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

@@ -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
 

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 <[email protected]>"]
 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 = ">=3.8"
 stopit = ">=1.1"
 Flask = ">=2.2.5"
 Flask-Cors = ">=3.0.9"
 gen3authz = ">=0.2"
-PyYAML = "~5.3.1"
+PyYAML = ">=5.4.1"
 dicttoxml = ">=1.5"
 SQLAlchemy = "1.3.5"
 graphene = ">=2.0,<3"
@@ -40,7 +40,7 @@ mock = ">=1.0"
 pytest-flask = ">=0.15"
 pytest-cov = ">=2.8"
 indexclient = ">=2.1.1"
-sheepdog = {git = "https://[email protected]/uc-cdis/sheepdog.git", rev = "5.1.2" }
+sheepdog = {git = "https://[email protected]/uc-cdis/sheepdog.git", rev = "5.1.3" }
 
 [tool.poetry.plugins."peregrine.modules"]
 "system" = "peregrine=peregrine.api:main"