antibody-utils 0.1.0__tar.gz

antibody_utils-0.1.0/LICENCE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, University of Oxford
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

antibody_utils-0.1.0/PKG-INFO

@@ -0,0 +1,122 @@
+Metadata-Version: 2.4
+Name: antibody-utils
+Version: 0.1.0
+Summary: Utilities for antibody sequence and structure analysis.
+Keywords: antibody,immunoglobulin,CDR,numbering,bioinformatics
+Author: Benjamin Heathcote Williams
+Author-email: Benjamin Heathcote Williams <benjaminhwilliams@users.noreply.github.com>
+License-Expression: BSD-3-Clause
+License-File: LICENCE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Dist: gemmi
+Requires-Dist: numpy
+Requires-Dist: platformdirs ; extra == 'canonicals'
+Requires-Dist: anarcii>=2 ; extra == 'numbering'
+Maintainer: Oxford Protein Informatics Group
+Maintainer-email: Oxford Protein Informatics Group <opig@stats.ox.ac.uk>
+Requires-Python: >=3.11
+Project-URL: Documentation, https://antibody-utils.readthedocs.io
+Project-URL: Source, https://github.com/oxpig/antibody-utils
+Project-URL: Issues, https://github.com/oxpig/antibody-utils/issues
+Provides-Extra: canonicals
+Provides-Extra: numbering
+Description-Content-Type: text/markdown
+
+# antibody-utils
+
+[![Tests](https://github.com/oxpig/antibody-utils/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/oxpig/antibody-utils/actions/workflows/tests.yml)
+[![Documentation](https://readthedocs.org/projects/antibody-utils/badge/?version=latest)](https://antibody-utils.readthedocs.io/en/latest/)
+[![pre-commit.ci](https://results.pre-commit.ci/badge/github/oxpig/antibody-utils/main.svg)](https://results.pre-commit.ci/latest/github/oxpig/antibody-utils/main)
+[![Coverage](https://codecov.io/gh/oxpig/antibody-utils/graph/badge.svg)](https://codecov.io/gh/oxpig/antibody-utils)
+[![PyPI](https://img.shields.io/pypi/v/antibody-utils)](https://pypi.org/project/antibody-utils/)
+[![Python versions](https://img.shields.io/pypi/pyversions/antibody-utils)](https://pypi.org/project/antibody-utils/)
+[![Downloads](https://static.pepy.tech/badge/antibody-utils/month)](https://pepy.tech/projects/antibody-utils)
+
+[![Licence: BSD-3-Clause](https://img.shields.io/badge/licence-BSD--3--Clause-blue)](LICENCE)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+
+Utilities for antibody sequence and structure analysis: numbering, region
+definitions, sequence comparison, VH/VL orientation and more.
+
+antibody-utils is developed by the
+[Oxford Protein Informatics Group](https://opig.stats.ox.ac.uk/).
+
+## Installation
+
+With [uv](https://docs.astral.sh/uv/), add antibody-utils to your project:
+
+```console
+uv add antibody-utils
+```
+
+Or with pip:
+
+```console
+pip install antibody-utils
+```
+
+To number raw sequences and structures with
+[ANARCII](https://github.com/oxpig/ANARCII), install the `numbering` extra:
+
+```console
+uv add "antibody-utils[numbering]"
+```
+
+```console
+pip install "antibody-utils[numbering]"
+```
+
+> [!TIP]
+> ANARCII depends on PyTorch.  On Linux, the default PyTorch wheels from PyPI
+> bundle CUDA libraries, a download of several gigabytes.  To get the build that
+> suits your machine (CPU-only, or your CUDA or ROCm version):
+>
+> - With uv's pip interface, let uv detect your hardware:
+>
+>   ```console
+>   uv pip install --torch-backend=auto "antibody-utils[numbering]"
+>   ```
+>
+>   `uv add` has no such flag; in a uv project, point `torch` at the right
+>   PyTorch index in your `pyproject.toml` instead, as described in
+>   [uv's PyTorch guide](https://docs.astral.sh/uv/guides/integration/pytorch/).
+>
+> - pip cannot detect your hardware, so install PyTorch first from the
+>   [PyTorch index](https://pytorch.org/get-started/locally/) for your platform,
+>   e.g. CPU-only:
+>
+>   ```console
+>   pip install torch --index-url https://download.pytorch.org/whl/cpu
+>   pip install "antibody-utils[numbering]"
+>   ```
+
+## Documentation
+
+See the [documentation](https://antibody-utils.readthedocs.io) for a user guide
+and API reference.
+
+## Citing
+
+If you use antibody-utils in published work, please cite it and the methods
+it implements; see [Citing](https://antibody-utils.readthedocs.io/en/latest/citing.html)
+in the documentation.
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for how to set up a development
+environment, run the tests and propose changes.
+
+## Licence
+
+BSD 3-Clause; see [LICENCE](LICENCE).

