diff --git a/CHANGELOG.rst b/CHANGELOG.rst index eef790ad..f5d9cb46 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,12 @@ foursight-cgap Change Log ---------- +4.0.1 +===== + +* Update magma to bring in fixes for creating and running MWFR + + 4.0.0 ===== diff --git a/poetry.lock b/poetry.lock index 75f2ab0e..a7ec9687 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "ansicon" version = "1.89.0" description = "Python wrapper for loading Jason Hood's ANSICON" +category = "dev" optional = false python-versions = "*" files = [ @@ -15,6 +16,7 @@ files = [ name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -26,6 +28,7 @@ files = [ name = "aws-requests-auth" version = "0.4.3" description = "AWS signature version 4 signing process for the python requests module" +category = "main" optional = false python-versions = "*" files = [ @@ -40,6 +43,7 @@ requests = ">=0.14.0" name = "backports-zoneinfo" version = "0.2.1" description = "Backport of the standard library zoneinfo module" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -68,6 +72,7 @@ tzdata = ["tzdata"] name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -86,6 +91,7 @@ lxml = ["lxml"] name = "benchmark-4dn" version = "0.5.23" description = "Benchmark functions that returns total space, mem, cpu given input size and parameters for the CWL workflows" +category = "main" optional = false python-versions = ">=3.5,<4.0" files = [ @@ -97,6 +103,7 @@ files = [ name = "blessed" version = "1.20.0" description = "Easy, practical library for making terminal apps, by providing an elegant, well-documented interface to Colors, Keyboard input, and screen Positioning capabilities." +category = "dev" optional = false python-versions = ">=2.7" files = [ @@ -111,17 +118,18 @@ wcwidth = ">=0.1.4" [[package]] name = "boto3" -version = "1.28.62" +version = "1.28.63" description = "The AWS SDK for Python" +category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.62-py3-none-any.whl", hash = "sha256:0dfa2fc96ccafce4feb23044d6cba8b25075ad428a0c450d369d099c6a1059d2"}, - {file = "boto3-1.28.62.tar.gz", hash = "sha256:148eeba0f1867b3db5b3e5ae2997d75a94d03fad46171374a0819168c36f7ed0"}, + {file = "boto3-1.28.63-py3-none-any.whl", hash = "sha256:65d052ec13197460586ee385aa2d6bba0e7378d2d2c7f3e93c044c43ae1ca782"}, + {file = "boto3-1.28.63.tar.gz", hash = "sha256:94218aba2feb5b404b665b8d76c172dc654f79b4c5fa0e9e92459c098da87bf4"}, ] [package.dependencies] -botocore = ">=1.31.62,<1.32.0" +botocore = ">=1.31.63,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.7.0,<0.8.0" @@ -130,13 +138,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.31.62" +version = "1.31.63" description = "Low-level, data-driven core of boto 3." +category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "botocore-1.31.62-py3-none-any.whl", hash = "sha256:be792d806afc064694a2d0b9b25779f3ca0c1584b29a35ac32e67f0064ddb8b7"}, - {file = "botocore-1.31.62.tar.gz", hash = "sha256:272b78ac65256b6294cb9cdb0ac484d447ad3a85642e33cb6a3b1b8afee15a4c"}, + {file = "botocore-1.31.63-py3-none-any.whl", hash = "sha256:cb9db5db5af865b1fc2e1405b967db5d78dd0f4d84e5dc1974e082733c1034b7"}, + {file = "botocore-1.31.63.tar.gz", hash = "sha256:6e582c811ea74f25bdb490ac372b2645de4a60286b42ddd8c69f3b6df82b6b12"}, ] [package.dependencies] @@ -154,6 +163,7 @@ crt = ["awscrt (==0.16.26)"] name = "cachetools" version = "5.3.1" description = "Extensible memoizing collections and decorators" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -165,6 +175,7 @@ files = [ name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -176,6 +187,7 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -240,6 +252,7 @@ pycparser = "*" name = "chalice" version = "1.29.0" description = "Microframework" +category = "dev" optional = false python-versions = "*" files = [ @@ -268,6 +281,7 @@ event-file-poller = ["watchdog (==2.3.1)"] name = "charset-normalizer" version = "2.0.12" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.5.0" files = [ @@ -282,6 +296,7 @@ unicode-backport = ["unicodedata2"] name = "click" version = "7.1.2" description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -293,6 +308,7 @@ files = [ name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -304,6 +320,7 @@ files = [ name = "coverage" version = "7.3.2" description = "Code coverage measurement for Python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -371,6 +388,7 @@ toml = ["tomli"] name = "cron-descriptor" version = "1.4.0" description = "A Python library that converts cron expressions into human readable strings." +category = "main" optional = false python-versions = "*" files = [ @@ -384,6 +402,7 @@ dev = ["polib"] name = "cryptography" version = "39.0.2" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -429,6 +448,7 @@ tox = ["tox"] name = "dcicutils" version = "8.0.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" +category = "main" optional = false python-versions = ">=3.8,<3.12" files = [ @@ -463,6 +483,7 @@ webtest = ">=2.0.34,<3.0.0" name = "decorator" version = "5.1.1" description = "Decorators for Humans" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -474,6 +495,7 @@ files = [ name = "docker" version = "4.4.4" description = "A Python library for the Docker Engine API." