diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5e3e7f64..e47ae07b 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -11,6 +11,7 @@ jobs:
         tox-action:
           - lint
           - pytest
+          - mypy
     steps:
       - uses: actions/checkout@v4
         with:
diff --git a/Makefile b/Makefile
index e7f6d6b4..ab106366 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,4 @@
 # Default tests run with make test and make quick-tests
-NOSE_TESTS?=tests ephemeris
 # Default environment for make tox
 ENV?=py37
 # Extra arguments supplied to tox command
@@ -72,17 +71,17 @@ setup-git-hook-lint:
 setup-git-hook-lint-and-test:
 	cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint-and-test .git/hooks/pre-commit
 
-flake8:
-	$(IN_VENV) flake8 --max-complexity 15 $(SOURCE_DIR)  $(TEST_DIR)
+format:
+	$(IN_VENV) isort $(SOURCE_DIR) $(TEST_DIR) && black $(SOURCE_DIR) $(TEST_DIR) && ruff --fix $(SOURCE_DIR) $(TEST_DIR)
 
 lint:
-	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
+	$(IN_VENV) tox -e py38-lint
 
 lint-readme:
 	$(IN_VENV) python setup.py check -r -s
 
 test:
-	$(IN_VENV) nosetests $(NOSE_TESTS)
+	$(IN_VENV) pytest $(TEST_DIR)
 
 tox:
 	$(IN_VENV) tox -e $(ENV) -- $(ARGS)
diff --git a/dev-requirements.txt b/dev-requirements.txt
index ae6e7192..ac858691 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -15,6 +15,9 @@ CommonMark
 pyflakes
 flake8
 flake8-import-order
+isort
+black
+ruff
 
 # For release
 wheel
diff --git a/docs/conf.py b/docs/conf.py
index c7a3b65c..f2768b0e 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -13,19 +13,19 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another
 # directory, add these directories to sys.path here. If the directory is
 # relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # Get the project root dir, which is the parent dir of this
 cwd = os.getcwd()
 project_root = os.path.dirname(cwd)
-source = (os.path.join(project_root, 'src'))
+source = os.path.join(project_root, "src")
 
