Enable style checking for entire code base

.github/workflows/test_and_deploy.yml

@@ -31,6 +31,22 @@ env:
 
 
 jobs:
+  lint:
+    name: Check code style
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install ruff
+      run: pip install ruff
+    - name: Check code formatting
+      run: ruff format --diff
+    - name: Lint code base
+      run: ruff check
+
+
   generate-wheels-matrix:
     name: "Generate wheels matrix"
     runs-on: "ubuntu-latest"
@@ -245,6 +261,7 @@ jobs:
     permissions:
       contents: write
     needs:
+    - lint
     - test-and-build
     - make-sdist
     - test-interfaces

.gitignore

@@ -39,7 +39,6 @@ htmlcov
 # Ignore all compiled python files (e.g. from running the unit tests)
 *.pyc
 *.pyo
-*.py{}
 *.py-e
 
 # Ignore potential directory created during install

doc/apidoc.py

@@ -3,17 +3,16 @@
 # information.
 
 __author__ = "Patrick Kunzmann"
-__all__ = ["create_api_doc", "skip_non_methods"]
+__all__ = ["create_api_doc", "skip_nonrelevant"]
 
-from os.path import join, isdir
-from os import listdir, makedirs
-from importlib import import_module
-import types
-import json
 import enum
-from textwrap import dedent
+import json
+import types
 from collections import OrderedDict
-
+from importlib import import_module
+from os import listdir, makedirs
+from os.path import isdir, join
+from textwrap import dedent
 
 _INDENT = " " * 4
 
@@ -24,7 +23,6 @@
     _pck_categories = json.load(file, object_pairs_hook=OrderedDict)
 
 
-
 def create_api_doc(src_path, doc_path):
     """
     Create *.rst files for API documentation.
@@ -40,11 +38,7 @@ def create_api_doc(src_path, doc_path):
     # Create directory to store apidoc
     if not isdir(doc_path):
         makedirs(doc_path)
-    package_list = _create_package_doc(
-        "biotite",
-        join(src_path, "biotite"),
-        doc_path
-    )
+    package_list = _create_package_doc("biotite", join(src_path, "biotite"), doc_path)
     _create_package_index(doc_path, package_list)
 
 
@@ -67,31 +61,35 @@ def _create_package_doc(pck, src_path, doc_path):
     module = import_module(pck)
     attr_list = dir(module)
     # Classify attribute names into classes and functions
-    class_list = [attr for attr in attr_list
-                  # Do not document private classes
-                  if attr[0] != "_"
-                  # Check if object is a class
-                  and isinstance(getattr(module, attr), type)]
-    func_list = [attr for attr in attr_list
-                 # Do not document private classes
-                 if attr[0] != "_"
-                 # All functions are callable...
-                 and callable(getattr(module, attr))
-                 # ...but classes are also callable
-                 and attr not in class_list
-                ]
+    class_list = [
+        attr
+        for attr in attr_list
+        # Do not document private classes
+        if attr[0] != "_"
+        # Check if object is a class
+        and isinstance(getattr(module, attr), type)
+    ]
+    func_list = [
+        attr
+        for attr in attr_list
+        # Do not document private classes
+        if attr[0] != "_"
+        # All functions are callable...
+        and callable(getattr(module, attr))
+        # ...but classes are also callable
+        and attr not in class_list
+    ]
     # Create *.rst files
     _create_package_page(doc_path, pck, class_list, func_list, sub_pck)
     for class_name in class_list:
         _create_class_page(doc_path, pck, class_name)
     for function_name in func_list:
         _create_function_page(doc_path, pck, function_name)
 
-    return([pck] + sub_pck)
+    return [pck] + sub_pck
 
 
-def _create_package_page(doc_path, package_name,
-                         classes, functions, subpackages):
+def _create_package_page(doc_path, package_name, classes, functions, subpackages):
     attributes = classes + functions
 
     # Get categories for this package
@@ -114,7 +112,6 @@ def _create_package_page(doc_path, package_name,
         misc_category_name = "Miscellaneous" if categories else "Content"
         categories[misc_category_name] = misc_attributes
 
-
     # String for categorized class and function enumeration
     category_strings = []
     for category, attrs in categories.items():
@@ -135,12 +132,11 @@ def _create_package_page(doc_path, package_name,
     attributes_string = "\n".join(category_strings)
 
     # String for subpackage enumeration
-    subpackages_string = "\n".join(
-        [_INDENT + pck for pck in subpackages]
-    )
+    subpackages_string = "\n".join([_INDENT + pck for pck in subpackages])
 
