diff --git a/.coveragerc b/.coveragerc
index a920d99..7235976 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,13 +1,28 @@
+# .coveragerc to control coverage.py
 [run]
+branch = True
 source = src
 omit = tests/*
 
+[paths]
+source =
+    src/
+    */site-packages/
+
 [report]
+# Regexes for lines to exclude from consideration
 exclude_lines =
+    # Have to re-enable the standard pragma
     pragma: no cover
+
+    # Don't complain about missing debug-only code:
     def __repr__
-    if self.debug:
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
     raise AssertionError
     raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
index 3a661e2..ccc7db7 100644
--- a/.github/workflows/publish-pypi.yml
+++ b/.github/workflows/publish-pypi.yml
@@ -9,12 +9,7 @@ jobs:
     name: Build and Test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      
-      - name: Set up uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          enable-cache: true
+      - uses: actions/checkout@v7
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
@@ -22,7 +17,7 @@ jobs:
           python-version: 3.12
 
       - name: Install tox
-        run: uv tool install tox --with tox-uv
+        run: python -m pip install tox
 
       - name: Test
         run: tox -e default
@@ -40,12 +35,7 @@ jobs:
     name: Build Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      
-      - name: Set up uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          enable-cache: true
+      - uses: actions/checkout@v7
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
@@ -53,7 +43,7 @@ jobs:
           python-version: 3.12
 
       - name: Install tox
-        run: uv tool install tox --with tox-uv
+        run: python -m pip install tox
 
       - name: Build docs
         run: tox -e docs
@@ -62,7 +52,7 @@ jobs:
         run: touch ./docs/_build/html/.nojekyll
 
       - name: Upload Pages artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v5
         with:
           path: ./docs/_build/html
 
@@ -77,7 +67,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: python-package-distributions
           path: dist/
@@ -98,4 +88,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 3350dd1..25083d6 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -36,12 +36,7 @@ jobs:
     runs-on: ${{ matrix.platform }}
     name: Python ${{ matrix.python }}, ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          enable-cache: true
+      - uses: actions/checkout@v7
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -49,14 +44,12 @@ jobs:
           python-version: ${{ matrix.python }}
 
       - name: Install tox
-        run: uv tool install tox --with tox-uv
-
-      - name: Install dependencies
-        run: uv sync --all-extras --python ${{ matrix.python }}
+        run: python -m pip install tox coverage
 
       - name: Run tests
-        run: |
-          tox -e default -- --cov --cov-branch --cov-report=xml
+        run: >-
+          tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
 
       - name: Check for codecov token availability
         id: codecov-check
@@ -71,7 +64,7 @@ jobs:
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v7
         if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           slug: ${{ github.repository }}
           flags: ${{ matrix.platform }} - py${{ matrix.python }}
diff --git a/README.md b/README.md
index 4080557..a5515d8 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,12 @@ To create a brand new repository, you can use the `hatchit` CLI command:
 hatchit my-awesome-package --description "A robust new tool" --license MIT
 ```
 
+By default, `hatchit` builds standard `tox` environments with pip installation. If you want to use the blazing fast `uv` ecosystem instead, just add `--use-uv`:
+
+```bash
+hatchit my-awesome-package --description "A robust new tool" --license MIT --use-uv
+```
+
 Alternatively, since `hatchit` is a 100% compatible Copier template, you can use `copier` directly to render the project!
 
 ```bash
@@ -50,13 +56,15 @@ That's it! You're ready to start writing code.
 
 ## Development Process
 
-`hatchit` structures your project around `tox` and `uv`. To run your tests during development:
+`hatchit` structures your project around `tox` for automated testing. To run your tests during development:
 
 ```bash
 cd my-awesome-package
 tox -e default
 ```
 
+If you configured the project with `--use-uv`, tox will automatically use `uv` under the hood!
+
 To build your documentation locally and preview:
 ```bash
 tox -e docs
diff --git a/add_biocframe_test.py b/add_biocframe_test.py
new file mode 100644
index 0000000..6ef69f1
--- /dev/null
+++ b/add_biocframe_test.py
@@ -0,0 +1,11 @@
+import re
+from pathlib import Path
+
+pyproj = Path("/home/jayaram/Projects/biocpy/biocutils/pyproject.toml")
+with open(pyproj, "r") as f:
+    content = f.read()
+
+content = content.replace('"pandas>=3.0.5",\n', '"pandas>=3.0.5",\n    "biocframe",\n    "iranges",\n')
+
+with open(pyproj, "w") as f:
+    f.write(content)
diff --git a/check_missing_testing.py b/check_missing_testing.py
new file mode 100644
index 0000000..742dfae
--- /dev/null
+++ b/check_missing_testing.py
@@ -0,0 +1,24 @@
+import os
+from pathlib import Path
+
+projects_dir = Path("/home/jayaram/Projects")
+missing_testing = []
+
+for pyproj in projects_dir.rglob("pyproject.toml"):
+    if ".venv" in str(pyproj) or ".tox" in str(pyproj) or "trash" in str(pyproj):
+        continue
+    
+    with open(pyproj, 'r') as f:
+        content = f.read()
+        
+    # only care if we just migrated it - we can tell if it has tox.ini with `extras = testing`
+    tox_file = pyproj.parent / "tox.ini"
+    if tox_file.exists():
+        with open(tox_file, 'r') as tf:
+            tox_content = tf.read()
+            if "extras = testing" in tox_content:
+                if "\ntesting =" not in content and "\ntesting=" not in content:
+                    missing_testing.append(str(pyproj))
+
+for p in sorted(missing_testing):
+    print(p)
diff --git a/check_uv.py b/check_uv.py
new file mode 100644
index 0000000..9c2a3ff
--- /dev/null
+++ b/check_uv.py
@@ -0,0 +1,23 @@
+import os
+import glob
+from pathlib import Path
+
+projects_dir = Path("/home/jayaram/Projects")
+uv_projects = []
+
+for pyproj in projects_dir.rglob("pyproject.toml"):
+    if ".venv" in str(pyproj) or ".tox" in str(pyproj):
+        continue
+    
+    project_root = pyproj.parent
+    workflows_dir = project_root / ".github" / "workflows"
+    run_tests = workflows_dir / "run-tests.yml"
+    
+    if run_tests.exists():
+        with open(run_tests, 'r') as f:
+            if 'setup-uv' in f.read():
+                uv_projects.append(str(project_root))
+
+print("Projects using uv:")
+for p in sorted(uv_projects):
+    print(p)
diff --git a/copier.yml b/copier.yml
index 405369e..d47cceb 100644
--- a/copier.yml
+++ b/copier.yml
@@ -39,10 +39,14 @@ github_username:
   type: str
   default: "YOUR_ORG_OR_USERNAME"
   help: GitHub Organization or Username
+use_uv:
+  type: bool
+  default: false
+  help: "Use uv for dependency management and tox running?"
