fix: ruff now uses afterpython/ruff.toml for the whole project, not only files inside afterpython/

- ap init adds [tool.ruff] extend = "afterpython/ruff.toml" to pyproject.toml,
  so plain ruff, ap format and editors find the config without --config
- src = ["..", "../src"] in ruff.toml keeps import sorting correct for files inside afterpython/
- ap init skips the ruff setup if a root ruff.toml/.ruff.toml or [tool.ruff] already exists;
  new `ap init ruff` re-runs it
- drop --config from ap check and the ruff pre-commit hooks

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Author: softwareentrepreneer

afterpython/.pre-commit-config.yaml

@@ -31,15 +31,9 @@ repos:
   - id: ruff-check
     stages:
     - pre-commit
-    args:
-    - --config
-    - ./afterpython/ruff.toml
   - id: ruff-format
     stages:
     - pre-commit
-    args:
-    - --config
-    - ./afterpython/ruff.toml
 - repo: local
   hooks:
   # same id twice so that SKIP=ap-commit skips both

afterpython/doc/package_maintenance/package_management.md

@@ -21,10 +21,24 @@ Example wrapper:
 ## Linting and Formatting
 `afterpython` uses [ruff] for linting and formatting, configured in `afterpython/ruff.toml`.
 
-Example wrapper:
-- `ap check` (alias: `ap lint`) runs `ruff check --config ./afterpython/ruff.toml`.
-
-Or you can just directly use `ruff` command as usual since it will automatically find the config file in `afterpython/ruff.toml`.
+`ap init` also adds this to your `pyproject.toml`, so that ruff always finds `afterpython/ruff.toml`:
+```toml
+[tool.ruff]
+extend = "afterpython/ruff.toml"
+```
+Keep all your ruff settings in `afterpython/ruff.toml`, not in `pyproject.toml` or a `ruff.toml` at the project root.
+If `ap init` finds an existing ruff config there, it skips the ruff setup; remove it and run `ap init ruff` to set it up again.
+
+Wrappers (all arguments are passed through to ruff):
+- `ap check` (alias: `ap lint`) runs `ruff check`, e.g. `ap check --fix`.
+- `ap format` runs `ruff format`, e.g. `ap format --check`.
+
+Or you can just directly use the `ruff` command (and ruff editor extensions) as usual, they use the same config.
+
+:::{note}
+Relative paths in `afterpython/ruff.toml` are resolved from `afterpython/`, not the project root,
+e.g. use `"../tests/*"` in `per-file-ignores` to target your project's `tests/` folder.
+:::
 
 
 ---

afterpython/ruff.toml

@@ -1,5 +1,12 @@
 # Ruff configuration
 # See More: https://docs.astral.sh/ruff/configuration/
+#
+# NOTE: relative paths in this file are resolved from afterpython/, not the
+# project root, e.g. use "../tests/*" to target the project's tests/ folder.
+
+# where your own (first-party) packages live, used by import sorting:
+# ".." = project root (flat layout), "../src" = src layout
+src = ["..", "../src"]
 
 line-length = 88
 target-version = "py311"

pyproject.toml

@@ -78,3 +78,6 @@ module-root = "src"
 
 [tool.pyright]
 typeCheckingMode = "basic"
+
+[tool.ruff]
+extend = "afterpython/ruff.toml"

src/afterpython/cli/commands/check.py

@@ -13,7 +13,7 @@
 )
 @click.pass_context
 def check(ctx):
-    """Run ruff linter (uses afterpython/ruff.toml if available)"""
+    """Run ruff linter"""
     from afterpython.utils import handle_passthrough_help
 
     # Show both our options and ruff's help and exit
@@ -23,14 +23,7 @@ def check(ctx):
         show_underlying=True,
     )
 
-    paths = ctx.obj["paths"]
-    ruff_toml = paths.afterpython_path / "ruff.toml"
-    if ruff_toml.exists():
-        click.echo(f"Using ruff configuration from {ruff_toml}")
-        result = subprocess.run(
-            ["ruff", "check", "--config", str(ruff_toml), *ctx.args], check=False
-        )
-    else:
-        result = subprocess.run(["ruff", "check", *ctx.args], check=False)
+    # no --config: ruff finds afterpython/ruff.toml via pyproject.toml's [tool.ruff] extend
+    result = subprocess.run(["ruff", "check", *ctx.args], check=False)
     if result.returncode != 0:
         raise Exit(result.returncode)