antibody_utils-0.1.0/README.md

@@ -0,0 +1,88 @@
+# antibody-utils
+
+[![Tests](https://github.com/oxpig/antibody-utils/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/oxpig/antibody-utils/actions/workflows/tests.yml)
+[![Documentation](https://readthedocs.org/projects/antibody-utils/badge/?version=latest)](https://antibody-utils.readthedocs.io/en/latest/)
+[![pre-commit.ci](https://results.pre-commit.ci/badge/github/oxpig/antibody-utils/main.svg)](https://results.pre-commit.ci/latest/github/oxpig/antibody-utils/main)
+[![Coverage](https://codecov.io/gh/oxpig/antibody-utils/graph/badge.svg)](https://codecov.io/gh/oxpig/antibody-utils)
+[![PyPI](https://img.shields.io/pypi/v/antibody-utils)](https://pypi.org/project/antibody-utils/)
+[![Python versions](https://img.shields.io/pypi/pyversions/antibody-utils)](https://pypi.org/project/antibody-utils/)
+[![Downloads](https://static.pepy.tech/badge/antibody-utils/month)](https://pepy.tech/projects/antibody-utils)
+
+[![Licence: BSD-3-Clause](https://img.shields.io/badge/licence-BSD--3--Clause-blue)](LICENCE)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+
+Utilities for antibody sequence and structure analysis: numbering, region
+definitions, sequence comparison, VH/VL orientation and more.
+
+antibody-utils is developed by the
+[Oxford Protein Informatics Group](https://opig.stats.ox.ac.uk/).
+
+## Installation
+
+With [uv](https://docs.astral.sh/uv/), add antibody-utils to your project:
+
+```console
+uv add antibody-utils
+```
+
+Or with pip:
+
+```console
+pip install antibody-utils
+```
+
+To number raw sequences and structures with
+[ANARCII](https://github.com/oxpig/ANARCII), install the `numbering` extra:
+
+```console
+uv add "antibody-utils[numbering]"
+```
+
+```console
+pip install "antibody-utils[numbering]"
+```
+
+> [!TIP]
+> ANARCII depends on PyTorch.  On Linux, the default PyTorch wheels from PyPI
+> bundle CUDA libraries, a download of several gigabytes.  To get the build that
+> suits your machine (CPU-only, or your CUDA or ROCm version):
+>
+> - With uv's pip interface, let uv detect your hardware:
+>
+>   ```console
+>   uv pip install --torch-backend=auto "antibody-utils[numbering]"
+>   ```
+>
+>   `uv add` has no such flag; in a uv project, point `torch` at the right
+>   PyTorch index in your `pyproject.toml` instead, as described in
+>   [uv's PyTorch guide](https://docs.astral.sh/uv/guides/integration/pytorch/).
+>
+> - pip cannot detect your hardware, so install PyTorch first from the
+>   [PyTorch index](https://pytorch.org/get-started/locally/) for your platform,
+>   e.g. CPU-only:
+>
+>   ```console
+>   pip install torch --index-url https://download.pytorch.org/whl/cpu
+>   pip install "antibody-utils[numbering]"
+>   ```
+
+## Documentation
+
+See the [documentation](https://antibody-utils.readthedocs.io) for a user guide
+and API reference.
+
+## Citing
+
+If you use antibody-utils in published work, please cite it and the methods
+it implements; see [Citing](https://antibody-utils.readthedocs.io/en/latest/citing.html)
+in the documentation.
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for how to set up a development
+environment, run the tests and propose changes.
+
+## Licence
+
+BSD 3-Clause; see [LICENCE](LICENCE).

