From 3f3f99f16dc8a56ac1c5408c30d17444ff139a83 Mon Sep 17 00:00:00 2001 From: Ian Boyes Date: Wed, 12 Jun 2024 10:59:40 -0700 Subject: [PATCH] feat: support jobs without `rights` field * Support jobs without `rights` field. * Prevent forward ref error. --- Dockerfile | 4 +- poetry.lock | 202 ++++++++++--------------------------------------- pyproject.toml | 2 +- 3 files changed, 41 insertions(+), 167 deletions(-) diff --git a/Dockerfile b/Dockerfile index 580135a..7795cb2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ WORKDIR SPAdes-3.15.5 ENV PREFIX=/build/spades RUN ./spades_compile.sh -FROM python:3.12-bookworm as deps +FROM python:3.12.3-bookworm as deps WORKDIR /app COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/ COPY --from=spades /build/spades /opt/spades @@ -47,7 +47,7 @@ RUN curl -sSL https://install.python-poetry.org | python - COPY poetry.lock pyproject.toml ./ RUN poetry install -FROM python:3.12-bookworm as base +FROM python:3.12.3-bookworm as base WORKDIR /app COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/ COPY --from=spades /build/spades /opt/spades diff --git a/poetry.lock b/poetry.lock index a5a56e6..33a0dd6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -106,21 +106,6 @@ yarl = ">=1.0,<2.0" [package.extras] speedups = ["Brotli", "aiodns", "brotlicffi"] -[[package]] -name = "aioredis" -version = "1.3.1" -description = "asyncio (PEP 3156) Redis support" -optional = false -python-versions = "*" -files = [ - {file = "aioredis-1.3.1-py3-none-any.whl", hash = "sha256:b61808d7e97b7cd5a92ed574937a079c9387fdadd22bfbfa7ad2fd319ecc26e3"}, - {file = "aioredis-1.3.1.tar.gz", hash = "sha256:15f8af30b044c771aee6787e5ec24694c048184c7b9e54c3b60c750a4b93273a"}, -] - -[package.dependencies] -async-timeout = "*" -hiredis = "*" - [[package]] name = "aiosignal" version = "1.3.1" @@ -154,17 +139,6 @@ types-python-dateutil = ">=2.8.10" doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] -[[package]] -name = "async-timeout" -version = "4.0.3" -description = "Timeout context manager for asyncio programs" -optional = false -python-versions = ">=3.7" -files = [ - {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"}, - {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"}, -] - [[package]] name = "attrs" version = "23.2.0" @@ -430,124 +404,6 @@ files = [ {file = "frozenlist-1.4.1.tar.gz", hash = "sha256:c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b"}, ] -[[package]] -name = "hiredis" -version = "2.3.2" -description = "Python wrapper for hiredis" -optional = false -python-versions = ">=3.7" -files = [ - {file = "hiredis-2.3.2-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:742093f33d374098aa21c1696ac6e4874b52658c870513a297a89265a4d08fe5"}, - {file = "hiredis-2.3.2-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:9e14fb70ca4f7efa924f508975199353bf653f452e4ef0a1e47549e208f943d7"}, - {file = "hiredis-2.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6d7302b4b17fcc1cc727ce84ded7f6be4655701e8d58744f73b09cb9ed2b13df"}, - {file = "hiredis-2.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ed63e8b75c193c5e5a8288d9d7b011da076cc314fafc3bfd59ec1d8a750d48c8"}, - {file = "hiredis-2.3.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:6b4edee59dc089bc3948f4f6fba309f51aa2ccce63902364900aa0a553a85e97"}, - {file = "hiredis-2.3.