From 932d4cf7853fc53038e790f5c25ba16e50ba15d3 Mon Sep 17 00:00:00 2001 From: Marcelo Costa Date: Sun, 10 Jan 2021 09:16:18 -0600 Subject: [PATCH 1/5] fix(dependencies): Fix poetry lock --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index d4342767f..06b1bb765 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,6 +31,7 @@ gen3authz = "^0.4.0" gen3cirrus = "^1.3.0" gen3config = "^0.1.7" gen3users = "^0.6.0" +idna = "^2.10" markdown = "^3.1.1" paramiko = "^2.6.0" psycopg2 = "^2.8.3" From 547c457ec08606054e9b12ff73f0713b11c1968d Mon Sep 17 00:00:00 2001 From: Marcelo Costa Date: Sun, 10 Jan 2021 09:17:09 -0600 Subject: [PATCH 2/5] new lock file --- poetry.lock | 699 ++++++++++++++++++++++++++++------------------------ 1 file changed, 376 insertions(+), 323 deletions(-) diff --git a/poetry.lock b/poetry.lock index 11f33208b..f981a1c1a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,6 +1,6 @@ [[package]] name = "addict" -version = "2.3.0" +version = "2.4.0" description = "Addict is a dictionary whose items can be set using both attribute and item syntax." category = "main" optional = false @@ -8,7 +8,7 @@ python-versions = "*" [[package]] name = "aniso8601" -version = "8.0.0" +version = "8.1.0" description = "A library for parsing ISO 8601 strings." category = "main" optional = false @@ -32,15 +32,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "20.2.0" +version = "20.3.0" description = "Classes Without Boilerplate" category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "sphinx-rtd-theme", "pre-commit"] -docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"] +docs = ["furo", "sphinx", "zope.interface"] tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"] @@ -79,7 +79,7 @@ xmltodict = ">=0.9,<1.0" [[package]] name = "babel" -version = "2.8.0" +version = "2.9.0" description = "Internationalization utilities" category = "main" optional = false @@ -109,7 +109,7 @@ cffi = ">=1.1" six = ">=1.4.1" [package.extras] -tests = ["pytest (>=3.2.1,<3.3.0 || >3.3.0)"] +tests = ["pytest (>=3.2.1,!=3.3.0)"] typecheck = ["mypy"] [[package]] @@ -157,7 +157,7 @@ python-versions = "*" [[package]] name = "cachetools" -version = "4.1.1" +version = "4.2.0" description = "Extensible memoizing collections and decorators" category = "main" optional = false @@ -209,6 +209,7 @@ description = "Collection of test data and tools" category = "dev" optional = false python-versions = "*" +develop = false [package.source] type = "git" @@ -218,7 +219,7 @@ resolved_reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024" [[package]] name = "certifi" -version = "2020.6.20" +version = "2020.12.5" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -226,7 +227,7 @@ python-versions = "*" [[package]] name = "cffi" -version = "1.14.3" +version = "1.14.4" description = "Foreign Function Interface for Python calling C code." category = "main" optional = false @@ -237,11 +238,11 @@ pycparser = "*" [[package]] name = "chardet" -version = "3.0.4" +version = "4.0.0" description = "Universal encoding detector for Python 2 and 3" category = "main" optional = false -python-versions = "*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "click" @@ -276,7 +277,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "coverage" -version = "5.3" +version = "5.3.1" description = "Code coverage measurement for Python" category = "dev" optional = false @@ -287,7 +288,7 @@ toml = ["toml"] [[package]] name = "coveralls" -version = "2.1.2" +version = "2.2.0" description = "Show coverage stats online via coveralls.io" category = "dev" optional = false @@ -314,11 +315,11 @@ cffi = ">=1.8,<1.11.3 || >1.11.3" six = ">=1.4.1" [package.extras] -docs = ["sphinx (>=1.6.5,<1.8.0 || >1.8.0)", "sphinx-rtd-theme"] +docs = ["sphinx (>=1.6.5,!