antibody_utils-0.1.0/pyproject.toml

@@ -0,0 +1,213 @@
+[build-system]
+requires = ["uv_build>=0.12.22,<0.13.0"]
+build-backend = "uv_build"
+
+[project]
+name = "antibody-utils"
+version = "0.1.0"
+description = "Utilities for antibody sequence and structure analysis."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "BSD-3-Clause"
+license-files = ["LICENCE"]
+keywords = [
+    "antibody",
+    "immunoglobulin",
+    "CDR",
+    "numbering",
+    "bioinformatics",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Typing :: Typed",
+]
+dependencies = [
+    "gemmi",
+    "numpy",
+]
+
+[[project.authors]]
+name = "Benjamin Heathcote Williams"
+email = "benjaminhwilliams@users.noreply.github.com"
+
+[[project.maintainers]]
+name = "Oxford Protein Informatics Group"
+email = "opig@stats.ox.ac.uk"
+
+[project.optional-dependencies]
+numbering = ["anarcii>=2"]
+canonicals = ["platformdirs"]
+
+[project.urls]
+Documentation = "https://antibody-utils.readthedocs.io"
+Source = "https://github.com/oxpig/antibody-utils"
+Issues = "https://github.com/oxpig/antibody-utils/issues"
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+    "--doctest-modules",
+]
+testpaths = [
+    "tests",
+    "src",
+    "docs",
+    "README.md",
+]
+doctest_optionflags = ["NORMALIZE_WHITESPACE"]
+markers = [
+    "numbering: requires the `numbering` extra (ANARCII)",
+    "pyigclassify2: requires a licensed copy of the PyIgClassify2 data",
+]
+
+[tool.coverage.run]
+source = ["antibody_utils"]
+
+[tool.ruff]
+src = [
+    "src",
+    "tests",
+]
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    "ERA",
+    "S",
+    "BLE",
+    "B",
+    "A",
+    "C4",
+    "DTZ",
+    "EXE",
+    "FA",
+    "ISC",
+    "ICN",
+    "LOG",
+    "G",
+    "PIE",
+    "T20",
+    "PYI",
+    "PT",
+    "RSE",
+    "RET",
+    "SIM",
+    "TID",
+    "TC",
+    "PTH",
+    "FLY",
+    "I",
+    "NPY",
+    "N",
+    "PERF",
+    "E",
+    "W",
+    "D",
+    "F",
+    "PGH",
+    "PLE",
+    "PLW",
+    "UP",
+    "FURB",
+    "RUF",
+]
+allowed-confusables = [
+    "–",
+    "α",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**/*.py" = [
+    "D",
+    "S101",
+]
+"scripts/**/*.py" = ["S310"]
+"docs/**/*.py" = ["D"]
+"docs/conf.py" = ["A001"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.typos.files]
+extend-exclude = ["tests/data/legacy/"]
+
+[tool.typos.default]
+locale = "en-gb"
+
+[tool.typos.default.extend-identifiers]
+NORMALIZE_WHITESPACE = "NORMALIZE_WHITESPACE"
+
+[tool.typos.default.extend-words]
+blosum = "blosum"
+ser = "ser"
+thr = "thr"
+
+[tool.bumpversion]
+parse = '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)'
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = true
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+moveable_tags = []
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = [
+    "uv lock",
+    "git add uv.lock",
+]
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = "version: {current_version}"
+replace = "version: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+regex = true
+search = 'date-released: \d{{4}}-\d{{2}}-\d{{2}}'
+replace = "date-released: {now:%Y-%m-%d}"
+
+[[tool.bumpversion.files]]
+filename = "CHANGELOG.md"
+search = "## Unreleased"
+replace = """
+## Unreleased
+
+## {new_version} ({now:%Y-%m-%d})"""
+
+[dependency-groups]
+dev = [
+    "bump-my-version>=1.4.1",
+    "pre-commit>=4.6.0",
+    "pytest>=9.1.1",
+    "pytest-cov>=7",
+    "sybil>=10.1.0",
+]
+docs = [
+    "furo",
+    "myst-parser",
+    "sphinx>=8",
+    "sphinx-autodoc-typehints",
+]