 # Insert the project root dir as the first element in the PYTHONPATH.
 # This lets us ensure that the source package is imported, and that its
@@ -39,27 +39,27 @@
 # -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinxarg.ext']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode", "sphinxarg.ext"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'Ephemeris'
-copyright = u'2017'
+project = "Ephemeris"
+copyright = "2017"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -72,42 +72,42 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to
 # some non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', '_*']
+exclude_patterns = ["_build", "_*"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built
 # documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output -------------------------------------------
@@ -120,79 +120,79 @@
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as
 # html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the
 # top of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon
 # of the docs.  This file should be a Windows icon file (.ico) being
 # 16x16 or 32x32 pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets)
 # here, relative to this directory. They are copied after the builtin
 # static files, so a file named "default.css" will overwrite the builtin
 # "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page
 # bottom, using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names
 # to template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer.
 # Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer.
 # Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages
 # will contain a <link> tag referring to it.  The value of this option
 # must be the base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'ephemerisdoc'
+htmlhelp_basename = "ephemerisdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -200,10 +200,8 @@
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #'preamble': '',
 }
@@ -212,30 +210,34 @@
 # (source start file, target name, title, author, documentclass
 # [howto/manual]).
 latex_documents = [
-    ('index', 'ephemeris.tex',
-     u'Ephemeris Documentation',
-     u'Galaxy Project and Community', 'manual'),
+    (
+        "index",
+        "ephemeris.tex",
+        "Ephemeris Documentation",
+        "Galaxy Project and Community",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at
 # the top of the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings
 # are parts, not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output ------------------------------------
@@ -243,13 +245,17 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'ephemeris',
-     u'Ephemris Documentation',
-     [u'Galaxy Project and Community'], 1)
+    (
+        "index",
+        "ephemeris",
+        "Ephemris Documentation",
+        ["Galaxy Project and Community"],
+        1,
+    )
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -258,22 +264,25 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'ephemeris',
-     u'Ephemeris Documentation',
-     u'Galaxy Project and Community',
-     'ephemeris',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        "index",
+        "ephemeris",
+        "Ephemeris Documentation",
+        "Galaxy Project and Community",
+        "ephemeris",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..0de1521d
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,28 @@
+[tool.black]
+line-length = 120
+target-version = ["py37"]
+
+[tool.isort]
+combine_as_imports = true
+force_alphabetical_sort_within_sections = true
+# Override force_grid_wrap value from profile=black, but black is still happy
+force_grid_wrap = 2
+# Same line length as for black
+line_length = 120
+no_lines_before = "LOCALFOLDER"
+profile = "black"
+reverse_relative = true
+skip_gitignore = true
+
+[tool.ruff]
+# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
+# flake8-logging-format (G) and pyupgrade (UP)
+select = ["E", "F", "B", "G", "UP"]
+target-version = "py38"
+# Exceptions:
+# B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
+# B9 flake8-bugbear opinionated warnings
+# E402 module level import not at top of file # TODO, we would like to improve this.
+# E501 is line length (delegated to black)
+# G* are TODOs
+ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"]
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index a7b38839..b0622c93 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -3,6 +3,7 @@
 # pull message down and embed, use arg parse, handle multiple, etc...
 import os
 import sys
+
 try:
     import requests
 except ImportError:
@@ -46,7 +47,7 @@ def extend(from_str, line):
         message = commit["message"]
         message = get_first_sentence(message)
     elif requests is not None and ident.startswith("pr"):
-        pull_request = ident[len("pr"):]
+        pull_request = ident[len("pr") :]
         api_url = urljoin(PROJECT_API, "pulls/%s" % pull_request)
         req = requests.get(api_url).json()
         print(api_url)
@@ -56,7 +57,7 @@ def extend(from_str, line):
             message = message.rstrip(".")
             message += " (thanks to `@%s`_)." % req["user"]["login"]
     elif requests is not None and ident.startswith("issue"):
-        issue = ident[len("issue"):]
+        issue = ident[len("issue") :]
         api_url = urljoin(PROJECT_API, "issues/%s" % issue)
         req = requests.get(api_url).json()
         message = req["title"]
@@ -66,12 +67,12 @@ def extend(from_str, line):
     to_doc = message + " "
 
     if ident.startswith("pr"):
-        pull_request = ident[len("pr"):]
+        pull_request = ident[len("pr") :]
         text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL)
         history = extend(".. github_links", text)
         to_doc += "`Pull Request {0}`_".format(pull_request)
     elif ident.startswith("issue"):
-        issue = ident[len("issue"):]
+        issue = ident[len("issue") :]
         text = ".. _Issue {0}: {1}/issues/{0}".format(issue, PROJECT_URL)
         history = extend(".. github_links", text)
         to_doc += "`Issue {0}`_".format(issue)
@@ -94,7 +95,7 @@ def get_first_sentence(message):
 
 def wrap(message):
     wrapper = textwrap.TextWrapper(initial_indent="* ")
-    wrapper.subsequent_indent = '  '
+    wrapper.subsequent_indent = "  "
     wrapper.width = 78
     return "\n".join(wrapper.wrap(message))
 
diff --git a/scripts/commit_version.py b/scripts/commit_version.py
index fa33fd37..6051c967 100644
--- a/scripts/commit_version.py
+++ b/scripts/commit_version.py
@@ -6,7 +6,6 @@
 import subprocess
 import sys
 
-
 PROJECT_DIRECTORY = os.path.join(os.path.dirname(__file__), "..")
 
 
@@ -17,7 +16,7 @@ def main(argv):
     with open(history_path, "r") as f:
         history = f.read()
     today = datetime.datetime.today()
-    today_str = today.strftime('%Y-%m-%d')
+    today_str = today.strftime("%Y-%m-%d")
     history = history.replace(".dev0", " (%s)" % today_str)
     with open(history_path, "w") as f:
         f.write(history)
@@ -25,13 +24,19 @@ def main(argv):
     source_mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, "__init__.py")
     with open(source_mod_path, "r") as f:
         mod = f.read()
-    mod = re.sub("__version__ = '[\d\.]*\.dev0'",
-                 "__version__ = '%s'" % version,
-                 mod)
+    mod = re.sub("__version__ = '[\d\.]*\.dev0'", "__version__ = '%s'" % version, mod)
     with open(source_mod_path, "w") as f:
         mod = f.write(mod)
-    shell(["git", "commit", "-m", "Version %s" % version,
-           "HISTORY.rst", "%s/__init__.py" % source_dir])
+    shell(
+        [
+            "git",
+            "commit",
+            "-m",
+            "Version %s" % version,
+            "HISTORY.rst",
+            "%s/__init__.py" % source_dir,
+        ]
+    )
     shell(["git", "tag", version])
 
