From 70def633f16d0eaef80a5c3e12500d394a4d6eba Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 20 Jan 2021 22:36:57 +0000
Subject: [PATCH 1/3] Replace pipenv with poetry. Update all dependencies

---
 Makefile                                      |  16 +-
 lib/galaxy/dependencies/conda-file.sh         |  26 --
 lib/galaxy/dependencies/dev-requirements.txt  | 233 +++++++++++++++++-
 lib/galaxy/dependencies/lint-requirements.txt |   4 +
 .../dependencies/pinned-lint-requirements.txt |  11 +
 .../dependencies/pinned-requirements.txt      | 190 +++++++++++++-
 .../default/pinned-dev-requirements.txt       |  74 ------
 .../pipfiles/default/pinned-requirements.txt  | 194 ---------------
 .../dependencies/pipfiles/docker/Dockerfile   |  15 --
 .../dependencies/pipfiles/docker/Makefile     |   7 -
 .../pipfiles/docker/docker_script.sh          |   5 -
 .../dependencies/pipfiles/flake8/Pipfile      |  15 --
 .../pipfiles/flake8/pinned-requirements.txt   |  18 --
 lib/galaxy/dependencies/pipfiles/update.sh    |  60 -----
 lib/galaxy/dependencies/update.sh             |  21 ++
 .../dependencies/update_lint_requirements.sh  |  12 +
 .../default/Pipfile => pyproject.toml         | 147 +++++------
 scripts/common_startup.sh                     |   2 +-
 tox.ini                                       |   3 +-
 19 files changed, 550 insertions(+), 503 deletions(-)
 delete mode 100755 lib/galaxy/dependencies/conda-file.sh
 mode change 120000 => 100644 lib/galaxy/dependencies/dev-requirements.txt
 create mode 100644 lib/galaxy/dependencies/lint-requirements.txt
 create mode 100644 lib/galaxy/dependencies/pinned-lint-requirements.txt
 mode change 120000 => 100644 lib/galaxy/dependencies/pinned-requirements.txt
 delete mode 100644 lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
 delete mode 100644 lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
 delete mode 100644 lib/galaxy/dependencies/pipfiles/docker/Dockerfile
 delete mode 100644 lib/galaxy/dependencies/pipfiles/docker/Makefile
 delete mode 100644 lib/galaxy/dependencies/pipfiles/docker/docker_script.sh
 delete mode 100644 lib/galaxy/dependencies/pipfiles/flake8/Pipfile
 delete mode 100644 lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
 delete mode 100755 lib/galaxy/dependencies/pipfiles/update.sh
 create mode 100755 lib/galaxy/dependencies/update.sh
 create mode 100755 lib/galaxy/dependencies/update_lint_requirements.sh
 rename lib/galaxy/dependencies/pipfiles/default/Pipfile => pyproject.toml (68%)

diff --git a/Makefile b/Makefile
index 938f7bf63fd..a2fa6ec4956 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 # Location of virtualenv used for development.
 VENV?=.venv
 # Source virtualenv to execute command (flake8, sphinx, twine, etc...)
-IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
 RELEASE_CURR:=16.01
 RELEASE_CURR_MINOR_NEXT:=$(shell $(IN_VENV) python scripts/bootstrap_history.py --print-next-minor-version)
 RELEASE_NEXT:=16.04
@@ -55,9 +55,6 @@ open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in bro
 open-project: ## open project on github
 	$(OPEN_RESOURCE) $(PROJECT_URL)
 
-lint: ## check style using tox and flake8 for Python 2 and Python 3
-	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
-
 uwsgi-rebuild-validation: ## rebuild uwsgi_config.yml kwalify schema against latest uwsgi master.
 	$(CONFIG_MANAGE) build_uwsgi_yaml
 
@@ -132,14 +129,11 @@ release-check-blocking-prs: ## Check github for release blocking PRs
 release-bootstrap-history: ## bootstrap history for a new release
 	$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
 
-build-dependencies-docker: ## Builds the docker container used for dependency updates
-	$(MAKE) -C lib/galaxy/dependencies/pipfiles/docker
+update-lint-requirements:
+	./lib/galaxy/dependencies/update_lint_requirements.sh
 
-update-dependencies:  build-dependencies-docker ## update linting + dev dependencies
-	sh lib/galaxy/dependencies/pipfiles/update.sh -d
-
-update-and-commit-dependencies: build-dependencies-docker ## update and commit linting + dev dependencies
-	sh lib/galaxy/dependencies/pipfiles/update.sh -d -c
+update-dependencies: update-lint-requirements ## update pinned and dev dependencies
+	$(IN_VENV) ./lib/galaxy/dependencies/update.sh
 
