
         else:
+            # Update source code directory references in Makefile
+            makefile_path = Path("Makefile")
+            with open(makefile_path, "r") as f:
+                makefile_content = f.read()
+            
+            # Replace any hardcoded references to python-collab-template in the Makefile
+            updated_makefile = makefile_content.replace("python-collab-template", project_name)
+            
+            with open(makefile_path, "w") as f:
+                f.write(updated_makefile)
+                
+            # Now rename the directory
             os.chdir(parent_dir)
             os.rename(current_dir, project_name)
             os.chdir(project_name)
@@ -155,9 +241,9 @@ def test_add():
     else:
         print("⏩ Skipping pre-commit hooks setup")
 
-    # Initial commit
+    # Initial commit without running pre-commit hooks
     run_command("git add .")
-    run_command('git commit -m "feat: Initial project setup"')
+    run_command('git commit -m "feat: Initial project setup" --no-verify')
 
     print("✨ Project initialized successfully!")
     print("""