Merge pull request #193 from pharmaverse/sort-deps

Add uv-based dependency sorting script and sort dependencies

Author: elong0527

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## rtflite (development version)
+
+### Maintenance
+
+- Add a script to automate sorting dependencies in `pyproject.toml` and
+  re-sort pyproject dependencies using the script (#193).
+
 ## rtflite 2.5.3
 
 ### Documentation

docs/changelog.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## rtflite (development version)
+
+### Maintenance
+
+- Add a script to automate sorting dependencies in `pyproject.toml` and
+  re-sort pyproject dependencies using the script (#193).
+
 ## rtflite 2.5.3
 
 ### Documentation

pyproject.toml

@@ -7,10 +7,10 @@ authors = [
     { name = "Nan Xiao", email = "me@nanx.me" },
 ]
 dependencies = [
-    "pydantic>=2.0.0",
-    "pillow>=8.0.0",
     "narwhals>=1.0.0",
+    "pillow>=8.0.0",
     "polars>=1.0.0",
+    "pydantic>=2.0.0",
 ]
 readme = "README.md"
 requires-python = ">= 3.10"
@@ -100,20 +100,20 @@ exclude = [
 
 [dependency-groups]
 dev = [
-    "pytest>=8.3.3",
-    "pytest-cov>=6.0.0",
-    "pytest-r-snapshot>=0.1.0",
-    "zensical>=0.0.15",
-    "mkdocstrings-python>=1.12.2",
-    "markdown-exec[ansi]>=1.11.0",
     "griffe-pydantic>=1.1.8",
-    "ruff>=0.7.4",
     "isort>=5.13.2",
-    "mypy>=1.17.1",
+    "markdown-exec[ansi]>=1.11.0",
     "matplotlib>=3.10.5",
+    "mkdocstrings-python>=1.12.2",
+    "mypy>=1.17.1",
     "pandas>=2.2.3",
-    "pyarrow >= 21.0.0; python_version < '3.14'",
-    "pyarrow >= 22.0.0; python_version >= '3.14'",
+    "pyarrow>=21.0.0 ; python_version < '3.14'",
+    "pyarrow>=22.0.0 ; python_version >= '3.14'",
+    "pytest>=8.3.3",
+    "pytest-cov>=6.0.0",
+    "pytest-r-snapshot>=0.1.0",
+    "ruff>=0.7.4",
+    "zensical>=0.0.15",
 ]
 
 [tool.ruff.lint]