 node-deps: ## Install NodeJS dependencies.
 ifndef YARN
diff --git a/lib/galaxy/dependencies/conda-file.sh b/lib/galaxy/dependencies/conda-file.sh
deleted file mode 100755
index e9291c6a2d8..00000000000
--- a/lib/galaxy/dependencies/conda-file.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-#
-# Conda does not have all of Galaxy's dependencies, and the list of which ones it does is always changing. As a result,
-# it's not possible to keep a conda requirements file up to date. However, with Conda >= 4.4, we can use Conda itself to
-# determine which dependencies it can install. Pip will be used (upon Galaxy startup) to install the rest.
-#
-# You should use this script like so:
-#
-# conda create --override-channels -c conda-forge -c bioconda -c defaults \
-#     -n <env> --file <(lib/galaxy/dependencies/conda-file.sh) python=2.7
-
-here=$(dirname $0)
-
-if ! command -v conda >/dev/null; then
-    printf "$0: command not found: conda\n" >&2
-    printf "hint: did you run 'conda activate base'?\n" >&2
-    exit 1
-fi
-
-printf "Filtering out Galaxy requirements not available from Conda:" >&2
-egrep -iv $( \
-    conda create --override-channels -c conda-forge -c bioconda -c defaults \
-        -n _gx_test_env --dry-run --file <(sed 's/;.*//' $here/pinned-requirements.txt) python=2.7 2>&1 \
-        | grep '^\s*-' | grep -v https: | awk '{print $NF}' | paste -s -d'|' \
-) $here/pinned-requirements.txt | sed 's/;.*//'
-printf " done\n" >&2
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
deleted file mode 120000
index ff2937ac59c..00000000000
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-pipfiles/default/pinned-dev-requirements.txt
\ No newline at end of file
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
new file mode 100644
index 00000000000..91a8791ac52
--- /dev/null
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -0,0 +1,232 @@
+--extra-index-url https://wheels.galaxyproject.org/simple
+
+adal==1.2.5
+aiofiles==0.6.0
+alabaster==0.7.12; python_version >= "3.5"
+amqp==5.0.3; python_version >= "3.6"
+appdirs==1.4.4; python_version >= "3.6"
+argcomplete==1.12.2; python_version >= "3.6" and python_version < "4"
+atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
+attmap==0.12.11
+attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+babel==2.9.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+bagit==1.7.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.4.0" and python_version < "4" and python_version >= "3.6"
+bcrypt==3.2.0; python_version >= "3.6"
+bdbag==1.5.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4")
+beaker==1.11.0
+bioblend==0.14.0; python_version >= "3.5"
+bleach==3.2.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+boltons==20.2.1
+boto3==1.16.57
+boto==2.49.0
+botocore==1.19.57
+bx-python==0.8.9; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
+cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
+cachetools==4.2.0; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
+certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+cffi==1.14.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
+chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+cheetah3==3.2.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+click==7.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+cliff==3.6.0; python_version >= "3.6"
+cloudauthz==0.6.0
+cloudbridge==2.1.0
+cmd2==1.4.0; python_version >= "3.6"
+colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
+coloredlogs==15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
+commonmark==0.9.1
+coverage==5.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+cryptography==3.3.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
+cwltool==3.0.20201109103151; python_version >= "3.6" and python_version < "4"
+dataclasses==0.8; python_version >= "3.6" and python_version < "3.7"
+debtcollector==2.2.0; python_version >= "3.6"
+decorator==4.4.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.6"
+defusedxml==0.7.0rc2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.0"
+deprecated==1.2.11; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+deprecation==2.1.0
+dictobj==0.4
+docopt==0.6.2
+docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+dogpile.cache==1.1.1; python_version >= "3.6"
+ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+fabric3==1.14.post1
+fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
+fastapi==0.63.0; python_version >= "3.6"
+funcsigs==1.0.2
+future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+galaxy-sequence-utils==1.1.5
+google-api-core==1.25.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+google-api-python-client==1.12.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+google-auth-httplib2==0.0.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+google-auth==1.24.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+googleapis-common-protos==1.52.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+gunicorn==20.0.4; python_version >= "3.4"
+gxformat2==0.15.0
+h11==0.12.0; python_version >= "3.6"
+h5py==3.1.0; python_version >= "3.6"
+httplib2==0.18.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+humanfriendly==9.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
+idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+imagesize==1.2.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5"
+importlib-metadata==3.4.0; python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
+importlib-resources==5.1.0; python_version < "3.7" and python_version >= "3.6"
+iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+isa-rwval==0.10.9
+iso8601==0.1.13; python_version >= "3.6"
+isodate==0.6.0; python_version >= "3.6" and python_version < "4"
+jinja2==2.11.2; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5"
+jmespath==0.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
+jsonpatch==1.28; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+jsonpointer==2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+keystoneauth1==4.3.0; python_version >= "3.6"
+kombu==5.0.2; python_version >= "3.6"
+lockfile==0.12.2; python_version >= "3.6" and python_version < "4"
+lxml==4.6.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+mako==1.1.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+markdown==3.3.3; python_version >= "3.6"
+markupsafe==1.1.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+mercurial==5.6.1
+mirakuru==2.3.0; python_version >= "3.6"
+mistune==0.8.4; python_version >= "3.6" and python_version < "4"
+msgpack==1.0.2; python_version >= "3.6"
+munch==2.5.0; python_version >= "3.6"
+mypy-extensions==0.4.3; python_version >= "3.6" and python_version < "4"
+netaddr==0.8.0; python_version >= "3.6"
+netifaces==0.10.9; python_version >= "3.6"
+networkx==1.11; python_version >= "3.6" and python_version < "4"
+nodeenv==1.5.0
+nose==1.3.7
+nosehtml==0.4.6
+numpy==1.19.5; python_version >= "3.6"
+oauth2client==4.1.3
+oauthlib==3.1.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+openstacksdk==0.52.0; python_version >= "3.6"
+os-client-config==2.1.0; python_version >= "3.6"
+os-service-types==1.7.0; python_version >= "3.6"
+osc-lib==2.3.1; python_version >= "3.6"
+oslo.config==8.4.0; python_version >= "3.6"
+oslo.context==3.1.1; python_version >= "3.6"
+oslo.i18n==5.0.1; python_version >= "3.6"
+oslo.log==4.4.0; python_version >= "3.6"
+oslo.serialization==4.0.1; python_version >= "3.6"
+oslo.utils==4.7.0; python_version >= "3.6"
+oyaml==1.0
+packaging==20.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+paramiko==2.7.2
+parsley==1.3
+paste==3.5.0
+pastedeploy==2.1.1
+pastescript==3.2.0
+pbr==5.5.1; python_version >= "3.6"
+pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+port-for==0.4; python_version >= "3.6"
+prettytable==0.7.2; python_version >= "3.6"
+protobuf==3.14.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+prov==1.5.1; python_version >= "3.6" and python_version < "4"
+psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+pulsar-galaxy-lib==0.14.0.dev4
+py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
+pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+pycryptodome==3.9.9; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
+pydot==1.4.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
+pyeventsystem==0.1.0
+pyfaidx==0.5.9.2
+pygithub==1.54.1; python_version >= "3.6"
+pygments==2.7.4; python_version >= "3.5"
+pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
+pyjwt==1.7.1; python_version >= "3.6"
+pykwalify==1.8.0
+pynacl==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+pyperclip==1.8.1; python_version >= "3.6"
+pyreadline==2.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" and sys_platform == "win32" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" and sys_platform == "win32"
+pysam==0.16.0.1
+pytest-cov==2.11.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+pytest-html==3.1.1; python_version >= "3.6"
+pytest-metadata==1.11.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
+pytest-mock==3.5.1; python_version >= "3.5"
+pytest-postgresql==2.5.2; python_version >= "3.6"
+pytest-pythonpath==0.7.3
+pytest-shard==0.1.2; python_version >= "3.6"
+pytest==6.2.1; python_version >= "3.6"
+python-dateutil==2.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
+python-irodsclient==0.8.5
+python-jose==3.2.0
+python-keystoneclient==4.1.1; python_version >= "3.6"
+python-neutronclient==7.2.1; python_version >= "3.6"
+python-novaclient==17.2.1; python_version >= "3.6"
+python-swiftclient==3.10.1
+python3-openid==3.2.0; python_version >= "3.0"
+pytz==2020.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
+pyuwsgi==2.0.19.1.post0
+pyyaml==5.4.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
+rdflib-jsonld==0.5.0; python_version >= "3.6" and python_version < "4"
+rdflib==4.2.2; python_version >= "3.6" and python_version < "4"
+recommonmark==0.7.1
+refgenconf==0.9.3
+repoze.lru==0.7
+requests-oauthlib==1.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+requests-toolbelt==0.9.1; python_version >= "3.5"
+requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+requestsexceptions==1.4.0; python_version >= "3.6"
+responses==0.12.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+rfc3986==1.4.0; python_version >= "3.6"
+routes==2.5.1
+rsa==4.7; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
+ruamel.yaml.clib==0.2.2; platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"
+ruamel.yaml==0.16.5; python_version >= "3.6" and python_version < "4"
+s3transfer==0.3.4
+schema-salad==7.0.20201119201711; python_version >= "3.6" and python_version < "4"
+selenium==3.141.0
+setuptools-scm==5.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+shellescape==3.4.1; python_version >= "3.6" and python_version < "4"
+simplejson==3.17.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
+six==1.15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version >= "3.6" and python_version < "4"
+snowballstemmer==2.1.0; python_version >= "3.5"
+social-auth-core==3.3.0
+sortedcontainers==2.3.0
+sphinx-markdown-tables==0.0.15
+sphinx-rtd-theme==0.5.1
+sphinx==3.4.3; python_version >= "3.5"
+sphinxcontrib-applehelp==1.0.2; python_version >= "3.5"
+sphinxcontrib-devhelp==1.0.2; python_version >= "3.5"
+sphinxcontrib-htmlhelp==1.0.3; python_version >= "3.5"
+sphinxcontrib-jsmath==1.0.1; python_version >= "3.5"
+sphinxcontrib-qthelp==1.0.3; python_version >= "3.5"
+sphinxcontrib-serializinghtml==1.1.4; python_version >= "3.5"
+sqlalchemy-migrate==0.13.0
+sqlalchemy-utils==0.36.7
+sqlalchemy==1.3.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+sqlitedict==1.7.0
+sqlparse==0.4.1; python_version >= "3.5"
+starlette==0.13.6; python_version >= "3.6" and python_version < "4.0"
+stevedore==3.3.0; python_version >= "3.6"
+svgwrite==1.4.1; python_version >= "3.6"
+tempita==0.5.2
+tenacity==6.3.1
+testfixtures==6.17.1
+toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+tqdm==4.56.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+twill==2.0.1
+typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8"
+tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version < "4"
+ubiquerg==0.6.1
+unidecode==1.1.2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.0"
+uritemplate==3.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+urllib3==1.26.2; python_version >= "2.7" and python_full_version < "3.0.0" and python_version != "3.4" or python_full_version >= "3.5.0" and python_version < "4" and python_version != "3.4"
+uvicorn==0.13.3
+vine==5.0.0; python_version >= "3.6"
+watchdog==1.0.2; python_version >= "3.6"
+wcwidth==0.2.5; python_version >= "3.6"
+webencodings==0.5.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+webob==1.8.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+whoosh==2.7.4
+wrapt==1.12.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+xmlrunner==1.7.7
+yacman==0.7.0
+zipp==3.4.0; python_version < "3.7" and python_version >= "3.6"
+zipstream-new==1.1.8
diff --git a/lib/galaxy/dependencies/lint-requirements.txt b/lib/galaxy/dependencies/lint-requirements.txt
new file mode 100644
index 00000000000..98ec924ae6d
--- /dev/null
+++ b/lib/galaxy/dependencies/lint-requirements.txt
@@ -0,0 +1,4 @@
+flake8
+flake8-bugbear
+flake8-import-order
+mypy
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
new file mode 100644
index 00000000000..62b69cd286d
--- /dev/null
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -0,0 +1,11 @@
+attrs==20.3.0
+flake8==3.8.4
+flake8-bugbear==20.11.1
+flake8-import-order==0.18.1
+mccabe==0.6.1
+mypy==0.790
+mypy-extensions==0.4.3
+pycodestyle==2.6.0
+pyflakes==2.2.0
+typed-ast==1.4.2
+typing-extensions==3.7.4.3
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
deleted file mode 120000
index 26ec2b5e875..00000000000
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-pipfiles/default/pinned-requirements.txt
\ No newline at end of file
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
new file mode 100644
index 00000000000..0057ce73582
--- /dev/null
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -0,0 +1,189 @@
+--extra-index-url https://wheels.galaxyproject.org/simple
+
+adal==1.2.5
+aiofiles==0.6.0
+amqp==5.0.3; python_version >= "3.6"
+appdirs==1.4.4; python_version >= "3.6"
+argcomplete==1.12.2; python_version >= "3.6" and python_version < "4"
+attmap==0.12.11
+attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+babel==2.9.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+bagit==1.7.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.4.0" and python_version < "4" and python_version >= "3.6"
+bcrypt==3.2.0; python_version >= "3.6"
+bdbag==1.5.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4")
+beaker==1.11.0
+bioblend==0.14.0; python_version >= "3.5"
+bleach==3.2.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+boltons==20.2.1
+boto3==1.16.57
+boto==2.49.0
+botocore==1.19.57
+bx-python==0.8.9; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
+cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
+cachetools==4.2.0; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
+certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+cffi==1.14.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
+chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+cheetah3==3.2.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+click==7.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+cliff==3.6.0; python_version >= "3.6"