 
diff --git a/scripts/new_version.py b/scripts/new_version.py
index 9ac9dbb5..f7d63cd9 100644
--- a/scripts/new_version.py
+++ b/scripts/new_version.py
@@ -6,7 +6,6 @@
 import sys
 from distutils.version import StrictVersion
 
-
 PROJECT_DIRECTORY = os.path.join(os.path.dirname(__file__), "..")
 
 
@@ -33,27 +32,37 @@ def main(argv):
 
     def extend(from_str, line):
         from_str += "\n"
-        return history.replace(from_str, from_str + line + "\n" )
+        return history.replace(from_str, from_str + line + "\n")
 
-    history = extend(".. to_doc", """
+    history = extend(
+        ".. to_doc",
+        """
 ---------------------
 %s.dev0
 ---------------------
 
-    """ % new_version)
+    """
+        % new_version,
+    )
     with open(history_path, "w") as f:
         f.write(history)
 
     source_mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, "__init__.py")
     with open(source_mod_path, "r") as f:
         mod = f.read()
-    mod = re.sub("__version__ = '[\d\.]+'",
-                 "__version__ = '%s.dev0'" % new_version,
-                 mod, 1)
+    mod = re.sub("__version__ = '[\d\.]+'", "__version__ = '%s.dev0'" % new_version, mod, 1)
     with open(source_mod_path, "w") as f:
         mod = f.write(mod)
-    shell(["git", "commit", "-m", "Starting work on %s" % new_version,
-           "HISTORY.rst", "%s/__init__.py" % source_dir])
+    shell(
+        [
+            "git",
+            "commit",
+            "-m",
+            "Starting work on %s" % new_version,
+            "HISTORY.rst",
+            "%s/__init__.py" % source_dir,
+        ]
+    )
 
 
 def shell(cmds, **kwds):
diff --git a/scripts/print_version_for_release.py b/scripts/print_version_for_release.py
index 7ee52cc1..289e3cb9 100644
--- a/scripts/print_version_for_release.py
+++ b/scripts/print_version_for_release.py
@@ -1,16 +1,16 @@
 from __future__ import print_function
-from distutils.version import LooseVersion
+
 import ast
 import re
 import sys
+from distutils.version import LooseVersion
 
 source_dir = sys.argv[1]
 
-_version_re = re.compile(r'__version__\s+=\s+(.*)')
+_version_re = re.compile(r"__version__\s+=\s+(.*)")
 
-with open('%s/__init__.py' % source_dir, 'rb') as f:
-    version = str(ast.literal_eval(_version_re.search(
-        f.read().decode('utf-8')).group(1)))
+with open("%s/__init__.py" % source_dir, "rb") as f:
+    version = str(ast.literal_eval(_version_re.search(f.read().decode("utf-8")).group(1)))
 
 # Strip .devN
 version_tuple = LooseVersion(version).version[0:3]
diff --git a/setup.py b/setup.py
index 19506109..5b1f7bc8 100644
--- a/setup.py
+++ b/setup.py
@@ -4,18 +4,22 @@
 import ast
 import os
 import re
-from setuptools import setup, find_packages
+
+from setuptools import (
+    find_packages,
+    setup,
+)
 
 SOURCE_DIR = "src/ephemeris"
 
-_version_re = re.compile(r'__version__\s+=\s+(.*)')
+_version_re = re.compile(r"__version__\s+=\s+(.*)")
 