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:a6481c3b7673a86276220140456c2a6fbfe8d1fb5c613b4728293c8634134824"}, - {file = "hiredis-2.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:684840b014ce83541a087fcf2d48227196576f56ae3e944d4dfe14c0a3e0ccb7"}, - {file = "hiredis-2.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:1c4c0bcf786f0eac9593367b6279e9b89534e008edbf116dcd0de956524702c8"}, - {file = "hiredis-2.3.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:66ab949424ac6504d823cba45c4c4854af5c59306a1531edb43b4dd22e17c102"}, - {file = "hiredis-2.3.2-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:322c668ee1c12d6c5750a4b1057e6b4feee2a75b3d25d630922a463cfe5e7478"}, - {file = "hiredis-2.3.2-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:bfa73e3f163c6e8b2ec26f22285d717a5f77ab2120c97a2605d8f48b26950dac"}, - {file = "hiredis-2.3.2-cp310-cp310-musllinux_1_1_s390x.whl", hash = "sha256:7f39f28ffc65de577c3bc0c7615f149e35bc927802a0f56e612db9b530f316f9"}, - {file = "hiredis-2.3.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:55ce31bf4711da879b96d511208efb65a6165da4ba91cb3a96d86d5a8d9d23e6"}, - {file = "hiredis-2.3.2-cp310-cp310-win32.whl", hash = "sha256:3dd63d0bbbe75797b743f35d37a4cca7ca7ba35423a0de742ae2985752f20c6d"}, - {file = "hiredis-2.3.2-cp310-cp310-win_amd64.whl", hash = "sha256:ea002656a8d974daaf6089863ab0a306962c8b715db6b10879f98b781a2a5bf5"}, - {file = "hiredis-2.3.2-cp311-cp311-macosx_10_15_universal2.whl", hash = "sha256:adfbf2e9c38b77d0db2fb32c3bdaea638fa76b4e75847283cd707521ad2475ef"}, - {file = "hiredis-2.3.2-cp311-cp311-macosx_10_15_x86_64.whl", hash = "sha256:80b02d27864ebaf9b153d4b99015342382eeaed651f5591ce6f07e840307c56d"}, - {file = "hiredis-2.3.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:bd40d2e2f82a483de0d0a6dfd8c3895a02e55e5c9949610ecbded18188fd0a56"}, - {file = "hiredis-2.3.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:dfa904045d7cebfb0f01dad51352551cce1d873d7c3f80c7ded7d42f8cac8f89"}, - {file = "hiredis-2.3.2-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:28bd184b33e0dd6d65816c16521a4ba1ffbe9ff07d66873c42ea4049a62fed83"}, - {file = "hiredis-2.3.2-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:f70481213373d44614148f0f2e38e7905be3f021902ae5167289413196de4ba4"}, - {file = "hiredis-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eb8797b528c1ff81eef06713623562b36db3dafa106b59f83a6468df788ff0d1"}, - {file = "hiredis-2.3.2-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:02fc71c8333586871602db4774d3a3e403b4ccf6446dc4603ec12df563127cee"}, - {file = "hiredis-2.3.2-cp311-cp311-musllinux_1_1_aarch64.whl", hash = "sha256:0da56915bda1e0a49157191b54d3e27689b70960f0685fdd5c415dacdee2fbed"}, - {file = "hiredis-2.3.2-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:e2674a5a3168349435b08fa0b82998ed2536eb9acccf7087efe26e4cd088a525"}, - {file = "hiredis-2.3.2-cp311-cp311-musllinux_1_1_ppc64le.whl", hash = "sha256:dc1c3fd49930494a67dcec37d0558d99d84eca8eb3f03b17198424538f2608d7"}, - {file = "hiredis-2.3.2-cp311-cp311-musllinux_1_1_s390x.whl", hash = "sha256:14c7b43205e515f538a9defb4e411e0f0576caaeeda76bb9993ed505486f7562"}, - {file = "hiredis-2.3.