+cloudauthz==0.6.0
+cloudbridge==2.1.0
+cmd2==1.4.0; python_version >= "3.6"
+colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+coloredlogs==15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
+cryptography==3.3.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
+cwltool==3.0.20201109103151; python_version >= "3.6" and python_version < "4"
+dataclasses==0.8; python_version >= "3.6" and python_version < "3.7"
+debtcollector==2.2.0; python_version >= "3.6"
+decorator==4.4.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.6"
+defusedxml==0.7.0rc2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.0"
+deprecation==2.1.0
+dictobj==0.4
+docopt==0.6.2
+docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+dogpile.cache==1.1.1; python_version >= "3.6"
+ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+fabric3==1.14.post1
+fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
+fastapi==0.63.0; python_version >= "3.6"
+funcsigs==1.0.2
+future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+galaxy-sequence-utils==1.1.5
+google-api-core==1.25.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+google-api-python-client==1.12.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+google-auth-httplib2==0.0.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+google-auth==1.24.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+googleapis-common-protos==1.52.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+gxformat2==0.15.0
+h11==0.12.0; python_version >= "3.6"
+h5py==3.1.0; python_version >= "3.6"
+httplib2==0.18.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+humanfriendly==9.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
+idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+importlib-metadata==3.4.0; python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7")
+importlib-resources==5.1.0; python_version < "3.7" and python_version >= "3.6"
+isa-rwval==0.10.9
+iso8601==0.1.13; python_version >= "3.6"
+isodate==0.6.0; python_version >= "3.6" and python_version < "4"
+jmespath==0.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
+jsonpatch==1.28; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+jsonpointer==2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+keystoneauth1==4.3.0; python_version >= "3.6"
+kombu==5.0.2; python_version >= "3.6"
+lockfile==0.12.2; python_version >= "3.6" and python_version < "4"
+lxml==4.6.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+mako==1.1.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+markdown==3.3.3; python_version >= "3.6"
+markupsafe==1.1.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+mercurial==5.6.1
+mistune==0.8.4; python_version >= "3.6" and python_version < "4"
+msgpack==1.0.2; python_version >= "3.6"
+munch==2.5.0; python_version >= "3.6"
+mypy-extensions==0.4.3; python_version >= "3.6" and python_version < "4"
+netaddr==0.8.0; python_version >= "3.6"
+netifaces==0.10.9; python_version >= "3.6"
+networkx==1.11; python_version >= "3.6" and python_version < "4"
+nodeenv==1.5.0
+nose==1.3.7
+numpy==1.19.5; python_version >= "3.6"
+oauth2client==4.1.3
+oauthlib==3.1.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+openstacksdk==0.52.0; python_version >= "3.6"
+os-client-config==2.1.0; python_version >= "3.6"
+os-service-types==1.7.0; python_version >= "3.6"
+osc-lib==2.3.1; python_version >= "3.6"
+oslo.config==8.4.0; python_version >= "3.6"
+oslo.context==3.1.1; python_version >= "3.6"
+oslo.i18n==5.0.1; python_version >= "3.6"
+oslo.log==4.4.0; python_version >= "3.6"
+oslo.serialization==4.0.1; python_version >= "3.6"
+oslo.utils==4.7.0; python_version >= "3.6"
+oyaml==1.0
+packaging==20.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
+paramiko==2.7.2
+parsley==1.3
+paste==3.5.0
+pastedeploy==2.1.1
+pastescript==3.2.0
+pbr==5.5.1; python_version >= "3.6"
+prettytable==0.7.2; python_version >= "3.6"
+protobuf==3.14.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+prov==1.5.1; python_version >= "3.6" and python_version < "4"
+psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+pulsar-galaxy-lib==0.14.0.dev4
+pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
+pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
+pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+pycryptodome==3.9.9; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
+pydot==1.4.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
+pyeventsystem==0.1.0
+pyfaidx==0.5.9.2
+pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
+pyjwt==1.7.1
+pykwalify==1.8.0
+pynacl==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+pyperclip==1.8.1; python_version >= "3.6"
+pyreadline==2.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" and sys_platform == "win32" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" and sys_platform == "win32"
+pysam==0.16.0.1
+python-dateutil==2.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
+python-jose==3.2.0
+python-keystoneclient==4.1.1; python_version >= "3.6"
+python-neutronclient==7.2.1; python_version >= "3.6"
+python-novaclient==17.2.1; python_version >= "3.6"
+python-swiftclient==3.10.1
+python3-openid==3.2.0; python_version >= "3.0"
+pytz==2020.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
+pyuwsgi==2.0.19.1.post0
+pyyaml==5.4.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
+rdflib-jsonld==0.5.0; python_version >= "3.6" and python_version < "4"
+rdflib==4.2.2; python_version >= "3.6" and python_version < "4"
+refgenconf==0.9.3
+repoze.lru==0.7
+requests-oauthlib==1.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+requests-toolbelt==0.9.1; python_version >= "3.5"
+requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+requestsexceptions==1.4.0; python_version >= "3.6"
+rfc3986==1.4.0; python_version >= "3.6"
+routes==2.5.1
+rsa==4.7; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
+ruamel.yaml.clib==0.2.2; platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"
+ruamel.yaml==0.16.5; python_version >= "3.6" and python_version < "4"
+s3transfer==0.3.4
+schema-salad==7.0.20201119201711; python_version >= "3.6" and python_version < "4"
+setuptools-scm==5.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
+shellescape==3.4.1; python_version >= "3.6" and python_version < "4"
+simplejson==3.17.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
+six==1.15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version >= "3.6" and python_version < "4"
+social-auth-core==3.3.0
+sortedcontainers==2.3.0
+sqlalchemy-migrate==0.13.0
+sqlalchemy-utils==0.36.7
+sqlalchemy==1.3.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
+sqlitedict==1.7.0
+sqlparse==0.4.1; python_version >= "3.5"
+starlette==0.13.6; python_version >= "3.6" and python_version < "4.0"
+stevedore==3.3.0; python_version >= "3.6"
+svgwrite==1.4.1; python_version >= "3.6"
+tempita==0.5.2
+tenacity==6.3.1
+tqdm==4.56.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8"
+tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version < "4"
+ubiquerg==0.6.1
+unidecode==1.1.2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.0"
+uritemplate==3.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+urllib3==1.26.2; python_version >= "2.7" and python_full_version < "3.0.0" and python_version != "3.4" or python_full_version >= "3.5.0" and python_version < "4" and python_version != "3.4"
+uvicorn==0.13.3
+vine==5.0.0; python_version >= "3.6"
+wcwidth==0.2.5; python_version >= "3.6"
+webencodings==0.5.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+webob==1.8.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
