From 8057bf6dd90449dde8752c0ff99dda5e086bb925 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 24 Aug 2026 21:43:51 -0700 Subject: [PATCH 01/10] refactor: transition to copier --- .zenodo.json | 14 + copier.yml | 36 + pyproject.toml | 6 +- src/hatchit/scaffold.py | 321 +-- .../github_workflows/publish-pypi.yml | 52 - .../templates/github_workflows/run-tests.yml | 73 - src/hatchit/templates/root/AUTHORS.md | 3 - src/hatchit/templates/root/CITATION.cff | 10 - .../templates/root => template}/.coveragerc | 0 .../root => template}/.gitattributes | 0 .../.github}/dependabot.yml | 0 .../.github/workflows}/pre-commit.yml | 0 .../.github/workflows}/publish-pypi.yml | 0 .../.github/workflows}/run-tests.yml | 0 .../gitignore.template => template/.gitignore | 0 .../.pre-commit-config.yaml | 7 + .../root => template}/.readthedocs.yml | 0 .../templates/root => template}/.zenodo.json | 6 +- template/AUTHORS.md | 3 + .../templates/root => template}/CHANGELOG.md | 0 template/CITATION.cff | 10 + .../root => template}/CONTRIBUTING.md | 0 .../templates/root => template}/LICENSE.md | 2 +- template/README.md | 23 + .../templates => template}/docs/Makefile | 0 .../docs/_static/.gitignore | 0 .../templates => template}/docs/authors.md | 0 .../templates => template}/docs/changelog.md | 0 .../templates => template}/docs/conf.py | 14 +- .../docs/contributing.md | 0 .../templates => template}/docs/index.md | 2 +- .../templates => template}/docs/license.md | 0 .../templates => template}/docs/readme.md | 0 .../docs/requirements.txt | 0 template/pyproject.toml.jinja | 54 + .../__init__.py | 11 + .../py.typed | 0 template/tests/test_basic.py.jinja | 5 + .../tox/uv_tox.ini => template/tox.ini | 0 tests/test_cli.py | 3 +- tests/test_scaffold.py | 3 +- uv.lock | 1891 +++++++++++++++++ 42 files changed, 2099 insertions(+), 450 deletions(-) create mode 100644 .zenodo.json create mode 100644 copier.yml delete mode 100644 src/hatchit/templates/github_workflows/publish-pypi.yml delete mode 100644 src/hatchit/templates/github_workflows/run-tests.yml delete mode 100644 src/hatchit/templates/root/AUTHORS.md delete mode 100644 src/hatchit/templates/root/CITATION.cff rename {src/hatchit/templates/root => template}/.coveragerc (100%) rename {src/hatchit/templates/root => template}/.gitattributes (100%) rename {src/hatchit/templates/github => template/.github}/dependabot.yml (100%) rename {src/hatchit/templates/uv_github_workflows => template/.github/workflows}/pre-commit.yml (100%) rename {src/hatchit/templates/uv_github_workflows => template/.github/workflows}/publish-pypi.yml (100%) rename {src/hatchit/templates/uv_github_workflows => template/.github/workflows}/run-tests.yml (100%) rename src/hatchit/templates/gitignore/gitignore.template => template/.gitignore (100%) rename src/hatchit/templates/precommit/pre-commit-config.yaml => template/.pre-commit-config.yaml (89%) rename {src/hatchit/templates/root => template}/.readthedocs.yml (100%) rename {src/hatchit/templates/root => template}/.zenodo.json (64%) create mode 100644 template/AUTHORS.md rename {src/hatchit/templates/root => template}/CHANGELOG.md (100%) create mode 100644 template/CITATION.cff rename {src/hatchit/templates/root => template}/CONTRIBUTING.md (100%) rename {src/hatchit/templates/root => template}/LICENSE.md (95%) create mode 100644 template/README.md rename {src/hatchit/templates => template}/docs/Makefile (100%) rename {src/hatchit/templates => template}/docs/_static/.gitignore (100%) rename {src/hatchit/templates => template}/docs/authors.md (100%) rename {src/hatchit/templates => template}/docs/changelog.md (100%) rename {src/hatchit/templates => template}/docs/conf.py (95%) rename {src/hatchit/templates => template}/docs/contributing.md (100%) rename {src/hatchit/templates => template}/docs/index.md (97%) rename {src/hatchit/templates => template}/docs/license.md (100%) rename {src/hatchit/templates => template}/docs/readme.md (100%) rename {src/hatchit/templates => template}/docs/requirements.txt (100%) create mode 100644 template/pyproject.toml.jinja create mode 100644 template/src/{{ project_name|replace('-', '_') }}/__init__.py create mode 100644 template/src/{{ project_name|replace('-', '_') }}/py.typed create mode 100644 template/tests/test_basic.py.jinja rename src/hatchit/templates/tox/uv_tox.ini => template/tox.ini (100%) create mode 100644 uv.lock diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..bacfb27 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,14 @@ +{ + "title": "hatchit", + "description": "Modern Python project scaffolder combining uv and hatch", + "creators": [ + { + "name": "Jayaram Kancherla", + "affiliation": "YOUR_AFFILIATION", + "orcid": "0000-0000-0000-0000" + } + ], + "access_right": "open", + "license": "MIT", + "upload_type": "software" +} diff --git a/copier.yml b/copier.yml new file mode 100644 index 0000000..c3e6202 --- /dev/null +++ b/copier.yml @@ -0,0 +1,36 @@ +_subdirectory: template + +# Project Info +project_name: + type: str + help: Name of the project (e.g. my-awesome-package) +description: + type: str + default: "Add a short description here!" + help: Short description of the project +license: + type: str + default: MIT + help: License for the project + +# Author Info +author_name: + type: str + default: "First Author" + help: Name of the author +author_email: + type: str + default: "first.author@example.com" + help: Email of the author +github_username: + type: str + default: "YOUR_ORG_OR_USERNAME" + help: GitHub Organization or Username + +# Tasks to run after generation +_tasks: + - "uv lock" + - "git init" + - "git add ." + # Use ignore_errors because git commit might fail if git user isn't configured, or we can just run it. + - "git commit -m 'chore: initial setup' || true" diff --git a/pyproject.toml b/pyproject.toml index 7985fd8..aa99644 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ authors = [ { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" } ] requires-python = ">=3.12" -dependencies = ["uv"] +dependencies = ["uv", "copier>=9.0.0"] keywords = ["scaffold", "uv", "hatch", "project", "generator"] classifiers = [ "Development Status :: 4 - Beta", @@ -32,6 +32,10 @@ hatchit = "hatchit.cli:main" requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" +[tool.hatch.build.targets.wheel.force-include] +"copier.yml" = "hatchit/copier.yml" +"template" = "hatchit/template" + [tool.hatch.version] source = "vcs" fallback-version = "0.1.0" diff --git a/src/hatchit/scaffold.py b/src/hatchit/scaffold.py index ddca951..669ef47 100644 --- a/src/hatchit/scaffold.py +++ b/src/hatchit/scaffold.py @@ -1,8 +1,7 @@ -import datetime -import shutil import subprocess from pathlib import Path from warnings import warn +import copier __author__ = "Jayaram Kancherla" __copyright__ = "Jayaram Kancherla" @@ -14,9 +13,7 @@ def create_hatchit_repository(project_path: str, description: str, license: str) This function initializes a new Python project at the specified `project_path` using the `uv` tool and `hatch` for version management and project scaffolding. - It sets up a basic project structure, including source code, tests, documentation, - and configuration files. The function also customizes certain files based on the - provided `description` and `license`. + It uses `copier` under the hood to render the project template. Args: project_path: @@ -34,307 +31,41 @@ def create_hatchit_repository(project_path: str, description: str, license: str) ... description="My new project", ... license="MIT", ... ) - - CLI usage: - $ hatchit my_project --description "My new project" --license MIT """ if description is None: description = "Add a short description here!" - subprocess.run(["uv", "init", "--no-workspace", "--lib", project_path], check=True) - - # Clear out the dummy hello function generated by uv init - init_path = Path(project_path) / "src" / project_path.split("/")[-1].replace("-", "_") / "__init__.py" - if init_path.exists(): - with open(init_path, "w") as init_f: - init_content = """from importlib.metadata import PackageNotFoundError, version # pragma: no cover - -try: - dist_name = __name__ - __version__ = version(dist_name) -except PackageNotFoundError: # pragma: no cover - __version__ = "unknown" -finally: - del version, PackageNotFoundError -""" - init_f.write(init_content) - - modified_files = [] - template_dir = Path(__file__).parent / "templates" - - # Add GitHub Actions - gh_actions_dir = Path(project_path) / ".github" / "workflows" - gh_actions_dir.mkdir(parents=True, exist_ok=True) - - for workflow in ["run-tests.yml", "publish-pypi.yml", "pre-commit.yml"]: - src = template_dir / "uv_github_workflows" / workflow - dst = gh_actions_dir / workflow - shutil.copy2(src, dst) - modified_files.append(dst) - - # Add dependabot.yml - dependabot_src = template_dir / "github" / "dependabot.yml" - dependabot_dst = Path(project_path) / ".github" / "dependabot.yml" - shutil.copy2(dependabot_src, dependabot_dst) - modified_files.append(dependabot_dst) - - # Add tox.ini - tox_src = template_dir / "tox" / "uv_tox.ini" - tox_dst = Path(project_path) / "tox.ini" - shutil.copy2(tox_src, tox_dst) - modified_files.append(tox_dst) - - # Add comprehensive .gitignore - gitignore_src = template_dir / "gitignore" / "gitignore.template" - gitignore_dst = Path(project_path) / ".gitignore" - shutil.copy2(gitignore_src, gitignore_dst) - modified_files.append(gitignore_dst) - - proj_name = Path(project_path).parts[-1] - try: git_name = subprocess.check_output(["git", "config", "user.name"], text=True).strip() git_email = subprocess.check_output(["git", "config", "user.email"], text=True).strip() - except Exception as _: + except Exception: warn("Git user.name and user.email not configured. Using default values.") git_name = "First Author" git_email = "first.author@example.com" - - # Add top-level root files - for root_file in [ - "CHANGELOG.md", - "CONTRIBUTING.md", - "LICENSE.md", - "AUTHORS.md", - ".coveragerc", - ".readthedocs.yml", - "CITATION.cff", - ".gitattributes", - ".zenodo.json", - ]: - src = template_dir / "root" / root_file - dst = Path(project_path) / root_file - if src.exists(): - if root_file == "LICENSE.md": - with open(src, "r") as f: - content = f.read() - - with open(dst, "w") as f: - f.write(content.replace("REPLACE_PROJECT_NAME", proj_name)) - elif root_file == "AUTHORS.md": - with open(src, "r") as f: - content = f.read() - - with open(dst, "w") as f: - f.write(content.replace("First Author ", f"{git_name} <{git_email}>")) - elif root_file == "CITATION.cff": - name_parts = git_name.split(" ", 1) - given_names = name_parts[0] - family_names = name_parts[1] if len(name_parts) > 1 else "" - today_str = datetime.date.today().strftime("%Y-%m-%d") - - with open(src, "r") as f: - content = f.read() - - with open(dst, "w") as f: - f.write( - content - .replace("REPLACE_PROJECT_NAME", proj_name) - .replace("YOUR_FIRST_NAME", given_names) - .replace("YOUR_LAST_NAME", family_names) - .replace("REPLACE_DATE", today_str) - ) - elif root_file == ".zenodo.json": - with open(src, "r") as f: - content = f.read() - - with open(dst, "w") as f: - f.write( - content - .replace("REPLACE_PROJECT_NAME", proj_name) - .replace("REPLACE_DESCRIPTION", description) - .replace("YOUR_NAME", git_name) - ) - else: - shutil.copy2(src, dst) - - modified_files.append(dst) - - # Add pre-commit config - precommit_src = template_dir / "precommit" / "pre-commit-config.yaml" - precommit_dst = Path(project_path) / ".pre-commit-config.yaml" - shutil.copy2(precommit_src, precommit_dst) - modified_files.append(precommit_dst) - - # Modify README - readme_path = Path(project_path) / "README.md" - - new_readme = f"""[![PyPI-Server](https://img.shields.io/pypi/v/{proj_name}.svg)](https://pypi.org/project/{proj_name}/) -![Unit tests](https://github.com/YOUR_ORG_OR_USERNAME/{proj_name}/actions/workflows/run-tests.yml/badge.svg) - -# {proj_name} - -> {description} - -A longer description of your project goes here... - -## Install - -To get started, install the package from [PyPI](https://pypi.org/project/{proj_name}/) - -```bash -pip install {proj_name} -``` - - - -## Note - -This project has been set up using [hatchit](https://github.com/biocpy/hatchit) -and [uv](https://docs.astral.sh/uv/). -""" - - with open(readme_path, "w") as f: - f.write(new_readme) - modified_files.append(readme_path) - - # Add docs - docs_dir = Path(project_path) / "docs" - src_docs_dir = template_dir / "docs" - shutil.copytree(src_docs_dir, docs_dir, dirs_exist_ok=True) - - pkg_name = proj_name.replace("-", "_") - - conf_py_path = docs_dir / "conf.py" - if conf_py_path.exists(): - with open(conf_py_path, "r") as f: - content = f.read() - - with open(conf_py_path, "w") as f: - f.write(content.replace("REPLACE_PROJECT_NAME", pkg_name).replace("YOUR_NAME", git_name)) - - modified_files.append(conf_py_path) - - index_md_path = docs_dir / "index.md" - if index_md_path.exists(): - with open(index_md_path, "r") as f: - content = f.read() - - with open(index_md_path, "w") as f: - f.write(content.replace("REPLACE_PROJECT_NAME", proj_name)) - - modified_files.append(index_md_path) - - for f in docs_dir.glob("**/*"): - if f.is_file() and f not in modified_files: - modified_files.append(f) - - # Modify pyproject.toml - pyprj_path = Path(project_path) / "pyproject.toml" - with open(pyprj_path, "r") as f: - pyprj_content = f.read() - - ruff_config = """ -[tool.ruff] -line-length = 120 -src = ["src"] -exclude = ["tests", "docs"] - -[tool.ruff.lint] -extend-ignore = ["F821"] - -[tool.ruff.lint.pydocstyle] -convention = "google" - -[tool.ruff.lint.per-file-ignores] -"__init__.py" = ["E402", "F401"] - -[tool.ruff.format] -docstring-code-format = true -docstring-code-line-length = 20 - -[tool.mypy] -strict = true - -[tool.pytest.ini_options] -addopts = "--cov --cov-report term-missing" -testpaths = ["tests"] -""" - - import re - - # Remove hardcoded version and replace with dynamic versioning - pyprj_content = re.sub(r'version\s*=\s*"[^"]+"\n', 'dynamic = ["version"]\n', pyprj_content) - - # Replace build-system with hatchling and hatch-vcs - build_system = """[build-system] -requires = ["hatchling", "hatch-vcs"] -build-backend = "hatchling.build" - -[tool.hatch.version] -source = "vcs" -fallback-version = "0.1.0" -""" - pyprj_content = re.sub( - r'\[build-system\].*?build-backend\s*=\s*"[^"]+"\n', build_system, pyprj_content, flags=re.DOTALL - ) - - pyprj_content = pyprj_content.replace('description = "Add your description here"', f'description = "{description}"') - - with open(pyprj_path, "w") as f: - f.write(pyprj_content + ruff_config) - modified_files.append(pyprj_path) - - # tests directory - tests_dir = Path(project_path) / "tests" - tests_dir.mkdir(parents=True, exist_ok=True) - test_file = tests_dir / "test_basic.py" - - pkg_name = proj_name.replace("-", "_") - test_content = f"""import {pkg_name} - -def test_import(): - '''Test that the package can be imported.''' - assert {pkg_name}.__name__ == "{pkg_name}" -""" - with open(test_file, "w") as f: - f.write(test_content) - - modified_files.append(test_file) - - # Install dev dependencies - subprocess.run( - [ - "uv", - "add", - "--dev", - "pytest", - "pytest-cov", - "sphinx", - "myst-nb", - "furo", - "sphinx-autodoc-typehints", - "linkify-it-py", - "mypy", - ], - cwd=project_path, - check=True, - ) - + try: - subprocess.run(["git", "init"], cwd=project_path, check=True, capture_output=True) - subprocess.run(["git", "add", "."], cwd=project_path, check=True, capture_output=True) - - # Check if git user config exists before committing - name_configured = subprocess.run(["git", "config", "user.name"], capture_output=True).returncode == 0 - email_configured = subprocess.run(["git", "config", "user.email"], capture_output=True).returncode == 0 - - if name_configured and email_configured: - subprocess.run( - ["git", "commit", "-m", "chore: initial setup"], cwd=project_path, check=True, capture_output=True - ) + # Check if gh CLI is installed for github username, or extract from remote if any. + # Defaults to a placeholder + github_username = "YOUR_ORG_OR_USERNAME" except Exception: - warn("Git is not installed or not configured. Skipping git initialization and commit.") - pass + github_username = "YOUR_ORG_OR_USERNAME" + + proj_name = Path(project_path).parts[-1] + data = { + "project_name": proj_name, + "description": description, + "license": license, + "author_name": git_name, + "author_email": git_email, + "github_username": github_username, + } + + template_dir = Path(__file__).parent.parent.parent + if not (template_dir / "copier.yml").exists(): + # Fallback for when the package is installed + template_dir = Path(__file__).parent + + copier.run_copy(str(template_dir), project_path, data=data, unsafe=True) + print("hatchit complete! 