antibody_utils-0.1.0/pyproject.toml.orig

@@ -0,0 +1,185 @@
+[build-system]
+requires = ["uv_build>=0.12.22,<0.13.0"]
+build-backend = "uv_build"
+
+[project]
+name = "antibody-utils"
+version = "0.1.0"
+description = "Utilities for antibody sequence and structure analysis."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "BSD-3-Clause"
+license-files = ["LICENCE"]
+authors = [
+  { name = "Benjamin Heathcote Williams", email = "benjaminhwilliams@users.noreply.github.com" },
+]
+maintainers = [
+  { name = "Oxford Protein Informatics Group", email = "opig@stats.ox.ac.uk" },
+]
+keywords = ["antibody", "immunoglobulin", "CDR", "numbering", "bioinformatics"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Typing :: Typed",
+]
+dependencies = [
+  "gemmi",
+  "numpy",
+]
+
+[project.optional-dependencies]
+numbering = ["anarcii>=2"]
+canonicals = ["platformdirs"]
+
+[project.urls]
+Documentation = "https://antibody-utils.readthedocs.io"
+Source = "https://github.com/oxpig/antibody-utils"
+Issues = "https://github.com/oxpig/antibody-utils/issues"
+
+[tool.pytest.ini_options]
+addopts = [
+  "--import-mode=importlib",
+  # Run docstring examples as tests; `conftest.py` does the same for Markdown.
+  "--doctest-modules",
+]
+testpaths = ["tests", "src", "docs", "README.md"]
+doctest_optionflags = ["NORMALIZE_WHITESPACE"]
+markers = [
+  "numbering: requires the `numbering` extra (ANARCII)",
+  "pyigclassify2: requires a licensed copy of the PyIgClassify2 data",
+]
+
+[tool.coverage.run]
+source = ["antibody_utils"]
+
+[tool.ruff]
+src = ["src", "tests"]
+line-length = 88
+lint.select = [
+  "ERA",  # eradicate - https://docs.astral.sh/ruff/rules/#eradicate-era
+  "S",    # flake8-bandit - https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+  "BLE",  # flake8-blind-except - https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
+  "B",    # flake8-bugbear - https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+  "A",    # flake8-builtins - https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+  "C4",   # flake8-comprehensions - https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+  "DTZ",  # flake8-datetimez - https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  "EXE",  # flake8-executable - https://docs.astral.sh/ruff/rules/#flake8-executable-exe
+  "FA",   # flake8-future-annotations - https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
+  "ISC",  # flake8-implicit-str-concat - https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
+  "ICN",  # flake8-import-conventions - https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
+  "LOG",  # flake8-logging - https://docs.astral.sh/ruff/rules/#flake8-logging-log
+  "G",    # flake8-logging-format - https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  "PIE",  # flake8-pie - https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+  "T20",  # flake8-print - https://docs.astral.sh/ruff/rules/#flake8-print-t20
+  "PYI",  # flake8-pyi - https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi
+  "PT",   # flake8-pytest-style - https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+  "RSE",  # flake8-raise - https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+  "RET",  # flake8-return - https://docs.astral.sh/ruff/rules/#flake8-return-ret