+whoosh==2.7.4
+wrapt==1.12.1; python_version >= "3.6"
+yacman==0.7.0
+zipp==3.4.0; python_version < "3.7" and python_version >= "3.6"
+zipstream-new==1.1.8
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
deleted file mode 100644
index 99638356df3..00000000000
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ /dev/null
@@ -1,74 +0,0 @@
-#
-# These requirements were autogenerated by pipenv
-# To regenerate from the project's Pipfile, run:
-#
-#    pipenv lock --requirements --dev-only
-#
-
--i https://wheels.galaxyproject.org/simple
---extra-index-url https://pypi.python.org/simple
-alabaster==0.7.12
-attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-babel==2.9.0
-certifi==2020.12.5
-chardet==3.0.4
-commonmark==0.9.1
-coverage==5.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
-deprecated==1.2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-docutils==0.16
-gunicorn==20.0.4
-idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-imagesize==1.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-importlib-metadata==3.1.1; python_version == '3.6' and python_version < '3.8'
-iniconfig==1.1.1
-jinja2==2.11.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-lxml==4.6.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.3.3
-markupsafe==1.1.1
-mirakuru==2.3.0; python_version >= '3.6'
-nose==1.3.7
-nosehtml==0.4.6
-packaging==20.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-port-for==0.4
-prettytable==0.7.2
-psutil==5.7.3
-py==1.9.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pygithub==1.54
-pygments==2.7.3; python_version >= '3.5'
-pyjwt==1.7.1
-pyparsing==2.4.7
-pytest-cov==2.10.1
-pytest-html==3.1.0
-pytest-metadata==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-pytest-mock==3.3.1
-pytest-postgresql==2.5.2
-pytest-pythonpath==0.7.3
-pytest-shard==0.1.1
-pytest==6.1.2
-python-irodsclient==0.8.5
-pytz==2020.4
-recommonmark==0.6.0
-requests==2.24.0
-responses==0.12.1
-selenium==3.141.0
-six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-snowballstemmer==2.0.0
-sphinx-markdown-tables==0.0.15
-sphinx-rtd-theme==0.5.0
-sphinx==3.3.1
-sphinxcontrib-applehelp==1.0.2; python_version >= '3.5'
-sphinxcontrib-devhelp==1.0.2; python_version >= '3.5'
-sphinxcontrib-htmlhelp==1.0.3; python_version >= '3.5'
-sphinxcontrib-jsmath==1.0.1; python_version >= '3.5'
-sphinxcontrib-qthelp==1.0.3; python_version >= '3.5'
-sphinxcontrib-serializinghtml==1.1.4; python_version >= '3.5'
-testfixtures==6.16.0
-toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-twill==2.0.1
-urllib3==1.25.11; python_version != '3.4'
-watchdog==1.0.0
-wcwidth==0.2.5; sys_platform != 'win32'
-wrapt==1.12.1
-xmlrunner==1.7.7
-zipp==3.4.0; python_version < '3.8'
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
deleted file mode 100644
index 672dc270335..00000000000
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ /dev/null
@@ -1,194 +0,0 @@
-#
-# These requirements were autogenerated by pipenv
-# To regenerate from the project's Pipfile, run:
-#
-#    pipenv lock --requirements
-#
-
--i https://wheels.galaxyproject.org/simple
---extra-index-url https://pypi.python.org/simple
-adal==1.2.5
-aiofiles==0.6.0
-amqp==5.0.2; python_version >= '3.6'
-appdirs==1.4.4
-argcomplete==1.12.2
-attmap==0.12.11
-attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-babel==2.9.0
-bagit==1.7.0
-bcrypt==3.2.0; python_version >= '3.6'
-bdbag==1.5.6
-beaker==1.11.0
-bioblend==0.14.0
-bleach==3.2.1
-boltons==20.2.1
-boto3==1.16.33
-boto==2.49.0
-botocore==1.19.33
-bx-python==0.8.9
-cachecontrol==0.11.7
-cached-property==1.5.2; python_version < '3.8'
-cachetools==4.1.1; python_version ~= '3.5'
-certifi==2020.12.5
-cffi==1.14.4
-chardet==3.0.4
-cheetah3==3.2.6
-click==7.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-cliff==3.5.0; python_version >= '3.6'
-cloudauthz==0.6.0
-cloudbridge==2.1.0
-cmd2==1.4.0; python_version >= '3.5'
-colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-coloredlogs==14.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-cryptography==3.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-cwltool==3.0.20201109103151
-dataclasses==0.8; python_version < '3.7'
-debtcollector==2.2.0; python_version >= '3.6'
-decorator==4.4.2
-defusedxml==0.6.0; python_version >= '3.0'
-deprecation==2.1.0
-dictobj==0.4
-docopt==0.6.2
-docutils==0.16
-dogpile.cache==1.1.1; python_version >= '3.6'
-ecdsa==0.14.1; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-fabric3==1.14.post1
-fastapi-utils==0.2.1
-fastapi==0.62.0
-future==0.18.2
-galaxy-sequence-utils==1.1.5
-google-api-core==1.23.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-google-api-python-client==1.12.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-google-auth-httplib2==0.0.4
-google-auth==1.23.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-googleapis-common-protos==1.52.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-gxformat2==0.15.0
-h11==0.11.0
-h5py==3.1.0
-httplib2==0.18.1
-humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-importlib-metadata==3.1.1; python_version == '3.6' and python_version < '3.8'
-importlib-resources==3.3.0; python_version < '3.7'
-isa-rwval==0.10.9
-iso8601==0.1.13
-isodate==0.6.0
-jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-jsonpatch==1.28; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-jsonpointer==2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-keystoneauth1==4.3.0; python_version >= '3.6'
-kombu==5.0.2
-lockfile==0.12.2
-lxml==4.6.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-mako==1.1.3
-markdown==3.3.3
-markupsafe==1.1.1
-mercurial==5.6.1
-mistune==0.8.4
-msgpack==1.0.0
-munch==2.5.0
-mypy-extensions==0.4.3
-netaddr==0.8.0
-netifaces==0.10.9
-networkx==1.11
-nodeenv==1.5.0
-nose==1.3.7
-numpy==1.19.4
-oauth2client==4.1.3
-oauthlib==3.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-openstacksdk==0.52.0; python_version >= '3.6'
-os-client-config==2.1.0
-os-service-types==1.7.0
-osc-lib==2.3.0; python_version >= '3.6'
-oslo.config==8.4.0; python_version >= '3.6'
-oslo.context==3.1.1; python_version >= '3.6'
-oslo.i18n==5.0.1; python_version >= '3.6'
-oslo.log==4.4.0; python_version >= '3.6'
-oslo.serialization==4.0.1; python_version >= '3.6'
-oslo.utils==4.7.0; python_version >= '3.6'
-oyaml==1.0
-packaging==20.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-paramiko==2.7.2
-parsley==1.3
-paste==3.5.0
-pastedeploy==2.1.1
-pastescript==3.2.0
-pbr==5.5.1; python_version >= '2.6'
-prettytable==0.7.2
-protobuf==3.14.0
-prov==1.5.1
-psutil==5.7.3
-pulsar-galaxy-lib==0.14.0.dev4
-pyasn1-modules==0.2.8
-pyasn1==0.4.8
-pycparser==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pycryptodome==3.9.9
-pydantic==1.7.3; python_version >= '3.6'
-pydot==1.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyeventsystem==0.1.0
-pyfaidx==0.5.9.2
-pyinotify==0.9.6; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
-pyjwt==1.7.1
-pykwalify==1.7.0
-pynacl==1.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyparsing==2.4.7
-pyperclip==1.8.1
-pysam==0.16.0.1
-python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-python-jose==3.2.0
-python-keystoneclient==4.1.1; python_version >= '3.6'
-python-neutronclient==7.2.1; python_version >= '3.6'
-python-novaclient==17.2.1; python_version >= '3.6'
-python-swiftclient==3.10.1
-python3-openid==3.2.0; python_version >= '3.0'
-pytz==2020.4
-pyuwsgi==2.0.19.1.post0
-pyyaml==5.3.1
-rdflib-jsonld==0.5.0
-rdflib==4.2.2
-refgenconf==0.9.3
-repoze.lru==0.7
-requests-oauthlib==1.3.0
-requests-toolbelt==0.9.1
-requests==2.24.0
-requestsexceptions==1.4.0
-rfc3986==1.4.0
-routes==2.5.1