 
-with open('%s/__init__.py' % SOURCE_DIR, 'rb') as f:
-    init_contents = f.read().decode('utf-8')
+with open("%s/__init__.py" % SOURCE_DIR, "rb") as f:
+    init_contents = f.read().decode("utf-8")
 
     def get_var(var_name):
-        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        pattern = re.compile(r"%s\s+=\s+(.*)" % var_name)
         match = pattern.search(init_contents).group(1)
         return str(ast.literal_eval(match))
 
@@ -25,9 +29,9 @@ def get_var(var_name):
     PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
     PROJECT_EMAIL = get_var("PROJECT_EMAIL")
 
-TEST_DIR = 'tests'
-PROJECT_DESCRIPTION = 'Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.'
-ENTRY_POINTS = '''
+TEST_DIR = "tests"
+PROJECT_DESCRIPTION = "Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows."
+ENTRY_POINTS = """
         [console_scripts]
         get-tool-list=ephemeris.get_tool_list_from_galaxy:main
         shed-tools=ephemeris.shed_tools:main
@@ -39,7 +43,7 @@ def get_var(var_name):
         install_tool_deps=ephemeris.install_tool_deps:main
         install-tool-deps=ephemeris.install_tool_deps:main
         set-library-permissions=ephemeris.set_library_permissions:main
-'''
+"""
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
 }
@@ -47,8 +51,8 @@ def get_var(var_name):
     SOURCE_DIR: SOURCE_DIR,
 }
 
-readme = open('README.rst').read()
-history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+readme = open("README.rst").read()
+history = open("HISTORY.rst").read().replace(".. :changelog:", "")
 
 if os.path.exists("requirements.txt"):
     requirements = open("requirements.txt").read().split("\n")
@@ -66,36 +70,36 @@ def get_var(var_name):
     name=PROJECT_NAME,
     version=version,
     description=PROJECT_DESCRIPTION,
-    long_description=readme + '\n\n' + history,
+    long_description=readme + "\n\n" + history,
     author=PROJECT_AUTHOR,
     author_email=PROJECT_EMAIL,
     url=PROJECT_URL,
-    packages=find_packages('src'),
+    packages=find_packages("src"),
     entry_points=ENTRY_POINTS,
     package_data=PACKAGE_DATA,
-    package_dir={'': 'src'},
+    package_dir={"": "src"},
     include_package_data=True,
     install_requires=requirements,
     license="AFL",
     zip_safe=False,
     python_requires=">=3.7",
-    keywords='galaxy',
+    keywords="galaxy",
     classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Intended Audience :: Developers',
-        'Environment :: Console',
-        'License :: OSI Approved :: Academic Free License (AFL)',
-        'Operating System :: POSIX',
-        'Topic :: Software Development',
-        'Topic :: Software Development :: Code Generators',
-        'Topic :: Software Development :: Testing',
-        'Natural Language :: English',
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Developers",
+        "Environment :: Console",
+        "License :: OSI Approved :: Academic Free License (AFL)",
+        "Operating System :: POSIX",
+        "Topic :: Software Development",
+        "Topic :: Software Development :: Code Generators",
+        "Topic :: Software Development :: Testing",
+        "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
     test_suite=TEST_DIR,
-    tests_require=test_requirements
+    tests_require=test_requirements,
 )
diff --git a/src/ephemeris/__init__.py b/src/ephemeris/__init__.py
index 51910180..2a1d461d 100644
--- a/src/ephemeris/__init__.py
+++ b/src/ephemeris/__init__.py
@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import yaml
 from bioblend import galaxy
 
@@ -10,18 +8,13 @@
 PROJECT_URL = "https://github.com/galaxyproject/ephemeris"
 PROJECT_AUTHOR = "Galaxy Project and Community"
 PROJECT_EMAIL = "jmchilton@gmail.com"
-RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
-    PROJECT_USERAME,
-    PROJECT_NAME,
-)
+RAW_CONTENT_URL = f"https://raw.github.com/{PROJECT_USERAME}/{PROJECT_NAME}/master/"
 
 
 def check_url(url, log=None):
     if not url.startswith("http"):
         if log:
-            log.warning(
-                "URL should start with http:// or https://. https:// chosen by default."
-            )
+            log.warning("URL should start with http:// or https://. https:// chosen by default.")
         url = "https://" + url
     return url
 