 
 # Tasks to run after generation
 _tasks:
-  - "uv lock"
+  - "{% if use_uv %}uv lock{% else %}echo Skip uv lock{% endif %}"
   - "git init"
   - "git add ."
   # Use ignore_errors because git commit might fail if git user isn't configured, or we can just run it.
diff --git a/docs/requirements.txt b/docs/requirements.txt
new file mode 100644
index 0000000..d097ae7
--- /dev/null
+++ b/docs/requirements.txt
@@ -0,0 +1,5 @@
+sphinx>=7.0.0
+furo
+myst-nb
+sphinx-autodoc-typehints
+linkify-it-py
diff --git a/fix_biocutils.py b/fix_biocutils.py
new file mode 100644
index 0000000..297c396
--- /dev/null
+++ b/fix_biocutils.py
@@ -0,0 +1,95 @@
+import re
+from pathlib import Path
+
+repo = Path("/home/jayaram/Projects/biocpy/biocutils")
+
+# 1. Fix pyproject.toml
+pyproj = repo / "pyproject.toml"
+with open(pyproj, "r") as f:
+    content = f.read()
+
+# Remove the duplicate dev group
+content = re.sub(r'\[project\.optional-dependencies\]\ndev = \[\n(    ".*?",\n)*\]\n?', '', content)
+with open(pyproj, "w") as f:
+    f.write(content.strip() + "\n")
+
+
+# 2. Fix tox.ini
+tox_ini = repo / "tox.ini"
+tox_content = """# Tox configuration file
+# Read more under https://tox.wiki/
+
+[tox]
+minversion = 4.0
+envlist = default
+
+[testenv]
+description = Invoke pytest to run automated tests
+extras = testing
+commands =
+    pytest {posargs}
+
+[testenv:typecheck]
+description = Run static type checking with mypy
+deps = mypy
+commands =
+    mypy src/
+
+[testenv:lint]
+description = Perform static analysis and style checks
+deps = ruff
+skip_install = True
+commands =
+    ruff check {posargs:.}
+    ruff format --check {posargs:.}
+
+[testenv:{build,clean}]
+description =
+    build: Build the package
+    clean: Remove old distribution files
+deps = build
+skip_install = True
+commands =
+    clean: python -c 'import shutil; [shutil.rmtree(p, True) for p in ("build", "dist", "docs/_build")]'
+    clean: python -c 'import pathlib, shutil; [shutil.rmtree(p, True) for p in pathlib.Path("src").glob("*.egg-info")]'
+    build: python -m build {posargs}
+
+[testenv:{docs,doctests,linkcheck}]
+description =
+    docs: Invoke sphinx-build to build the docs
+    doctests: Invoke sphinx-build to run doctests
+    linkcheck: Check for broken links in the documentation
+deps =
+    -r {toxinidir}/docs/requirements.txt
+setenv =
+    DOCSDIR = {toxinidir}/docs
+    BUILDDIR = {toxinidir}/docs/_build
+    docs: BUILD = html
+    doctests: BUILD = doctest
+    linkcheck: BUILD = linkcheck
+commands =
+    sphinx-apidoc -f -o "{env:DOCSDIR}/api" src/
+    sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs}
+
+[testenv:publish]
+description =
+    Publish the package you have been developing to a package index server.
+skip_install = True
+deps = twine
+commands =
+    python -m twine upload {posargs:dist/*}
+"""
+with open(tox_ini, "w") as f:
+    f.write(tox_content)
+
+# 3. Fix run-tests.yml
+run_tests = repo / ".github" / "workflows" / "run-tests.yml"
+with open(run_tests, "r") as f:
+    content = f.read()
+
+content = re.sub(r'\n\s*- name: Set up uv\n\s*uses: astral-sh/setup-uv@v5\n\s*with:\n\s*enable-cache: true\n', '', content)
+content = content.replace("uv tool install tox --with tox-uv", "python -m pip install tox")
+content = re.sub(r'\n\s*- name: Install dependencies\n\s*run: uv sync --all-extras --python \$\{\{ matrix\.python \}\}\n', '', content)
+with open(run_tests, "w") as f:
+    f.write(content)
+
diff --git a/fix_hatchit.py b/fix_hatchit.py
new file mode 100644
index 0000000..ad7b702
--- /dev/null
+++ b/fix_hatchit.py
@@ -0,0 +1,11 @@
+import sys
+sys.path.append("/home/jayaram/.gemini/antigravity-ide/brain/9bc824b7-d246-454a-b7c0-32f2b65d7d0d/scratch")
+import migrate_to_pip
+from pathlib import Path
+
+root = Path("/home/jayaram/Projects/biocpy/hatchit")
+migrate_to_pip.process_tox_ini(root / "tox.ini")
+migrate_to_pip.process_pyproject_toml(root / "pyproject.toml")
+migrate_to_pip.process_github_action(root / ".github" / "workflows" / "run-tests.yml")
+migrate_to_pip.process_github_action(root / ".github" / "workflows" / "publish-pypi.yml")
+migrate_to_pip.process_readthedocs(root / ".readthedocs.yml")
diff --git a/fix_hatchit2.py b/fix_hatchit2.py
new file mode 100644
index 0000000..271d4a5
--- /dev/null
+++ b/fix_hatchit2.py
@@ -0,0 +1,12 @@
+import sys
+from pathlib import Path
+
+# Load functions from our existing scripts
+import imp
+fix_tox_ini = imp.load_source('fix_tox_ini', 'fix_tox_ini.py')
+fix_tox_skip_install = imp.load_source('fix_tox_skip_install', 'fix_tox_skip_install.py')
+
+root = Path("/home/jayaram/Projects/biocpy/hatchit")
+fix_tox_ini.fix_tox(root / "tox.ini")
+fix_tox_skip_install.fix_tox(root / "tox.ini")
+fix_tox_skip_install.fix_pyproject(root / "pyproject.toml")
diff --git a/fix_missing_testing.py b/fix_missing_testing.py
new file mode 100644
index 0000000..123ceb8