     # Assemble page
-    file_content = dedent(f"""
+    file_content = (
+        dedent(f"""
 
         ``{package_name}``
         {"=" * (len(package_name) + 4)}
@@ -150,16 +146,21 @@ def _create_package_page(doc_path, package_name,
 
         .. currentmodule:: {package_name}
 
-    """) + attributes_string
+    """)
+        + attributes_string
+    )
     if len(subpackages) > 0:
-        file_content += dedent(f"""
+        file_content += (
+            dedent("""
 
         Subpackages
         -----------
 
         .. autosummary::
 
-    """) + subpackages_string
+    """)
+            + subpackages_string
+        )
     with open(join(doc_path, f"{package_name}.rst"), "w") as f:
         f.write(file_content)
 
@@ -201,18 +202,19 @@ def _create_function_page(doc_path, package_name, function_name):
 
 def _create_package_index(doc_path, package_list):
     # String for package enumeration
-    packages_string = "\n".join(
-        [_INDENT + pck for pck in sorted(package_list)]
-    )
+    packages_string = "\n".join([_INDENT + pck for pck in sorted(package_list)])
 
-    file_content = dedent(f"""
+    file_content = (
+        dedent("""
         API Reference
         =============
 
         .. autosummary::
             :toctree:
 
-    """) + packages_string
+    """)
+        + packages_string
+    )
     with open(join(doc_path, "index.rst"), "w") as f:
         f.write(file_content)
 
@@ -249,20 +251,21 @@ def _is_relevant_type(obj):
         # These are some special built-in Python methods
         return False
     return (
-        # Functions
-        type(obj) in [
-            types.FunctionType, types.BuiltinFunctionType, types.MethodType
-        ]
-    ) | (
-        # Functions from C-extensions
-        type(obj).__name__ in [
-            "cython_function_or_method",
-            "fused_cython_function"
-        ]
-    ) | (
-        # Enum instance
-        isinstance(obj, enum.Enum)
-    ) | (
-        # Inner class
-        isinstance(obj, type)
-    )
+        (
+            # Functions
+            type(obj)
+            in [types.FunctionType, types.BuiltinFunctionType, types.MethodType]
+        )
+        | (
+            # Functions from C-extensions
+            type(obj).__name__ in ["cython_function_or_method", "fused_cython_function"]
+        )
+        | (
+            # Enum instance
+            isinstance(obj, enum.Enum)
+        )
+        | (
+            # Inner class
+            isinstance(obj, type)
+        )
+    )

doc/bibliography.py

@@ -5,14 +5,14 @@
 __author__ = "Patrick Kunzmann"
 
 import warnings
-from pybtex.richtext import Text, Tag, HRef
+from pybtex.richtext import HRef, Tag, Text
 from pybtex.style.formatting import BaseStyle
 
 
 class IEEEStyle(BaseStyle):
     def format_article(self, param):
         entry = param["entry"]
-        
+
         try:
             authors = []
             for author in entry.persons["author"]:
@@ -28,7 +28,7 @@ def format_article(self, param):
                     text += " "
                 text += " ".join([s for s in author.last_names])
                 authors.append(Text(text + ", "))
-            
+
             title = ""
             in_protected = False
             for char in entry.fields["title"]:
@@ -46,34 +46,34 @@ def format_article(self, param):
                         else:
                             title += char.lower()
             title = Text('"', title, '," ')
-            
+
             journal = Text(Tag("em", entry.fields["journal"]), ", ")
-            
+
             if "volume" in entry.fields:
                 volume = Text("vol. ", entry.fields["volume"], ", ")
             else:
                 volume = Text()
-            
+
             if "pages" in entry.fields:
                 pages = Text("pp. ", entry.fields["pages"], ", ")
             else:
                 pages = Text()
-            
+
             date = entry.fields["year"]
             if "month" in entry.fields:
                 date = entry.fields["month"] + " " + date
             date = Text(date, ". ")
-            
-            if "doi" in entry.fields: 
-                doi = Text("doi: ", HRef(
-                    "https://doi.org/" + entry.fields["doi"],
-                    entry.fields["doi"]
-                ))
+
+            if "doi" in entry.fields:
+                doi = Text(
+                    "doi: ",
+                    HRef("https://doi.org/" + entry.fields["doi"], entry.fields["doi"]),
+                )
             else:
                 doi = Text()
-            
+
             return Text(*authors, title, journal, volume, pages, date, doi)
-        
-        except:
+
+        except Exception:
             warnings.warn(f"Invalid BibTeX entry '{entry.key}'")
-            return Text(entry.key)
+            return Text(entry.key)