@@ -42,24 +35,20 @@ def get_galaxy_connection(args, file=None, log=None, login_required=True):
     api_key = args.api_key or file_content.get("api_key")
 
     if args.user and args.password:
-        return galaxy.GalaxyInstance(
-            url=galaxy_url, email=args.user, password=args.password
-        )
+        return galaxy.GalaxyInstance(url=galaxy_url, email=args.user, password=args.password)
     elif api_key:
         return galaxy.GalaxyInstance(url=galaxy_url, key=api_key)
     elif not login_required:
         return galaxy.GalaxyInstance(url=galaxy_url)
     else:
-        raise ValueError(
-            "Missing api key or user & password combination, in order to make a galaxy connection."
-        )
+        raise ValueError("Missing api key or user & password combination, in order to make a galaxy connection.")
 
 
 def load_yaml_file(filename):
     """
     Load YAML from the `tool_list_file` and return a dict with the content.
     """
-    with open(filename, "r") as f:
+    with open(filename) as f:
         dictionary = yaml.safe_load(f)
     return dictionary
 
diff --git a/src/ephemeris/common_parser.py b/src/ephemeris/common_parser.py
index aa69ad54..cf56a753 100644
--- a/src/ephemeris/common_parser.py
+++ b/src/ephemeris/common_parser.py
@@ -16,23 +16,22 @@ class RawDescriptionHideUnderscoresHelpFormatter(HideUnderscoresHelpFormatter, a
     pass
 
 
-class ArgumentDefaultsHideUnderscoresHelpFormatter(HideUnderscoresHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
+class ArgumentDefaultsHideUnderscoresHelpFormatter(
+    HideUnderscoresHelpFormatter, argparse.ArgumentDefaultsHelpFormatter
+):
     pass
 
 
 def get_common_args(login_required=True, log_file=False):
     parser = argparse.ArgumentParser(add_help=False)
     general_group = parser.add_argument_group("General options")
-    general_group.add_argument(
-        "-v", "--verbose", help="Increase output verbosity.", action="store_true"
-    )
+    general_group.add_argument("-v", "--verbose", help="Increase output verbosity.", action="store_true")
     if log_file:
         general_group.add_argument(
             "--log-file",
             "--log_file",
             dest="log_file",
-            help="Where the log file should be stored. "
-            "Default is a file in your system's temp folder",
+            help="Where the log file should be stored. " "Default is a file in your system's temp folder",
             default=None,
         )
 
diff --git a/src/ephemeris/ephemeris_log.py b/src/ephemeris/ephemeris_log.py
index c5d8f2b7..626ee1a7 100644
--- a/src/ephemeris/ephemeris_log.py
+++ b/src/ephemeris/ephemeris_log.py
@@ -59,5 +59,5 @@ def setup_global_logger(name, log_file=None):
         log_file = temp.name
     file_handler = logging.FileHandler(log_file)
     logger.addHandler(file_handler)
-    logger.info("Storing log file in: {0}".format(log_file))
+    logger.info(f"Storing log file in: {log_file}")
     return logger
diff --git a/src/ephemeris/generate_tool_list_from_ga_workflow_files.py b/src/ephemeris/generate_tool_list_from_ga_workflow_files.py
index 7d1dc0f9..8f1c3bb2 100644
--- a/src/ephemeris/generate_tool_list_from_ga_workflow_files.py
+++ b/src/ephemeris/generate_tool_list_from_ga_workflow_files.py
@@ -49,24 +49,19 @@ def _parser():
         "--panel_label",
         dest="panel_label",
         default="Tools from workflows",
-        help="The name of the panel where the tools will show up in Galaxy."
-        'If not specified: "Tools from workflows"',
+        help="The name of the panel where the tools will show up in Galaxy." 'If not specified: "Tools from workflows"',
     )
     return parser
 
 
 def get_workflow_dictionary(json_file):
-    with open(json_file, "r") as File:
+    with open(json_file) as File:
         mydict = json.load(File)
     return mydict
 