--- /dev/null
+++ b/fix_missing_testing.py
@@ -0,0 +1,18 @@
+from pathlib import Path
+
+paths = [
+    Path("/home/jayaram/Projects/biocpy/biostrings/pyproject.toml"),
+    Path("/home/jayaram/Projects/biocpy/iranges/pyproject.toml")
+]
+
+for p in paths:
+    if not p.exists(): continue
+    with open(p, 'r') as f:
+        content = f.read()
+    
+    if "testing = [" not in content:
+        content = content.replace("[project.optional-dependencies]", 
+                                  "[project.optional-dependencies]\ntesting = [\n    \"pytest>=9.1.1\",\n    \"pytest-cov>=7.1.0\",\n]\n")
+        with open(p, 'w') as f:
+            f.write(content)
+
diff --git a/fix_pyproject_metadata.py b/fix_pyproject_metadata.py
new file mode 100644
index 0000000..eda34f8
--- /dev/null
+++ b/fix_pyproject_metadata.py
@@ -0,0 +1,102 @@
+import os
+import tomllib
+from pathlib import Path
+import re
+
+def process_pyproject(path):
+    with open(path, 'r') as f:
+        content = f.read()
+    
+    try:
+        data = tomllib.loads(content)
+    except Exception as e:
+        print(f"Failed to parse TOML {path}: {e}")
+        return
+        
+    project_data = data.get('project', {})
+    org_name = path.parent.parent.name
+    repo_name = path.parent.name
+    
+    # Capitalization logic for GitHub URL conventions
+    if org_name == "biocpy":
+        org_url = "BiocPy"
+    else:
+        org_url = org_name
+
+    # 1. Keywords
+    if "keywords" not in project_data:
+        # insert after requires-python
+        keyword_str = 'keywords = [\n    "bioinformatics",\n]\n'
+        content = re.sub(r'(requires-python = ".*?"\n)', r'\1' + keyword_str, content)
+        
+    # 2. Classifiers
+    if "classifiers" not in project_data:
+        classifier_str = """classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Typing :: Typed",
+]
+"""
+        # insert after requires-python or keywords
+        if "keywords = [" in content:
+            # find end of keywords block
+            content = re.sub(r'(keywords = \[.*?\]\n)', r'\1' + classifier_str, content, flags=re.DOTALL)
+        else:
+            content = re.sub(r'(requires-python = ".*?"\n)', r'\1' + classifier_str, content)
+
+    # 3. License
+    if "license" not in project_data:
+        # inject [project.license] block before [project.optional-dependencies] or [build-system]
+        license_str = '\n[project.license]\nfile = "LICENSE.txt"\n'
+        if "[project.urls]" in content:
+            content = content.replace("[project.urls]", license_str + "\n[project.urls]")
+        elif "[project.optional-dependencies]" in content:
+            content = content.replace("[project.optional-dependencies]", license_str + "\n[project.optional-dependencies]")
+        else:
+            content = content.replace("[build-system]", license_str + "\n[build-system]")
+
+    # 4. URLs
+    if "urls" not in project_data:
+        urls_str = f"""\n[project.urls]
+Homepage = "https://github.com/{org_url}/{repo_name}"
+Documentation = "https://{org_url.lower()}.github.io/{repo_name}/"
+Source = "https://github.com/{org_url}/{repo_name}"
+"Bug Tracker" = "https://github.com/{org_url}/{repo_name}/issues"
+"""
+        if "[project.optional-dependencies]" in content:
+            content = content.replace("[project.optional-dependencies]", urls_str + "\n[project.optional-dependencies]")
+        else:
+            content = content.replace("[build-system]", urls_str + "\n[build-system]")
+
+    with open(path, 'w') as f:
+        f.write(content)
+
+
+def main():
+    projects_dir = Path("/home/jayaram/Projects")
+    for pyproj in projects_dir.rglob("pyproject.toml"):
+        if ".venv" in str(pyproj) or ".tox" in str(pyproj) or "trash" in str(pyproj):
+            continue
+        
+        # Ensure it has a standard build system to avoid touching random pyprojects
+        with open(pyproj, 'r') as f:
+            if "hatchling" not in f.read() and "setuptools" not in f.read():
+                continue
+                
+        print(f"Fixing metadata for {pyproj}")
+        process_pyproject(pyproj)
+
+if __name__ == "__main__":
+    main()
diff --git a/fix_toml_duplicate.py b/fix_toml_duplicate.py
new file mode 100644
index 0000000..d5ef7a6
--- /dev/null
+++ b/fix_toml_duplicate.py
@@ -0,0 +1,50 @@
+import os
+import glob
+from pathlib import Path
+import re
+
+def fix_pyproject_toml(path):
+    if not path.exists(): return
+    with open(path, 'r') as f:
+        content = f.read()
+    
+    # We replaced [dependency-groups] with [project.optional-dependencies]
+    # But if it had [project.optional-dependencies] earlier, it's invalid.
+    
+    # Let's check if there are two [project.optional-dependencies]
+    if content.count("[project.optional-dependencies]") > 1:
+        # We need to extract the second block (which was dev = [...])
