apply ruff rules (#45)

Closes #26.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: njzjz

.pre-commit-config.yaml

@@ -16,6 +16,8 @@ repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.2.0
     hooks:
+    - id: ruff
+      args: [ --fix ]
     - id: ruff-format
 # numpydoc
 -   repo: https://github.com/Carreau/velin

dargs/__init__.py

@@ -1,3 +1,3 @@
-from .dargs import Argument, Variant, ArgumentEncoder
+from .dargs import Argument, ArgumentEncoder, Variant
 
 __all__ = ["Argument", "Variant", "ArgumentEncoder"]

dargs/dargs.py

@@ -1,5 +1,4 @@
-r"""
-Some (ocaml) pseudo-code here to show the intended type structure::
+r"""Some (ocaml) pseudo-code here to show the intended type structure.
 
     type args = {key: str; value: data; optional: bool; doc: str} list
     and  data =
@@ -40,7 +39,11 @@
 HookArgKType = Callable[["Argument", dict, List[str]], None]
 HookArgVType = Callable[["Argument", Any, List[str]], None]
 HookVrntType = Callable[["Variant", dict, List[str]], None]
-_DUMMYHOOK = lambda a, x, p: None  # for doing nothing in traversing
+
+
+def _DUMMYHOOK(a, x, p):
+    # for doing nothing in traversing
+    pass
 
 
 class _Flags(Enum):
@@ -68,19 +71,19 @@ def __str__(self) -> str:
 
 
 class ArgumentKeyError(ArgumentError):
-    """Error class for missing or invalid argument keys"""
+    """Error class for missing or invalid argument keys."""
 
     pass
 
 
 class ArgumentTypeError(ArgumentError):
-    """Error class for invalid argument data types"""
+    """Error class for invalid argument data types."""
 
     pass
 
 
 class ArgumentValueError(ArgumentError):
-    """Error class for missing or invalid argument values"""
+    """Error class for missing or invalid argument values."""
 
     pass
 
@@ -169,8 +172,12 @@ def __init__(
     def __eq__(self, other: "Argument") -> bool:
         # do not compare doc and default
         # since they do not enter to the type checking
-        fkey = lambda f: f.name
-        vkey = lambda v: v.flag_name
+        def fkey(f):
+            return f.name
+
+        def vkey(v):
+            return v.flag_name
+
         return (
             self.name == other.name
             and set(self.dtype) == set(other.dtype)
@@ -204,7 +211,7 @@ def __getitem__(self, key: str) -> "Argument":
             return self[skey][rkey]
 
     @property
-    def I(self):
+    def I(self):  # noqa:E743
         # return a dummy argument that only has self as a sub field
         # can be used in indexing
         return Argument("_", dict, [self])
@@ -227,7 +234,7 @@ def _reorg_dtype(self):
         if (
             self.optional
             and self.default is not _Flags.NONE
-            and all([not isinstance_annotation(self.default, tt) for tt in self.dtype])
+            and all(not isinstance_annotation(self.default, tt) for tt in self.dtype)
         ):
             self.dtype.add(type(self.default))
         # and make it compatible with `isinstance`
@@ -473,7 +480,7 @@ def normalize(
         do_alias: bool = True,
         trim_pattern: Optional[str] = None,
     ):
-        """Modify `argdict` so that it meets the Argument structure
+        """Modify `argdict` so that it meets the Argument structure.
 
         Normalization can add default values to optional args,
         substitute alias by its standard names, and discard unnecessary
@@ -526,7 +533,7 @@ def normalize_value(
         do_alias: bool = True,
         trim_pattern: Optional[str] = None,
     ):
-        """Modify the value so that it meets the Argument structure
+        """Modify the value so that it meets the Argument structure.
 
         Same as `normalize({self.name: value})[self.name]`.
 
@@ -611,7 +618,7 @@ def gen_doc_head(self, path: Optional[List[str]] = None, **kwargs) -> str:
         if self.optional:
             typesig += ", optional"
             if self.default == "":
-                typesig += f", default: (empty string)"
+                typesig += ", default: (empty string)"
             elif self.default is not _Flags.NONE:
                 typesig += f", default: ``{self.default}``"
         if self.alias:
@@ -733,7 +740,7 @@ def set_default(self, default_tag: Union[bool, str]):
             self.default_tag = default_tag
 
