From dc1dff97e67890460ace2e3ad6603a1bf7205bc8 Mon Sep 17 00:00:00 2001 From: Benjamin Capodanno Date: Fri, 16 Oct 2026 16:08:30 -0700 Subject: [PATCH] chore(deps): depend on bbi-variant-annotation from PyPI and bump to 2026.3.1 PyPI rejects packages whose metadata names a git dependency, which blocked publishing mavedb 2026.3.0. variant-annotation is now on PyPI as bbi-variant-annotation 1.2.0b3, built from the same code as the v1.2.0-beta.1 tag; it still imports as variant_annotation. --- poetry.lock | 71 ++++++++++++++++++++---------------------- pyproject.toml | 11 +++---- src/mavedb/__init__.py | 2 +- 3 files changed, 39 insertions(+), 45 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8455104b..f204b6ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -204,6 +204,37 @@ files = [ [package.dependencies] cryptography = "*" +[[package]] +name = "bbi-variant-annotation" +version = "1.2.0b3" +description = "Genetic variant mapping and annotation pipeline" +optional = true +python-versions = ">=3.11" +groups = ["main"] +markers = "extra == \"server\"" +files = [ + {file = "bbi_variant_annotation-1.2.0b3-py3-none-any.whl", hash = "sha256:df1903b7db4c0e117ef0e1758df33a6f808ded032847e24d42a613c12151a286"}, + {file = "bbi_variant_annotation-1.2.0b3.tar.gz", hash = "sha256:7f609f3f46dc9c3b6e2d121ecfe90b9b0297318e11cdc8e7a62554566cd5c11b"}, +] + +[package.dependencies] +biopython = "*" +boto3 = "*" +click = "*" +openpyxl = "*" +pandas = ">=2.2.1,<3.0.0" +python-dotenv = "*" +redis = "*" +requests = "*" +variant-translation = "1.2.0" + +[package.extras] +dev = ["ruff"] +gnomad = ["hail"] +liftover = ["pyliftover"] +publish = ["build", "twine"] +tests = ["pytest"] + [[package]] name = "beautifulsoup4" version = "4.14.3" @@ -4935,42 +4966,6 @@ dev = ["Cython (>=3.0,<4.0)", "setuptools (>=60)"] docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinx_rtd_theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)"] test = ["aiohttp (>=3.10.5)", "flake8 (>=6.1,<7.0)", "mypy (>=0.800)", "psutil", "pyOpenSSL (>=25.3.0,<25.4.0)", "pycodestyle (>=2.11.0,<2.12.0)"] -[[package]] -name = "variant-annotation" -version = "1.2.0-beta.1" -description = "Genetic variant mapping and annotation pipeline" -optional = true -python-versions = ">=3.11" -groups = ["main"] -markers = "extra == \"server\"" -files = [] -develop = false - -[package.dependencies] -biopython = "*" -boto3 = "*" -click = "*" -openpyxl = "*" -pandas = ">=2.2.1,<3.0.0" -python-dotenv = "*" -redis = "*" -requests = "*" -variant-translation = "1.2.0" - -[package.extras] -dev = ["ruff"] -gnomad = ["hail"] -liftover = ["pyliftover"] -mapping = ["dcd-mapping @ git+https://github.com/VariantEffect/dcd_mapping2.git@v2026.1.2"] -publish = ["build", "twine"] -tests = ["pytest"] - -[package.source] -type = "git" -url = "https://github.com/bbi-lab/variant-annotation.git" -reference = "v1.2.0-beta.1" -resolved_reference = "350b53bae5e99d30ecf6f33821c3df70f5c76a65" - [[package]] name = "variant-translation" version = "1.2.0" @@ -5297,9 +5292,9 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_it type = ["pytest-mypy"] [extras] -server = ["aiocache", "alembic", "alembic-utils", "arq", "authlib", "biocommons", "boto3", "cdot", "cryptography", "fastapi", "hgvs", "orcid", "psycopg2", "pyathena", "python-jose", "python-multipart", "requests", "slack-sdk", "starlette", "starlette-context", "uvicorn", "variant-annotation", "watchtower"] +server = ["aiocache", "alembic", "alembic-utils", "arq", "authlib", "bbi-variant-annotation", "biocommons", "boto3", "cdot", "cryptography", "fastapi", "hgvs", "orcid", "psycopg2", "pyathena", "python-jose", "python-multipart", "requests", "slack-sdk", "starlette", "starlette-context", "uvicorn", "watchtower"] [metadata] lock-version = "2.1" python-versions = "^3.11" -content-hash = "5a24b728c64c490a22d95d754e2ffaa6bf7615d01de828803a69f3bfb5e82030" +content-hash = "3354617968bfec911fcc172ceedfceeecf71b415356f757f2173c3ac45a4ca0d" diff --git a/pyproject.toml b/pyproject.toml index 126b5606..d382064d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "mavedb" -version = "2026.3.0" +version = "2026.3.1" description = "API for MaveDB, the database of Multiplexed Assays of Variant Effect." license = "AGPL-3.0-only" readme = "README.md" @@ -65,7 +65,7 @@ starlette = { version = "^1.7.0", optional = true } starlette-context = { version = "^0.3.6", optional = true } slack-sdk = { version = "~3.21.3", optional = true } uvicorn = { extras = ["standard"], version = "*", optional = true } -variant-annotation = { git = "https://github.com/bbi-lab/variant-annotation.git", tag = "v1.2.0-beta.1", optional = true } +bbi-variant-annotation = { version = "1.2.0b3", optional = true } watchtower = { version = "~3.2.0", optional = true } asyncclick = "^8.3.0.7" filelock = "^3.29.0" @@ -96,7 +96,7 @@ SQLAlchemy = { extras = ["mypy"], version = "~2.0.0" } [tool.poetry.extras] -server = ["aiocache", "alembic", "alembic-utils", "arq", "authlib", "biocommons", "boto3", "cdot", "cryptography", "fastapi", "hgvs", "orcid", "psycopg2", "python-jose", "python-multipart", "pyathena", "requests", "starlette", "starlette-context", "slack-sdk", "uvicorn", "variant-annotation", "watchtower"] +server = ["aiocache", "alembic", "alembic-utils", "arq", "authlib", "biocommons", "boto3", "cdot", "cryptography", "fastapi", "hgvs", "orcid", "psycopg2", "python-jose", "python-multipart", "pyathena", "requests", "starlette", "starlette-context", "slack-sdk", "uvicorn", "bbi-variant-annotation", "watchtower"] [tool.mypy] @@ -107,9 +107,8 @@ plugins = [ ] mypy_path = "mypy_stubs" -# variant-annotation is a git-pinned dependency (not yet published to PyPI) that ships -# no py.typed marker. Treat it as untyped rather than maintaining drift-prone local -# stubs for an actively-developed internal library. +# bbi-variant-annotation (imported as variant_annotation) ships no py.typed marker. Treat it as +# untyped rather than maintaining drift-prone local stubs for an actively-developed internal library. [[tool.mypy.overrides]] module = "variant_annotation.*" ignore_missing_imports = true diff --git a/src/mavedb/__init__.py b/src/mavedb/__init__.py index 4d74f711..24284f22 100644 --- a/src/mavedb/__init__.py +++ b/src/mavedb/__init__.py @@ -6,7 +6,7 @@ logger = module_logging.getLogger(__name__) __project__ = "mavedb-api" -__version__ = "2026.3.0" +__version__ = "2026.3.1" logger.info(f"MaveDB {__version__}")