style: format with Ruff

.github/workflows/python-package.yml

@@ -5,37 +5,27 @@ on:
   pull_request:
 
 jobs:
-  # codechecks:
-  #   runs-on: ubuntu-latest
-
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Set up Python
-  #       uses: actions/setup-python@v4
-  #       with:
-  #         python-version: "3.10"
-  #         cache: "pip"
-  #         cache-dependency-path: "**/setup.cfg"
-
-  #     - name: Install dependencies
-  #       run: |
-  #         pip install -e .[dev]
-
-  #     - name: Lint with flake8
-  #       run: |
-  #         # stop the build if there are Python syntax errors or undefined names
-  #         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-  #         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-  #         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-  #     - name: Format check with isort
-  #       run: |
-  #         isort --check src
-
-  #     - name: Format check with black
-  #       run: |
-  #         black --check src
+  cqa:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/pyproject.yaml'
+
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --use-deprecated=legacy-resolver -e .[dev]
+
+    - name: Format check with Ruff
+      run: |
+        ruff format --check .
 
   test:
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff-format
+      args: [ --check ]

Makefile

@@ -107,9 +107,9 @@ tox:
 .PHONY: reformat
 reformat:
 	@if ! git diff --cached --exit-code >/dev/null; then echo "Repository not clean" 1>&2; exit 1; fi
-	black src tests
+	ruff format src tests
 	isort src tests
-	git commit -a -m "reformatted with black and isort"
+	git commit -a -m "reformatted with ruff and isort"
 
 #=> docs -- make sphinx docs
 .PHONY: docs

docs/conf.py

@@ -6,55 +6,61 @@
 try:
     # get release from hgvs if available
     import hgvs
+
     release = str(hgvs.__version__)
 except ModuleNotFoundError:
     # else get release from first tag (raise exception if not available)
     import subprocess
+
     release = subprocess.check_output(["git", "describe", "--tags"]).decode().strip().split()[0]
 version = re.sub(r"\.post\d+$", "", release)
 
 
-project = u'HGVS'
-authors = project + ' Contributors'
-copyright = u'2021, ' + authors
+project = "HGVS"
+authors = project + " Contributors"
+copyright = "2021, " + authors
 
-extlinks = {'issue': ('https://github.com/biocommons/hgvs/issues/%s', 'issue '), }
+extlinks = {
+    "issue": ("https://github.com/biocommons/hgvs/issues/%s", "issue "),
+}
 
-man_pages = [('index', project, project + u' Documentation', [project + u' Contributors'], 1)]
+man_pages = [("index", project, project + " Documentation", [project + " Contributors"], 1)]
 
 # even for local builds
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 #
 # Boilerplate
 
-autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance']    #, 'inherited-members']
-autoclass_content = 'both'
-exclude_patterns = ['build', 'static', 'templates', 'themes']
+autodoc_default_flags = ["members", "undoc-members", "show-inheritance"]  # , 'inherited-members']
+autoclass_content = "both"
+exclude_patterns = ["build", "static", "templates", "themes"]
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.coverage',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
 ]
-html_favicon = 'static/favicon.ico'
-html_logo = 'static/hgvs-logo.png'
-html_static_path = ['static']
-html_title = '{project} {release}'.format(project=project, release=release)
-intersphinx_mapping = {'http://docs.python.org/': None, }
-master_doc = 'index'
-pygments_style = 'sphinx'
-source_suffix = '.rst'
-templates_path = ['templates']
+html_favicon = "static/favicon.ico"
+html_logo = "static/hgvs-logo.png"
+html_static_path = ["static"]
+html_title = "{project} {release}".format(project=project, release=release)
+intersphinx_mapping = {
+    "http://docs.python.org/": None,
+}
+master_doc = "index"
+pygments_style = "sphinx"
+source_suffix = ".rst"
+templates_path = ["templates"]
 
 
 # rst_epilog is appended to all rst files
 # it's a good place to define global aliases
 # If ends in .rst, sphinx will append it to itself :-(
-rst_epilog_fn = os.path.join(os.path.dirname(__file__), 'rst_epilog')
+rst_epilog_fn = os.path.join(os.path.dirname(__file__), "rst_epilog")
 rst_epilog = open(rst_epilog_fn).read()
 
 # <LICENSE>

docs/contributing.rst

@@ -35,7 +35,7 @@ Highlights
   close to it).
 
 * Abide by current `code style`_.  Use ``make reformat`` to reformat all
-  code with `yapf`_ prior to submitting a PR.
+  code with `ruff`_ prior to submitting a PR.
 
 * Email the `hgvs-discuss`_ mailing list if you have questions.
 
@@ -158,11 +158,11 @@ setting UTA_DB_URL.  The format is
 ``postgresql://<user>:<pass>@<host>/<db>/<schema>``. For example:
 
    ``postgresql://anonymous:[email protected]/uta/uta_20140210``
-  
-explicitly selects the public database, and 
+
+explicitly selects the public database, and
 
    ``postgresql://localhost/uta/uta_20140210``
- 
+
 selects a local instance.  Developers can test connectivity like this:
 
    ``$ UTA_DB_URL=postgresql://localhost/uta/uta_20140210 make test-quick``
@@ -215,7 +215,7 @@ changes::
   spaces_before_comment = 4
   split_before_named_assigns = True
 
-These code conventions are uniformly enforce by yapf_.  The entire code
+These code conventions are uniformly enforce by ruff_.  The entire code
 base is periodically automatically reformatted for consistency.
 
 
@@ -232,13 +232,13 @@ understand the code.
   variable names. |eg| ``var_c`` in a function argument list signifies
   that a SequenceVariant object with type='c' is expected.
 
