Fix most formatting errors.

docs/__init__.py

@@ -0,0 +1 @@
+"""Documentation."""

docs/conf.py

@@ -1,6 +1,5 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-#
+"""Configuration of the Sphinx documentation."""
+
 # rdata documentation build configuration file, created by
 # sphinx-quickstart on Tue Aug 7 12:49:32 2018.
 #
@@ -27,7 +26,7 @@
 # General information about the project.
 project = "rdata"
 author = "Carlos Ramos Carreño"
-copyright = "2018, Carlos Ramos Carreño"
+copyright = "2018, Carlos Ramos Carreño"  # noqa: A001
 github_url = "https://github.com/vnmabus/rdata"
 rtd_version = os.environ.get("READTHEDOCS_VERSION")
 rtd_version_type = os.environ.get("READTHEDOCS_VERSION_TYPE")
@@ -44,7 +43,7 @@
 try:
     release = importlib.metadata.version("rdata")
 except importlib.metadata.PackageNotFoundError:
-    print(
+    print(  # noqa: T201
         f"To build the documentation, The distribution information of\n"
         f"{project} has to be available.  Either install the package\n"
         f"into your development environment or run 'setup.py develop'\n"
@@ -57,8 +56,6 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -166,7 +163,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, "rdata", "rdata Documentation", [author], 1)
+    (master_doc, "rdata", "rdata Documentation", [author], 1),
 ]
 
 # -- Options for Texinfo output -------------------------------------------
@@ -194,15 +191,6 @@
 epub_publisher = author
 epub_copyright = copyright
 
-# The unique identifier of the text. This can be a ISBN number
-# or the project homepage.
-#
-# epub_identifier = ''
-
-# A unique identification for the text.
-#
-# epub_uid = ''
-
 # A list of files that should not be packed into the epub file.
 epub_exclude_files = ["search.html"]
 

examples/__init__.py

@@ -0,0 +1 @@
+"""Documentation examples."""

examples/plot_cran.py

@@ -105,6 +105,7 @@
 
 
 def graph_constructor(obj, attrs):
+    """Construct graph object from R representation."""
     n_vertices = int(obj[0][0])
     is_directed = obj[1]
     edge_from = obj[2].astype(int)
@@ -119,7 +120,7 @@ def graph_constructor(obj, attrs):
     vertex_attrs = obj[8][2]
     edge_attrs = obj[8][3]
 
-    graph = igraph.Graph(
+    return igraph.Graph(
         n=n_vertices,
         directed=is_directed,
         edges=list(zip(edge_from, edge_to)),
@@ -128,8 +129,6 @@ def graph_constructor(obj, attrs):
         edge_attrs=edge_attrs,
     )
 
-    return graph
-
 
 # %%
 # We create a dict with all the constructors that we want to apply.

examples/plot_example.py

@@ -15,6 +15,7 @@
 
 @interact(files=FileUpload(accept="*.rd*", multiple=True))
 def convert_from_file(files):
+    """Open a rds or rdata file and display its contents as Python objects."""
     for f in files:
         parsed = rdata.parser.parse_data(f.content)
         converted = rdata.conversion.convert(parsed)

pyproject.toml

@@ -88,6 +88,21 @@ ignore = [
 	"TID252", # relative imports allowed
 ]
 
+[tool.ruff.per-file-ignores]
+"plot_*.py" = [
+	"ANN", # no type hints in examples
+	"ARG001", # Some unused args are needed
+	"B018", # single object expressions are not useless in examples (they display the object)
+	"D205", # examples do not have a blank line in docstring
+	"D415", # first line in examples does not end with period
+	"ERA001", # Commented code may be useful for the reader
+	"S310", # URLs in examples have been validated
+	"T201", # print allowed in examples
+]
+
+[tool.ruff.isort]
+combine-as-imports = true
+
 [tool.ruff.pydocstyle]
 convention = "google"
 

rdata/__init__.py

@@ -2,10 +2,12 @@
 from __future__ import annotations
 
 from importlib.resources import files
-from typing import Final
+from typing import TYPE_CHECKING, Final
 
