Update project files

Author: avalentino

.flake8

@@ -3,14 +3,27 @@
 # max-complexity = 10
 doctests = true
 # https://github.com/psf/black/blob/main/docs/guides/using_black_with_other_tools.md
+# - E203: whitespace before ‘,’, ‘;’, or ‘:’
+# - E701: multiple statements on one line (colon)
+# - E704: multiple statements on one line (def)
+# + W504: line break after binary operator
+# https://www.pydocstyle.org/en/stable/error_codes.html
+# - D105: undocumented-magic-method
+# - D107: undocumented-public-init
+# https://github.com/gforcada/flake8-builtins?tab=readme-ov-file#rules
+# - A003: A class attribute is shadowing a Python builtin.
+# - A005: A module is shadowing a Python builtin module (e.g: logging or socket)
+# https://github.com/PyCQA/flake8-bugbear?tab=readme-ov-file#list-of-warnings
+# + B950: (smart) Line too long
+# https://github.com/orsinium-labs/flake8-todos
+# - T003: add link on issue into TODO.
+# https://github.com/plinss/flake8-noqa?tab=readme-ov-file#error-codes
+# NQA102: "# noqa: X000" has no matching violations
+# misc
+# - I  # flake8-import-order: not compatible with isort
+# - SC  # flake8-spellcheck: too aggressive
+# - CNL  # flake8-class-newline: incompatible with black
 extend-ignore = E203,E501,E701,W503,SC,CNL
-# extend-ignore = I  # flake8-import-order: not compatible with isort
-# extend-ignore = SC  # flake8-spellcheck: too aggressive
-# extend-ignore = CNL  # flake8-class-newline: incompatible with black
-# extend-ignore = A003,A005  # Python builtin is shadowed by class attribute / module
-# https://docs.astral.sh/ruff/rules/#pydocstyle-d
-# extend-ignore = D105  # undocumented-magic-method
-# extend-ignore = D107  # undocumented-public-init
 extend-select = W504,B950
 per-file-ignores =
     */tests/test_*.py: D,T003
@@ -19,6 +32,7 @@ per-file-ignores =
     bpack/codecs.py: A005
     bpack/typing.py: A005
     bpack/tests/test_future_annotations.py: D,T003,NQA102
+    bpack/tests/test_backends_codec.py: D,T003, BLK100
 statistics = True
 count = True
 extend-exclude = examples/*

.github/workflows/ci.yml

@@ -21,6 +21,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
+          fetch-depth: 0
           submodules: 'true'
 
       - name: Set up Python

.github/workflows/lint.yml

@@ -35,16 +35,31 @@ jobs:
 
       - name: Lint (flake8)
         run: |
+          python -m flake8 --version
           python -m flake8 --count --show-source --statistics ${PACKAGE}
 
       - name: Lint (pydocstyle)
         run: |
+          python -m pydocstyle --version
           python -m pydocstyle --count ${PACKAGE}
 
       - name: Lint (isort)
         run: |
+          python -m isort --version
           python -m isort --check ${PACKAGE}
 
       - name: Lint (black)
         run: |
+          python -m black --version
           python -m black --check ${PACKAGE}
+          # python -m black --diff ${PACKAGE}
+
+      # - name: Lint (mypy)
+      #   run: |
+      #     python -m mypy --version
+      #     python -m mypy ${PACKAGE}
+
+      # - name: Lint (ruff)
+      #   run: |
+      #     ruff --version
+      #     ruff check ${PACKAGE}

.gitignore

@@ -1,6 +1,6 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -46,7 +46,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
+*.py.cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -94,23 +94,36 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
 # poetry
 #   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
 #poetry.lock
+#poetry.toml
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
 #pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
+#pdm.toml
 .pdm-python
 .pdm-build/
 
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
@@ -123,6 +136,7 @@ celerybeat.pid
 
 # Environments
 .env
+.envrc
 .venv
 env/
 venv/
@@ -159,7 +173,35 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-/.idea/
-
-# VSCode
-/.vscode
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+.vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -15,14 +15,14 @@ repos:
     -   id: detect-private-key
 
 # -   repo: https://github.com/astral-sh/ruff-pre-commit
-#     rev: v0.7.0
+#     rev: v0.12.5
 #     hooks:
 #     -   id: ruff
-#         args: [ --fix ]
+#         args: [--fix]
 #     -   id: ruff-format
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.20.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
@@ -35,7 +35,7 @@ repos:
             )
 
 -   repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
+    rev: 7.3.0
     hooks:
     -   id: flake8
 
@@ -46,24 +46,33 @@ repos:
         exclude: tests|examples|data|docs
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
     -   id: isort
         name: isort (python)
 
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
     -   id: black
         language_version: python3.10
+    -   id: black-jupyter
+        language_version: python3.10
 