🚀 💥") diff --git a/src/hatchit/templates/github_workflows/publish-pypi.yml b/src/hatchit/templates/github_workflows/publish-pypi.yml deleted file mode 100644 index 405fee0..0000000 --- a/src/hatchit/templates/github_workflows/publish-pypi.yml +++ /dev/null @@ -1,52 +0,0 @@ -name: Publish to PyPI - -on: - push: - tags: "*" - -jobs: - build: - runs-on: ubuntu-latest - permissions: - id-token: write - repository-projects: write - contents: write - pages: write - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python 3.12 - uses: actions/setup-python@v5 - with: - python-version: 3.12 - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install tox - - - name: Test with tox - run: | - tox - - - name: Build Project and Publish - run: | - python -m tox -e clean,build - - # This uses the trusted publisher workflow so no token is required. - - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - - - name: Build docs - run: | - tox -e docs - - - run: touch ./docs/_build/html/.nojekyll - - - name: GH Pages Deployment - uses: JamesIves/github-pages-deploy-action@v4 - with: - branch: gh-pages # The branch the action should deploy to. - folder: ./docs/_build/html - clean: true # Automatically remove deleted files from the deploy branch diff --git a/src/hatchit/templates/github_workflows/run-tests.yml b/src/hatchit/templates/github_workflows/run-tests.yml deleted file mode 100644 index e0f247d..0000000 --- a/src/hatchit/templates/github_workflows/run-tests.yml +++ /dev/null @@ -1,73 +0,0 @@ -name: Test the library - -on: - push: - branches: - - master # for legacy repos - - main - pull_request: - branches: - - master # for legacy repos - - main - workflow_dispatch: # Allow manually triggering the workflow - schedule: - # Run roughly every 15 days at 00:00 UTC - # (useful to check if updates on dependencies break the package) - - cron: "0 0 1,16 * *" - -permissions: - contents: read - -concurrency: - group: >- - ${{ github.workflow }}-${{ github.ref_type }}- - ${{ github.event.pull_request.number || github.sha }} - cancel-in-progress: true - -jobs: - test: - strategy: - matrix: - python: ["3.10", "3.11", "3.12", "3.13", "3.14"] - platform: - - ubuntu-latest - - macos-latest - - windows-latest - runs-on: ${{ matrix.platform }} - name: Python ${{ matrix.python }}, ${{ matrix.platform }} - steps: - - uses: actions/checkout@v4 - - - uses: actions/setup-python@v5 - id: setup-python - with: - python-version: ${{ matrix.python }} - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install tox coverage - - - name: Run tests - run: >- - pipx run --python '${{ steps.setup-python.outputs.python-path }}' - 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 - 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 }} diff --git a/src/hatchit/templates/root/AUTHORS.md b/src/hatchit/templates/root/AUTHORS.md deleted file mode 100644 index 64b8f8f..0000000 --- a/src/hatchit/templates/root/AUTHORS.md +++ /dev/null @@ -1,3 +0,0 @@ -# Authors - -* First Author diff --git a/src/hatchit/templates/root/CITATION.cff b/src/hatchit/templates/root/CITATION.cff deleted file mode 100644 index c3a0b5e..0000000 --- a/src/hatchit/templates/root/CITATION.cff +++ /dev/null @@ -1,10 +0,0 @@ -cff-version: 1.2.0 -message: "If you use this software, please cite it as below." -authors: -- family-names: "YOUR_LAST_NAME" - given-names: "YOUR_FIRST_NAME" - orcid: "https://orcid.org/0000-0000-0000-0000" -title: "REPLACE_PROJECT_NAME" -version: 0.1.0 -date-released: REPLACE_DATE -url: "https://github.com/YOUR_ORG_OR_USERNAME/REPLACE_PROJECT_NAME" diff --git a/src/hatchit/templates/root/.coveragerc b/template/.coveragerc similarity index 100% rename from src/hatchit/templates/root/.coveragerc rename to template/.coveragerc diff --git a/src/hatchit/templates/root/.gitattributes b/template/.gitattributes similarity index 100% rename from src/hatchit/templates/root/.gitattributes rename to template/.gitattributes diff --git a/src/hatchit/templates/github/dependabot.yml b/template/.github/dependabot.yml similarity index 100% rename from src/hatchit/templates/github/dependabot.yml rename to template/.github/dependabot.yml diff --git a/src/hatchit/templates/uv_github_workflows/pre-commit.yml b/template/.github/workflows/pre-commit.yml similarity index 100% rename from src/hatchit/templates/uv_github_workflows/pre-commit.yml rename to template/.github/workflows/pre-commit.yml diff --git a/src/hatchit/templates/uv_github_workflows/publish-pypi.yml b/template/.github/workflows/publish-pypi.yml similarity index 100% rename from src/hatchit/templates/uv_github_workflows/publish-pypi.yml rename to template/.github/workflows/publish-pypi.yml diff --git a/src/hatchit/templates/uv_github_workflows/run-tests.yml b/template/.github/workflows/run-tests.yml similarity index 100% rename from src/hatchit/templates/uv_github_workflows/run-tests.yml rename to template/.github/workflows/run-tests.yml diff --git a/src/hatchit/templates/gitignore/gitignore.template b/template/.gitignore similarity index 100% rename from src/hatchit/templates/gitignore/gitignore.template rename to template/.gitignore diff --git a/src/hatchit/templates/precommit/pre-commit-config.yaml b/template/.pre-commit-config.yaml similarity index 89% rename from src/hatchit/templates/precommit/pre-commit-config.yaml rename to template/.pre-commit-config.yaml index 863ce2d..af3eb03 100644 --- a/src/hatchit/templates/precommit/pre-commit-config.yaml +++ b/template/.pre-commit-config.yaml @@ -53,3 +53,10 @@ repos: # rev: v2.2.5 # hooks: # - id: codespell + +- repo: https://github.com/PyCQA/bandit + rev: 1.7.9 + hooks: + - id: bandit + args: ["-c", "pyproject.toml"] + additional_dependencies: ["bandit[toml]"] diff --git a/src/hatchit/templates/root/.readthedocs.yml b/template/.readthedocs.yml similarity index 100% rename from src/hatchit/templates/root/.readthedocs.yml rename to template/.readthedocs.yml diff --git a/src/hatchit/templates/root/.zenodo.json b/template/.zenodo.json similarity index 64% rename from src/hatchit/templates/root/.zenodo.json rename to template/.zenodo.json index ad4c80e..9bff420 100644 --- a/src/hatchit/templates/root/.zenodo.json +++ b/template/.zenodo.json @@ -1,9 +1,9 @@ { - "title": "REPLACE_PROJECT_NAME", - "description": "REPLACE_DESCRIPTION", + "title": "{{ project_name }}", + "description": "{{ description }}", "creators": [ { - "name": "YOUR_NAME", + "name": "{{ author_name }}", "affiliation": "YOUR_AFFILIATION", "orcid": "0000-0000-0000-0000" } diff --git a/template/AUTHORS.md b/template/AUTHORS.md new file mode 100644 index 0000000..5e771cb --- /dev/null +++ b/template/AUTHORS.md @@ -0,0 +1,3 @@ +# Authors + +* {{ author_name }} <{{ author_email }}> diff --git a/src/hatchit/templates/root/CHANGELOG.md b/template/CHANGELOG.md similarity index 100% rename from src/hatchit/templates/root/CHANGELOG.md rename to template/CHANGELOG.md diff --git a/template/CITATION.cff b/template/CITATION.cff new file mode 100644 index 0000000..63270e5 --- /dev/null +++ b/template/CITATION.cff @@ -0,0 +1,10 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." +authors: +- family-names: "{% if names|length > 1 %}{{ names[1] }}{% endif %}" + given-names: "{% set names = author_name.split(' ', 1) %}{{ names[0] }}" + orcid: "https://orcid.org/0000-0000-0000-0000" +title: "{{ project_name }}" +version: 0.1.0 +date-released: {% now 'utc', '%Y-%m-%d' %} +url: "https://github.com/YOUR_ORG_OR_USERNAME/{{ project_name }}" diff --git a/src/hatchit/templates/root/CONTRIBUTING.md b/template/CONTRIBUTING.md similarity index 100% rename from src/hatchit/templates/root/CONTRIBUTING.md rename to template/CONTRIBUTING.md diff --git a/src/hatchit/templates/root/LICENSE.md b/template/LICENSE.md similarity index 95% rename from src/hatchit/templates/root/LICENSE.md rename to template/LICENSE.md index b8e0639..bea5c9c 100644 --- a/src/hatchit/templates/root/LICENSE.md +++ b/template/LICENSE.md @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2024 REPLACE_PROJECT_NAME authors +Copyright (c) 2024 {{ project_name }} authors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/template/README.md b/template/README.md new file mode 100644 index 0000000..7cd038b --- /dev/null +++ b/template/README.md @@ -0,0 +1,23 @@ +[![PyPI-Server](https://img.shields.io/pypi/v/{{ project_name }}.svg)](https://pypi.org/project/{{ project_name }}/) +![Unit tests](https://github.com/{{ github_username }}/{{ project_name }}/actions/workflows/run-tests.yml/badge.svg) + +# {{ project_name }} + +> {{ description }} + +A longer description of your project goes here... + +## Install + +To get started, install the package from [PyPI](https://pypi.org/project/{{ project_name }}/) + +```bash +pip install {{ project_name }} +``` + + + +## Note + +This project has been set up using [hatchit](https://github.com/biocpy/hatchit) +and [uv](https://docs.astral.sh/uv/). diff --git a/src/hatchit/templates/docs/Makefile b/template/docs/Makefile similarity index 100% rename from src/hatchit/templates/docs/Makefile rename to template/docs/Makefile diff --git a/src/hatchit/templates/docs/_static/.gitignore b/template/docs/_static/.gitignore similarity index 100% rename from src/hatchit/templates/docs/_static/.gitignore rename to template/docs/_static/.gitignore diff --git a/src/hatchit/templates/docs/authors.md b/template/docs/authors.md similarity index 100% rename from src/hatchit/templates/docs/authors.md