scripts/sort_deps.py

@@ -0,0 +1,283 @@
+"""Sort pyproject.toml dependencies by re-adding them with uv.
+
+This script reads dependency declarations from pyproject.toml, removes them with
+`uv remove`, and re-adds them with `uv add` so uv's automatic sorting is applied.
+"""
+
+from __future__ import annotations
+
+import argparse
+import re
+import shlex
+import subprocess
+import sys
+from pathlib import Path
+
+try:
+    import tomllib
+except ImportError as exc:  # pragma: no cover - tomllib is Python 3.11+
+    print("This script requires Python 3.11+ (tomllib).", file=sys.stderr)
+    raise SystemExit(1) from exc
+
+
+NAME_RE = re.compile(r"^\s*([A-Za-z0-9][A-Za-z0-9._-]*)")
+
+
+def load_pyproject(path: Path) -> dict:
+    """Load a pyproject.toml file into a dict.
+
+    Args:
+        path: Path to pyproject.toml.
+
+    Returns:
+        Parsed TOML content.
+    """
+    if not path.is_file():
+        raise FileNotFoundError(f"pyproject.toml not found: {path}")
+    with path.open("rb") as handle:
+        return tomllib.load(handle)
+
+
+def ensure_string_list(value: object, location: str) -> list[str]:
+    """Validate a TOML value is a list of strings.
+
+    Args:
+        value: Value to validate.
+        location: Friendly location string for error messages.
+
+    Returns:
+        The original list, typed as list[str].
+
+    Raises:
+        TypeError: If the value is not a list of strings.
+    """
+    if value is None:
+        return []
+    if not isinstance(value, list):
+        raise TypeError(f"Expected {location} to be a list of strings.")
+    for item in value:
+        if not isinstance(item, str):
+            raise TypeError(f"Expected {location} to contain only strings.")
+    return value
+
+
+def ensure_mapping(value: object, location: str) -> dict[str, list[str]]:
+    """Validate a TOML table of dependency groups.
+
+    Args:
+        value: Value to validate.
+        location: Friendly location string for error messages.
+
+    Returns:
+        Mapping of group name to dependency list.
+
+    Raises:
+        TypeError: If the value is not a string-keyed mapping of lists.
+    """
+    if value is None:
+        return {}
+    if not isinstance(value, dict):
+        raise TypeError(f"Expected {location} to be a table of lists.")
+    result: dict[str, list[str]] = {}
+    for key, entries in value.items():
+        if not isinstance(key, str):
+            raise TypeError(f"Expected {location} keys to be strings.")
+        result[key] = ensure_string_list(entries, f"{location}.{key}")
+    return result
+
+
+def extract_name(requirement: str) -> str:
+    """Extract the package name from a requirement string.
+
+    Args:
+        requirement: PEP 508-style requirement string.
+
+    Returns:
+        The package name.
+
+    Raises:
+        ValueError: If the requirement cannot be parsed.
+    """
+    match = NAME_RE.match(requirement)
+    if not match:
+        raise ValueError(f"Unable to parse dependency name from: {requirement!r}")
+    return match.group(1)
+
+
+def unique_in_order(items: list[str]) -> list[str]:
+    """Return unique items while preserving first-seen order.
+
+    Args:
+        items: Items to de-duplicate.
+
+    Returns:
+        Unique items in their original order.
+    """
+    seen: set[str] = set()
+    result: list[str] = []
+    for item in items:
+        if item in seen:
+            continue
+        seen.add(item)
+        result.append(item)
+    return result
+
+
+def run_uv(command: list[str], cwd: Path, dry_run: bool) -> None:
+    """Run a uv command, or print it when in dry-run mode.
+
+    Args:
+        command: Command and arguments to execute.
+        cwd: Working directory for the uv invocation.
+        dry_run: When true, print the command without executing it.
+    """
+    printable = shlex.join(command)
+    if dry_run:
+        print(f"[dry-run] {printable}")
+        return
+    print(f"[run] {printable}")
+    subprocess.run(command, cwd=cwd, check=True)
+
+
+def remove_and_add(
+    *,
+    requirements: list[str],
+    remove_flags: list[str],
+    add_flags_prefix: list[str],
+    add_flags_suffix: list[str],
+    cwd: Path,
+    dry_run: bool,
+) -> None:
+    """Remove and re-add requirements using uv with the given flags.
+
+    Args:
+        requirements: Requirement strings to manage.
+        remove_flags: Flags passed to `uv remove`.
+        add_flags_prefix: Flags placed before requirements in `uv add`.
+        add_flags_suffix: Flags placed after requirements in `uv add`.
+        cwd: Working directory for uv commands.
+        dry_run: When true, print commands without executing them.
+    """
+    if not requirements:
+        return
+    names = unique_in_order([extract_name(req) for req in requirements])
+    if names:
+        run_uv(["uv", "remove", *remove_flags, *names], cwd=cwd, dry_run=dry_run)
+    run_uv(
+        ["uv", "add", *add_flags_prefix, *requirements, *add_flags_suffix],
+        cwd=cwd,
+        dry_run=dry_run,
+    )
+
+
+def reset_python_version_markers(path: Path, *, dry_run: bool) -> None:
+    """Replace python_full_version markers with python_version in pyproject.toml.
+
+    Args:
+        path: Path to pyproject.toml.
+        dry_run: When true, print the change without writing the file.
+    """
+    content = path.read_text(encoding="utf-8")
+    updated = content.replace("python_full_version", "python_version")
+    if updated == content:
+        return
+    if dry_run:
+        print(f"[dry-run] replace python_full_version markers in {path}")
+        return
+    path.write_text(updated, encoding="utf-8")
+
+
+def parse_args() -> argparse.Namespace:
+    """Parse CLI arguments for the script."""
+    default_pyproject = Path(__file__).resolve().parents[1] / "pyproject.toml"
+    parser = argparse.ArgumentParser(
+        description="Re-add dependencies with uv to sort them in pyproject.toml."
+    )
+    parser.add_argument(
+        "--pyproject",
+        type=Path,
+        default=default_pyproject,
+        help="Path to pyproject.toml (default: repo root).",
+    )
+    parser.add_argument(
+        "--no-sync",
+        action="store_true",
+        help="Pass --no-sync to uv commands.",
+    )
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Print uv commands without executing them.",
+    )
+    return parser.parse_args()
+
+
+def main() -> int:
+    """Entry point for sorting dependencies via uv."""
+    args = parse_args()
+    pyproject_path = args.pyproject
+    if pyproject_path.is_dir():
+        pyproject_path = pyproject_path / "pyproject.toml"
+    data = load_pyproject(pyproject_path)
+    root = pyproject_path.parent
+    no_sync = ["--no-sync"] if args.no_sync else []
+
+    project = data.get("project", {})
+    dependencies = ensure_string_list(
+        project.get("dependencies"), "project.dependencies"
+    )
+    optional_dependencies = ensure_mapping(
+        project.get("optional-dependencies"), "project.optional-dependencies"
+    )
+    dependency_groups = ensure_mapping(
+        data.get("dependency-groups"), "dependency-groups"
+    )
+
+    remove_and_add(
+        requirements=dependencies,
+        remove_flags=no_sync,
+        add_flags_prefix=no_sync,
+        add_flags_suffix=[],
+        cwd=root,
+        dry_run=args.dry_run,
+    )
+
+    for group, requirements in dependency_groups.items():
+        add_suffix: list[str]
+        if group == "dev":
+            remove_flags = [*no_sync, "--dev"]
+            add_prefix = [*no_sync, "--dev"]
+            add_suffix = []
+        else:
+            remove_flags = [*no_sync, "--group", group]
+            add_prefix = [*no_sync, "--group", group]
+            add_suffix = []
+        remove_and_add(
+            requirements=requirements,
+            remove_flags=remove_flags,
+            add_flags_prefix=add_prefix,
+            add_flags_suffix=add_suffix,
+            cwd=root,
+            dry_run=args.dry_run,
+        )
+
+    for group, requirements in optional_dependencies.items():
+        remove_flags = [*no_sync, "--optional", group]
+        add_prefix = [*no_sync]
+        add_suffix = ["--optional", group]
+        remove_and_add(
+            requirements=requirements,
+            remove_flags=remove_flags,
+            add_flags_prefix=add_prefix,
+            add_flags_suffix=add_suffix,
+            cwd=root,
+            dry_run=args.dry_run,
+        )
+
+    reset_python_version_markers(pyproject_path, dry_run=args.dry_run)
+
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())