=1.8.0)", "sphinx-rtd-theme"] docstest = ["doc8", "pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"] idna = ["idna (>=2.1)"] pep8test = ["flake8", "flake8-import-order", "pep8-naming"] -test = ["pytest (>=3.6.0,<3.9.0 || >3.9.0,<3.9.1 || >3.9.1,<3.9.2 || >3.9.2)", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,<3.79.2 || >3.79.2)"] +test = ["pytest (>=3.6.0,!=3.9.0,!=3.9.1,!=3.9.2)", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] [[package]] name = "debtcollector" @@ -343,7 +344,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*" [[package]] name = "dnspython" -version = "2.0.0" +version = "2.1.0" description = "DNS toolkit" category = "main" optional = false @@ -374,7 +375,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "ecdsa" -version = "0.16.0" +version = "0.16.1" description = "ECDSA cryptographic signature library (pure python)" category = "main" optional = false @@ -389,7 +390,7 @@ gmpy2 = ["gmpy2"] [[package]] name = "email-validator" -version = "1.1.1" +version = "1.1.2" description = "A robust email syntax and deliverability validation library for Python 2.x/3.x." category = "main" optional = false @@ -420,7 +421,7 @@ dotenv = ["python-dotenv"] [[package]] name = "flask-cors" -version = "3.0.9" +version = "3.0.10" description = "A Flask extension adding a decorator for CORS support" category = "main" optional = false @@ -530,11 +531,11 @@ PyYAML = ">=5.1,<6.0" [[package]] name = "google-api-core" -version = "1.23.0" +version = "1.24.1" description = "Google API client core library" category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [package.dependencies] google-auth = ">=1.21.1,<2.0dev" @@ -567,16 +568,16 @@ uritemplate = ">=3.0.0,<4dev" [[package]] name = "google-auth" -version = "1.22.1" +version = "1.24.0" description = "Google Authentication Library" category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [package.dependencies] cachetools = ">=2.0.0,<5.0" pyasn1-modules = ">=0.2.1" -rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.5\""} +rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.6\""} six = ">=1.9.0" [package.extras] @@ -597,39 +598,40 @@ six = "*" [[package]] name = "google-cloud-core" -version = "1.4.3" +version = "1.5.0" description = "Google Cloud API client core library" category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [package.dependencies] -google-api-core = ">=1.19.0,<2.0.0dev" +google-api-core = ">=1.21.0,<2.0.0dev" +six = ">=1.12.0" [package.extras] grpc = ["grpcio (>=1.8.2,<2.0dev)"] [[package]] name = "google-cloud-storage" -version = "1.32.0" +version = "1.35.0" description = "Google Cloud Storage API client library" category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [package.dependencies] google-auth = ">=1.11.0,<2.0dev" google-cloud-core = ">=1.4.1,<2.0dev" -google-resumable-media = ">=1.0.0,<2.0dev" +google-resumable-media = ">=1.2.0,<2.0dev" requests = ">=2.18.0,<3.0.0dev" [[package]] name = "google-crc32c" -version = "1.0.0" +version = "1.1.0" description = "A python wrapper of the C library 'Google CRC32C'" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.dependencies] cffi = ">=1.0.0" @@ -639,11 +641,11 @@ testing = ["pytest"] [[package]] name = "google-resumable-media" -version = "1.1.0" +version = "1.2.0" description = "Utilities for Google Media Downloads and Resumable Uploads" category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [package.dependencies] google-crc32c = {version = ">=1.0,<2.0dev", markers = "python_version >= \"3.5\""} @@ -685,32 +687,34 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "2.0.0" +version = "3.3.0" description = "Read metadata from Python packages" category = "main" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] +typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} zipp = ">=0.5" [package.extras] -docs = ["sphinx", "rst.linker"] -testing = ["packaging", "pep517", "importlib-resources (>=1.3)"] +docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"] +testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "jaraco.test (>=3.2.0)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" -version = "3.0.0" +version = "5.0.0" description = "Read resources from Python packages" category = "main" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] zipp = {version = ">=0.4", markers = "python_version < \"3.8\""} [package.extras] -docs = ["sphinx", "rst.linker", "jaraco.packaging"] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "pytest-black (>=0.3.7)", "pytest-mypy"] [[package]] name = "iso8601" @@ -752,7 +756,7 @@ python-versions = "*" [[package]] name = "markdown" -version = "3.3.2" +version = "3.3.3" description = "Python implementation of Markdown." category = "main" optional = false @@ -790,7 +794,7 @@ test = ["unittest2 (>=1.1.0)"] [[package]] name = "more-itertools" -version = "8.5.0" +version = "8.6.0" description = "More routines for operating on iterables, beyond itertools" category = "dev" optional = false @@ -823,7 +827,7 @@ zipp = "*" [package.extras] acm = ["cryptography (>=2.3.0)"] -all = ["cryptography (>=2.3.0)", "PyYAML (>=5.1)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "ecdsa (<0.15)", "docker (>=2.5.1)", "jsondiff (>=1.1.2)", "aws-xray-sdk (>=0.93,<0.96 || >0.96)", "idna (>=2.5,<3)", "cfn-lint (>=0.4.0)", "sshpubkeys (>=3.1.0,<4.0)", "sshpubkeys (>=3.1.0)"] +all = ["cryptography (>=2.3.0)", "PyYAML (>=5.1)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "ecdsa (<0.15)", "docker (>=2.5.1)", "jsondiff (>=1.1.2)", "aws-xray-sdk (>=0.93,!=0.96)", "idna (>=2.5,<3)", "cfn-lint (>=0.4.0)", "sshpubkeys (>=3.1.0,<4.0)", "sshpubkeys (>=3.1.0)"] awslambda = ["docker (>=2.5.1)"] batch = ["docker (>=2.5.1)"] cloudformation = ["PyYAML (>=5.1)", "cfn-lint (>=0.4.0)"] @@ -832,11 +836,11 @@ ec2 = ["cryptography (>=2.3.0)", "sshpubkeys (>=3.1.0,<4.0)", "sshpubkeys (>=3.1 iam = ["cryptography (>=2.3.0)"] iotdata = ["jsondiff (>=1.1.2)"] server = ["flask"] -xray = ["aws-xray-sdk (>=0.93,<0.96 || >0.96)"] +xray = ["aws-xray-sdk (>=0.93,!=0.96)"] [[package]] name = "msgpack" -version = "1.0.0" +version = "1.0.2" description = "MessagePack (de)serializer." category = "main" optional = false @@ -878,7 +882,7 @@ six = ">=1.6.1" [[package]] name = "oslo.config" -version = "8.3.2" +version = "8.4.0" description = "Oslo Configuration API" category = "main" optional = false @@ -894,6 +898,10 @@ requests = ">=2.18.0" rfc3986 = ">=1.2.0" stevedore = ">=1.20.0" +[package.extras] +rst_generator = ["rst2txt (>=1.1.0)", "sphinx (>=1.8.0,!=2.1.0)"] +test = ["bandit (>=1.6.0,<1.7.0)", "coverage (>=4.0,!=4.4)", "fixtures (>=3.0.0)", "hacking (>=3.0.1,<3.1.0)", "mypy (>=0.720)", "oslo.log (>=3.36.0)", "oslotest (>=3.2.0)", "pre-commit (>=2.6.0)", "requests-mock (>=1.5.0)", "stestr (>=2.1.0)", "testscenarios (>=0.4)", "testtools (>=2.2.0)"] + [[package]] name = "oslo.i18n" version = "5.0.1" @@ -922,7 +930,7 @@ pytz = ">=2013.6" [[package]] name = "oslo.utils" -version = "4.6.0" +version = "4.7.0" description = "Oslo Utility library" category = "main" optional = false @@ -942,7 +950,7 @@ six = ">=1.10.0" [[package]] name = "packaging" -version = "20.4" +version = "20.8" description = "Core utilities for Python packages" category = "main" optional = false @@ -950,7 +958,6 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.dependencies] pyparsing = ">=2.0.2" -six = "*" [[package]] name = "paramiko" @@ -1003,7 +1010,7 @@ python-versions = "*" [[package]] name = "protobuf" -version = "3.13.0" +version = "3.14.0" description = "Protocol Buffers" category = "main" optional = false @@ -1022,7 +1029,7 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" [[package]] name = "py" -version = "1.9.0" +version = "1.10.