 # -   repo: https://github.com/pre-commit/mirrors-mypy
-#     rev: v1.12.0
+#     rev: v1.17.0
 #     hooks:
 #     -   id: mypy
+#         additional_dependencies:
+#         -   tokenize-rt==3.2.0
+#         -   numpy>=1.21
 
-# -   repo: https://github.com/codespell-project/codespell
-#     rev: v2.2.4
-#     hooks:
-#     -   id: codespell
-#         additional_dependencies: [tomli]
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+    -   id: codespell
+        additional_dependencies: [tomli]
+        exclude: |
+            (?x)^(
+                docs/spelling_wordlist.txt
+            )

.readthedocs.yml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3"
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
@@ -24,6 +24,6 @@ formats:
 
 python:
   install:
+    - requirements: docs/requirements-docs.txt
     - method: pip
       path: .
-    - requirements: docs/requirements-docs.txt

Makefile

@@ -47,8 +47,10 @@ clean:
 
 cleaner: clean
 	$(RM) -r .coverage htmlcov
-	$(RM) -r .pytest_cache .tox
-	$(RM) -r .mypy_cache .ruff_cache
+	$(RM) -r .pytest_cache
+	$(RM) -r .tox
+	$(RM) -r .mypy_cache
+	$(RM) -r .ruff_cache
 	$(RM) -r .ipynb_checkpoints
 
 distclean: cleaner
@@ -59,12 +61,16 @@ lint:
 	$(PYTHON) -m pydocstyle --count $(TARGET)
 	$(PYTHON) -m isort --check $(TARGET)
 	$(PYTHON) -m black --check $(TARGET)
+	# $(PYTHON) -m fawltydeps
 	# $(PYTHON) -m mypy --check-untyped-defs --ignore-missing-imports $(TARGET)
 	# ruff check $(TARGET)
+	codespell
 
 docs:
 	mkdir -p docs/_static
 	$(MAKE) -C docs html
+	$(MAKE) -C docs linkcheck
+	$(MAKE) -C docs spelling
 
 api:
 	$(RM) -r docs/api

bpack/bs.py

@@ -234,7 +234,7 @@ def packbits(
     Please note that no check that the input values actually fits in the
     specified number of bits is performed is performed.
 
-    The function return a sting of bytes including same number of samples
+    The function return a string of bytes including same number of samples
     of the input plus possibly some padding bit (at the end) to fill an
     integer number of bytes.
 
@@ -244,7 +244,7 @@ def packbits(
     if (nsamples * bits_per_sample) % 8:
         warnings.warn(
             f"packing {nsamples} with {bits_per_sample} bits per "
-            f"sample requires padding"
+            "sample requires padding"
         )
     encoder_ = _get_sequence_codec(
         nsamples, bits_per_sample, signed=signed, byteorder=byteorder

bpack/codecs.py

@@ -31,7 +31,7 @@ def _check_descriptor(cls, descriptor):
         if bpack.baseunits(descriptor) is not cls.baseunits:
             raise ValueError(
                 f"{cls.__module__}.{cls.__name__} "
-                f"only accepts descriptors with base units "
+                "only accepts descriptors with base units "
                 f"'{cls.baseunits.value}'"
             )
 

bpack/descriptors.py

@@ -125,7 +125,7 @@ def _validate_signed(self):
         if not isinstance(self.signed, bool):
             raise TypeError(
                 f"invalid 'signed' parameter: {self.signed!r} "
-                f"(must be a bool or None)"
+                "(must be a bool or None)"
             )
 
     def _validate_repeat(self):
@@ -144,7 +144,7 @@ def __post_init__(self):
         """Finalize BinFieldDescriptor instance initialization."""
         if isinstance(self.type, str):
             raise TypeError(
-                f"the 'type' parameter cannot be a string "
+                "the 'type' parameter cannot be a string "
                 f"(type_: {self.type!r})"
             )
 
@@ -170,21 +170,21 @@ def validate(self):
             self._validate_signed()
             if not self.is_int_type():
                 warnings.warn(
-                    f"the 'signed' parameter will be ignored for non-integer "
+                    "the 'signed' parameter will be ignored for non-integer "
                     f"type: '{self.type!r}'"
                 )
         if self.repeat is not None:
             self._validate_repeat()
             if not self.is_sequence_type() and self.repeat is not None:
                 raise TypeError(
-                    f"repeat parameter specified for non-sequence type: "
+                    "repeat parameter specified for non-sequence type: "
                     f"{self.type!r}"
                 )
         if bpack.utils.is_enum_type(self.type):
             self._validate_enum_type()
         elif self.is_sequence_type() and self.repeat is None:
             raise TypeError(
-                f"no 'repeat' parameter specified for sequence type "
+                "no 'repeat' parameter specified for sequence type "
                 f"{self.type!r}"
             )