rename to template/docs/authors.md diff --git a/src/hatchit/templates/docs/changelog.md b/template/docs/changelog.md similarity index 100% rename from src/hatchit/templates/docs/changelog.md rename to template/docs/changelog.md diff --git a/src/hatchit/templates/docs/conf.py b/template/docs/conf.py similarity index 95% rename from src/hatchit/templates/docs/conf.py rename to template/docs/conf.py index 72704b2..7af8616 100644 --- a/src/hatchit/templates/docs/conf.py +++ b/template/docs/conf.py @@ -34,7 +34,7 @@ from sphinx import apidoc output_dir = os.path.join(__location__, "api") -module_dir = os.path.join(__location__, "../src/REPLACE_PROJECT_NAME") +module_dir = os.path.join(__location__, "../src/{{ project_name|replace("-", "_") }}") try: shutil.rmtree(output_dir) except FileNotFoundError: @@ -105,8 +105,8 @@ master_doc = "index" # General information about the project. -project = "REPLACE_PROJECT_NAME" -copyright = "2026, YOUR_NAME" +project = "{{ project_name|replace("-", "_") }}" +copyright = "2026, {{ author_name }}" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -118,7 +118,7 @@ # just set them both to the same value. try: from importlib.metadata import version as get_version - version = get_version("REPLACE_PROJECT_NAME") + version = get_version("{{ project_name|replace("-", "_") }}") except Exception: version = "unknown" @@ -186,7 +186,7 @@ "color-brand-primary": "#4c9aff", "color-brand-content": "#4c9aff", }, - "source_repository": "https://github.com/YOUR_ORG_OR_USERNAME/REPLACE_PROJECT_NAME", + "source_repository": "https://github.com/YOUR_ORG_OR_USERNAME/{{ project_name|replace("-", "_") }}", "source_branch": "main", "source_directory": "docs/", } @@ -257,7 +257,7 @@ # html_file_suffix = None # Output file base name for HTML help builder. -htmlhelp_basename = "REPLACE_PROJECT_NAME-doc" +htmlhelp_basename = "{{ project_name|replace("-", "_") }}-doc" # -- Options for LaTeX output ------------------------------------------------ @@ -274,7 +274,7 @@ # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ("index", "user_guide.tex", "REPLACE_PROJECT_NAME Documentation", "YOUR_NAME", "manual") + ("index", "user_guide.tex", "{{ project_name|replace("-", "_") }} Documentation", "{{ author_name }}", "manual") ] # The name of an image file (relative to this directory) to place at the top of diff --git a/src/hatchit/templates/docs/contributing.md b/template/docs/contributing.md similarity index 100% rename from src/hatchit/templates/docs/contributing.md rename to template/docs/contributing.md diff --git a/src/hatchit/templates/docs/index.md b/template/docs/index.md similarity index 97% rename from src/hatchit/templates/docs/index.md rename to template/docs/index.md index 47207b3..aa6896f 100644 --- a/src/hatchit/templates/docs/index.md +++ b/template/docs/index.md @@ -1,4 +1,4 @@ -# REPLACE_PROJECT_NAME +# {{ project_name }} Add a short description here! diff --git a/src/hatchit/templates/docs/license.md b/template/docs/license.md similarity index 100% rename from src/hatchit/templates/docs/license.md rename to template/docs/license.md diff --git a/src/hatchit/templates/docs/readme.md b/template/docs/readme.md similarity index 100% rename from src/hatchit/templates/docs/readme.md rename to template/docs/readme.md diff --git a/src/hatchit/templates/docs/requirements.txt b/template/docs/requirements.txt similarity index 100% rename from src/hatchit/templates/docs/requirements.txt rename to template/docs/requirements.txt diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja new file mode 100644 index 0000000..13390e1 --- /dev/null +++ b/template/pyproject.toml.jinja @@ -0,0 +1,54 @@ +[project] +name = "{{ project_name }}" +dynamic = ["version"] +description = "{{ description }}" +readme = "README.md" +requires-python = ">=3.12" +authors = [ + { name = "{{ author_name }}", email = "{{ author_email }}" } +] + +[build-system] 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project_name|replace('-', '_') }}/__init__.py @@ -0,0 +1,11 @@ +from importlib.metadata import PackageNotFoundError, version # pragma: no cover + +try: + dist_name = __name__ + __version__ = version(dist_name) +except PackageNotFoundError: # pragma: no cover + __version__ = "unknown" +finally: + del version, PackageNotFoundError + +__all__ = ["__version__"] diff --git a/template/src/{{ project_name|replace('-', '_') }}/py.typed b/template/src/{{ project_name|replace('-', '_') }}/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/template/tests/test_basic.py.jinja b/template/tests/test_basic.py.jinja new file mode 100644 index 0000000..73ccc9e --- /dev/null +++ b/template/tests/test_basic.py.jinja @@ -0,0 +1,5 @@ +import {{ project_name|replace('-', '_') }} + +def test_import(): + '''Test that the package can be imported.''' + assert {{ project_name|replace('-', '_') }}.__name__ == "{{ project_name|replace('-', '_') }}" diff --git a/src/hatchit/templates/tox/uv_tox.ini 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data=data, unsafe=True) + copier.run_copy(str(template_dir), project_path, data=data, vcs_ref="HEAD", unsafe=True) print("hatchit complete! 🚀 💥") From e8c9f8f2a5276e9d57ef5f06c23296e4cf44a57e Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 24 Aug 2026 21:45:47 -0700 Subject: [PATCH 03/10] fix: test_scaffold.py expects exact project_name and update README.md --- README.md | 9 +- tests/test_scaffold.py | 2 +- uv.lock | 199 ++++++++++++++++++++++++++++++++++++++++- 3 files changed, 207 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 2e9b06b..b2f40f7 100644 --- a/README.md +++ b/README.md @@ -14,12 +14,19 @@ pip install hatchit ## Quickstart Tutorial -To create a brand new repository, simply run the `hatchit` CLI command: +To create a brand new repository, you can use the `hatchit` CLI command: ```bash hatchit my-awesome-package --description "A robust new tool" --license MIT ``` +Alternatively, since `hatchit` is a 100% compatible Copier template, you 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22:44:15 -0700 Subject: [PATCH 04/10] update doc and action templates --- README.md | 15 +- template/.github/workflows/publish-pypi.yml | 104 +++++-- template/.github/workflows/run-tests.yml | 16 +- template/docs/Makefile | 29 -- template/docs/conf.py | 322 ++------------------ template/docs/index.md | 37 ++- template/docs/requirements.txt | 9 - template/pyproject.toml.jinja | 21 ++ template/tox.ini | 1 + 9 files changed, 153 insertions(+), 401 deletions(-) delete mode 100644 template/docs/Makefile delete mode 100644 template/docs/requirements.txt diff --git a/README.md b/README.md index b2f40f7..9aed70f 100644 --- a/README.md +++ b/README.md @@ -36,14 +36,17 @@ create_hatchit_repository(project_path = "my-awesome-package", description = "ne This will generate the project in the `my-awesome-package` directory and initialize a fresh Git repository. -## After setup +## What's Next? (After Setup Checklist) -- The GitHub workflows use "trusted publisher workflow" to publish packages to PyPI. Read more instructions [here](https://docs.pypi.org/trusted-publishers/). -- Install [tox](https://tox.wiki/en/4.23.2/) to handle package tasks. GitHub Actions relies on the tox configuration to test, generate documentation, and publish packages. -- (Optional) Enable the [pre-commit.ci](https://pre-commit.ci/) bot for your repository. -- (Optional) Install [ruff](https://docs.astral.sh/ruff/) for code formatting. -- (Optional) Setup [codecov](https://about.codecov.io/) for coverage reports. +Now that your project is perfectly scaffolded, there are just a few quick things you'll want to configure to get the full automated experience working for you: +1. **Update `pyproject.toml` keywords**: We've added a few placeholder keywords (like `"TODO"`, `"FIXME"`) to your `pyproject.toml`. Swap those out with relevant keywords for your package to make it more discoverable on PyPI! +2. **Setup PyPI Trusted Publishing**: We use GitHub Actions for publishing. You don't need any secrets! Instead, head over to PyPI, create a "Pending Publisher", and link it to your GitHub repository. [Read more here](https://docs.pypi.org/trusted-publishers/). +3. **Configure Codecov (Optional)**: If you want test coverage reports, head to [Codecov](https://about.codecov.io/), link your repo, grab your token, and add it as a `CODECOV_TOKEN` secret in your GitHub repository. +4. **Activate pre-commit.ci (Optional)**: If you want automated PRs keeping your code perfectly formatted, enable the [pre-commit.ci](https://pre-commit.ci/) bot on your repo. +5. **Enable GitHub Pages (Optional)**: The publishing workflow automatically builds your Sphinx docs. To serve them, go to your repository settings, navigate