From 3ae1385eab34cb2836f569ef6ca82650d2fae6da Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 21 Apr 2025 08:43:33 -0400 Subject: [PATCH] poetry CLI alias for sample_annotator/gold_tool.py --- poetry.lock | 1006 ++++++++++++++++++++++++------------------------ pyproject.toml | 2 + 2 files changed, 515 insertions(+), 493 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8fb0dc3..1bf71c0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "alabaster" @@ -6,7 +6,6 @@ version = "1.0.0" description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.10" -groups = ["main"] files = [ {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, @@ -18,7 +17,6 @@ version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" -groups = ["main", "dev"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -30,7 +28,6 @@ version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" optional = false python-versions = "*" -groups = ["main"] files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] @@ -41,7 +38,6 @@ version = "1.3.0" description = "Better dates & times for Python" optional = false python-versions = ">=3.8" -groups = ["main"] files = [ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, @@ -61,19 +57,18 @@ version = "25.3.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.8" -groups = ["main", "dev"] files = [ {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"}, {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"}, ] [package.extras] -benchmark = ["cloudpickle ; 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documents" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"}, {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"}, @@ -3394,7 +3439,6 @@ version = "2.1.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"}, {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"}, @@ -3411,7 +3455,6 @@ version = "4.1" description = "Extension to include jQuery on newer Sphinx releases" optional = false python-versions = ">=2.7" -groups = ["main"] files = [ {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"}, {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"}, @@ -3426,7 +3469,6 @@ version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" optional = false python-versions = ">=3.5" -groups = ["main"] files = [ {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"}, {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"}, @@ -3441,7 +3483,6 @@ version = "2.0.0" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"}, {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"}, @@ -3458,7 +3499,6 @@ version = "2.0.0" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"}, {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"}, @@ -3475,7 +3515,6 @@ version = "2.0.40" description = "Database Abstraction Library" optional = false python-versions = ">=3.7" -groups = ["main", "dev"] files = [ {file = "SQLAlchemy-2.0.40-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:ae9597cab738e7cc823f04a704fb754a9249f0b6695a6aeb63b74055cd417a96"}, {file = "SQLAlchemy-2.0.40-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:37a5c21ab099a83d669ebb251fddf8f5cee4d75ea40a5a1653d9c43d60e20867"}, @@ -3571,7 +3610,6 @@ version = "1.0.1" description = "" optional = false python-versions = "*" -groups = ["main"] files = [ {file = "stemming-1.0.1.tar.gz", hash = "sha256:59678702e1d06caffecee82910f048edf12ad89dcf430776b4b05bfb8850bc51"}, {file = "stemming-1.0.1.zip", hash = "sha256:3a812fbe64a8c74e95651f5a48bae3a7a47282aa58cd5a61f3384e73674ac23d"}, @@ -3583,7 +3621,6 @@ version = "3.6.0" description = "threadpoolctl" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "threadpoolctl-3.6.0-py3-none-any.whl", hash = "sha256:43a0b8fd5a2928500110039e43a5eed8480b918967083ea48dc3ab9f13c4a7fb"}, {file = "threadpoolctl-3.6.0.tar.gz", hash = "sha256:8ab8b4aa3491d812b623328249fab5302a68d2d71745c8a4c719a2fcaba9f44e"}, @@ -3595,8 +3632,6 @@ version = "2.2.1" description = "A lil' TOML parser" optional = false python-versions = ">=3.8" -groups = ["main", "dev"] -markers = "python_version < \"3.11\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -3638,7 +3673,6 @@ version = "4.20.0" description = "tox is a generic virtualenv management and test command line tool" optional = false python-versions = ">=3.8" -groups = ["dev"] files = [ {file = "tox-4.20.0-py3-none-any.whl", hash = "sha256:21a8005e3d3fe5658a8e36b8ca3ed13a4230429063c5cc2a2fdac6ee5aa0de34"}, {file = "tox-4.20.0.tar.gz", hash = "sha256:5b78a49b6eaaeab3ae4186415e7c97d524f762ae967c63562687c3e5f0ec23d5"}, @@ -3658,7 +3692,7 @@ virtualenv = ">=20.26.3" [package.extras] docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-argparse-cli (>=1.17)", "sphinx-autodoc-typehints (>=2.4)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=24.8)"] -testing = ["build[virtualenv] (>=1.2.2)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.2)", "devpi-process (>=1)", "diff-cover (>=9.1.1)", "distlib (>=0.3.8)", "flaky (>=3.8.1)", "hatch-vcs (>=0.4)", "hatchling (>=1.25)", "psutil (>=6)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-xdist (>=3.6.1)", "re-assert (>=1.1)", "setuptools (>=74.1.2)", "time-machine (>=2.15) ; implementation_name != \"pypy\"", "wheel (>=0.44)"] +testing = ["build[virtualenv] (>=1.2.2)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.2)", "devpi-process (>=1)", "diff-cover (>=9.1.1)", "distlib (>=0.3.8)", "flaky (>=3.8.1)", "hatch-vcs (>=0.4)", "hatchling (>=1.25)", "psutil (>=6)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-xdist (>=3.6.1)", "re-assert (>=1.1)", "setuptools (>=74.1.2)", "time-machine (>=2.15)", "wheel (>=0.44)"] [[package]] name = "tqdm" @@ -3666,7 +3700,6 @@ version = "4.67.1" description = "Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" -groups = ["main", "dev"] files = [ {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"}, {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"}, @@ -3688,7 +3721,6 @@ version = "4.4.2" description = "Run-time type checker for Python" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "typeguard-4.4.2-py3-none-any.whl", hash = "sha256:77a78f11f09777aeae7fa08585f33b5f4ef0e7335af40005b0c422ed398ff48c"}, {file = "typeguard-4.4.2.tar.gz", hash = "sha256:a6f1065813e32ef365bc3b3f503af8a96f9dd4e0033a02c28c4a4983de8c6c49"}, @@ -3699,7 +3731,7 @@ typing_extensions = ">=4.10.0" [package.extras] doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"] -test = ["coverage[toml] (>=7)", "mypy (>=1.2.0) ; platform_python_implementation != \"PyPy\"", "pytest (>=7)"] +test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"] [[package]] name = "types-python-dateutil" @@ -3707,7 +3739,6 @@ version = "2.9.0.20241206" description = "Typing stubs for python-dateutil" optional = false python-versions = ">=3.8" -groups = ["main"] files = [ {file = "types_python_dateutil-2.9.0.20241206-py3-none-any.whl", hash = "sha256:e248a4bc70a486d3e3ec84d0dc30eec3a5f979d6e7ee4123ae043eedbb987f53"}, {file = "types_python_dateutil-2.9.0.20241206.tar.gz", hash = "sha256:18f493414c26ffba692a72369fea7a154c502646301ebfe3d56a04b3767284cb"}, @@ -3719,7 +3750,6 @@ version = "78.1.0.20250329" description = "Typing stubs for setuptools" optional = false python-versions = ">=3.9" -groups = ["dev"] files = [ {file = "types_setuptools-78.1.0.20250329-py3-none-any.whl", hash = "sha256:ea47eab891afb506f470eee581dcde44d64dc99796665da794da6f83f50f6776"}, {file = "types_setuptools-78.1.0.20250329.tar.gz", hash = "sha256:31e62950c38b8cc1c5114b077504e36426860a064287cac11b9666ab3a483234"}, @@ -3734,7 +3764,6 @@ version = "4.13.