-rsa==4.6; python_version >= '3.5'
-ruamel.yaml.clib==0.2.2; python_version < '3.8' and platform_python_implementation == 'CPython'
-ruamel.yaml==0.16.5
-s3transfer==0.3.3
-schema-salad==7.0.20201119201711; python_version >= '3.6'
-setuptools-scm==4.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-shellescape==3.4.1
-simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
-six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-social-auth-core[openidconnect]==3.3.0
-sortedcontainers==2.3.0
-sqlalchemy-migrate==0.13.0
-sqlalchemy-utils==0.36.7
-sqlalchemy==1.3.20
-sqlitedict==1.7.0
-sqlparse==0.4.1
-starlette==0.13.6; python_version >= '3.6'
-stevedore==3.3.0; python_version >= '3.6'
-svgwrite==1.4
-tempita==0.5.2
-tenacity==6.2.0
-tqdm==4.54.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-typing-extensions==3.7.4.3; python_version < '3.8'
-tzlocal==2.1
-ubiquerg==0.6.1
-unidecode==1.1.1; python_version >= '3.0'
-uritemplate==3.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-urllib3==1.25.11; python_version != '3.4'
-uvicorn==0.13.0
-vine==5.0.0; python_version >= '3.6'
-wcwidth==0.2.5; sys_platform != 'win32'
-webencodings==0.5.1
-webob==1.8.6
-whoosh==2.7.4
-wrapt==1.12.1
-yacman==0.7.0
-zipp==3.4.0; python_version < '3.8'
-zipstream-new==1.1.8
diff --git a/lib/galaxy/dependencies/pipfiles/docker/Dockerfile b/lib/galaxy/dependencies/pipfiles/docker/Dockerfile
deleted file mode 100644
index be4763d5186..00000000000
--- a/lib/galaxy/dependencies/pipfiles/docker/Dockerfile
+++ /dev/null
@@ -1,15 +0,0 @@
-FROM python:3.6
-
-ENV DEBIAN_FRONTEND noninteractive
-ENV LC_ALL C.UTF-8
-ENV LANG C.UTF-8
-
-# Install Pipenv
-RUN apt-get update && apt-get -y upgrade
-RUN pip install pipenv
-
-ADD docker_script.sh /docker_script.sh
-
-WORKDIR /working
-
-CMD bash /docker_script.sh
diff --git a/lib/galaxy/dependencies/pipfiles/docker/Makefile b/lib/galaxy/dependencies/pipfiles/docker/Makefile
deleted file mode 100644
index 64560d35f8e..00000000000
--- a/lib/galaxy/dependencies/pipfiles/docker/Makefile
+++ /dev/null
@@ -1,7 +0,0 @@
-all:
-	if ! docker inspect galaxy/update-python-dependencies >/dev/null 2>&1; then \
-		docker build --no-cache -t galaxy/update-python-dependencies .; \
-	fi
-
-clean:
-	docker rmi --force galaxy/update-python-dependencies
diff --git a/lib/galaxy/dependencies/pipfiles/docker/docker_script.sh b/lib/galaxy/dependencies/pipfiles/docker/docker_script.sh
deleted file mode 100644
index 0f6e7dd8b41..00000000000
--- a/lib/galaxy/dependencies/pipfiles/docker/docker_script.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-
-pipenv lock -v
-pipenv lock -r > pinned-requirements.txt
-pipenv lock -r --dev-only > pinned-dev-requirements.txt
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile
deleted file mode 100644
index 37e5ba2e60b..00000000000
--- a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile
+++ /dev/null
@@ -1,15 +0,0 @@
-[[source]]
-url = "https://pypi.python.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[dev-packages]
-
-
-[packages]
-flake8 = "*"
-flake8-bugbear = "*"
-flake8-import-order = "*"
-
-[requires]
-python_version = "3.6"
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
deleted file mode 100644
index 2f35a72138d..00000000000
--- a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-#
-# These requirements were autogenerated by pipenv
-# To regenerate from the project's Pipfile, run:
-#
-#    pipenv lock --requirements
-#
-
--i https://pypi.python.org/simple
-attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-flake8-bugbear==20.11.1
-flake8-import-order==0.18.1
-flake8==3.8.4
-importlib-metadata==3.1.1; python_version < '3.8'
-mccabe==0.6.1
-pycodestyle==2.6.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyflakes==2.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-typing-extensions==3.7.4.3; python_version < '3.8'
-zipp==3.4.0; python_version >= '3.6'
diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh
deleted file mode 100755
index 18f03853393..00000000000
--- a/lib/galaxy/dependencies/pipfiles/update.sh
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/bin/sh
-set -e
-
-usage() {
-cat << EOF
-Usage: ${0##*/} [-c] [-d]
-
-Use pipenv to regenerate locked and hashed versions of Galaxy dependencies.
-Use -c to automatically commit these changes (be sure you have no staged git
-changes).
-Use -d to rebuild with Pipenv from the galaxy/update-python-dependencies
-container. This container can be built by running 'make' from the docker
-subdirectory.
-
-EOF
-}
-
-commit=0
-docker=0
-while getopts ":hcd" opt; do
-    case "$opt" in
-        c)
-            commit=1
-            ;;
-        d)
-            docker=1
-            ;;
-        h)
-            usage
-            exit 0
-            ;;
-        *)
-            usage >&2
-            exit 1
-            ;;
-    esac
-done
-
-THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
-ENVS="flake8
-default"
-
-export PIPENV_IGNORE_VIRTUALENVS=1
-for env in $ENVS; do
-    cd "$THIS_DIRECTORY/$env"
-    if [ "$docker" -eq 1 ]; then
-        docker run -v "$(pwd):/working" -t 'galaxy/update-python-dependencies'
-    else
-        sh ../docker/docker_script.sh
-    fi
-
-    if ! grep '==' pinned-dev-requirements.txt ; then
-        rm -f pinned-dev-requirements.txt
-    fi
-done
-
-if [ "$commit" -eq 1 ]; then
-	git add -u "$THIS_DIRECTORY"
-	git commit -m "Rev and re-lock Galaxy dependencies"
-fi
diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh
new file mode 100755
index 00000000000..b874c9abf07
--- /dev/null
+++ b/lib/galaxy/dependencies/update.sh
@@ -0,0 +1,21 @@
+#!/bin/sh
+set -e
+
+# You can pass one or more package specifications to this script to add only
+# them without updating all the rest of the requirements.
+
+if [ -z "$VIRTUAL_ENV" ]; then
+    echo "Please run this script inside a virtual environment!"
+    exit 1
+fi
+
+THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
+
+pip install --upgrade pip setuptools poetry
+if [ $# -gt 0 ]; then
+    poetry add --lock "$@"
+else
+    poetry update -vv --lock
+fi
+poetry export -f requirements.txt --without-hashes --output "$THIS_DIRECTORY/pinned-requirements.txt"
+poetry export --dev -f requirements.txt --without-hashes --output "$THIS_DIRECTORY/dev-requirements.txt"
diff --git a/lib/galaxy/dependencies/update_lint_requirements.sh b/lib/galaxy/dependencies/update_lint_requirements.sh
new file mode 100755
index 00000000000..53fc1293b06
--- /dev/null
+++ b/lib/galaxy/dependencies/update_lint_requirements.sh
@@ -0,0 +1,12 @@
+#!/bin/sh
+set -e
+
+THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
+
+LINT_VENV=$(mktemp -d "${TMPDIR:-/tmp}/lint_venv.XXXXXXXXXX")
+virtualenv -p python3 "${LINT_VENV}"
+. "${LINT_VENV}/bin/activate"
+pip install --upgrade pip setuptools
+pip install -r "${THIS_DIRECTORY}/lint-requirements.txt"
+pip freeze -l > "${THIS_DIRECTORY}/pinned-lint-requirements.txt"
+rm -rf "${LINT_VENV}"
diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/pyproject.toml
similarity index 68%
rename from lib/galaxy/dependencies/pipfiles/default/Pipfile
rename to pyproject.toml
index fc391f87850..ed7b211549e 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/pyproject.toml
@@ -1,14 +1,79 @@
-[[source]]
-url = "https://wheels.galaxyproject.org/simple"
-verify_ssl = true
+[tool.poetry]
 name = "galaxy"
+version = "21.01"
+description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
+authors = ["Galaxy Contributors"]
+license = "AFL-3.0"
+readme = "README.rst"
+homepage = "https://galaxyproject.org/"
+repository = "https://github.com/galaxyproject/galaxy/"
+documentation = "https://docs.galaxyproject.org/"
 