+        # and move it to the first block.
+        
+        # 1. Find the second block
+        # It's at the end of the file in our case, but let's be robust
+        parts = content.split("[project.optional-dependencies]")
+        
+        # parts[0] is everything before first block
+        # parts[1] is the first block
+        # parts[2] is the second block (dev)
+        
+        # We want to append parts[2] to parts[1]
+        
+        new_content = parts[0] + "[project.optional-dependencies]" + parts[1].rstrip() + "\n" + parts[2].lstrip()
+        
+        with open(path, 'w') as f:
+            f.write(new_content)
+            
+def main():
+    projects_dir = Path("/home/jayaram/Projects")
+    for pyproj in projects_dir.rglob("pyproject.toml"):
+        if ".venv" in str(pyproj) or ".tox" in str(pyproj) or "trash" in str(pyproj):
+            continue
+        
+        try:
+            fix_pyproject_toml(pyproj)
+            # test validity
+            import tomllib
+            with open(pyproj, 'rb') as f:
+                tomllib.load(f)
+        except Exception as e:
+            print(f"Failed on {pyproj}: {e}")
+
+if __name__ == "__main__":
+    main()
diff --git a/fix_tox_docs.py b/fix_tox_docs.py
new file mode 100644
index 0000000..17ae302
--- /dev/null
+++ b/fix_tox_docs.py
@@ -0,0 +1,69 @@
+import os
+from pathlib import Path
+import re
+
+def create_docs_requirements(repo_root):
+    docs_dir = repo_root / "docs"
+    docs_dir.mkdir(exist_ok=True)
+    req_file = docs_dir / "requirements.txt"
+    if not req_file.exists():
+        req_file.write_text("sphinx>=7.0.0\nfuro\nmyst-nb\nsphinx-autodoc-typehints\nlinkify-it-py\n")
+
+def fix_tox(path):
+    if not path.exists(): return
+    with open(path, 'r') as f:
+        content = f.read()
+    
+    # split by testenv blocks
+    blocks = re.split(r'(\[testenv\]|\[testenv:.*?\])', content)
+    
+    for i in range(1, len(blocks), 2):
+        header = blocks[i]
+        body = blocks[i+1]
+        
+        if header == "[testenv:typecheck]":
+            body = body.replace("skip_install = True\n", "")
+            if "extras = dev\n" in body:
+                body = body.replace("extras = dev\n", "deps = mypy\n")
+            elif "extras = testing\n" in body:
+                body = body.replace("extras = testing\n", "deps = mypy\n")
+            elif "deps = mypy" not in body:
+                # Add deps = mypy after the description or at the beginning
+                if "description =" in body:
+                    body = body.replace("description =", "deps = mypy\ndescription =", 1)
+                else:
+                    body = "deps = mypy\n" + body
+                    
+        elif "docs" in header and "linkcheck" in header: # [testenv:{docs,doctests,linkcheck}]
+            body = body.replace("skip_install = True\n", "")
+            if "extras = dev\n" in body:
+                body = body.replace("extras = dev\n", "")
+            elif "extras = testing\n" in body:
+                body = body.replace("extras = testing\n", "")
+                
+            if "deps =" not in body:
+                deps_str = "deps =\n    -r {toxinidir}/docs/requirements.txt\n"
+                if "setenv =" in body:
+                    body = body.replace("setenv =", deps_str + "setenv =", 1)
+                else:
+                    body = deps_str + body
+            
+            # create the requirements.txt file for this repo if it's missing
+            repo_root = path.parent
+            create_docs_requirements(repo_root)
+
+        blocks[i+1] = body
+        
+    new_content = "".join(blocks)
+    with open(path, 'w') as f:
+        f.write(new_content)
+
+def main():
+    projects_dir = Path("/home/jayaram/Projects")
+    for tox in projects_dir.rglob("tox.ini"):
+        if ".venv" in str(tox) or ".tox" in str(tox) or "trash" in str(tox):
+            continue
+        fix_tox(tox)
+
+if __name__ == "__main__":
+    main()
diff --git a/fix_tox_ini.py b/fix_tox_ini.py
new file mode 100644
index 0000000..736b304
--- /dev/null
+++ b/fix_tox_ini.py
@@ -0,0 +1,51 @@
+import os
+import glob
+from pathlib import Path
+import re
+
+def fix_tox(path):
+    if not path.exists(): return
+    with open(path, 'r') as f:
+        content = f.read()
+    
+    # split by testenv blocks
+    blocks = re.split(r'(\[testenv:.*?\])', content)
+    # blocks[0] is everything before the first [testenv:...]
+    # blocks[1] is [testenv:...]
+    # blocks[2] is the content of that block, etc.
+    
+    for i in range(1, len(blocks), 2):
+        header = blocks[i]
+        body = blocks[i+1]
+        
+        # Remove deps = twine from non-publish blocks
+        if "publish" not in header:
+            body = body.replace("deps = twine\n", "")
+            
+        # Also clean up any potential duplicate deps in publish itself?
+        # A block might have two "deps = twine".