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" -groups = ["main", "dev"] files = [ {file = "typing_extensions-4.13.2-py3-none-any.whl", hash = "sha256:a439e7c04b49fec3e5d3e2beaa21755cadbbdc391694e28ccdd36ca4a1408f8c"}, {file = "typing_extensions-4.13.2.tar.gz", hash = "sha256:e6c81219bd689f51865d9e372991c540bda33a0379d5573cddb9a3a23f7caaef"}, @@ -3746,7 +3775,6 @@ version = "0.4.0" description = "Runtime typing introspection tools" optional = false python-versions = ">=3.9" -groups = ["main", "dev"] files = [ {file = "typing_inspection-0.4.0-py3-none-any.whl", hash = "sha256:50e72559fcd2a6367a19f7a7e610e6afcb9fac940c650290eed893d61386832f"}, {file = "typing_inspection-0.4.0.tar.gz", hash = "sha256:9765c87de36671694a67904bf2c96e395be9c6439bb6c87b5142569dcdd65122"}, @@ -3761,7 +3789,6 @@ version = "2025.2" description = "Provider of IANA time zone data" optional = false python-versions = ">=2" -groups = ["main", "dev"] files = [ {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"}, {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"}, @@ -3773,7 +3800,6 @@ version = "1.3.0" description = "RFC 6570 URI Template Processor" optional = false python-versions = ">=3.7" -groups = ["main"] files = [ {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"}, {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"}, @@ -3788,14 +3814,13 @@ version = "2.4.0" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.9" -groups = ["main", "dev"] files = [ {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"}, {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"}, ] [package.extras] -brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -3806,7 +3831,6 @@ version = "20.30.0" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" -groups = ["dev"] files = [ {file = "virtualenv-20.30.0-py3-none-any.whl", hash = "sha256:e34302959180fca3af42d1800df014b35019490b119eba981af27f2fa486e5d6"}, {file = "virtualenv-20.30.0.tar.gz", hash = "sha256:800863162bcaa5450a6e4d721049730e7f2dae07720e0902b0e4040bd6f9ada8"}, @@ -3819,7 +3843,7 @@ platformdirs = ">=3.9.1,<5" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] name = "watchdog" @@ -3827,7 +3851,6 @@ version = "6.0.0" description = "Filesystem events monitoring" optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "watchdog-6.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d1cdb490583ebd691c012b3d6dae011000fe42edb7a82ece80965b42abd61f26"}, {file = "watchdog-6.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bc64ab3bdb6a04d69d4023b29422170b74681784ffb9463ed4870cf2f3e66112"}, @@ -3870,7 +3893,6 @@ version = "24.11.1" description = "A library for working with the color formats defined by HTML and CSS." optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"}, {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"}, @@ -3882,7 +3904,6 @@ version = "1.4.0" description = "Wikipedia API for Python" optional = false python-versions = "*" -groups = ["main"] files = [ {file = "wikipedia-1.4.0.tar.gz", hash = "sha256:db0fad1829fdd441b1852306e9856398204dc0786d2996dd2e0c8bb8e26133b2"}, ] @@ -3897,7 +3918,6 @@ version = "1.17.2" description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" -groups = ["main", "dev"] files = [ {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3d57c572081fed831ad2d26fd430d565b76aa277ed1d30ff4d40670b1c0dd984"}, {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b5e251054542ae57ac7f3fba5d10bfff615b6c2fb09abeb37d2f1463f841ae22"}, @@ -3981,6 +4001,6 @@ files = [ ] [metadata] -lock-version = "2.1" +lock-version = "2.0" python-versions = "^3.10" content-hash = "15f4a19d5b34822a1522ed68afd4e0967e10b30317fafdbfc1b8a08a0bd52708" diff --git a/pyproject.toml b/pyproject.toml index 030f3f2..ff9f470 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -79,3 +79,5 @@ gold-to-mongo = "sample_annotator.gold_to_mongo:main" rel_to_oxygen_example = "sample_annotator.rel_to_oxygen_example:cli" xlsx-to-tsv = "sample_annotator.file_utils.xlsx_to_tsv:xlsx_to_tsv" rebuild-gold-cache = "sample_annotator.rebuild_gold_cache:rebuild_gold_cache" +gold-tool = "sample_annotator.gold_tool:cli" +