-:hgvs*: a string representing an HGVS variant name.  
+:hgvs*: a string representing an HGVS variant name.
 
 :var*: a :class:`hgvs.variant.SequenceVariant` object
 
-:pos: 
+:pos:
 
-:posedit: 
+:posedit:
 
 :hgvs_position:
 

docs/rst_epilog

@@ -17,7 +17,7 @@
 .. _peg: http://en.wikipedia.org/wiki/Parsing_expression_grammar
 .. _pep8: https://www.python.org/dev/peps/pep-0008/
 .. _uta: https://github.com/biocommons/uta/
-.. _yapf: https://github.com/google/yapf
+.. _ruff: https://docs.astral.sh/ruff/
 
 
 .. |eg| replace:: *e.g.,*

pyproject.toml

@@ -103,10 +103,6 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.black]
-line-length = 100
-
-
 # [tool.flake8]
 # flake8 does not support configuration in pyproject.toml
 # https://github.com/PyCQA/flake8/issues/234#issuecomment-812800832
@@ -120,4 +116,9 @@ disable = "R0913"
 
 
 [tool.pylint.format]
-max-line-length = "120"
+max-line-length = "100"
+
+
+[tool.ruff]
+src = ["src", "test"]
+line-length = 100

sbin/generate_parser.py

@@ -18,7 +18,7 @@
     grammar_file = os.path.join(hgvs_base_dir, "src/hgvs/_data/hgvs.pymeta")
     generated_code_dir = os.path.join(hgvs_base_dir, "src/hgvs/generated")
 
-    grammar_hash = hashlib.md5(open(grammar_file, 'rb').read()).hexdigest()
+    grammar_hash = hashlib.md5(open(grammar_file, "rb").read()).hexdigest()
     prefix_length = len(hgvs_base_dir) + 1  # extra to also remove slash
 
     header_template = """# --------------------------------------------------
@@ -31,11 +31,13 @@
 #  Python version: {python_version}
 # --------------------------------------------------
 """
-    header = header_template.format(generate_script=script_path[prefix_length:],
-                                    grammar_file=grammar_file[prefix_length:],
-                                    grammar_hash=grammar_hash,
-                                    parsley_version=parsley.__version__,
-                                    python_version=sys.version)
+    header = header_template.format(
+        generate_script=script_path[prefix_length:],
+        grammar_file=grammar_file[prefix_length:],
+        grammar_hash=grammar_hash,
+        parsley_version=parsley.__version__,
+        python_version=sys.version,
+    )
 
     g = OMeta(open(grammar_file).read(), name="Grammar")
     tree = g.parseGrammar("Grammar")

setup.cfg

@@ -28,22 +28,22 @@ hgvs =
 
 [options.extras_require]
 dev =
-    black
     flake8
     ipython
     isort
     jupyter
+    pre-commit ~= 3.4
     pytest >= 5.3
     pytest-cov >= 2.8
     pytest-recording
     restview
+    ruff == 0.4.4
     setuptools
     sphinx
     sphinx_rtd_theme
     sphinxcontrib-fulltoc >= 1.1
     tox
     vcrpy
-    yapf
 
 
 [aliases]

setup.py

@@ -1,2 +1,3 @@
 from setuptools import setup
+
 setup(use_scm_version=True)

src/hgvs/alignmentmapper.py

@@ -26,7 +26,6 @@
 #    g.   ... 123   124   125   126   127   128   129   130   131   132   133 ...
 #
 
-
 from bioutils.coordinates import strand_int_to_pm
 from six.moves import range
 

src/hgvs/config.py

@@ -31,6 +31,7 @@
 import re
 from configparser import ConfigParser, ExtendedInterpolation
 from copy import copy
+
 try:
     from importlib.resources import files as resources_files
 except ImportError:

src/hgvs/dataproviders/interface.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Defines the abstract data provider interface
-
-"""
+"""Defines the abstract data provider interface"""
 
 import abc
 import os

src/hgvs/dataproviders/seqfetcher.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""provides sequencing fetching from NCBI and Ensembl
-
-"""
+"""provides sequencing fetching from NCBI and Ensembl"""
 
 import logging
 import os

src/hgvs/edit.py

@@ -8,6 +8,7 @@
 location).
 
 """
+
 import abc
 
 import attr
@@ -50,7 +51,7 @@ def _del_ins_lengths(self, ilen):
     @property
     @abc.abstractmethod
     def type(self):
-        """ return the type of this Edit """
+        """return the type of this Edit"""
         pass
 
 

src/hgvs/exceptions.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""defined exceptions used by the hgvs package
-
-"""
+"""defined exceptions used by the hgvs package"""
 
 
 class HGVSError(Exception):

src/hgvs/extras/babelfish.py

@@ -1,4 +1,5 @@
 """translate between HGVS and other formats"""
+
 import os
 
 from bioutils.assemblies import make_ac_name_map, make_name_ac_map

src/hgvs/hgvsposition.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Represent partial HGVS tags that refer to a position without alleles
-
-"""
+"""Represent partial HGVS tags that refer to a position without alleles"""
 
 import attr
 

src/hgvs/normalizer.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
-"""hgvs.normalizer
-"""
+"""hgvs.normalizer"""
 
 import copy
 import logging
@@ -444,6 +443,7 @@ def _normalize_alleles(self, var, boundary):
 
         return base + start, base + stop, (ref, alt)
 
+
 # <LICENSE>
 # Copyright 2018 HGVS Contributors (https://github.com/biocommons/hgvs)
 #