+        # We can just deduplicate lines starting with deps =
+        lines = body.split('\n')
+        new_lines = []
+        seen_deps = set()
+        for line in lines:
+            if line.startswith("deps ="):
+                if line in seen_deps:
+                    continue
+                seen_deps.add(line)
+            new_lines.append(line)
+        blocks[i+1] = '\n'.join(new_lines)
+        
+    new_content = "".join(blocks)
+    with open(path, 'w') as f:
+        f.write(new_content)
+        
+def main():
+    projects_dir = Path("/home/jayaram/Projects")
+    for tox in projects_dir.rglob("tox.ini"):
+        if ".venv" in str(tox) or ".tox" in str(tox) or "trash" in str(tox):
+            continue
+        fix_tox(tox)
+
+if __name__ == "__main__":
+    main()
diff --git a/fix_tox_skip_install.py b/fix_tox_skip_install.py
new file mode 100644
index 0000000..a1d06e5
--- /dev/null
+++ b/fix_tox_skip_install.py
@@ -0,0 +1,77 @@
+import os
+import glob
+from pathlib import Path
+import re
+
+def fix_tox(path):
+    if not path.exists(): return
+    with open(path, 'r') as f:
+        content = f.read()
+    
+    # split by testenv blocks
+    blocks = re.split(r'(\[testenv\]|\[testenv:.*?\])', content)
+    
+    for i in range(1, len(blocks), 2):
+        header = blocks[i]
+        body = blocks[i+1]
+        
+        if header == "[testenv]":
+            # Remove skip_install = True
+            body = body.replace("skip_install = True\n", "")
+            # Change extras = dev to extras = testing
+            body = body.replace("extras = dev", "extras = testing")
+        
+        blocks[i+1] = body
+        
+    new_content = "".join(blocks)
+    with open(path, 'w') as f:
+        f.write(new_content)
+
+def fix_pyproject(path):
+    if not path.exists(): return
+    with open(path, 'r') as f:
+        content = f.read()
+        
+    # We want to remove the 'dev = [...]' block inside project.optional-dependencies 
+    # if it's at the end of the file. 
+    # Or actually, we can just remove it using regex since it looks like:
+    # dev = [
+    #     ...
+    # ]
+    
+    # A safer way is to just find [project.optional-dependencies]\ndev = [ ... ]
+    # and remove it if it exists.
+    # It might be just `dev = [ ... ]` at the end of the file if we merged it earlier.
+    
+    # We can just read the lines, and if we encounter `dev = [`, we delete until `]`
+    lines = content.split('\n')
+    new_lines = []
+    in_dev = False
+    
+    for line in lines:
+        if line.startswith("dev = ["):
+            in_dev = True
+            continue
+        if in_dev:
+            if line.strip() == "]":
+                in_dev = False
+            continue
+        new_lines.append(line)
+        
+    with open(path, 'w') as f:
+        f.write('\n'.join(new_lines))
+
+def main():
+    projects_dir = Path("/home/jayaram/Projects")
+    for tox in projects_dir.rglob("tox.ini"):
+        if ".venv" in str(tox) or ".tox" in str(tox) or "trash" in str(tox):
+            continue
+        fix_tox(tox)
+        
+    for pyproj in projects_dir.rglob("pyproject.toml"):
+        if ".venv" in str(pyproj) or ".tox" in str(pyproj) or "trash" in str(pyproj):
+            continue
+        fix_pyproject(pyproj)
+
+if __name__ == "__main__":
+    main()
diff --git a/fix_uv_run_leftovers.py b/fix_uv_run_leftovers.py
new file mode 100644
index 0000000..543b58c
--- /dev/null
+++ b/fix_uv_run_leftovers.py
@@ -0,0 +1,18 @@
+from pathlib import Path
+
+projects_dir = Path("/home/jayaram/Projects")
+for tox in projects_dir.rglob("tox.ini"):
+    if ".venv" in str(tox) or ".tox" in str(tox) or "trash" in str(tox):
+        continue
+        
+    with open(tox, 'r') as f:
+        content = f.read()
+        
+    original = content
+    content = content.replace("uv run --all-extras ", "")
+    content = content.replace("uv run ", "")
+    
+    if content != original:
+        with open(tox, 'w') as f:
+            f.write(content)
+            
diff --git a/fix_yaml_jinja.py b/fix_yaml_jinja.py
new file mode 100644
index 0000000..fab1f05
--- /dev/null
+++ b/fix_yaml_jinja.py
@@ -0,0 +1,16 @@
+import re
+import glob
+import os
+
+files = glob.glob("template/.github/workflows/*.jinja")
+for f in files:
+    with open(f, 'r') as file:
+        content = file.read()
+    
+    # We want to replace ${{ ... }} with {% raw %}${{ ... }}{% endraw %}
+    # But only if it's not already wrapped.
+    content = re.sub(r'(?<!{% raw %})(\${{.*?}})(?!{% endraw %})', r'{% raw %}\1{% endraw %}', content)
+    
+    with open(f, 'w') as file:
+        file.write(content)
+
diff --git a/install_coverage.py b/install_coverage.py
new file mode 100644
index 0000000..21f30c5
--- /dev/null
+++ b/install_coverage.py
@@ -0,0 +1,30 @@
+import os
+from pathlib import Path
+
+def update_tox_install(path):
+    with open(path, 'r') as f:
+        content = f.read()
+
+    # The block we are looking for is:
+    #       - name: Install tox
+    #         run: python -m pip install tox
+
+    # Replace with:
+    #       - name: Install tox
+    #         run: python -m pip install tox coverage
+
+    content = content.replace("python -m pip install tox\n", "python -m pip install tox coverage\n")
+
+    with open(path, 'w') as f:
+        f.write(content)
+
+def main():
+    projects_dir = Path("/home/jayaram/Projects")
+    for action_file in projects_dir.rglob("run-tests.yml*"):
+        if ".venv" in str(action_file) or ".tox" in str(action_file) or "trash" in str(action_file):
+            continue
+            
+        update_tox_install(action_file)
+
+if __name__ == "__main__":
+    main()
diff --git a/pyproject.toml b/pyproject.toml
index e2757cd..5913898 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,10 @@ classifiers = [
     "Topic :: Software Development :: Code Generators",
 ]
 
+
+[project.license]
+file = "LICENSE.txt"
+
 [project.urls]
 Homepage = "https://github.com/biocpy/hatchit"
 Documentation = "https://biocpy.github.io/hatchit"
@@ -99,14 +103,12 @@ testpaths = [
     "tests",
 ]
 
-[dependency-groups]
-dev = [
-    "pytest",
-    "pytest-cov",
-    "sphinx",
-    "myst-nb",
-    "furo",
-    "sphinx-autodoc-typehints",
-    "linkify-it-py",
-    "mypy",
+[project.optional-dependencies]
+testing = [
+    "pytest>=9.1.1",
+    "pytest-cov>=7.1.0",
 ]
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B110"]
diff --git a/src/hatchit/cli.py b/src/hatchit/cli.py
index 547e992..9c4ae08 100644
--- a/src/hatchit/cli.py
+++ b/src/hatchit/cli.py
@@ -14,6 +14,7 @@ def main():
     parser.add_argument("project_path", help="Path where the new project should be created.")
     parser.add_argument("--description", default="Add a short description here!", help="Optional project description.")
     parser.add_argument("--license", default="MIT", help="License to use. Defaults to MIT.")