-[[source]]
-url = "https://pypi.python.org/simple"
-verify_ssl = true
-name = "pypi"
+[[tool.poetry.source]]
+name = "galaxyproject"
+url = "https://wheels.galaxyproject.org/simple"
 
-[dev-packages]
+[tool.poetry.dependencies]
+aiofiles = "*"
+Babel = "*"
+bdbag = "*"
+Beaker = "1.11.0"
+bioblend = "*"
+bleach = "*"
+boltons = "*"
+boto = "*"
+bx-python = "*"
+Cheetah3 = "*"
+cloudauthz = "==0.6.0"
+cloudbridge = "*"
+cwltool = "==3.0.20201109103151"
+dictobj = "*"
+docutils = "*"
+Fabric3 = "*"
+fastapi = "*"
+fastapi-utils = "*"
+future = "*"
+galaxy_sequence_utils = "*"
+gxformat2 = "*"
+h5py = "!=2.7.0, !=2.7.1"
+isa-rwval = "*"
+kombu = "*"
+Mako = "*"
+Markdown = "*"
+MarkupSafe = "*"
+Mercurial = "*"
+nodeenv = "*"
+nose = "*"
+numpy = "*"
+paramiko = "*"
+Parsley = "*"
+Paste = "*"
+psutil = "*"
+pulsar-galaxy-lib = "==0.14.0.dev4"
+pycryptodome = "*"
+pykwalify = "*"
+pyparsing = "*"
+pysam = "*"
+python = "^3.6"
+pyuwsgi = "*"
+PyYAML = "*"
+refgenconf = ">=0.7.0"
+requests = "*"
+Routes = "*"
+social-auth-core = {version = "==3.3.0", extras = ["openidconnect"]}
+sortedcontainers = "*"
+SQLAlchemy = "*"
+sqlalchemy-migrate = "*"
+SQLAlchemy-Utils = "!=0.36.8"  # https://github.com/kvesteri/sqlalchemy-utils/issues/462
+sqlitedict = "*"
+sqlparse = "*"
+svgwrite = "*"
+uvicorn = "*"
+WebOb = "*"
+Whoosh = "*"
+zipstream-new = "*"
+
+[tool.poetry.dev-dependencies]
 gunicorn = "*"
 lxml = "!=4.2.2"
 NoseHTML = "*"
@@ -16,6 +81,7 @@ pygithub = "*"
 pytest = "*"
 pytest-cov = "*"
 pytest-html = "*"
+python-irodsclient = "*"
 pytest-mock = "*"
 pytest-pythonpath = "*"
 pytest-postgresql = "*"
@@ -29,68 +95,3 @@ sphinx_rtd_theme = "*"
 testfixtures = "*"
 twill = "*"
 watchdog = "*"
-python-irodsclient = "*"
-
-[packages]
-numpy = "*"
-bx-python = "*"
-MarkupSafe = "*"
-Markdown = "*"
-# Optional requirement for markdown export.
-# Weasyprint = "==0.42"
-PyYAML = "*"
-SQLAlchemy = "*"
-SQLAlchemy-Utils = "!=0.36.8"  # https://github.com/kvesteri/sqlalchemy-utils/issues/462
-Mercurial = "*"
-nodeenv = "*"
-pycryptodome = "*"
-pyuwsgi = "*"
-pysam = "*"
-bdbag = "*"
-bleach = "*"
-cwltool = "==3.0.20201109103151"
-isa-rwval = "*"
-boltons = "*"
-Paste = "*"
-docutils = "*"
-uvicorn = "*"
-fastapi = "*"
-fastapi-utils = "*"
-aiofiles = "*"
-Routes = "*"
-WebOb = "*"
-Mako = "*"
-Babel = "*"
-Beaker = "*"
-dictobj = "*"
-nose = "*"
-Parsley = "*"
-sortedcontainers = "*"
-Whoosh = "*"
-galaxy_sequence_utils = "*"
-h5py = "!=2.7.0, !=2.7.1"
-pykwalify = "*"
-"Cheetah3" = "*"
-requests = "<2.25"  # PyGitHub 1.54 requires requests < 2.25
-bioblend = "*"
-boto = "*"
-kombu = "*"
-psutil = "*"
-pulsar-galaxy-lib = "==0.14.0.dev4"
-sqlalchemy-migrate = "*"
-sqlitedict = "*"
-sqlparse = "*"
-svgwrite = "*"
-pyparsing = "*"
-"Fabric3" = "*"
-paramiko = "*"
-cloudbridge = "*"
-social-auth-core = {version = "==3.3.0", extras = ['openidconnect']}
-cloudauthz = "==0.6.0"
-gxformat2 = "*"
-refgenconf = ">=0.7.0"
-future = "*"
-zipstream-new = "*"
-
-[requires]
-python_version = "3.6"
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index bba0815904b..5902644992c 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -192,7 +192,7 @@ fi
 