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:7bac7e02915b970c3723a7a7c5df4ba7a11a3426d2a3f181e041aa506a1ff028"}, - {file = "hiredis-2.3.2-cp311-cp311-win32.whl", hash = "sha256:63a090761ddc3c1f7db5e67aa4e247b4b3bb9890080bdcdadd1b5200b8b89ac4"}, - {file = "hiredis-2.3.2-cp311-cp311-win_amd64.whl", hash = "sha256:70d226ab0306a5b8d408235cabe51d4bf3554c9e8a72d53ce0b3c5c84cf78881"}, - {file = "hiredis-2.3.2-cp312-cp312-macosx_10_15_universal2.whl", hash = "sha256:5c614552c6bd1d0d907f448f75550f6b24fb56cbfce80c094908b7990cad9702"}, - {file = "hiredis-2.3.2-cp312-cp312-macosx_10_15_x86_64.whl", hash = "sha256:9c431431abf55b64347ddc8df68b3ef840269cb0aa5bc2d26ad9506eb4b1b866"}, - {file = "hiredis-2.3.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:a45857e87e9d2b005e81ddac9d815a33efd26ec67032c366629f023fe64fb415"}, - {file = "hiredis-2.3.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e138d141ec5a6ec800b6d01ddc3e5561ce1c940215e0eb9960876bfde7186aae"}, - {file = "hiredis-2.3.2-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:387f655444d912a963ab68abf64bf6e178a13c8e4aa945cb27388fd01a02e6f1"}, - {file = "hiredis-2.3.2-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:4852f4bf88f0e2d9bdf91279892f5740ed22ae368335a37a52b92a5c88691140"}, - {file = "hiredis-2.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d711c107e83117129b7f8bd08e9820c43ceec6204fff072a001fd82f6d13db9f"}, - {file = "hiredis-2.3.2-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:92830c16885f29163e1c2da1f3c1edb226df1210ec7e8711aaabba3dd0d5470a"}, - {file = "hiredis-2.3.2-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:16b01d9ceae265d4ab9547be0cd628ecaff14b3360357a9d30c029e5ae8b7e7f"}, - {file = "hiredis-2.3.2-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:5986fb5f380169270a0293bebebd95466a1c85010b4f1afc2727e4d17c452512"}, - {file = "hiredis-2.3.2-cp312-cp312-musllinux_1_1_ppc64le.whl", hash = "sha256:49532d7939cc51f8e99efc326090c54acf5437ed88b9c904cc8015b3c4eda9c9"}, - {file = "hiredis-2.3.2-cp312-cp312-musllinux_1_1_s390x.whl", hash = "sha256:8f34801b251ca43ad70691fb08b606a2e55f06b9c9fb1fc18fd9402b19d70f7b"}, - {file = "hiredis-2.3.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:7298562a49d95570ab1c7fc4051e72824c6a80e907993a21a41ba204223e7334"}, - {file = "hiredis-2.3.2-cp312-cp312-win32.whl", hash = "sha256:e1d86b75de787481b04d112067a4033e1ecfda2a060e50318a74e4e1c9b2948c"}, - {file = "hiredis-2.3.2-cp312-cp312-win_amd64.whl", hash = "sha256:6dbfe1887ffa5cf3030451a56a8f965a9da2fa82b7149357752b67a335a05fc6"}, - {file = "hiredis-2.3.2-cp37-cp37m-macosx_10_15_x86_64.whl", hash = "sha256:4fc242e9da4af48714199216eb535b61e8f8d66552c8819e33fc7806bd465a09"}, - {file = "hiredis-2.3.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e81aa4e9a1fcf604c8c4b51aa5d258e195a6ba81efe1da82dea3204443eba01c"}, - {file = "hiredis-2.3.2-cp37-cp37m-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:419780f8583ddb544ffa86f9d44a7fcc183cd826101af4e5ffe535b6765f5f6b"}, - {file = "hiredis-2.3.2-cp37-cp37m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:6871306d8b98a15e53a5f289ec1106a3a1d43e7ab6f4d785f95fcef9a7bd9504"}, - {file = "hiredis-2.3.