-from . import conversion, parser
-from .parser._parser import Traversable
+from . import conversion as conversion, parser as parser
+
+if TYPE_CHECKING:
+    from .parser._parser import Traversable
 
 
 def _get_test_data_path() -> Traversable:

rdata/conversion/__init__.py

@@ -1,3 +1,4 @@
+"""Utilities for converting R objects to Python ones."""
 from ._conversion import (
     DEFAULT_CLASS_MAP as DEFAULT_CLASS_MAP,
     Converter as Converter,

rdata/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for the rdata package."""

rdata/tests/test_rdata.py

@@ -4,7 +4,7 @@
 from collections import ChainMap
 from fractions import Fraction
 from types import SimpleNamespace
-from typing import Any, Dict
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -15,16 +15,16 @@
 TESTDATA_PATH = rdata.TESTDATA_PATH
 
 
-class SimpleTests(unittest.TestCase):  # noqa:WPS214
+class SimpleTests(unittest.TestCase):
     """Collection of simple test cases."""
 
     def test_opened_file(self) -> None:
         """Test that an opened file can be passed to parse_file."""
-        with open(TESTDATA_PATH / "test_vector.rda") as f:
+        with (TESTDATA_PATH / "test_vector.rda").open() as f:
             parsed = rdata.parser.parse_file(f)
             converted = rdata.conversion.convert(parsed)
 
-            self.assertIsInstance(converted, dict)
+            assert isinstance(converted, dict)
 
     def test_opened_string(self) -> None:
         """Test that a string can be passed to parse_file."""
@@ -33,7 +33,7 @@ def test_opened_string(self) -> None:
         )
         converted = rdata.conversion.convert(parsed)
 
-        self.assertIsInstance(converted, dict)
+        assert isinstance(converted, dict)
 
     def test_logical(self) -> None:
         """Test parsing of logical vectors."""
@@ -228,9 +228,9 @@ def test_list(self) -> None:
             "test_list":
                 [
                     np.array([1.0]),
-                    ['a', 'b', 'c'],
+                    ["a", "b", "c"],
                     np.array([2.0, 3.0]),
-                    ['hi'],
+                    ["hi"],
                 ],
         })
 
@@ -251,7 +251,7 @@ def test_expression(self) -> None:
         np.testing.assert_equal(converted, {
             "test_expression": rdata.conversion.RExpression([
                 rdata.conversion.RLanguage(
-                    ['^', 'base', 'exponent'],
+                    ["^", "base", "exponent"],
                     attributes={},
                 ),
             ]),
@@ -275,7 +275,7 @@ def test_minimal_function_uncompiled(self) -> None:
 
         converted_fun = converted["test_minimal_function_uncompiled"]
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_fun,
             rdata.conversion.RFunction,
         )
@@ -297,7 +297,7 @@ def test_minimal_function(self) -> None:
 
         converted_fun = converted["test_minimal_function"]
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_fun,
             rdata.conversion.RFunction,
         )
@@ -307,7 +307,7 @@ def test_minimal_function(self) -> None:
 
         converted_body = converted_fun.body
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_body,
             rdata.conversion.RBytecode,
         )
@@ -329,17 +329,17 @@ def test_empty_function_uncompiled(self) -> None:
 
         converted_fun = converted["test_empty_function_uncompiled"]
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_fun,
             rdata.conversion.RFunction,
         )
 
         np.testing.assert_equal(converted_fun.environment, ChainMap({}))
         np.testing.assert_equal(converted_fun.formals, None)
-        self.assertIsInstance(converted_fun.body, rdata.conversion.RLanguage)
+        assert isinstance(converted_fun.body, rdata.conversion.RLanguage)
         np.testing.assert_equal(
             converted_fun.source,
-            "test_empty_function_uncompiled <- function() {}\n",  # noqa:P103
+            "test_empty_function_uncompiled <- function() {}\n",
         )
 
     def test_empty_function(self) -> None:
@@ -351,7 +351,7 @@ def test_empty_function(self) -> None:
 
         converted_fun = converted["test_empty_function"]
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_fun,
             rdata.conversion.RFunction,
         )
@@ -361,7 +361,7 @@ def test_empty_function(self) -> None:
 
