diff --git a/bento_reference_service/sql/migrate_v0_2.sql b/bento_reference_service/sql/migrate_v0_2.sql index a889dfc..b6745bc 100644 --- a/bento_reference_service/sql/migrate_v0_2.sql +++ b/bento_reference_service/sql/migrate_v0_2.sql @@ -1,5 +1,6 @@ -- Run these commands before migrating to v0.2.x +DROP TABLE genome_feature_parents CASCADE; DROP TABLE genome_feature_annotations CASCADE; DROP TABLE genome_features CASCADE; DROP TABLE IF EXISTS genome_feature_type_synonyms; -- from v0.1, now unused diff --git a/poetry.lock b/poetry.lock index 9068615..20bc8ca 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "aiofiles" -version = "23.2.1" +version = "24.1.0" description = "File support for asyncio." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "aiofiles-23.2.1-py3-none-any.whl", hash = "sha256:19297512c647d4b27a2cf7c34caa7e405c0d60b5560618a29a9fe027b18b0107"}, - {file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"}, + {file = "aiofiles-24.1.0-py3-none-any.whl", hash = "sha256:b4ec55f4195e3eb5d7abd1bf7e061763e864dd4954231fb8539a0ef8bb8260e5"}, + {file = "aiofiles-24.1.0.tar.gz", hash = "sha256:22a075c9e5a3810f0c2e48f3008c94d68c65d763b9b03857924c99e57355166c"}, ] [[package]] @@ -257,17 +257,17 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "bento-lib" -version = "11.11.0" +version = "11.11.2" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = "<4.0,>=3.10" files = [ - {file = "bento_lib-11.11.0-py3-none-any.whl", hash = "sha256:3ba1e6edfbc4900f12d65e3065dba1460eec8f9438fa2eed065881a63d091a50"}, - {file = "bento_lib-11.11.0.tar.gz", hash = "sha256:b1b6e26d78109f49a93ed23817dae97c456c09715b677df9fa90d992c25d90cd"}, + {file = "bento_lib-11.11.2-py3-none-any.whl", hash = "sha256:684edb7d084ca8b401d3beb9e6b50a108e00dc7bceca2829992908563ce45f62"}, + {file = "bento_lib-11.11.2.tar.gz", hash = "sha256:ec9056ce22a2be6fe5bd6075e6f69ea32f821c024710ed3daa5807905a6e4bc7"}, ] [package.dependencies] -aiofiles = ">=23.2.1,<24.0.0" +aiofiles = ">=23.2.1,<25" aiohttp = ">=3.9.4,<4" fastapi = {version = ">=0.104,<0.112", optional = true, markers = "extra == \"fastapi\""} jsonschema = ">=4.20.0,<5" @@ -647,17 +647,17 @@ test = ["pytest (>=6)"] [[package]] name = "fasta-checksum-utils" -version = "0.4.2" +version = "0.4.3" description = "Library and command-line utility for checksumming FASTA files and individual contigs." optional = false python-versions = "<4.0.0,>=3.9.1" files = [ - {file = "fasta_checksum_utils-0.4.2-py3-none-any.whl", hash = "sha256:909f3355e57c9ef50d619fe16c01ce394f26dee9e18645beaaf045a765fdd60a"}, - {file = "fasta_checksum_utils-0.4.2.tar.gz", hash = "sha256:601a7d465b905dbcc43d47e347ab003d39bd312a00895914926a88ddba46e556"}, + {file = "fasta_checksum_utils-0.4.3-py3-none-any.whl", hash = "sha256:53e6b796915c7d346890fbae34d58379d71b924282a71cb419e2e0e6585a337a"}, + {file = "fasta_checksum_utils-0.4.3.tar.gz", hash = "sha256:1f1ad64cc11b14c3743391b252e24649487f5c795660582a3386f2f607d21038"}, ] [package.dependencies] -aiofiles = ">=23.2.1,<24.0.0" +aiofiles = ">=23.2.1,<25" aiohttp = ">=3.9.3,<4.0.0" pysam = ">=0.22.0,<0.23.0" @@ -1643,13 +1643,13 @@ files = [ [[package]] name = "pytest" -version = "8.2.2" +version = "8.3.1" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" files = [ - {file = "pytest-8.2.2-py3-none-any.whl", hash = "sha256:c434598117762e2bd304e526244f67bf66bbd7b5d6cf22138be51ff661980343"}, - {file = "pytest-8.2.2.tar.gz", hash = "sha256:de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977"}, + {file = "pytest-8.3.1-py3-none-any.whl", hash = "sha256:e9600ccf4f563976e2c99fa02c7624ab938296551f280835ee6516df8bc4ae8c"}, + {file = "pytest-8.3.1.tar.gz", hash = "sha256:7e8e5c5abd6e93cb1cc151f23e57adc31fcf8cfd2a3ff2da63e23f732de35db6"}, ] [package.dependencies] @@ -1657,7 +1657,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" -pluggy = ">=1.5,<2.0" +pluggy = ">=1.5,<2" tomli = {version = ">=1", markers = "python_version < \"3.11\""} [package.extras] @@ -1665,13 +1665,13 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments [[package]] name = "pytest-asyncio" -version = "0.23.7" +version = "0.23.8" description = "Pytest support for asyncio" optional = false python-versions = ">=3.8" files = [ - {file = "pytest_asyncio-0.23.7-py3-none-any.whl", hash = "sha256:009b48127fbe44518a547bddd25611551b0e43ccdbf1e67d12479f569832c20b"}, - {file = "pytest_asyncio-0.23.7.tar.gz", hash = "sha256:5f5c72948f4c49e7db4f29f2521d4031f1c27f86e57b046126654083d4770268"}, + {file = "pytest_asyncio-0.23.8-py3-none-any.whl", hash = "sha256:50265d892689a5faefb84df80819d1ecef566eb3549cf915dfb33569359d1ce2"}, + {file = "pytest_asyncio-0.23.8.tar.gz", hash = "sha256:759b10b33a6dc61cce40a8bd5205e302978bbbcc00e279a8b61d9a6a3c82e4d3"}, ] [package.dependencies] @@ -2178,13 +2178,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "uvicorn" -version = "0.30.1" +version = "0.30.3" description = "The lightning-fast ASGI server." optional = false python-versions = ">=3.8" files = [ - {file = "uvicorn-0.30.1-py3-none-any.whl", hash = "sha256:cd17daa7f3b9d7a24de3617820e634d0933b69eed8e33a516071174427238c81"}, - {file = "uvicorn-0.30.1.tar.gz", hash = "sha256:d46cd8e0fd80240baffbcd9ec1012a712938754afcf81bce56c024c1656aece8"}, + {file = "uvicorn-0.30.3-py3-none-any.whl", hash = "sha256:94a3608da0e530cea8f69683aa4126364ac18e3826b6630d1a65f4638aade503"}, + {file = "uvicorn-0.30.3.tar.gz", hash = "sha256:0d114d0831ff1adbf231d358cbf42f17333413042552a624ea6a9b4c33dcfd81"}, ] [package.dependencies] @@ -2557,4 +2557,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10.0" -content-hash = "4bd4662a9a831f711a7536e74ab3fe5bf33b985678aa5020864c56e36f81fc22" +content-hash = "ff036d0335307dd9628e2b4cbc9bb7a530a43513fd40b5571e7169c242f30f63" diff --git a/pyproject.toml b/pyproject.toml index e69bb70..4d25398 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_reference_service" -version = "0.2.1" +version = "0.2.2" description = "Reference data (genomes & annotations) service for the Bento platform." authors = [ "David Lougheed ", @@ -27,8 +27,8 @@ classifiers = [ python = "^3.10.0" fastapi = {extras = ["all"], version = "^0.111.1"} pydantic = "^2.6.1" -bento-lib = {extras = ["fastapi"], version = "^11.11.0"} -aiofiles = "^23.2.1" +bento-lib = {extras = ["fastapi"], version = "^11.11.2"} +aiofiles = "^24.1.0" pysam = "~0.22.0" jsonschema = "^4.21.1" pydantic-settings = "^2.1.0" @@ -44,7 +44,7 @@ pytest = "^8.2.1" pytest-asyncio = "^0.23.5" pytest-cov = "^5.0.0" tox = "^4.12.1" -fasta-checksum-utils = "^0.4.1" +fasta-checksum-utils = "^0.4.3" [tool.black] line_length = 120