 requirement_args="-r requirements.txt"
 if [ $DEV_WHEELS -eq 1 ]; then
-    requirement_args="$requirement_args -r ${GALAXY_DEV_REQUIREMENTS}"
+    requirement_args="-r ${GALAXY_DEV_REQUIREMENTS}"
 fi
 
 [ "$CI" = 'true' ] && export PIP_PROGRESS_BAR=off
diff --git a/tox.ini b/tox.ini
index bbbdc82dc0c..0c67927158b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -28,9 +28,8 @@ setenv =
     check_indexes: GALAXY_TEST_FORCE_DATABASE_MIGRATION=1
     check_indexes: GALAXY_SKIP_CLIENT_BUILD=1
 deps =
-    lint,lint_docstring,lint_docstring_include_list: -rlib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+    lint,lint_docstring,lint_docstring_include_list,mypy: -rlib/galaxy/dependencies/pinned-lint-requirements.txt
     unit: mock-ssh-server
-    mypy: mypy
 
 [testenv:mulled]
 commands =  bash run_tests.sh --skip-venv -u test/unit/tool_util/mulled

From 582398d35afd20961fa562c670c2fb1ca19d1e5f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 20 Jan 2021 09:42:08 -0500
Subject: [PATCH 2/3] Fix jwt usage for 2.0 compat

---
 lib/galaxy/authnz/custos_authnz.py              | 6 +++---
 lib/galaxy/webapps/galaxy/controllers/authnz.py | 2 +-
 test/unit/authnz/test_custos_authnz.py          | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index 32180411516..39c5b5d3653 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -77,7 +77,7 @@ class CustosAuthnz(IdentityProvider):
         # Get nonce from token['id_token'] and validate. 'nonce' in the
         # id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME
         # cookie.
-        id_token_decoded = jwt.decode(id_token, verify=False)
+        id_token_decoded = jwt.decode(id_token, options={"verify_signature": False})
         nonce_hash = id_token_decoded['nonce']
         self._validate_nonce(trans, nonce_hash)
 
@@ -144,7 +144,7 @@ class CustosAuthnz(IdentityProvider):
         # Get nonce from token['id_token'] and validate. 'nonce' in the
         # id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME
         # cookie.
-        userinfo = jwt.decode(id_token, verify=False)
+        userinfo = jwt.decode(id_token, options={"verify_signature": False})
 
         # Get userinfo and create Galaxy user record
         email = userinfo['email']
@@ -180,7 +180,7 @@ class CustosAuthnz(IdentityProvider):
                 raise Exception("User is not associated with provider {}".format(self.config["provider"]))
             if len(provider_tokens) > 1:
                 for idx, token in enumerate(provider_tokens):
-                    id_token_decoded = jwt.decode(token.id_token, verify=False)
+                    id_token_decoded = jwt.decode(token.id_token, options={"verify_signature": False})
                     if (id_token_decoded['email'] == email):
                         index = idx
             trans.sa_session.delete(provider_tokens[index])
diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py
index 8b28a5f44e9..f3b11fcde4b 100644
--- a/lib/galaxy/webapps/galaxy/controllers/authnz.py
+++ b/lib/galaxy/webapps/galaxy/controllers/authnz.py
@@ -42,7 +42,7 @@ class OIDC(JSAppLauncher):
             rtv.append({'id': trans.app.security.encode_id(authnz.id), 'provider': authnz.provider, 'email': authnz.uid})
         # Add cilogon and custos identities
         for token in trans.user.custos_auth:
-            userinfo = jwt.decode(token.id_token, verify=False)
+            userinfo = jwt.decode(token.id_token, options={"verify_signature": False})
             rtv.append({'id': trans.app.security.encode_id(token.id), 'provider': token.provider, 'email': userinfo['email']})
         return rtv
 
diff --git a/test/unit/authnz/test_custos_authnz.py b/test/unit/authnz/test_custos_authnz.py
index 2b71f40d16b..c74de23feea 100644
--- a/test/unit/authnz/test_custos_authnz.py
+++ b/test/unit/authnz/test_custos_authnz.py
@@ -83,7 +83,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
 
     @property
     def test_id_token(self):
-        return jwt.encode({'nonce': self.test_nonce_hash}, key=None, algorithm=None).decode()
+        return jwt.encode({'nonce': self.test_nonce_hash}, key=None, algorithm=None)
 
     def mock_create_oauth2_session(self, custos_authnz):
         orig_create_oauth2_session = custos_authnz._create_oauth2_session
@@ -365,7 +365,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
             'email': self.test_email,
             'preferred_username': self.test_username,
             'sub': self.test_sub},
-            key=None, algorithm=None).decode()
+            key=None, algorithm=None)
 
         self._raw_token = {
             "access_token": self.test_access_token,

From 4339fd72c08201f67a40c90171d7b80ad7df9b9f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 21 Jan 2021 20:28:57 +0000
Subject: [PATCH 3/3] Make tests work with both PyJWT 1.7.1 and 2.0.1

---
 test/unit/authnz/test_custos_authnz.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/unit/authnz/test_custos_authnz.py b/test/unit/authnz/test_custos_authnz.py
index c74de23feea..4a201a5cd9f 100644
--- a/test/unit/authnz/test_custos_authnz.py
+++ b/test/unit/authnz/test_custos_authnz.py
@@ -15,6 +15,7 @@ import requests
 
 from galaxy.authnz import custos_authnz
 from galaxy.model import CustosAuthnzToken, User
+from galaxy.util import unicodify
 from ..unittest_utils.galaxy_mock import MockTrans
 
 
@@ -83,7 +84,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
 
     @property
     def test_id_token(self):
-        return jwt.encode({'nonce': self.test_nonce_hash}, key=None, algorithm=None)
+        return unicodify(jwt.encode({'nonce': self.test_nonce_hash}, key=None, algorithm=None))
 
     def mock_create_oauth2_session(self, custos_authnz):
         orig_create_oauth2_session = custos_authnz._create_oauth2_session
@@ -360,12 +361,12 @@ class CustosAuthnzTestCase(unittest.TestCase):
         )
         self.assertEqual(0, len(self.trans.sa_session.items))
 
-        test_id_token = jwt.encode({
+        test_id_token = unicodify(jwt.encode({
             'nonce': self.test_nonce_hash,
             'email': self.test_email,
             'preferred_username': self.test_username,
-            'sub': self.test_sub},
-            key=None, algorithm=None)
+            'sub': self.test_sub
+        }, key=None, algorithm=None))
 
         self._raw_token = {
             "access_token": self.test_access_token,