to "Pages", and select **GitHub Actions** as the "Source". The deployment workflow will automatically publish the built artifact to your site! + +That's it! You're ready to start writing code. ## Development Process diff --git a/template/.github/workflows/publish-pypi.yml b/template/.github/workflows/publish-pypi.yml index 81ef189..68e2196 100644 --- a/template/.github/workflows/publish-pypi.yml +++ b/template/.github/workflows/publish-pypi.yml @@ -1,53 +1,101 @@ -name: Publish to PyPI +name: Publish to PyPI and GitHub Pages on: push: tags: "*" jobs: - build: + build-and-test: + name: Build and Test runs-on: ubuntu-latest - permissions: - id-token: write - repository-projects: write - contents: write - pages: write - steps: - uses: actions/checkout@v4 + + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true - name: Set up Python 3.12 uses: actions/setup-python@v5 with: python-version: 3.12 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install uv tox - uv sync + - name: Install tox + run: uv tool install tox --with tox-uv - name: Test - run: | - tox -e default + run: tox -e default - name: Build Project - run: | - tox -e build + run: tox -e build - # This uses the trusted publisher workflow so no token is required. - - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Store the distribution packages + uses: actions/upload-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + build-docs: + 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 + + - 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 - name: Build docs - run: | - tox -e docs + run: tox -e docs + + - name: Add .nojekyll + run: touch ./docs/_build/html/.nojekyll - - run: touch ./docs/_build/html/.nojekyll + - name: Upload Pages artifact + uses: actions/upload-pages-artifact@v3 + with: + path: ./docs/_build/html - - name: GH Pages Deployment - uses: JamesIves/github-pages-deploy-action@v4 + publish-pypi: + name: Publish to PyPI + needs: build-and-test + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/{{ project_name|replace('-', '_') }} + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 with: - branch: gh-pages # The branch the action should deploy to. - folder: ./docs/_build/html - clean: true # Automatically remove deleted files from the deploy branch + name: python-package-distributions + path: dist/ + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + deploy-pages: + name: Deploy GitHub Pages + needs: build-docs + runs-on: ubuntu-latest + permissions: + pages: write + id-token: write + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/template/.github/workflows/run-tests.yml b/template/.github/workflows/run-tests.yml index 22de18b..4aa904e 100644 --- a/template/.github/workflows/run-tests.yml +++ b/template/.github/workflows/run-tests.yml @@ -38,16 +38,18 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - id: setup-python + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + + - name: Set up Python + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install uv tox - uv sync + - name: Install tox + run: uv tool install tox --with tox-uv - name: Run tests run: | diff --git a/template/docs/Makefile b/template/docs/Makefile deleted file mode 100644 index 31655dd..0000000 --- a/template/docs/Makefile +++ /dev/null @@ -1,29 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build -AUTODOCDIR = api - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1) -$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/") -endif - -.PHONY: help clean Makefile - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -clean: - rm -rf $(BUILDDIR)/* $(AUTODOCDIR) - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/template/docs/conf.py b/template/docs/conf.py index 7af8616..d0383fc 100644 --- a/template/docs/conf.py +++ b/template/docs/conf.py @@ -1,333 +1,51 @@ -# This file is execfile()d with the current directory set to its containing dir. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html -# -# All configuration values have a default; values that are commented out -# serve to show the default. - import os import sys -import shutil - -# -- Path setup -------------------------------------------------------------- - -__location__ = os.path.dirname(__file__) -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -sys.path.insert(0, os.path.join(__location__, "../src")) +sys.path.insert(0, os.path.abspath("../src")) -# -- Run sphinx-apidoc ------------------------------------------------------- -# This hack is necessary since RTD does not issue `sphinx-apidoc` before running -# `sphinx-build -b html . _build/html`. See Issue: -# https://github.com/readthedocs/readthedocs.org/issues/1139 -# DON'T FORGET: Check the box "Install your project inside a virtualenv using -# setup.py install" in the RTD Advanced Settings. -# Additionally it helps us to avoid running apidoc manually - -try: # for Sphinx >= 1.7 - from sphinx.ext import apidoc -except ImportError: - from sphinx import apidoc - -output_dir = os.path.join(__location__, "api") -module_dir = os.path.join(__location__, "../src/{{ project_name|replace("-", "_") }}") -try: - shutil.rmtree(output_dir) -except FileNotFoundError: - pass +project = "{{ project_name|replace('-', '_') }}" +copyright = "2026, {{ author_name }}" +author = "{{ author_name }}" try: - import sphinx - - cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}" - - args = cmd_line.split(" ") - if tuple(sphinx.__version__.split(".")) >= ("1", "7"): - # This is a rudimentary parse_version to avoid external dependencies - args = args[1:] - - apidoc.main(args) -except Exception as e: - print("Running `sphinx-apidoc` failed!\n{}".format(e)) - -# -- General configuration --------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' + from importlib.metadata import version + release = version(project) +except Exception: + release = "unknown" -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. extensions = [ "sphinx.ext.autodoc", - "sphinx.ext.intersphinx", - "sphinx.ext.todo", "sphinx.ext.autosummary", "sphinx.ext.viewcode", - "sphinx.ext.coverage", - "sphinx.ext.doctest", - "sphinx.ext.ifconfig", - "sphinx.ext.mathjax", "sphinx.ext.napoleon", + "sphinx.ext.intersphinx", + "myst_nb", + "sphinx_autodoc_typehints", ] -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - - -# Enable markdown -extensions.append("myst_parser") - -# Configure MyST-Parser myst_enable_extensions = [ - "amsmath", "colon_fence", "deflist", - "dollarmath", "html_image", "linkify", "replacements", "smartquotes", - "substitution", "tasklist", ] -# The suffix of source filenames. -source_suffix = [".rst", ".md"] - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = "index" - -# General information about the project. -project = "{{ project_name|replace("-", "_") }}" -copyright = "2026, {{ author_name }}" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# version: The short X.Y version. -# release: The full version, including alpha/beta/rc tags. -# If you don’t need the separation provided between version and release, -# just set them both to the same value. -try: - from importlib.metadata import version as get_version - version = get_version("{{ project_name|replace("-", "_") }}") -except Exception: - version = "unknown" - -if not version or version.lower() == "unknown": - version = os.getenv("READTHEDOCS_VERSION", "unknown") # automatically set by RTD - -release = version - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. +templates_path = ["_templates"] exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"] - -# The reST default role (used for this markup: `text`) to use for all documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -# keep_warnings = False - -# If this is True, todo emits a warning for each TODO entries. The default is False. -todo_emit_warnings = True - - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = "alabaster" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -html_theme_options = { - "light_css_variables": { - "color-brand-primary": "#0052cc", - "color-brand-content": "#0052cc", - }, - "dark_css_variables": { - "color-brand-primary": "#4c9aff", - "color-brand-content": "#4c9aff", - }, - "source_repository": "https://github.com/YOUR_ORG_OR_USERNAME/{{ project_name|replace("-", "_") }}", - "source_branch": "main", - "source_directory": "docs/", -} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = "" - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". +html_theme = "furo" html_static_path = ["_static"] -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = "{{ project_name|replace("-", "_") }}-doc" - - -# -- Options for LaTeX output ------------------------------------------------ - -latex_elements = { - # The paper size ("letterpaper" or "a4paper"). - # "papersize": "letterpaper", - # The font size ("10pt", "11pt" or "12pt"). - # "pointsize": "10pt", - # Additional stuff for the LaTeX preamble. - # "preamble": "", -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ("index", "user_guide.tex", "{{ project_name|replace("-", "_") }} Documentation", "{{ author_name }}", "manual") -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = "" - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - -# -- External mapping -------------------------------------------------------- -python_version = ".".join(map(str, sys.version_info[0:2])) -intersphinx_mapping = { - "sphinx": ("https://www.sphinx-doc.org/en/master", None), - "python": ("https://docs.python.org/" + python_version, None), - "matplotlib": ("https://matplotlib.org", None), - "numpy": ("https://numpy.org/doc/stable", None), - "sklearn": ("https://scikit-learn.org/stable", None), - "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None), - "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), - "setuptools": ("https://setuptools.pypa.io/en/stable/", None), -} - -print(f"loading configurations for {project} {version} ...", file=sys.stderr) - -# -- Biocsetup configuration ------------------------------------------------- - -# Enable execution of code chunks in markdown -extensions.remove('myst_parser') -extensions.append('myst_nb') - -# Less verbose api documentation -extensions.append('sphinx_autodoc_typehints') - +# Autosummary settings +autosummary_generate = True autodoc_default_options = { - "special-members": True, + "members": True, + "show-inheritance": True, "undoc-members": True, - "exclude-members": "__weakref__, __dict__, __str__, __module__", } -autosummary_generate = True -autosummary_imported_members = True - -html_theme = "furo" +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), +} diff --git a/template/docs/index.md b/template/docs/index.md index aa6896f..e55592f 100644 --- a/template/docs/index.md +++ b/template/docs/index.md @@ -1,39 +1,36 @@ -# {{ project_name }} +# Welcome to {{ project_name }} -Add a short description here! +**{{ description }}** +## Quick Start -## Note - -> This is the main page of your project's [Sphinx] documentation. It is -> formatted in [Markdown]. Add additional pages by creating md-files in -> `docs` or rst-files (formatted in [reStructuredText]) and adding links to -> them in the `Contents` section below. -> -> Please check [Sphinx] and [MyST] for more information -> about how to document your project and how to configure your preferences. - +```bash +pip install {{ project_name }} +``` -## Contents +Check out the [Overview](readme.md) for more detailed instructions and tutorials! ```{toctree} :maxdepth: 2 +:hidden: +Home Overview +Module Reference +``` + +```{toctree} +:maxdepth: 1 +:hidden: +:caption: Project Info + Contributions & Help License Authors Changelog -Module Reference ``` ## Indices and tables * {ref}`genindex` * {ref}`modindex` -* {ref}`search` - -[Sphinx]: http://www.sphinx-doc.org/ -[Markdown]: https://daringfireball.net/projects/markdown/ -[reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html -[MyST]: https://myst-parser.readthedocs.io/en/latest/ diff --git a/template/docs/requirements.txt b/template/docs/requirements.txt deleted file mode 100644 index a1b9d2b..0000000 --- a/template/docs/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -# Requirements file for ReadTheDocs, check .readthedocs.yml. -# To build the module reference correctly, make sure every external package -# under `install_requires` in `setup.cfg` is also listed here! -# sphinx_rtd_theme -myst-parser[linkify] -sphinx>=3.2.1 -myst-nb -furo -sphinx-autodoc-typehints diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja index 13390e1..4cfd36d 100644 --- a/template/pyproject.toml.jinja +++ b/template/pyproject.toml.jinja @@ -7,6 +7,27 @@ requires-python = ">=3.12" authors = [ { name = "{{ author_name }}", email = "{{ author_email }}" } ] +keywords = [ + "FIXME", + "TODO", +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Developers", + "License :: OSI Approved :: {{ license }} License", + "Programming Language :: Python :: 3", + "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", +] + +[project.urls] +Homepage = "https://github.com/{{ github_username }}/{{ project_name }}" +Documentation = "https://github.com/{{ github_username }}/{{ project_name }}" +Repository = "https://github.com/{{ github_username }}/{{ project_name }}" +"Bug Tracker" = "https://github.com/{{ github_username }}/{{ project_name }}/issues" [build-system] requires = ["hatchling", "hatch-vcs"] diff --git a/template/tox.ini b/template/tox.ini index 4b4791a..dbc5d26 100644 --- a/template/tox.ini +++ b/template/tox.ini @@ -48,6 +48,7 @@ setenv = 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} [testenv:publish] From e0d89cbb9d18ebf13fd4ad5ef6063d034d866348 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 22:55:01 -0700 Subject: [PATCH 05/10] update the repo package structurewith the template --- .github/workflows/pre-commit.yml | 28 +-- .github/workflows/publish-pypi.yml | 104 ++++++--- .github/workflows/run-tests.yml | 18 +- .python-version | 1 - .zenodo.json | 14 -- docs/Makefile | 29 --- docs/api/modules.rst | 4 +- docs/conf.py | 324 ++--------------------------- docs/index.md | 25 ++- docs/requirements.txt | 9 - template/docs/conf.py | 6 +- tox.ini | 1 + 12 files changed, 152 insertions(+), 411 deletions(-) delete mode 100644 .python-version delete mode 100644 .zenodo.json delete mode 100644 docs/Makefile delete mode 100644 docs/requirements.txt diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index d638c47..e752aca 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -1,16 +1,16 @@ -name: pre-commit +# name: pre-commit -on: - pull_request: - push: - branches: [main] +# on: +# pull_request: +# push: +# branches: [main] -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: - python-version: '3.12' - - uses: pre-commit/action@v3.0.1 +# jobs: +# pre-commit: +# runs-on: ubuntu-latest +# steps: +# - uses: actions/checkout@v4 +# - uses: actions/setup-python@v5 +# with: +# python-version: '3.12' +# - uses: pre-commit/action@v3.0.1 diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 81ef189..68e2196 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -1,53 +1,101 @@ -name: Publish to PyPI +name: Publish to PyPI and GitHub Pages on: push: tags: "*" jobs: - build: + build-and-test: + name: Build and Test runs-on: ubuntu-latest - permissions: - id-token: write - repository-projects: write - contents: write - pages: write - steps: - uses: actions/checkout@v4 + + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true - name: Set up Python 3.12 uses: actions/setup-python@v5 with: python-version: 3.12 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install uv tox - uv sync + - name: Install tox + run: uv tool install tox --with tox-uv - name: Test - run: | - tox -e default + run: tox -e default - name: Build Project - run: | - tox -e build + run: tox -e build - # This uses the trusted publisher workflow so no token is required. - - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Store the distribution packages + uses: actions/upload-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + build-docs: + 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 + + - 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 - name: Build docs - run: | - tox -e docs + run: tox -e docs + + - name: Add .nojekyll + run: touch ./docs/_build/html/.nojekyll - - run: touch ./docs/_build/html/.nojekyll + - name: Upload Pages artifact + uses: actions/upload-pages-artifact@v3 + with: + path: ./docs/_build/html - - name: GH Pages Deployment - uses: JamesIves/github-pages-deploy-action@v4 + publish-pypi: + name: Publish to PyPI + needs: build-and-test + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/{{ project_name|replace('-', '_') }} + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 with: - branch: gh-pages # The branch the action should deploy to. - folder: ./docs/_build/html - clean: true # Automatically remove deleted files from the deploy branch + name: python-package-distributions + path: dist/ + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + deploy-pages: + name: Deploy GitHub Pages + needs: build-docs + runs-on: ubuntu-latest + permissions: + pages: write + id-token: write + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index d84e762..4aa904e 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -28,7 +28,7 @@ jobs: test: strategy: matrix: - python: ["3.12", "3.13", "3.14"] + python: ["3.10", "3.11", "3.12", "3.13", "3.14"] platform: - ubuntu-latest - macos-latest @@ -38,16 +38,18 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - id: setup-python + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + + - name: Set up Python + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install uv tox - uv sync + - name: Install tox + run: uv tool install tox --with tox-uv - name: Run tests run: | diff --git a/.python-version b/.python-version deleted file mode 100644 index e4fba21..0000000 --- a/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.12 diff --git a/.zenodo.json b/.zenodo.json deleted file mode 100644 index bacfb27..0000000 --- a/.zenodo.