 
-def translate_workflow_dictionary_to_tool_list(
-    workflow_dictionary, panel_label: str
-) -> List[InstallRepoDict]:
-    starting_tool_list = extract_tool_shed_repositories_from_workflow_dict(
-        workflow_dictionary
-    )
+def translate_workflow_dictionary_to_tool_list(workflow_dictionary, panel_label: str) -> List[InstallRepoDict]:
+    starting_tool_list = extract_tool_shed_repositories_from_workflow_dict(workflow_dictionary)
     tool_list: List[InstallRepoDict] = []
     for tool in starting_tool_list:
         sub_dic: InstallRepoDict = {
@@ -85,9 +80,7 @@ def extract_tool_shed_repositories_from_workflow_dict(workflow_dictionary):
     for step in workflow_dictionary["steps"].values():
         subworkflow = step.get("subworkflow")
         if subworkflow:
-            tool_list.extend(
-                extract_tool_shed_repositories_from_workflow_dict(subworkflow)
-            )
+            tool_list.extend(extract_tool_shed_repositories_from_workflow_dict(subworkflow))
         tsr = step.get("tool_shed_repository")
         if tsr:
             tool_list.append(tsr)
@@ -119,8 +112,7 @@ def reduce_tool_list(tool_list: List[InstallRepoDict]) -> List[InstallRepoDict]:
             if (
                 tool["name"] == current_tool["name"]
                 and tool["owner"] == current_tool["owner"]
-                and tool["tool_panel_section_label"]
-                == current_tool["tool_panel_section_label"]
+                and tool["tool_panel_section_label"] == current_tool["tool_panel_section_label"]
                 and tool["tool_shed_url"] == current_tool["tool_shed_url"]
             ):
                 current_tool["revisions"].extend(tool["revisions"])
@@ -129,38 +121,26 @@ def reduce_tool_list(tool_list: List[InstallRepoDict]) -> List[InstallRepoDict]:
     return tool_list
 
 
-def generate_repo_list_from_workflow(
-    workflow_files: Iterable[str], panel_label: str
-) -> List[InstallRepoDict]:
+def generate_repo_list_from_workflow(workflow_files: Iterable[str], panel_label: str) -> List[InstallRepoDict]:
     intermediate_tool_list: List[InstallRepoDict] = []
     for workflow in workflow_files:
         workflow_dictionary = get_workflow_dictionary(workflow)
-        intermediate_tool_list += translate_workflow_dictionary_to_tool_list(
-            workflow_dictionary, panel_label
-        )
+        intermediate_tool_list += translate_workflow_dictionary_to_tool_list(workflow_dictionary, panel_label)
     return reduce_tool_list(intermediate_tool_list)
 
 
-def generate_tool_list_from_workflow(
-    workflow_files: Iterable[str], panel_label: str, output_file: str
-):
+def generate_tool_list_from_workflow(workflow_files: Iterable[str], panel_label: str, output_file: str):
     """
     :rtype: object
     """
 
-    convert_dict = {
-        "tools": generate_repo_list_from_workflow(
-            workflow_files=workflow_files, panel_label=panel_label
-        )
-    }
+    convert_dict = {"tools": generate_repo_list_from_workflow(workflow_files=workflow_files, panel_label=panel_label)}
     print_yaml_tool_list(convert_dict, output_file)
 
 
 def main(argv=None):
     options = _parser().parse_args(argv)
-    generate_tool_list_from_workflow(
-        options.workflow_files, options.panel_label, options.output_file
-    )
+    generate_tool_list_from_workflow(options.workflow_files, options.panel_label, options.output_file)
 
 
 if __name__ == "__main__":
diff --git a/src/ephemeris/get_tool_list_from_galaxy.py b/src/ephemeris/get_tool_list_from_galaxy.py
index d92b25e6..4d8578bf 100644
--- a/src/ephemeris/get_tool_list_from_galaxy.py
+++ b/src/ephemeris/get_tool_list_from_galaxy.py
@@ -41,9 +41,7 @@ def handle_tool(tool_elem):
         if tsr["name"] != name or tsr["owner"] != owner:
             return
 
