From 61cb197bcf4167ff2c89ccbc08285334a037a6b7 Mon Sep 17 00:00:00 2001 From: George Thomas <98996322+george42-ctds@users.noreply.github.com> Date: Fri, 17 Nov 2023 10:32:32 -0800 Subject: [PATCH] Fix/upgrade pyyaml (#208) * (fix PXP-11163): upgrade pyyaml, gen3dictionary * (fix PXP-11163): remove broken codacy badge, add coverage * (fix PXP-11163): use latest tag for sheepdog, bump peregrine version --- README.md | 3 +- poetry.lock | 94 +++++++++++++++++++++++++++++--------------------- pyproject.toml | 10 +++--- 3 files changed, 60 insertions(+), 47 deletions(-) diff --git a/README.md b/README.md index 9ab2f48..0b8f7e8 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,7 @@ # Peregrine [![Build Status](https://travis-ci.org/uc-cdis/peregrine.svg?branch=master)](https://travis-ci.org/uc-cdis/peregrine) -[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Grade) -[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Coverage) +[![Coverage Status](https://coveralls.io/repos/github/uc-cdis/peregrine/badge.svg)](https://coveralls.io/github/uc-cdis/peregrine) Query interface to get insights into data in Gen3 Commons diff --git a/poetry.lock b/poetry.lock index e6954f7..dd5264f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -136,13 +136,13 @@ files = [ [[package]] name = "botocore" -version = "1.32.0" +version = "1.32.2" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">= 3.7" files = [ - {file = 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= "sheepdog" -version = "5.1.2" +version = "5.1.3" description = "Gen3 Submission Service" optional = false python-versions = ">=3.9,<3.10" @@ -1659,21 +1673,21 @@ cdiserrors = ">=1.0.0" cdislogging = ">=1.0.0" cdispyutils = ">=2.0.1" datamodelutils = ">=1.0.0" -dictionaryutils = ">=3.4.6" +dictionaryutils = ">=3.4.10" envelopes = ">=0.4" Flask = ">=2.2.5" Flask-SQLAlchemy-Session = ">=1.1" fuzzywuzzy = ">=0.6.1" gen3authz = ">=1.0.4" gen3datamodel = ">=3.1.0" -gen3dictionary = ">=2.0.1" +gen3dictionary = ">=2.0.3" graphene = ">=2.0.1" indexclient = ">=2.1.1" jsonschema = ">=3.2" lxml = ">=4.6.5" psqlgraph = ">=3.0.1" psycopg2 = ">=2.8.4" -PyYAML = "~5.3.1" +PyYAML = ">=5.4.1" requests = ">=2.31.0,<3.0.0" simplejson = ">=3.8.1" sqlalchemy = ">=1.3.*" @@ -1682,8 +1696,8 @@ urllib3 = "<2.0.0" [package.source] type = "git" url = "https://git@github.com/uc-cdis/sheepdog.git" -reference = "5.1.2" -resolved_reference = "d2893b13166ca9c6d78072bbf389752e462974aa" +reference = "5.1.3" +resolved_reference = "359c764c8b312d0ac6707b1c2bee130f4ac0b44e" [[package]] name = "simplejson" @@ -1939,4 +1953,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "33ad2ff1caa7f2abbd6798abb6f82a9d8781c4dd10c011411063ca7627243cca" +content-hash = "5334077b7c6c00df770dde0670497df907545e06959a65c14b4aef1563fe61a3" diff --git a/pyproject.toml b/pyproject.toml index bea73f3..6b2479a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "peregrine" -version = "3.0.1" +version = "3.2.2" description = "Query interface to get insights into data in Gen3 Commons" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -15,14 +15,14 @@ python = ">=3.9,<3.10" authutils = ">=6.2.0" datamodelutils = ">=1.0" defusedxml = ">=0.5" -dictionaryutils = ">=3.0" -gen3dictionary = ">=2.0" +dictionaryutils = ">=3.4.10" +gen3dictionary = ">=2.0.3" simplejson = 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