     def extend_choices(self, choices: Optional[Iterable["Argument"]]):
-        """Add a list of choice Arguments to the current Variant"""
+        """Add a list of choice Arguments to the current Variant."""
         # choices is a list of arguments
         # whose name is treated as the switch tag
         # we convert it into a dict for better reference
@@ -760,7 +767,7 @@ def add_choice(
         *args,
         **kwargs,
     ) -> "Argument":
-        """Add a choice Argument to the current Variant"""
+        """Add a choice Argument to the current Variant."""
         if isinstance(tag, Argument):
             newarg = tag
         else:
@@ -835,7 +842,7 @@ def gen_doc(
         if kwargs.get("make_link"):
             if not kwargs.get("make_anchor"):
                 raise ValueError("`make_link` only works with `make_anchor` set")
-            fnstr, target = make_ref_pair(path + [self.flag_name], fnstr, "flag")
+            fnstr, target = make_ref_pair([*path, self.flag_name], fnstr, "flag")
             body_list.append(target + "\n")
         for choice in self.choice_dict.values():
             body_list.append("")
@@ -986,7 +993,7 @@ def isinstance_annotation(value, dtype) -> bool:
 
 
 class ArgumentEncoder(json.JSONEncoder):
-    """Extended JSON Encoder to encode Argument object:
+    """Extended JSON Encoder to encode Argument object.
 
     Examples
     --------

dargs/sphinx.py

@@ -20,7 +20,7 @@
 where `_test_argument` returns an :class:`Argument <dargs.Argument>`. A :class:`list` of :class:`Argument <dargs.Argument>` is also accepted.
 """
 import sys
-from typing import List
+from typing import ClassVar, List
 
 from docutils.parsers.rst import Directive
 from docutils.parsers.rst.directives import unchanged
@@ -34,13 +34,13 @@
 
 
 class DargsDirective(Directive):
-    """dargs directive"""
+    """dargs directive."""
 
-    has_content = True
-    option_spec = dict(
-        module=unchanged,
-        func=unchanged,
-    )
+    has_content: ClassVar[bool] = True
+    option_spec: ClassVar[dict] = {
+        "module": unchanged,
+        "func": unchanged,
+    }
 
     def run(self):
         if "module" in self.options and "func" in self.options:
@@ -58,11 +58,8 @@ def run(self):
 
         if not hasattr(mod, attr_name):
             raise self.error(
-                (
-                    'Module "%s" has no attribute "%s"\n'
-                    "Incorrect argparse :module: or :func: values?"
-                )
-                % (module_name, attr_name)
+                f'Module "{module_name}" has no attribute "{attr_name}"\n'
+                "Incorrect argparse :module: or :func: values?"
             )
         func = getattr(mod, attr_name)
         arguments = func()
@@ -78,7 +75,7 @@ def run(self):
                 make_anchor=True, make_link=True, use_sphinx_domain=True
             )
             rsts.extend(rst.split("\n"))
-        self.state_machine.insert_input(rsts, "%s:%s" % (module_name, attr_name))
+        self.state_machine.insert_input(rsts, f"{module_name}:{attr_name}")
         return []
 
 
@@ -88,17 +85,17 @@ class DargsObject(ObjectDescription):
     This directive creates a signature node for an argument.
     """
 
-    option_spec = dict(
-        path=unchanged,
-    )
+    option_spec: ClassVar[dict] = {
+        "path": unchanged,
+    }
 
     def handle_signature(self, sig, signode):
         signode += addnodes.desc_name(sig, sig)
         return sig
 
     def add_target_and_index(self, name, sig, signode):
         path = self.options["path"]
-        targetid = "%s:%s" % (self.objtype, path)
+        targetid = f"{self.objtype}:{path}"
         if targetid not in self.state.document.ids:
             signode["names"].append(targetid)
             signode["ids"].append(targetid)
@@ -108,16 +105,15 @@ def add_target_and_index(self, name, sig, signode):
             inv = self.env.domaindata["dargs"]["arguments"]
             if targetid in inv:
                 self.state.document.reporter.warning(
-                    'Duplicated argument "%s" described in "%s".'
-                    % (targetid, self.env.doc2path(inv[targetid][0])),
+                    f'Duplicated argument "{targetid}" described in "{self.env.doc2path(inv[targetid][0])}".',
                     line=self.lineno,
                 )
             inv[targetid] = (self.env.docname, self.objtype)
 
         self.indexnode["entries"].append(
             (
                 "pair",
-                "%s ; %s (%s) " % (name, path, self.objtype.title()),
+                f"{name}; {path} ({self.objtype.title()})",
                 targetid,
                 "main",
                 None,
@@ -133,25 +129,25 @@ class DargsDomain(Domain):
     - dargs::argument role
     """
 
-    name = "dargs"
-    label = "dargs"
-    object_types = {
+    name: ClassVar[str] = "dargs"
+    label: ClassVar[str] = "dargs"
+    object_types: ClassVar[dict] = {
         "argument": ObjType("argument", "argument"),
     }
-    directives = {
+    directives: ClassVar[dict] = {
         "argument": DargsObject,
     }
-    roles = {
+    roles: ClassVar[dict] = {
         "argument": XRefRole(),
     }
 