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "title": "hatchit", - "description": "Modern Python project scaffolder combining uv and hatch", - "creators": [ - { - "name": "Jayaram Kancherla", - "affiliation": "YOUR_AFFILIATION", - "orcid": "0000-0000-0000-0000" - } - ], - "access_right": "open", - "license": "MIT", - "upload_type": "software" -} diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 31655dd..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,29 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build -AUTODOCDIR = api - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1) -$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/") -endif - -.PHONY: help clean Makefile - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -clean: - rm -rf $(BUILDDIR)/* $(AUTODOCDIR) - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/api/modules.rst b/docs/api/modules.rst index 23a6cad..c48b07e 100644 --- a/docs/api/modules.rst +++ b/docs/api/modules.rst @@ -1,5 +1,5 @@ -hatchit -======= +src +=== .. toctree:: :maxdepth: 4 diff --git a/docs/conf.py b/docs/conf.py index a586fc4..2fcf0f9 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,333 +1,53 @@ -# This file is execfile()d with the current directory set to its containing dir. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html -# -# All configuration values have a default; values that are commented out -# serve to show the default. - import os import sys -import shutil - -# -- Path setup -------------------------------------------------------------- - -__location__ = os.path.dirname(__file__) -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -sys.path.insert(0, os.path.join(__location__, "../src")) +sys.path.insert(0, os.path.abspath("../src")) -# -- Run sphinx-apidoc ------------------------------------------------------- -# This hack is necessary since RTD does not issue `sphinx-apidoc` before running -# `sphinx-build -b html . _build/html`. See Issue: -# https://github.com/readthedocs/readthedocs.org/issues/1139 -# DON'T FORGET: Check the box "Install your project inside a virtualenv using -# setup.py install" in the RTD Advanced Settings. -# Additionally it helps us to avoid running apidoc manually - -try: # for Sphinx >= 1.7 - from sphinx.ext import apidoc -except ImportError: - from sphinx import apidoc - -output_dir = os.path.join(__location__, "api") -module_dir = os.path.join(__location__, "../src/hatchit") -try: - shutil.rmtree(output_dir) -except FileNotFoundError: - pass +project = "hatchit" +copyright = "2026, Jayaram Kancherla" +author = "Jayaram Kancherla" try: - import sphinx - - cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir} {os.path.join(module_dir, 'templates')}" - - args = cmd_line.split(" ") - if tuple(sphinx.__version__.split(".")) >= ("1", "7"): - # This is a rudimentary parse_version to avoid external dependencies - args = args[1:] - - apidoc.main(args) -except Exception as e: - print("Running `sphinx-apidoc` failed!\n{}".format(e)) - -# -- General configuration --------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' + from importlib.metadata import version as get_version + version = get_version(project) + release = version +except Exception: + version = "unknown" + release = "unknown" -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. extensions = [ "sphinx.ext.autodoc", - "sphinx.ext.intersphinx", - "sphinx.ext.todo", "sphinx.ext.autosummary", "sphinx.ext.viewcode", - "sphinx.ext.coverage", - "sphinx.ext.doctest", - "sphinx.ext.ifconfig", - "sphinx.ext.mathjax", "sphinx.ext.napoleon", + "sphinx.ext.intersphinx", + "myst_nb", + "sphinx_autodoc_typehints", ] -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - - -# Enable markdown -extensions.append("myst_parser") - -# Configure MyST-Parser myst_enable_extensions = [ - "amsmath", "colon_fence", "deflist", - "dollarmath", "html_image", "linkify", "replacements", "smartquotes", - "substitution", "tasklist", ] -# The suffix of source filenames. -source_suffix = [".rst", ".md"] - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = "index" - -# General information about the project. -project = "hatchit" -copyright = "2026, Jayaram Kancherla" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# version: The short X.Y version. -# release: The full version, including alpha/beta/rc tags. -# If you don’t need the separation provided between version and release, -# just set them both to the same value. -try: - from importlib.metadata import version as get_version - version = get_version("hatchit") -except Exception: - version = "unknown" - -if not version or version.lower() == "unknown": - version = os.getenv("READTHEDOCS_VERSION", "unknown") # automatically set by RTD - -release = version - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. +templates_path = ["_templates"] exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"] - -# The reST default role (used for this markup: `text`) to use for all documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -# keep_warnings = False - -# If this is True, todo emits a warning for each TODO entries. The default is False. -todo_emit_warnings = True - - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = "alabaster" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -html_theme_options = { - "light_css_variables": { - "color-brand-primary": "#0052cc", - "color-brand-content": "#0052cc", - }, - "dark_css_variables": { - "color-brand-primary": "#4c9aff", - "color-brand-content": "#4c9aff", - }, - "source_repository": "https://github.com/YOUR_ORG_OR_USERNAME/hatchit", - "source_branch": "main", - "source_directory": "docs/", -} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = "" - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". +html_theme = "furo" html_static_path = ["_static"] -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = "hatchit-doc" - - -# -- Options for LaTeX output ------------------------------------------------ - -latex_elements = { - # The paper size ("letterpaper" or "a4paper"). - # "papersize": "letterpaper", - # The font size ("10pt", "11pt" or "12pt"). - # "pointsize": "10pt", - # Additional stuff for the LaTeX preamble. - # "preamble": "", -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ("index", "user_guide.tex", "hatchit Documentation", "Jayaram Kancherla", "manual") -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = "" - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - -# -- External mapping -------------------------------------------------------- -python_version = ".".join(map(str, sys.version_info[0:2])) -intersphinx_mapping = { - "sphinx": ("https://www.sphinx-doc.org/en/master", None), - "python": ("https://docs.python.org/" + python_version, None), - "matplotlib": ("https://matplotlib.org", None), - "numpy": ("https://numpy.org/doc/stable", None), - "sklearn": ("https://scikit-learn.org/stable", None), - "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None), - "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), - "setuptools": ("https://setuptools.pypa.io/en/stable/", None), -} - -print(f"loading configurations for {project} {version} ...", file=sys.stderr) - -# -- Biocsetup configuration ------------------------------------------------- - -# Enable execution of code chunks in markdown -extensions.remove('myst_parser') -extensions.append('myst_nb') - -# Less verbose api documentation -extensions.append('sphinx_autodoc_typehints') - +# Autosummary settings +autosummary_generate = True autodoc_default_options = { - "special-members": True, + "members": True, + "show-inheritance": True, "undoc-members": True, - "exclude-members": "__weakref__, __dict__, __str__, __module__", } -autosummary_generate = True -autosummary_imported_members = True - -html_theme = "furo" +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), +} diff --git a/docs/index.md b/docs/index.md index f5ac178..bc2f681 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,17 +4,38 @@ A modern, Python project scaffolder combining the blazing speed of `uv` with the `hatchit` generates publication-ready Python packages out-of-the-box, fully equipped with automated testing, documentation, and scientific publishing metadata. -## Contents +## Quick Start + +```bash +pip install hatchit +``` + +Check out the [Overview](readme.md) for more detailed instructions and tutorials! + ```{toctree} :maxdepth: 2 +:hidden: +Home readme setup development publishing +API +``` + +```{toctree} +:maxdepth: 1 +:hidden: +:caption: Project Info + contributing authors changelog license -API ``` + +## Indices and tables + +* {ref}`genindex` +* {ref}`modindex` diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index a1b9d2b..