src/afterpython/cli/commands/init.py

@@ -5,15 +5,65 @@
 
 import afterpython as ap
 
+# pyproject.toml's [tool.ruff] only points to afterpython/ruff.toml,
+# so that running `ruff` directly (or via editors) also uses afterpython/ruff.toml
+RUFF_EXTEND = "afterpython/ruff.toml"
+
+
+def _find_ruff_config_conflicts() -> list[str]:
+    """Find ruff configs at the project root that would compete with afterpython/ruff.toml."""
+    from afterpython.tools.pyproject import read_pyproject
+
+    conflicts = [
+        name
+        for name in ("ruff.toml", ".ruff.toml")
+        if (ap.paths.user_path / name).exists()
+    ]
+    tool_ruff = read_pyproject().get("tool", {}).get("ruff")
+    if tool_ruff is not None and tool_ruff.unwrap() != {"extend": RUFF_EXTEND}:
+        conflicts.append("[tool.ruff] in pyproject.toml")
+    return conflicts
+
+
+def init_ruff():
+    import tomlkit
+
+    from afterpython.tools.pyproject import read_pyproject, write_pyproject
+
+    if conflicts := _find_ruff_config_conflicts():
+        click.echo(
+            click.style(
+                f"Skipped ruff setup: found existing ruff config ({', '.join(conflicts)}).\n",
+                fg="yellow",
+                bold=True,
+            )
+            + "afterpython keeps all ruff settings in afterpython/ruff.toml, "
+            "and pyproject.toml's [tool.ruff] only points to it.\n"
+            "Until then, `ap check` and `ap format` will use your existing ruff config, "
+            "not afterpython's.\n"
+            "To fix: remove the config(s) above (keep a copy of any settings you want), "
+            "run `ap init ruff`, then add your settings to afterpython/ruff.toml."
+        )
+        return
 
-def init_ruff_toml():
     ruff_toml_path = ap.paths.afterpython_path / "ruff.toml"
     if ruff_toml_path.exists():
         click.echo(f"Ruff configuration file {ruff_toml_path} already exists")
-        return
-    ruff_template_path = ap.paths.templates_path / "ruff-template.toml"
-    shutil.copy(ruff_template_path, ruff_toml_path)
-    click.echo(f"Created {ruff_toml_path}")
+    else:
+        ruff_template_path = ap.paths.templates_path / "ruff-template.toml"
+        shutil.copy(ruff_template_path, ruff_toml_path)
+        click.echo(f"Created {ruff_toml_path}")
+
+    data = read_pyproject()
+    if "ruff" in data.get("tool", {}):
+        return  # already points to afterpython/ruff.toml (checked above)
+    if "tool" not in data:
+        data["tool"] = tomlkit.table(is_super_table=True)
+    ruff_table = tomlkit.table()
+    ruff_table["extend"] = RUFF_EXTEND
+    data["tool"]["ruff"] = ruff_table
+    write_pyproject(data)
+    click.echo(f'Added [tool.ruff] extend = "{RUFF_EXTEND}" to pyproject.toml')
 
 
 def init_faq():
@@ -110,9 +160,10 @@ def init(ctx, yes, skip_website: bool):
             init_prek()
 
         if yes or click.confirm(
-            f"\nCreate ruff.toml in {afterpython_path}?", default=True
+            f"\nCreate ruff.toml in {afterpython_path} (and point pyproject.toml's [tool.ruff] to it)?",
+            default=True,
         ):
-            init_ruff_toml()
+            init_ruff()
 
         if yes or click.confirm(
             "\nCreate release workflow in .github/workflows/release.yml?",
@@ -133,6 +184,16 @@ def init(ctx, yes, skip_website: bool):
         raise
 
 
+@init.command("ruff")
+def init_ruff_subcommand():
+    """Initialize ruff config (afterpython/ruff.toml + [tool.ruff] in pyproject.toml)
+
+    Use this to re-run the ruff setup, e.g. after removing a conflicting
+    ruff config that made `ap init` skip it.
+    """
+    init_ruff()
+
+
 @init.command("website")
 def init_website_subcommand():
     """Initialize project website (MyST config, template, deploy workflow)

src/afterpython/templates/pre-commit-config-template.yaml

@@ -29,15 +29,9 @@ repos:
   - id: ruff-check
     stages:
     - pre-commit
-    args:
-    - --config
-    - ./afterpython/ruff.toml
   - id: ruff-format
     stages:
     - pre-commit
-    args:
-    - --config
-    - ./afterpython/ruff.toml
 - repo: local
   hooks:
   # same id twice so that SKIP=ap-commit skips both

src/afterpython/templates/ruff-template.toml

@@ -1,5 +1,12 @@
 # Ruff configuration
 # See More: https://docs.astral.sh/ruff/configuration/
+#
+# NOTE: relative paths in this file are resolved from afterpython/, not the
+# project root, e.g. use "../tests/*" to target the project's tests/ folder.
+
+# where your own (first-party) packages live, used by import sorting:
+# ".." = project root (flat layout), "../src" = src layout
+src = ["..", "../src"]
 
 line-length = 88
 target-version = "py311"