+    parser.add_argument("--use-uv", action="store_true", help="Use uv for dependency management and tox running.")
 
     args = parser.parse_args()
 
@@ -24,7 +25,7 @@ def main():
         sys.exit(1)
 
     print(f"Hatching project at {project_path}...")
-    create_hatchit_repository(project_path=project_path, description=args.description, license=args.license)
+    create_hatchit_repository(project_path=project_path, description=args.description, license=args.license, use_uv=args.use_uv)
     print("Success! 🚀 💥")
 
 
diff --git a/src/hatchit/scaffold.py b/src/hatchit/scaffold.py
index 3c858fa..6dca8ef 100644
--- a/src/hatchit/scaffold.py
+++ b/src/hatchit/scaffold.py
@@ -8,7 +8,7 @@
 __license__ = "MIT"
 
 
-def create_hatchit_repository(project_path: str, description: str, license: str) -> None:
+def create_hatchit_repository(project_path: str, description: str, license: str, use_uv: bool = False) -> None:
     """Create a new Python project using uv and hatch.
 
     This function initializes a new Python project at the specified `project_path`
@@ -25,6 +25,9 @@ def create_hatchit_repository(project_path: str, description: str, license: str)
         license:
             The license to use for the project.
 
+        use_uv:
+            Whether to use uv for dependency management. Defaults to False.
+
     Example:
         >>> create_hatchit_repository(
         ...     "my_project",
@@ -59,6 +62,7 @@ def create_hatchit_repository(project_path: str, description: str, license: str)
         "author_name": git_name,
         "author_email": git_email,
         "github_username": github_username,
+        "use_uv": use_uv,
     }
 
     template_dir = Path(__file__).parent.parent.parent
diff --git a/template/.coveragerc b/template/.coveragerc
index a920d99..7235976 100644
--- a/template/.coveragerc
+++ b/template/.coveragerc
@@ -1,13 +1,28 @@
+# .coveragerc to control coverage.py
 [run]
+branch = True
 source = src
 omit = tests/*
 
+[paths]
+source =
+    src/
+    */site-packages/
+
 [report]
+# Regexes for lines to exclude from consideration
 exclude_lines =
+    # Have to re-enable the standard pragma
     pragma: no cover
+
+    # Don't complain about missing debug-only code:
     def __repr__
-    if self.debug:
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
     raise AssertionError
     raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
diff --git a/template/.github/workflows/pre-commit.yml b/template/.github/workflows/pre-commit.yml
index d638c47..e940068 100644
--- a/template/.github/workflows/pre-commit.yml
+++ b/template/.github/workflows/pre-commit.yml
@@ -9,7 +9,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
     - uses: actions/setup-python@v5
       with:
         python-version: '3.12'
diff --git a/template/.github/workflows/publish-pypi.yml b/template/.github/workflows/publish-pypi.yml.jinja
similarity index 79%
rename from template/.github/workflows/publish-pypi.yml
rename to template/.github/workflows/publish-pypi.yml.jinja
index 68e2196..674efa3 100644
--- a/template/.github/workflows/publish-pypi.yml
+++ b/template/.github/workflows/publish-pypi.yml.jinja
@@ -9,20 +9,27 @@ jobs:
     name: Build and Test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       
+{% if use_uv %}
       - name: Set up uv
         uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
+{% endif %}
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
           python-version: 3.12
 
+{% if use_uv %}
       - name: Install tox
         run: uv tool install tox --with tox-uv
+{% else %}
+      - name: Install tox
+        run: python -m pip install tox
+{% endif %}
 
       - name: Test
         run: tox -e default
@@ -40,20 +47,27 @@ jobs:
     name: Build Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       
+{% if use_uv %}
       - name: Set up uv
         uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
+{% endif %}
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
           python-version: 3.12
 
+{% if use_uv %}
       - name: Install tox
         run: uv tool install tox --with tox-uv
+{% else %}
+      - name: Install tox
+        run: python -m pip install tox
+{% endif %}
 
       - name: Build docs
         run: tox -e docs
@@ -62,7 +76,7 @@ jobs:
         run: touch ./docs/_build/html/.nojekyll
 
       - name: Upload Pages artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v5
         with:
           path: ./docs/_build/html
 
@@ -77,7 +91,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: python-package-distributions
           path: dist/
@@ -94,8 +108,8 @@ jobs:
       id-token: write
     environment:
       name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
+      url: {% raw %}${{ steps.deployment.outputs.page_url }}{% endraw %}
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5
diff --git a/template/.github/workflows/run-tests.yml b/template/.github/workflows/run-tests.yml.jinja
similarity index 51%
rename from template/.github/workflows/run-tests.yml
rename to template/.github/workflows/run-tests.yml.jinja
index 662c96f..70e4cf4 100644
--- a/template/.github/workflows/run-tests.yml
+++ b/template/.github/workflows/run-tests.yml.jinja
@@ -20,8 +20,8 @@ permissions:
 
 concurrency:
   group: >-
-    ${{ github.workflow }}-${{ github.ref_type }}-
-    ${{ github.event.pull_request.number || github.sha }}
+    {% raw %}${{ github.workflow }}{% endraw %}-{% raw %}${{ github.ref_type }}{% endraw %}-
+    {% raw %}${{ github.event.pull_request.number || github.sha }}{% endraw %}
   cancel-in-progress: true
 
 jobs:
@@ -33,45 +33,53 @@ jobs:
           - ubuntu-latest
           - macos-latest
           - windows-latest
-    runs-on: ${{ matrix.platform }}
-    name: Python ${{ matrix.python }}, ${{ matrix.platform }}
+    runs-on: {% raw %}${{ matrix.platform }}{% endraw %}