-    initial_data = {
+    initial_data: ClassVar[dict] = {
         "arguments": {},  # fullname -> docname, objtype
     }
 
     def resolve_xref(self, env, fromdocname, builder, typ, target, node, contnode):
         """Resolve cross-references."""
-        targetid = "%s:%s" % (typ, target)
+        targetid = f"{typ}:{target}"
         obj = self.data["arguments"].get(targetid)
         if obj is None:
             return None

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #

pyproject.toml

@@ -32,3 +32,34 @@ include = ["dargs*"]
 
 [tool.setuptools_scm]
 write_to = "dargs/_version.py"
+
+[tool.ruff.lint]
+select = [
+    "E", # errors
+    "F", # pyflakes
+    "D", # pydocstyle
+    "UP", # pyupgrade
+    "C4", # flake8-comprehensions
+    "RUF", # ruff
+    "I", # isort
+]
+
+ignore = [
+    "E501", # line too long
+    "F841", # local variable is assigned to but never used
+    "E741", # ambiguous variable name
+    "E402", # module level import not at top of file
+    "D100", # TODO: missing docstring in public module
+    "D101", # TODO: missing docstring in public class
+    "D102", # TODO: missing docstring in public method
+    "D103", # TODO: missing docstring in public function
+    "D104", # TODO: missing docstring in public package
+    "D105", # TODO: missing docstring in magic method
+    "D205", # 1 blank line required between summary line and description
+    "D401", # TODO: first line should be in imperative mood
+    "D404", # TODO: first word of the docstring should not be This
+]
+ignore-init-module-imports = true
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"

tests/__init__.py

@@ -0,0 +1,4 @@
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))

tests/context.py

@@ -1,4 +0,0 @@
-import sys, os
-
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
-import dargs

tests/dpmdargs.py

@@ -1,5 +1,4 @@
-from .context import dargs
-from dargs import dargs, Argument, Variant
+from dargs import Argument, Variant, dargs
 
 ACTIVATION_FN_DICT = {
     "relu": None,
@@ -140,7 +139,8 @@ def descrpt_se_a_tpe_args():
     doc_type_nlayer = "number of hidden layers of type embedding net"
     doc_numb_aparam = "dimension of atomic parameter. if set to a value > 0, the atomic parameters are embedded."
 
-    return descrpt_se_a_args() + [
+    return [
+        *descrpt_se_a_args(),
         Argument("type_nchanl", int, optional=True, default=4, doc=doc_type_nchanl),
         Argument("type_nlayer", int, optional=True, default=2, doc=doc_type_nlayer),
         Argument("numb_aparam", int, optional=True, default=0, doc=doc_numb_aparam),
@@ -202,7 +202,7 @@ def descrpt_se_ar_args():
 
 
 def descrpt_hybrid_args():
-    doc_list = f"A list of descriptor definitions"
+    doc_list = "A list of descriptor definitions"
 
     return [
         Argument(
@@ -243,7 +243,7 @@ def descrpt_variant_type_args():
     link_se_a_3be = make_link("se_a_3be", "model/descriptor[se_a_3be]")
     link_se_a_tpe = make_link("se_a_tpe", "model/descriptor[se_a_tpe]")
     link_hybrid = make_link("hybrid", "model/descriptor[hybrid]")
-    doc_descrpt_type = f"The type of the descritpor. See explanation below. \n\n\
+    doc_descrpt_type = "The type of the descritpor. See explanation below. \n\n\
 - `loc_frame`: Defines a local frame at each atom, and the compute the descriptor as local coordinates under this frame.\n\n\
 - `se_a`: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor.\n\n\
 - `se_r`: Used by the smooth edition of Deep Potential. Only the distance between atoms is used to construct the descriptor.\n\n\
@@ -391,7 +391,7 @@ def modifier_dipole_charge():
     doc_model_name = "The name of the frozen dipole model file."
     doc_model_charge_map = f"The charge of the WFCC. The list length should be the same as the {make_link('sel_type', 'model/fitting_net[dipole]/sel_type')}. "
     doc_sys_charge_map = f"The charge of real atoms. The list length should be the same as the {make_link('type_map', 'model/type_map')}"
-    doc_ewald_h = f"The grid spacing of the FFT grid. Unit is A"
+    doc_ewald_h = "The grid spacing of the FFT grid. Unit is A"
     doc_ewald_beta = f"The splitting parameter of Ewald sum. Unit is A^{-1}"
 
     return [

tests/test_checker.py

@@ -1,6 +1,6 @@
-from typing import List
-from .context import dargs
 import unittest
+from typing import List
+
 from dargs import Argument, Variant
 from dargs.dargs import ArgumentKeyError, ArgumentTypeError, ArgumentValueError