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -495,6 +517,7 @@ tls = ["cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] name = "docutils" version = "0.20.1" description = "Docutils -- Python Documentation Utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -506,6 +529,7 @@ files = [ name = "elasticsearch" version = "7.13.4" description = "Python client for Elasticsearch" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4" files = [ @@ -527,6 +551,7 @@ requests = ["requests (>=2.4.0,<3.0.0)"] name = "elasticsearch-dsl" version = "7.4.1" description = "Python client for Elasticsearch" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -546,6 +571,7 @@ develop = ["coverage (<5.0.0)", "mock", "pytest (>=3.0.0)", "pytest-cov", "pytes name = "exceptiongroup" version = "1.1.3" description = "Backport of PEP 654 (exception groups)" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -560,6 +586,7 @@ test = ["pytest (>=6)"] name = "flaky" version = "3.6.1" description = "Plugin for nose or pytest that automatically reruns flaky tests." +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -571,6 +598,7 @@ files = [ name = "foursight-core" version = "5.0.0" description = "Serverless Chalice Application for Monitoring" +category = "main" optional = false python-versions = ">=3.8,<3.12" files = [ @@ -605,6 +633,7 @@ tzlocal = ">=5.0.1,<6.0.0" name = "future" version = "0.18.3" description = "Clean single-source support for Python 3 and 2" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -615,6 +644,7 @@ files = [ name = "geocoder" version = "1.38.1" description = "Geocoder is a simple and consistent geocoding library." +category = "main" optional = false python-versions = "*" files = [ @@ -633,6 +663,7 @@ six = "*" name = "gitdb" version = "4.0.10" description = "Git Object Database" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -647,6 +678,7 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.37" description = "GitPython is a Python library used to interact with Git repositories" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -664,6 +696,7 @@ test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit" name = "google" version = "3.0.0" description = "Python bindings to the Google search engine." +category = "main" optional = false python-versions = "*" files = [ @@ -678,6 +711,7 @@ beautifulsoup4 = "*" name = "google-api-core" version = "2.12.0" description = "Google API client core library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -700,6 +734,7 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] name = "google-api-python-client" version = "1.12.11" description = "Google API Client Library for Python" +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -719,6 +754,7 @@ uritemplate = ">=3.0.0,<4dev" name = "google-auth" version = "2.23.3" description = "Google Authentication Library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -742,6 +778,7 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"] name = "google-auth-httplib2" version = "0.1.1" description = "Google Authentication Library: httplib2 transport" +category = "main" optional = false python-versions = "*" files = [ @@ -757,6 +794,7 @@ httplib2 = ">=0.19.0" name = "google-auth-oauthlib" version = "0.7.1" description = "Google Authentication Library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -773,13 +811,14 @@ tool = ["click (>=6.0.0)"] [[package]] name = "googleapis-common-protos" -version = "1.60.0" +version = "1.61.0" description = "Common protobufs used in Google APIs" +category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "googleapis-common-protos-1.60.0.tar.gz", hash = "sha256:e73ebb404098db405ba95d1e1ae0aa91c3e15a71da031a2eeb6b2e23e7bc3708"}, - {file = "googleapis_common_protos-1.60.0-py2.py3-none-any.whl", hash = "sha256:69f9bbcc6acde92cab2db95ce30a70bd2b81d20b12eff3f1aabaffcbe8a93918"}, + {file = "googleapis-common-protos-1.61.0.tar.gz", hash = "sha256:8a64866a97f6304a7179873a465d6eee97b7a24ec6cfd78e0f575e96b821240b"}, + {file = "googleapis_common_protos-1.61.0-py2.py3-none-any.whl", hash = "sha256:22f1915393bb3245343f6efe87f6fe868532efc12aa26b391b15132e1279f1c0"}, ] [package.dependencies] @@ -792,6 +831,7 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"] name = "httplib2" version = "0.22.0" description = "A comprehensive HTTP client library." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -806,6 +846,7 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 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python-versions = "*" files = [ @@ -875,6 +920,7 @@ ansicon = {version = "*", markers = "platform_system == \"Windows\""} name = "jmespath" version = "1.0.1" description = "JSON Matching Expressions" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -886,6 +932,7 @@ files = [ name = "jsonc-parser" version = "1.1.5" description = "A lightweight, native tool for parsing .jsonc files" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -895,13 +942,14 @@ files = [ [[package]] name = "magma-suite" -version = "2.0.0" +version = "2.1.1" description = "Collection of tools to manage meta-workflows automation." +category = "main" optional = false python-versions = ">=3.8,<3.12" files = [ - {file = "magma_suite-2.0.0-py3-none-any.whl", hash = "sha256:462845484ebf1edef187c74f4c470e49726c95ab30c90555ada112e2bbb90c95"}, - {file = "magma_suite-2.0.0.tar.gz", hash = "sha256:03577b5567ffe6fb99409d26575dd44b836a166b7ed9b8ec268b8e754d46403a"}, + {file = 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"pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "requests" version = "2.27.1" description = "Python HTTP for Humans." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -1463,6 +1553,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<5)"] name = "requests-oauthlib" version = "1.3.1" description = "OAuthlib authentication support for Requests." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1481,6 +1572,7 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"] name = "rfc3986" version = "1.5.0" description = "Validating URI References per RFC 3986" +category = "main" optional = false python-versions = "*" files = [ @@ -1495,6 +1587,7 @@ idna2008 = ["idna"] name = "rsa" version = "4.9" description = "Pure-Python RSA implementation" +category = "main" optional = false python-versions = ">=3.6,<4" files = [ @@ -1509,6 +1602,7 @@ pyasn1 = ">=0.1.3" name = "s3transfer" version = "0.7.0" description = "An Amazon S3 Transfer Manager" +category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -1526,6 +1620,7 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"] name = "setuptools" version = "68.2.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1542,6 +1637,7 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1553,6 +1649,7 @@ files = [ name = "smmap" version = "5.0.1" description = "A pure Python implementation of a sliding window memory map manager" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1564,6 +1661,7 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1575,6 +1673,7 @@ files = [ name = "structlog" version = "19.2.0" description = "Structured Logging for Python" +category = "main" optional = false python-versions = "*" files = [ @@ -1595,6 +1694,7 @@ tests = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest (>=3.3.0)", "pyth name = "tibanna" version = "5.1.0" description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud." +category = "main" optional = false python-versions = ">=3.8,<3.12" files = [ @@ -1613,6 +1713,7 @@ tomlkit = ">=0.11.0,<0.12.0" name = "tibanna-ff" version = "3.1.1" description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud." +category = "main" optional = false python-versions = ">=3.8,<3.12" files = [ @@ -1632,6 +1733,7 @@ tomlkit = ">=0.11.0,<0.12.0" name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1643,6 +1745,7 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1654,6 +1757,7 @@ files = [ name = "tomlkit" version = "0.11.8" description = "Style preserving TOML library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1665,6 +1769,7 @@ files = [ name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1685,6 +1790,7 @@ telegram = ["requests"] name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1696,6 +1802,7 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -1707,6 +1814,7 @@ files = [ name = "tzlocal" version = "5.1" description = "tzinfo object for the local timezone" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1725,6 +1833,7 @@ devenv = ["black", "check-manifest", "flake8", "pyroma", "pytest (>=4.3)", "pyte name = "uritemplate" version = "3.0.1" description = "URI templates" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1736,6 +1845,7 @@ files = [ name = "urllib3" version = "1.26.17" description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -1752,6 +1862,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "waitress" version = "2.1.2" description = "Waitress WSGI server" +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -1767,6 +1878,7 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "wcwidth" version = "0.2.8" description = "Measures the displayed width of unicode strings in a terminal" +category = "dev" optional = false python-versions = "*" files = [ @@ -1778,6 +1890,7 @@ files = [ name = "webob" version = "1.8.7" description = "WSGI request and response object" +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*" files = [ @@ -1793,6 +1906,7 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] name = "websocket-client" version = "1.6.4" description = "WebSocket client for Python with low level API options" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1809,6 +1923,7 @@ test = ["websockets"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" +category = "main" optional = false python-versions = "*" files = [ @@ -1830,6 +1945,7 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu name = "wheel" version = "0.41.2" description = "A built-package format for Python" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1843,4 +1959,4 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.12" -content-hash = "bb819ec8749404753ecd78c6b2051e48b0dbcb1393a96a7a959e11f34da3ff50" +content-hash = "f2c414cd6b8e5afd7ca95a7637e191683a44911846124db898e3682bdc05f504" diff --git a/pyproject.toml b/pyproject.toml index d2e473a7..2d971a10 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "foursight-cgap" -version = "4.0.0" +version = "4.0.1" description = "Serverless Chalice Application for Monitoring" authors = ["4DN-DCIC Team "] license = "MIT" @@ -24,7 +24,7 @@ elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" gitpython = "^3.1.2" pytz = "^2020.1" -magma-suite = "^2.0.0" +magma-suite = "^2.1.1" tibanna-ff = "^3.1.1" MarkupSafe = "^2.1.3" foursight-core = "^5.0.0"