         converted_body = converted_fun.body
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_body,
             rdata.conversion.RBytecode,
         )
@@ -371,7 +371,7 @@ def test_empty_function(self) -> None:
 
         np.testing.assert_equal(
             converted_fun.source,
-            "test_empty_function <- function() {}\n",  # noqa:P103
+            "test_empty_function <- function() {}\n",
         )
 
     def test_function(self) -> None:
@@ -383,7 +383,7 @@ def test_function(self) -> None:
 
         converted_fun = converted["test_function"]
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_fun,
             rdata.conversion.RFunction,
         )
@@ -393,7 +393,7 @@ def test_function(self) -> None:
 
         converted_body = converted_fun.body
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_body,
             rdata.conversion.RBytecode,
         )
@@ -418,7 +418,7 @@ def test_function_arg(self) -> None:
 
         converted_fun = converted["test_function_arg"]
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_fun,
             rdata.conversion.RFunction,
         )
@@ -428,7 +428,7 @@ def test_function_arg(self) -> None:
 
         converted_body = converted_fun.body
 
-        self.assertIsInstance(
+        assert isinstance(
             converted_body,
             rdata.conversion.RBytecode,
         )
@@ -495,7 +495,7 @@ def test_dataframe(self) -> None:
                             "value": pd.Series(
                                 [1, 2, 3],
                                 dtype=pd.Int32Dtype(),
-                            ).values,
+                            ).array,
                         },
                         index=pd.RangeIndex(start=1, stop=4),
                     ),
@@ -520,7 +520,7 @@ def test_dataframe_rds(self) -> None:
                             "value": pd.Series(
                                 [1, 2, 3],
                                 dtype=pd.Int32Dtype(),
-                            ).values,
+                            ).array,
                         },
                         index=pd.RangeIndex(start=1, stop=4),
                     ),
@@ -543,9 +543,9 @@ def test_dataframe_rownames(self) -> None:
                     "value": pd.Series(
                         [1, 2, 3],
                         dtype=pd.Int32Dtype(),
-                    ).values,
+                    ).array,
                 },
-                index=('Madrid', 'Frankfurt', 'Herzberg am Harz'),
+                index=("Madrid", "Frankfurt", "Herzberg am Harz"),
             ),
         )
 
@@ -572,7 +572,7 @@ def test_s4(self) -> None:
             "test_s4": SimpleNamespace(
                 age=np.array(28),
                 name=["Carlos"],
-                **{'class': ["Person"]},  # noqa: WPS517
+                **{"class": ["Person"]},
             ),
         })
 
@@ -583,8 +583,8 @@ def test_environment(self) -> None:
         )
         converted = rdata.conversion.convert(parsed)
 
-        dict_env = {'string': ['test']}
-        empty_global_env: Dict[str, Any] = {}
+        dict_env = {"string": ["test"]}
+        empty_global_env: dict[str, Any] = {}
 
         np.testing.assert_equal(converted, {
             "test_environment": ChainMap(dict_env, ChainMap(empty_global_env)),
@@ -608,17 +608,17 @@ def test_emptyenv(self) -> None:
         )
         converted = rdata.conversion.convert(parsed)
 
-        self.assertEqual(converted, {
+        assert converted == {
             "test_emptyenv": ChainMap({}),
-        })
+        }
 
     def test_list_attrs(self) -> None:
         """Test that lists accept attributes."""
         parsed = rdata.parser.parse_file(TESTDATA_PATH / "test_list_attrs.rda")
         converted = rdata.conversion.convert(parsed)
 
         np.testing.assert_equal(converted, {
-            "test_list_attrs": [['list'], [5]],
+            "test_list_attrs": [["list"], [5]],
         })
 
     def test_altrep_compact_intseq(self) -> None:
@@ -683,7 +683,7 @@ def test_altrep_deferred_string(self) -> None:
         converted = rdata.conversion.convert(parsed)
 
         np.testing.assert_equal(converted, {
-            "test_altrep_deferred_string": [  # noqa: WPS317
+            "test_altrep_deferred_string": [
                 "1", "2.3", "10000",
                 "1e+05", "-10000", "-1e+05",
                 "0.001", "1e-04", "1e-05",