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -# Requirements file for ReadTheDocs, check .readthedocs.yml. -# To build the module reference correctly, make sure every external package -# under `install_requires` in `setup.cfg` is also listed here! -# sphinx_rtd_theme -myst-parser[linkify] -sphinx>=3.2.1 -myst-nb -furo -sphinx-autodoc-typehints diff --git a/template/docs/conf.py b/template/docs/conf.py index d0383fc..3370b5e 100644 --- a/template/docs/conf.py +++ b/template/docs/conf.py @@ -8,9 +8,11 @@ author = "{{ author_name }}" try: - from importlib.metadata import version - release = version(project) + from importlib.metadata import version as get_version + version = get_version(project) + release = version except Exception: + version = "unknown" release = "unknown" extensions = [ diff --git a/tox.ini b/tox.ini index 4b4791a..dbc5d26 100644 --- a/tox.ini +++ b/tox.ini @@ -48,6 +48,7 @@ setenv = 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} [testenv:publish] From 0b4bec9e4704bdd1999408a01bd156a75a8643a5 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 22:56:37 -0700 Subject: [PATCH 06/10] update package metadata --- pyproject.toml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index aa99644..07e30d3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ authors = [ ] requires-python = ">=3.12" dependencies = ["uv", "copier>=9.0.0"] -keywords = ["scaffold", "uv", "hatch", "project", "generator"] +keywords = ["scaffold", "uv", "hatch", "project", "generator", "template", "copier", "packaging", "pypi"] classifiers = [ "Development Status :: 4 - Beta", "Programming Language :: Python :: 3", @@ -22,8 +22,10 @@ classifiers = [ ] [project.urls] +Homepage = "https://github.com/biocpy/hatchit" +Documentation = "https://biocpy.github.io/hatchit" Repository = "https://github.com/biocpy/hatchit" -Issues = "https://github.com/biocpy/hatchit/issues" +"Bug Tracker" = "https://github.com/biocpy/hatchit/issues" [project.scripts] hatchit = "hatchit.cli:main" From f739c4fd5bd2c5d97fbe15c21e046de9c25655b0 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 23:04:09 -0700 Subject: [PATCH 07/10] ssupport more licenses --- copier.yml | 9 + template/LICENSE.md | 21 - template/pyproject.toml.jinja | 10 +- ...'Apache-2.0' %}LICENSE.md{% endif %}.jinja | 176 +++++ ...SD-3-Clause' %}LICENSE.md{% endif %}.jinja | 24 + ...PL-3.0-only' %}LICENSE.md{% endif %}.jinja | 621 ++++++++++++++++++ ...nse == 'MIT' %}LICENSE.md{% endif %}.jinja | 21 + 7 files changed, 860 insertions(+), 22 deletions(-) delete mode 100644 template/LICENSE.md create mode 100644 template/{% if license == 'Apache-2.0' %}LICENSE.md{% endif %}.jinja create mode 100644 template/{% if license == 'BSD-3-Clause' %}LICENSE.md{% endif %}.jinja create mode 100644 template/{% if license == 'GPL-3.0-only' %}LICENSE.md{% endif %}.jinja create mode 100644 template/{% if license == 'MIT' %}LICENSE.md{% endif %}.jinja diff --git a/copier.yml b/copier.yml index c3e6202..c7c980b 100644 --- a/copier.yml +++ b/copier.yml @@ -12,6 +12,15 @@ license: type: str default: MIT help: License for the project + choices: + "Permissive - MIT": "MIT" + "Permissive - BSD-3-Clause": "BSD-3-Clause" + "Permissive - Apache-2.0": "Apache-2.0" + "Copyleft - GPL-3.0": "GPL-3.0-only" +copyright_year: + type: str + default: "{{ '%Y' | strftime }}" + help: "What is the starting year of the project? Used in copyright statements." # Author Info author_name: diff --git a/template/LICENSE.md b/template/LICENSE.md deleted file mode 100644 index bea5c9c..0000000 --- a/template/LICENSE.md +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2024 {{ project_name }} authors - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja index 4cfd36d..042f982 100644 --- a/template/pyproject.toml.jinja +++ b/template/pyproject.toml.jinja @@ -14,7 +14,15 @@ keywords = [ classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", - "License :: OSI Approved :: {{ license }} License", +{%- if license == "MIT" %} + "License :: OSI Approved :: MIT License", +{%- elif license == "BSD-3-Clause" %} + "License :: OSI Approved :: BSD License", +{%- elif license == "Apache-2.0" %} + "License :: OSI Approved :: Apache Software License", +{%- elif license == "GPL-3.0-only" %} + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", +{%- endif %} "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", diff --git a/template/{% if license == 'Apache-2.0' %}LICENSE.md{% endif %}.jinja b/template/{% if license == 'Apache-2.0' %}LICENSE.md{% endif %}.jinja new file mode 100644 index 0000000..4f6f639 --- /dev/null +++ b/template/{% if license == 'Apache-2.0' %}LICENSE.md{% endif %}.jinja @@ -0,0 +1,176 @@ + Apache License + Version 2.0, January 2004 + https://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS diff --git a/template/{% if license == 'MIT' %}LICENSE.md{% endif %}.jinja b/template/{% if license == 'MIT' %}LICENSE.md{% endif %}.jinja new file mode 100644 index 0000000..3034238 --- /dev/null +++ b/template/{% if license == 'MIT' %}LICENSE.md{% endif %}.jinja @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) {{ copyright_year }} {{ author_name }} + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of +the Software, and to permit persons to whom the Software is furnished to do so, +subject to the following conditions: + +The above copyright notice and this permission notice (including the next +paragraph) shall be included in all copies or substantial portions of the +Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. From 654cef9d751097233f1da99f8e6b0264b9c5668b Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 23:13:05 -0700 Subject: [PATCH 08/10] update changelog --- CHANGELOG.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index de395b6..83320af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,6 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased] +## 0.1.0 - 0.1.1 -### Added -- Initial project scaffolding. +- Switch to copier and modify the templates From ed03414cca2b6d059aea993c3d329fd9f7a2ae5f Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 23:16:31 -0700 Subject: [PATCH 09/10] fix tests for windows --- copier.yml | 4 ++++ .../__init__.py | 0 .../py.typed | 0 3 files changed, 4 insertions(+) rename template/src/{{{ project_name|replace('-', '_') }} => {{ python_package_name }}}/__init__.py (100%) rename template/src/{{{ project_name|replace('-', '_') }} => {{ python_package_name }}}/py.typed (100%) diff --git a/copier.yml b/copier.yml index c7c980b..405369e 100644 --- a/copier.yml +++ b/copier.yml @@ -4,6 +4,10 @@ _subdirectory: template project_name: type: str help: Name of the project (e.g. my-awesome-package) +python_package_name: + type: str + default: "{{ project_name|replace('-', '_') }}" + when: false description: type: str default: "Add a short description here!" diff --git a/template/src/{{ project_name|replace('-', '_') }}/__init__.py b/template/src/{{ python_package_name }}/__init__.py similarity index 100% rename from template/src/{{ project_name|replace('-', '_') }}/__init__.py rename to template/src/{{ python_package_name }}/__init__.py diff --git a/template/src/{{ project_name|replace('-', '_') }}/py.typed b/template/src/{{ python_package_name }}/py.typed similarity index 100% rename from template/src/{{ project_name|replace('-', '_') }}/py.typed rename to template/src/{{ python_package_name }}/py.typed From b41fd339c8533a78a648284786c61791189b065e Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 23:21:43 -0700 Subject: [PATCH 10/10] set defaults to true when running copier in ci --- src/hatchit/scaffold.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/hatchit/scaffold.py b/src/hatchit/scaffold.py index 7177526..3c858fa 100644 --- a/src/hatchit/scaffold.py +++ b/src/hatchit/scaffold.py @@ -66,6 +66,6 @@ def create_hatchit_repository(project_path: str, description: str, license: str) # Fallback for when the package is installed template_dir = Path(__file__).parent - copier.run_copy(str(template_dir), project_path, data=data, vcs_ref="HEAD", unsafe=True) + copier.run_copy(str(template_dir), project_path, data=data, vcs_ref="HEAD", unsafe=True, defaults=True) print("hatchit complete! 🚀 💥")