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:88cb0b35b63717ef1e41d62f4f8717166f7c6245064957907cfe177cc144357c"}, - {file = "hiredis-2.3.2-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:8c490191fa1218851f8a80c5a21a05a6f680ac5aebc2e688b71cbfe592f8fec6"}, - {file = "hiredis-2.3.2-cp37-cp37m-musllinux_1_1_aarch64.whl", hash = "sha256:4baf4b579b108062e91bd2a991dc98b9dc3dc06e6288db2d98895eea8acbac22"}, - {file = "hiredis-2.3.2-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:e627d8ef5e100556e09fb44c9571a432b10e11596d3c4043500080ca9944a91a"}, - {file = "hiredis-2.3.2-cp37-cp37m-musllinux_1_1_ppc64le.whl", hash = "sha256:ba3dc0af0def8c21ce7d903c59ea1e8ec4cb073f25ece9edaec7f92a286cd219"}, - {file = "hiredis-2.3.2-cp37-cp37m-musllinux_1_1_s390x.whl", hash = "sha256:56e9b7d6051688ca94e68c0c8a54a243f8db841911b683cedf89a29d4de91509"}, - {file = "hiredis-2.3.2-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:380e029bb4b1d34cf560fcc8950bf6b57c2ef0c9c8b7c7ac20b7c524a730fadd"}, - {file = "hiredis-2.3.2-cp37-cp37m-win32.whl", hash = "sha256:948d9f2ca7841794dd9b204644963a4bcd69ced4e959b0d4ecf1b8ce994a6daa"}, - {file = "hiredis-2.3.2-cp37-cp37m-win_amd64.whl", hash = "sha256:cfa67afe2269b2d203cd1389c00c5bc35a287cd57860441fb0e53b371ea6a029"}, - {file = "hiredis-2.3.2-cp38-cp38-macosx_10_15_universal2.whl", hash = "sha256:bcbe47da0aebc00a7cfe3ebdcff0373b86ce2b1856251c003e3d69c9db44b5a7"}, - {file = "hiredis-2.3.2-cp38-cp38-macosx_10_15_x86_64.whl", hash = "sha256:f2c9c0d910dd3f7df92f0638e7f65d8edd7f442203caf89c62fc79f11b0b73f8"}, - {file = "hiredis-2.3.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:01b6c24c0840ac7afafbc4db236fd55f56a9a0919a215c25a238f051781f4772"}, - {file = "hiredis-2.3.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c1f567489f422d40c21e53212a73bef4638d9f21043848150f8544ef1f3a6ad1"}, - {file = "hiredis-2.3.2-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:28adecb308293e705e44087a1c2d557a816f032430d8a2a9bb7873902a1c6d48"}, - {file = "hiredis-2.3.2-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:27e9619847e9dc70b14b1ad2d0fb4889e7ca18996585c3463cff6c951fd6b10b"}, - {file = "hiredis-2.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9a0026cfbf29f07649b0e34509091a2a6016ff8844b127de150efce1c3aff60b"}, - {file = "hiredis-2.3.2-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:f9de7586522e5da6bee83c9cf0dcccac0857a43249cb4d721a2e312d98a684d1"}, - {file = "hiredis-2.3.2-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:e58494f282215fc461b06709e9a195a24c12ba09570f25bdf9efb036acc05101"}, - {file = "hiredis-2.3.2-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:de3a32b4b76d46f1eb42b24a918d51d8ca52411a381748196241d59a895f7c5c"}, - {file = "hiredis-2.3.2-cp38-cp38-musllinux_1_1_ppc64le.whl", hash = "sha256:1979334ccab21a49c544cd1b8d784ffb2747f99a51cb0bd0976eebb517628382"}, - {file = "hiredis-2.3.2-cp38-cp38-musllinux_1_1_s390x.whl", hash = "sha256:0c0773266e1c38a06e7593bd08870ac1503f5f0ce0f5c63f2b4134b090b5d6a4"}, - {file = "hiredis-2.3.2-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:bd1cee053416183adcc8e6134704c46c60c3f66b8faaf9e65bf76191ca59a2f7"}, - {file = "hiredis-2.3.2-cp38-cp38-win32.whl", hash = "sha256:5341ce3d01ef3c7418a72e370bf028c7aeb16895e79e115fe4c954fff990489e"}, - {file = "hiredis-2.3.2-cp38-cp38-win_amd64.whl", hash = "sha256:8fc7197ff33047ce43a67851ccf190acb5b05c52fd4a001bb55766358f04da68"}, - {file = "hiredis-2.3.2-cp39-cp39-macosx_10_15_universal2.whl", hash = "sha256:f47775e27388b58ce52f4f972f80e45b13c65113e9e6b6bf60148f893871dc9b"}, - {file = "hiredis-2.3.2-cp39-cp39-macosx_10_15_x86_64.whl", hash = "sha256:9412a06b8a8e09abd6313d96864b6d7713c6003a365995a5c70cfb9209df1570"}, - {file = "hiredis-2.3.