+    name: Python {% raw %}${{ matrix.python }}{% endraw %}, {% raw %}${{ matrix.platform }}{% endraw %}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
+{% if use_uv %}
       - name: Set up uv
         uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
+{% endif %}
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python }}
+          python-version: {% raw %}${{ matrix.python }}{% endraw %}
 
+{% if use_uv %}
       - name: Install tox
         run: uv tool install tox --with tox-uv
 
       - name: Install dependencies
-        run: uv sync --all-extras --python ${{ matrix.python }}
+        run: uv sync --all-extras --python {% raw %}${{ matrix.python }}{% endraw %}
+{% else %}
+      - name: Install tox
+        run: python -m pip install tox coverage
+{% endif %}
 
       - name: Run tests
-        run: |
-          tox -e default -- --cov --cov-branch --cov-report=xml
+        run: >-
+          tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
 
       - name: Check for codecov token availability
         id: codecov-check
         shell: bash
         run: |
-          if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
+          if [ {% raw %}${{ secrets.CODECOV_TOKEN }}{% endraw %} != '' ]; then
             echo "codecov=true" >> $GITHUB_OUTPUT;
           else
             echo "codecov=false" >> $GITHUB_OUTPUT;
           fi
 
       - name: Upload coverage reports to Codecov with GitHub Action
-        uses: codecov/codecov-action@v5
-        if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-          slug: ${{ github.repository }}
-          flags: ${{ matrix.platform }} - py${{ matrix.python }}
+        uses: codecov/codecov-action@v7
+        if: {% raw %}${{ steps.codecov-check.outputs.codecov == 'true' }}{% endraw %}
+        with:
+          token: {% raw %}${{ secrets.CODECOV_TOKEN }}{% endraw %}
+          slug: {% raw %}${{ github.repository }}{% endraw %}
+          flags: {% raw %}${{ matrix.platform }}{% endraw %} - py{% raw %}${{ matrix.python }}{% endraw %}
diff --git a/template/.readthedocs.yml b/template/.readthedocs.yml.jinja
similarity index 92%
rename from template/.readthedocs.yml
rename to template/.readthedocs.yml.jinja
index da89049..e839c74 100644
--- a/template/.readthedocs.yml
+++ b/template/.readthedocs.yml.jinja
@@ -7,10 +7,12 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
+{% if use_uv %}
   jobs:
     post_install:
       - curl -LsSf https://astral.sh/uv/install.sh | sh
       - uv sync
+{% endif %}
 
 sphinx:
   configuration: docs/conf.py
diff --git a/template/README.md b/template/README.md.jinja
similarity index 93%
rename from template/README.md
rename to template/README.md.jinja
index 7cd038b..efb6da3 100644
--- a/template/README.md
+++ b/template/README.md.jinja
@@ -20,4 +20,7 @@ pip install {{ project_name }}
 ## Note
 
 This project has been set up using [hatchit](https://github.com/biocpy/hatchit)
+{%- if use_uv %}
 and [uv](https://docs.astral.sh/uv/).
+{%- else %}.
+{%- endif %}
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index 75225a7..abca07c 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -31,6 +31,9 @@ classifiers = [
     "Programming Language :: Python :: 3.14",
 ]
 
+[project.license]
+file = "LICENSE.txt"
+
 [project.urls]
 Homepage = "https://github.com/{{ github_username }}/{{ project_name }}"
 Documentation = "https://github.com/{{ github_username }}/{{ project_name }}"
@@ -70,6 +73,7 @@ strict = true
 addopts = "--cov --cov-report term-missing"
 testpaths = ["tests"]
 
+{% if use_uv %}
 [dependency-groups]
 dev = [
     "pytest",
@@ -81,3 +85,20 @@ dev = [
     "linkify-it-py",
     "mypy"
 ]
+{% else %}
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "sphinx",
+    "myst-nb",
+    "furo",
+    "sphinx-autodoc-typehints",
+    "linkify-it-py",
+    "mypy"
+]
+{% endif %}
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B110"]
diff --git a/template/tox.ini b/template/tox.ini.jinja
similarity index 50%
rename from template/tox.ini
rename to template/tox.ini.jinja
index d759a6a..d707e32 100644
--- a/template/tox.ini
+++ b/template/tox.ini.jinja
@@ -1,3 +1,4 @@
+{% if use_uv %}
 # Tox configuration file using uv as the backend runner
 # Read more under https://tox.wiki/
 
@@ -57,3 +58,67 @@ description =
 skip_install = True
 commands =
     uv publish {posargs:dist/*}
+{% else %}
+# Tox configuration file
+# Read more under https://tox.wiki/
+
+[tox]
+minversion = 4.0
+envlist = default
+
+[testenv]
+description = Invoke pytest to run automated tests
+extras = testing
+commands =
+    pytest {posargs}
+
+[testenv:typecheck]
+description = Run static type checking with mypy
+deps = mypy
+commands =
+    mypy src/
+
+[testenv:lint]
+description = Perform static analysis and style checks
+deps = ruff
+skip_install = True
+commands =
+    ruff check {posargs:.}
+    ruff format --check {posargs:.}
+
+[testenv:{build,clean}]
+description =
+    build: Build the package
+    clean: Remove old distribution files
+deps = build
+skip_install = True
+commands =
+    clean: python -c 'import shutil; [shutil.rmtree(p, True) for p in ("build", "dist", "docs/_build")]'
+    clean: python -c 'import pathlib, shutil; [shutil.rmtree(p, True) for p in pathlib.Path("src").glob("*.egg-info")]'
+    build: python -m build {posargs}
+
+[testenv:{docs,doctests,linkcheck}]
+description =
+    docs: Invoke sphinx-build to build the docs
+    doctests: Invoke sphinx-build to run doctests
+    linkcheck: Check for broken links in the documentation
+deps =
+    -r {toxinidir}/docs/requirements.txt
+setenv =
+    DOCSDIR = {toxinidir}/docs
+    BUILDDIR = {toxinidir}/docs/_build
+    docs: BUILD = html
+    doctests: BUILD = doctest
+    linkcheck: BUILD = linkcheck
+commands =
+    sphinx-apidoc -f -o "{env:DOCSDIR}/api" src/
+    sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs}
+
+[testenv:publish]
+description =
+    Publish the package you have been developing to a package index server.