+  "SIM",  # flake8-simplify - https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  "TID",  # flake8-tidy-imports - https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
+  "TC",   # flake8-type-checking - https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
+  "PTH",  # flake8-use-pathlib - https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+  "FLY",  # flynt - https://docs.astral.sh/ruff/rules/#flynt-fly
+  "I",    # isort - https://docs.astral.sh/ruff/rules/#isort-i
+  "NPY",  # NumPy-specific rules - https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
+  "N",    # pep8-naming - https://docs.astral.sh/ruff/rules/#pep8-naming-n
+  "PERF", # Perflint - https://docs.astral.sh/ruff/rules/#perflint-perf
+  "E",    # pycodestyle errors - https://docs.astral.sh/ruff/rules/#error-e
+  "W",    # pycodestyle warnings - https://docs.astral.sh/ruff/rules/#warning-w
+  "D",    # pydocstyle - https://docs.astral.sh/ruff/rules/#pydocstyle-d
+  "F",    # pyflakes rules - https://docs.astral.sh/ruff/rules/#pyflakes-f
+  "PGH",  # pygrep-hooks - https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+  "PLE",  # Pylint errors - https://docs.astral.sh/ruff/rules/#pylint-pl
+  "PLW",  # Pylint warnings - https://docs.astral.sh/ruff/rules/#pylint-pl
+  "UP",   # pyupgrade - https://docs.astral.sh/ruff/rules/#pyupgrade-up
+  "FURB", # refurb - https://docs.astral.sh/ruff/rules/#refurb-furb
+  "RUF",  # Ruff-specific rules - https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
+# En dashes (in page ranges) and α (in Cα) are intended.
+lint.allowed-confusables = ["–", "α"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**/*.py" = ["D", "S101"] # No docstrings required; allow assert statements
+"scripts/**/*.py" = ["S310"]    # URL fetches are the point of these scripts
+"docs/**/*.py" = ["D"]
+"docs/conf.py" = ["A001"] # Sphinx's `copyright` setting shadows the builtin
+
+[tool.typos.files]
+extend-exclude = ["tests/data/legacy/"]
+
+[tool.typos.default]
+locale = "en-gb"
+
+[tool.typos.default.extend-identifiers]
+NORMALIZE_WHITESPACE = "NORMALIZE_WHITESPACE" # doctest option flag
+
+[tool.typos.default.extend-words]
+blosum = "blosum" # BLOSUM substitution matrices
+ser = "ser"       # Residue name
+thr = "thr"       # Residue name
+
+[tool.bumpversion]
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = true
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+moveable_tags = []
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = ["uv lock", "git add uv.lock"]
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = "version: {current_version}"
+replace = "version: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+regex = true
+search = "date-released: \\d{{4}}-\\d{{2}}-\\d{{2}}"
+replace = "date-released: {now:%Y-%m-%d}"
+
+[[tool.bumpversion.files]]
+filename = "CHANGELOG.md"
+search = "## Unreleased"
+replace = "## Unreleased\n\n## {new_version} ({now:%Y-%m-%d})"
+
+[dependency-groups]
+dev = [
+    "bump-my-version>=1.4.1",
+    "pre-commit>=4.6.0",
+    "pytest>=9.1.1",
+    "pytest-cov>=7",
+    "sybil>=10.1.0",
+]
+docs = [
+    "furo",
+    "myst-parser",
+    "sphinx>=8",
+    "sphinx-autodoc-typehints",
+]

antibody_utils-0.1.0/src/antibody_utils/__init__.py

@@ -0,0 +1,5 @@
+"""Utilities for antibody sequence and structure analysis."""
+
+from importlib.metadata import version
+
+__version__ = version("antibody-utils")