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:f3020b60e3fc96d08c2a9b011f1c2e2a6bdcc09cb55df93c509b88be5cb791df"}, - {file = "hiredis-2.3.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:53d0f2c59bce399b8010a21bc779b4f8c32d0f582b2284ac8c98dc7578b27bc4"}, - {file = "hiredis-2.3.2-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:57c0d0c7e308ed5280a4900d4468bbfec51f0e1b4cde1deae7d4e639bc6b7766"}, - {file = "hiredis-2.3.2-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:1d63318ca189fddc7e75f6a4af8eae9c0545863619fb38cfba5f43e81280b286"}, - {file = "hiredis-2.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e741ffe4e2db78a1b9dd6e5d29678ce37fbaaf65dfe132e5b82a794413302ef1"}, - {file = "hiredis-2.3.2-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:eb98038ccd368e0d88bd92ee575c58cfaf33e77f788c36b2a89a84ee1936dc6b"}, - {file = "hiredis-2.3.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:eae62ed60d53b3561148bcd8c2383e430af38c0deab9f2dd15f8874888ffd26f"}, - {file = "hiredis-2.3.2-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:ca33c175c1cf60222d9c6d01c38fc17ec3a484f32294af781de30226b003e00f"}, - {file = "hiredis-2.3.2-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:0c5f6972d2bdee3cd301d5c5438e31195cf1cabf6fd9274491674d4ceb46914d"}, - {file = "hiredis-2.3.2-cp39-cp39-musllinux_1_1_s390x.whl", hash = "sha256:a6b54dabfaa5dbaa92f796f0c32819b4636e66aa8e9106c3d421624bd2a2d676"}, - {file = "hiredis-2.3.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:e96cd35df012a17c87ae276196ea8f215e77d6eeca90709eb03999e2d5e3fd8a"}, - {file = "hiredis-2.3.2-cp39-cp39-win32.whl", hash = "sha256:63b99b5ea9fe4f21469fb06a16ca5244307678636f11917359e3223aaeca0b67"}, - {file = "hiredis-2.3.2-cp39-cp39-win_amd64.whl", hash = "sha256:a50c8af811b35b8a43b1590cf890b61ff2233225257a3cad32f43b3ec7ff1b9f"}, - {file = "hiredis-2.3.2-pp310-pypy310_pp73-macosx_10_15_x86_64.whl", hash = "sha256:7e8bf4444b09419b77ce671088db9f875b26720b5872d97778e2545cd87dba4a"}, - {file = "hiredis-2.3.2-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5bd42d0d45ea47a2f96babd82a659fbc60612ab9423a68e4a8191e538b85542a"}, - {file = "hiredis-2.3.2-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:80441b55edbef868e2563842f5030982b04349408396e5ac2b32025fb06b5212"}, - {file = "hiredis-2.3.2-pp310-pypy310_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:ec444ab8f27562a363672d6a7372bc0700a1bdc9764563c57c5f9efa0e592b5f"}, - {file = "hiredis-2.3.2-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:f9f606e810858207d4b4287b4ef0dc622c2aa469548bf02b59dcc616f134f811"}, - {file = "hiredis-2.3.2-pp37-pypy37_pp73-macosx_10_15_x86_64.whl", hash = "sha256:c3dde4ca00fe9eee3b76209711f1941bb86db42b8a75d7f2249ff9dfc026ab0e"}, - {file = "hiredis-2.3.2-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d4dd676107a1d3c724a56a9d9db38166ad4cf44f924ee701414751bd18a784a0"}, - {file = "hiredis-2.3.2-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ce42649e2676ad783186264d5ffc788a7612ecd7f9effb62d51c30d413a3eefe"}, - {file = "hiredis-2.3.2-pp37-pypy37_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:8e3f8b1733078ac663dad57e20060e16389a60ab542f18a97931f3a2a2dd64a4"}, - {file = "hiredis-2.3.2-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:532a84a82156a82529ec401d1c25d677c6543c791e54a263aa139541c363995f"}, - {file = "hiredis-2.3.2-pp38-pypy38_pp73-macosx_10_15_x86_64.whl", hash = "sha256:4d59f88c4daa36b8c38e59ac7bffed6f5d7f68eaccad471484bf587b28ccc478"}, - {file = "hiredis-2.3.2-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a91a14dd95e24dc078204b18b0199226ee44644974c645dc54ee7b00c3157330"}, - {file = "hiredis-2.3.2-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bb777a38797c8c7df0444533119570be18d1a4ce5478dffc00c875684df7bfcb"}, - {file = "hiredis-2.3.2-pp38-pypy38_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:d47c915897a99d0d34a39fad4be97b4b709ab3d0d3b779ebccf2b6024a8c681e"}, - {file = "hiredis-2.3.2-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:333b5e04866758b11bda5f5315b4e671d15755fc6ed3b7969721bc6311d0ee36"}, - {file = "hiredis-2.3.2-pp39-pypy39_pp73-macosx_10_15_x86_64.whl", hash = "sha256:c8937f1100435698c18e4da086968c4b5d70e86ea718376f833475ab3277c9aa"}, - {file = "hiredis-2.3.2-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:fa45f7d771094b8145af10db74704ab0f698adb682fbf3721d8090f90e42cc49"}, - {file = "hiredis-2.3.2-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:33d5ebc93c39aed4b5bc769f8ce0819bc50e74bb95d57a35f838f1c4378978e0"}, - {file = "hiredis-2.3.2-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a797d8c7df9944314d309b0d9e1b354e2fa4430a05bb7604da13b6ad291bf959"}, - {file = "hiredis-2.3.2-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:e15a408f71a6c8c87b364f1f15a6cd9c1baca12bbc47a326ac8ab99ec7ad3c64"}, - {file = "hiredis-2.3.2.tar.gz", hash = "sha256:733e2456b68f3f126ddaf2cd500a33b25146c3676b97ea843665717bda0c5d43"}, -] - [[package]] name = "idna" version = "3.7" @@ -1080,6 +936,21 @@ files = [ [package.dependencies] six = ">=1.5" +[[package]] +name = "redis" +version = "5.0.5" +description = "Python client for Redis database and key-value store" +optional = false +python-versions = ">=3.7" +files = [ + {file = "redis-5.0.5-py3-none-any.whl", hash = "sha256:30b47d4ebb6b7a0b9b40c1275a19b87bb6f46b3bed82a89012cf56dea4024ada"}, + {file = "redis-5.0.5.tar.gz", hash = "sha256:3417688621acf6ee368dec4a04dd95881be24efd34c79f00d31f62bb528800ae"}, +] + +[package.extras] +hiredis = ["hiredis (>=1.0.0)"] +ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)"] + [[package]] name = "ruff" version = "0.1.15" @@ -1108,21 +979,22 @@ files = [ [[package]] name = "sentry-sdk" -version = "1.45.0" +version = "2.5.1" description = "Python client for Sentry (https://sentry.io)" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - {file = "sentry-sdk-1.45.0.tar.gz", hash = "sha256:509aa9678c0512344ca886281766c2e538682f8acfa50fd8d405f8c417ad0625"}, - {file = "sentry_sdk-1.45.0-py2.py3-none-any.whl", hash = "sha256:1ce29e30240cc289a027011103a8c83885b15ef2f316a60bcc7c5300afa144f1"}, + {file = "sentry_sdk-2.5.1-py2.py3-none-any.whl", hash = "sha256:1f87acdce4a43a523ae5aa21a3fc37522d73ebd9ec04b1dbf01aa3d173852def"}, + {file = "sentry_sdk-2.5.1.tar.gz", hash = "sha256:fbc40a78a8a9c6675133031116144f0d0940376fa6e4e1acd5624c90b0aaf58b"}, ] [package.dependencies] certifi = "*" -urllib3 = {version = ">=1.26.11", markers = "python_version >= \"3.6\""} +urllib3 = ">=1.26.11" [package.extras] aiohttp = ["aiohttp (>=3.5)"] +anthropic = ["anthropic (>=0.16)"] arq = ["arq (>=0.23)"] asyncpg = ["asyncpg (>=0.23)"] beam = ["apache-beam (>=2.12)"] @@ -1135,9 +1007,11 @@ django = ["django (>=1.8)"] falcon = ["falcon (>=1.4)"] fastapi = ["fastapi (>=0.79.0)"] flask = ["blinker (>=1.1)", "flask (>=0.11)", "markupsafe"] -grpcio = ["grpcio (>=1.21.1)"] +grpcio = ["grpcio (>=1.21.1)", "protobuf (>=3.8.0)"] httpx = ["httpx (>=0.16.0)"] huey = ["huey (>=2)"] +huggingface-hub = ["huggingface-hub (>=0.22)"] +langchain = ["langchain (>=0.0.210)"] loguru = ["loguru (>=0.5)"] openai = ["openai (>=1.0.0)", "tiktoken (>=0.3.0)"] opentelemetry = ["opentelemetry-distro (>=0.35b0)"] @@ -1251,49 +1125,49 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtool-core" -version = "11.1.0" +version = "14.0.1" description = "Core utilities for Virtool." optional = false -python-versions = ">3.8,<3.13" +python-versions = "<3.13,>=3.12" files = [ - {file = "virtool_core-11.1.0-py3-none-any.whl", hash = "sha256:4dd61940db57261e8311481f8fff26b0740daf8a50c359ebb48214a741f01341"}, - {file = "virtool_core-11.1.0.tar.gz", hash = "sha256:d25fd4e6b11c51c9b4684f5c2e18b00f30cd790aa50aadc0465900e7d9514918"}, + {file = "virtool_core-14.0.1-py3-none-any.whl", hash = "sha256:23ca5c161dd4b97736509f3d31f3077a3d81848f911a1f8b3dd8f573a2cda646"}, + {file = "virtool_core-14.0.1.tar.gz", hash = "sha256:fb9c627331391bf929eb8575b90cb3326aaf73761efa23e3dbe278a6691ce2c4"}, ] [package.dependencies] aiofiles = "0.7.0" -aioredis = ">=1.3.0,<2.0.0" arrow = ">=1.2.2,<2.0.0" dictdiffer = "0.8.1" -email-validator = ">=2.0.0.post2,<3.0.0" +email-validator = ">=2.1.1,<3.0.0" enum-tools = ">=0.11.0,<0.12.0" motor = ">=3.1.2,<4.0.0" motor-types = ">=1.0.0b3,<2.0.0" +orjson = ">=3.10.1,<4.0.0" pydantic = ">=1.8.2,<2.0.0" +redis = ">=5.0.3,<6.0.0" structlog = ">=23.1.0,<24.0.0" [[package]] name = "virtool-workflow" -version = "6.0.0" +version = "7.1.0" description = "A framework for developing bioinformatics workflows for Virtool." optional = false -python-versions = ">=3.10,<3.13" +python-versions = "<3.13,>=3.12" files = [ - {file = "virtool_workflow-6.0.0-py3-none-any.whl", hash = "sha256:c37fe9f94edc6aa1c400faf040a67f3d922f7f326f89689871a3f3e3aec0d8f0"}, - {file = "virtool_workflow-6.0.0.tar.gz", hash = "sha256:4d51b93f17073ec540bd39385cd5e16159342fbffca19b5924419eb1ff48fbd6"}, + {file = "virtool_workflow-7.1.0-py3-none-any.whl", hash = "sha256:3638498d7e20046e3243e9684ef4b639809bdac2832720a49bf34d1e1b3ecab3"}, + {file = "virtool_workflow-7.1.0.tar.gz", hash = "sha256:8e4d7aa50d8d6e2adfcf692f515333db7e447afb38af485624e738b99cf0ee56"}, ] [package.dependencies] aiofiles = ">=0.7.0,<0.8.0" aiohttp = ">=3.8.1,<4.0.0" -aioredis = "1.3.1" biopython = ">=1.81,<2.0" click = ">=8.1.7,<9.0.0" orjson = ">=3.9.9,<4.0.0" pydantic-factories = ">=1.17.3,<2.0.0" pyfixtures = ">=1.0.0,<2.0.0" -sentry-sdk = ">=1.5.7,<2.0.0" -virtool-core = ">=11.0.0,<12.0.0" +sentry-sdk = ">=2.3.1,<3.0.0" +virtool-core = ">=14.0.0,<15.0.0" [[package]] name = "yarl" @@ -1401,4 +1275,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "~3.12" -content-hash = "f553c9a177d8d84de1993b2043c8e78b3d01c610f61afd9ba8d43eb4f59abae6" +content-hash = "0173ebdcb23c97aefd7c9639d7dcb264078c5f4bdfe6abb68523dd477f0b5f77" diff --git a/pyproject.toml b/pyproject.toml index 453ecdc..45b5770 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ license = "MIT" [tool.poetry.dependencies] python = "~3.12" -virtool-workflow = "^6.0.0" +virtool-workflow = "^7.1.0" setuptools = "^70.0.0" [tool.poetry.group.dev.dependencies]