Make uv based config optional

.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__.:

.github/workflows/publish-pypi.yml

@@ -9,20 +9,15 @@ 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
         with:
           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
@@ -40,20 +35,15 @@ 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
         with:
           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

.github/workflows/run-tests.yml

@@ -36,27 +36,20 @@ 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
         with:
           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 }}

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

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)

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)

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)

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.

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx>=7.0.0
+furo
+myst-nb
+sphinx-autodoc-typehints
+linkify-it-py

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)
+

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")

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")

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)
+