+skip_install = True
+deps = twine
+commands =
+    python -m twine upload {posargs:dist/*}
+{% endif %}
diff --git a/test_copier.py b/test_copier.py
new file mode 100644
index 0000000..0c9fc50
--- /dev/null
+++ b/test_copier.py
@@ -0,0 +1,7 @@
+import copier
+import tempfile
+import os
+
+with tempfile.TemporaryDirectory() as temp_dir:
+    copier.run_copy(".", temp_dir, data={"project_name": "test", "description": "test", "license": "MIT", "use_uv": False}, vcs_ref="HEAD", unsafe=True, defaults=True)
+    print("Success")
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 6ca78ed..34bd3fb 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -19,6 +19,20 @@ def test_cli_execution(tmp_path):
     assert (project_path / "pyproject.toml").exists()
     assert (project_path / "CITATION.cff").exists()
     
+    # Run the CLI with --use-uv
+    project_path_uv = tmp_path / "cli_project_uv"
+    result_uv = subprocess.run(
+        ["hatchit", str(project_path_uv), "--description", "Test CLI package", "--use-uv"],
+        capture_output=True,
+        text=True
+    )
+    
+    assert result_uv.returncode == 0
+    assert "Hatching project" in result_uv.stdout
+    assert (project_path_uv / "pyproject.toml").exists()
+    with open(project_path_uv / "pyproject.toml") as f:
+        assert "[dependency-groups]" in f.read()
+    
     # Test error on non-empty directory
     (project_path / "extra.txt").touch()
     result_fail = subprocess.run(
diff --git a/tests/test_scaffold.py b/tests/test_scaffold.py
index 979e045..6388706 100644
--- a/tests/test_scaffold.py
+++ b/tests/test_scaffold.py
@@ -1,7 +1,7 @@
 from hatchit import create_hatchit_repository
 
 
-def test_create_hatchit_repository(tmp_path):
+def test_create_hatchit_repository_default(tmp_path):
     project_path = tmp_path / "my_test_project"
     
     create_hatchit_repository(
@@ -19,7 +19,26 @@ def test_create_hatchit_repository(tmp_path):
     assert (project_path / "docs" / "conf.py").exists()
     assert (project_path / ".github" / "workflows" / "run-tests.yml").exists()
     
-    # Verify pyproject.toml name interpolation
+    # Verify pyproject.toml name interpolation and pip structure
     with open(project_path / "pyproject.toml") as f:
         content = f.read()
         assert "my_test_project" in content
+        assert "[project.optional-dependencies]" in content
+        assert "[dependency-groups]" not in content
+
+def test_create_hatchit_repository_with_uv(tmp_path):
+    project_path = tmp_path / "my_uv_project"
+    
+    create_hatchit_repository(
+        project_path=str(project_path),
+        description="A test project",
+        license="MIT",
+        use_uv=True
+    )
+    
+    # Verify pyproject.toml name interpolation and uv structure
+    with open(project_path / "pyproject.toml") as f:
+        content = f.read()
+        assert "my_uv_project" in content
+        assert "[dependency-groups]" in content
+        assert "[project.optional-dependencies]" not in content
diff --git a/tox.ini b/tox.ini
index d759a6a..b08857b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -7,53 +7,56 @@ envlist = default
 
 [testenv]
 description = Invoke pytest to run automated tests
-allowlist_externals = uv
-skip_install = True
+extras = testing
 commands =
-    uv run --all-extras pytest {posargs}
+    pytest {posargs}
 
 [testenv:typecheck]
+deps = mypy
 description = Run static type checking with mypy
-skip_install = True
 commands =
-    uv run --all-extras mypy src/
+    mypy src/
 
 [testenv:lint]
 description = Perform static analysis and style checks
+deps = ruff
 skip_install = True
 commands =
-    uv run ruff check {posargs:.}
-    uv run ruff format --check {posargs:.}
+    ruff check {posargs:.}
+    ruff format --check {posargs:.}
 
 [testenv:{build,clean}]
 description =
     build: Build the package
     clean: Remove old distribution files
+deps = build
 skip_install = True
 commands =
     clean: python -c 'import shutil; [shutil.rmtree(p, True) for p in ("build", "dist", "docs/_build")]'
     clean: python -c 'import pathlib, shutil; [shutil.rmtree(p, True) for p in pathlib.Path("src").glob("*.egg-info")]'
-    build: uv build {posargs}
+    build: python -m build {posargs}
 
 [testenv:{docs,doctests,linkcheck}]
 description =
     docs: Invoke sphinx-build to build the docs
     doctests: Invoke sphinx-build to run doctests
     linkcheck: Check for broken links in the documentation
+deps =
+    -r {toxinidir}/docs/requirements.txt
 setenv =
     DOCSDIR = {toxinidir}/docs
     BUILDDIR = {toxinidir}/docs/_build
     docs: BUILD = html
     doctests: BUILD = doctest
     linkcheck: BUILD = linkcheck
-skip_install = True
 commands =
-    uv run sphinx-apidoc -f -o "{env:DOCSDIR}/api" src/
-    uv run sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs}
+    sphinx-apidoc -f -o "{env:DOCSDIR}/api" src/
+    sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs}
 
 [testenv:publish]
 description =
     Publish the package you have been developing to a package index server.
 skip_install = True
+deps = twine
 commands =
-    uv publish {posargs:dist/*}
+    python -m twine upload {posargs:dist/*}