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" category = "main" optional = false @@ -1057,7 +1064,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pycryptodome" -version = "3.9.8" +version = "3.9.9" description = "Cryptographic library for Python" category = "main" optional = false @@ -1090,7 +1097,7 @@ six = "*" [package.extras] docs = ["sphinx (>=1.6.5)", "sphinx-rtd-theme"] -tests = ["pytest (>=3.2.1,<3.3.0 || >3.3.0)", "hypothesis (>=3.27.0)"] +tests = ["pytest (>=3.2.1,!=3.3.0)", "hypothesis (>=3.27.0)"] [[package]] name = "pyparsing" @@ -1130,7 +1137,7 @@ coverage = ">=4.4" pytest = ">=3.6" [package.extras] -testing = ["fields", "hunter", "process-tests (2.0.2)", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"] [[package]] name = "pytest-flask" @@ -1203,7 +1210,7 @@ stevedore = ">=1.5.0" [[package]] name = "pytz" -version = "2020.1" +version = "2020.5" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -1219,7 +1226,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "requests" -version = "2.24.0" +version = "2.25.1" description = "Python HTTP for Humans." category = "main" optional = false @@ -1227,17 +1234,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.dependencies] certifi = ">=2017.4.17" -chardet = ">=3.0.2,<4" +chardet = ">=3.0.2,<5" idna = ">=2.5,<3" -urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26" +urllib3 = ">=1.21.1,<1.27" [package.extras] security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"] -socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"] +socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] [[package]] name = "responses" -version = "0.12.0" +version = "0.12.1" description = "A utility library for mocking out the `requests` Python library." category = "dev" optional = false @@ -1276,7 +1283,7 @@ idna2008 = ["idna"] [[package]] name = "rsa" -version = "4.6" +version = "4.7" description = "Pure-Python RSA implementation" category = "main" optional = false @@ -1306,7 +1313,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "sqlalchemy" -version = "1.3.20" +version = "1.3.22" description = "Database Abstraction Library" category = "main" optional = false @@ -1326,7 +1333,7 @@ pymysql = ["pymysql"] [[package]] name = "stevedore" -version = "3.2.2" +version = "3.3.0" description = "Manage dynamic plugins for Python applications" category = "main" optional = false @@ -1343,6 +1350,7 @@ description = "" category = "main" optional = false python-versions = "*" +develop = false [package.dependencies] boto = ">=2.36.0,<3.0.0" @@ -1360,6 +1368,14 @@ url = "https://github.com/uc-cdis/storage-client" reference = "1.0.1" resolved_reference = "885c59d83fc075527af44968c353d1ac93bec37e" +[[package]] +name = "typing-extensions" +version = "3.7.4.3" +description = "Backported and Experimental Type Hints for Python 3.5+" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "uritemplate" version = "3.0.1" @@ -1379,7 +1395,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" [package.extras] brotli = ["brotlipy (>=0.6.0)"] secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] -socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"] 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1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d4342767f..a0fb7cad7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ authlib = "^0.11" authutils = "^4.0.0" bcrypt = "^3.1.4" boto3 = "~1.9.91" -botocore = "~1.12.91" +botocore = "^1.12.253" cached_property = "^1.5.1" cdiserrors = "<2.0.0" cdislogging = "^1.0.0" From 3689f601fa05a7a563825746acf1aff184e94105 Mon Sep 17 00:00:00 2001 From: Marcelo Costa Date: Sun, 10 Jan 2021 09:26:44 -0600 Subject: [PATCH 4/5] add new lock file --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index f981a1c1a..b8d9926f2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1453,7 +1453,7 @@ testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake [metadata] lock-version = "1.1" python-versions = "^3.6" -content-hash = "b446f10bb06734b4b14212529bd1b8f7b239220ba2426d707811674ebc94c65d" +content-hash = 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