-        if tool_shed_url and format_tool_shed_url(
-            tsr["tool_shed"]
-        ) != format_tool_shed_url(tool_shed_url):
+        if tool_shed_url and format_tool_shed_url(tsr["tool_shed"]) != format_tool_shed_url(tool_shed_url):
             return
 
         if changeset_revision and changeset_revision != tsr["changeset_revision"]:
@@ -135,15 +133,9 @@ def record_repo(tool_elem):
                     tool_panel_section_id = None
                     tool_panel_section_label = None
                     for repo_with_panel in tools_with_panel:
-                        if the_same_repository(
-                            repo_with_panel, repo, check_revision=False
-                        ):
-                            tool_panel_section_id = repo_with_panel.get(
-                                "tool_panel_section_id"
-                            )
-                            tool_panel_section_label = repo_with_panel.get(
-                                "tool_panel_section_label"
-                            )
+                        if the_same_repository(repo_with_panel, repo, check_revision=False):
+                            tool_panel_section_id = repo_with_panel.get("tool_panel_section_id")
+                            tool_panel_section_label = repo_with_panel.get("tool_panel_section_label")
                             break
                     repositories.append(
                         dict(
@@ -189,17 +181,11 @@ def the_same_repository(repo_1_info, repo_2_info, check_revision=True):
     (either `tool_shed` or `tool_shed_url`).
     """
     # Sort from most unique to least unique for fast comparison.
-    if not check_revision or repo_1_info.get("changeset_revision") == repo_2_info.get(
-        "changeset_revision"
-    ):
+    if not check_revision or repo_1_info.get("changeset_revision") == repo_2_info.get("changeset_revision"):
         if repo_1_info.get("name") == repo_2_info.get("name"):
             if repo_1_info.get("owner") == repo_2_info.get("owner"):
-                t1ts = repo_1_info.get(
-                    "tool_shed", repo_1_info.get("tool_shed_url", None)
-                )
-                t2ts = repo_2_info.get(
-                    "tool_shed", repo_2_info.get("tool_shed_url", None)
-                )
+                t1ts = repo_1_info.get("tool_shed", repo_1_info.get("tool_shed_url", None))
+                t2ts = repo_2_info.get("tool_shed", repo_2_info.get("tool_shed_url", None))
                 if t1ts in t2ts or t2ts in t1ts:
                     return True
     return False
@@ -244,9 +230,7 @@ def merge_repository_changeset_revisions(repository_list):
 def _parser():
     """Creates the parser object."""
     parent = get_common_args(login_required=True)
-    parser = ArgumentParser(
-        parents=[parent], formatter_class=ArgumentDefaultsHideUnderscoresHelpFormatter
-    )
+    parser = ArgumentParser(parents=[parent], formatter_class=ArgumentDefaultsHideUnderscoresHelpFormatter)
     parser.add_argument(
         "-o",
         "--output-file",
@@ -286,8 +270,7 @@ def _parser():
         "--get-all-tools",
         "--get_all_tools",
         action="store_true",
-        help="Get all tools and revisions, not just those which are present on the web ui."
-        "Requires login details.",
+        help="Get all tools and revisions, not just those which are present on the web ui." "Requires login details.",
     )
     return parser
 
diff --git a/src/ephemeris/install_tool_deps.py b/src/ephemeris/install_tool_deps.py
index b1f632d4..8e776e13 100644
--- a/src/ephemeris/install_tool_deps.py
+++ b/src/ephemeris/install_tool_deps.py
@@ -27,9 +27,7 @@ def _parser():
         help="Path to a tool file, tool_conf file, or yaml file containing a sequence of tool ids",
         nargs="*",
     )
-    parser.add_argument(
-        "-i", "--id", help="Space-separated list of tool ids", nargs="*"
-    )
+    parser.add_argument("-i", "--id", help="Space-separated list of tool ids", nargs="*")
 
     return parser
 
@@ -70,35 +68,24 @@ def main(argv=None):
                         os.path.abspath(os.path.dirname(tool_conf_path)),
                     )
                     if tool_path:
-                        log.info("Searching for tools relative to " + tool_path)
+                        log.info("Searching for tools relative to %s", tool_path)
                     tools = root.findall(".//tool[@file]")
                     if len(tools) == 0:
                         log.warning("No tools found in tool_conf")
                         continue
 
                     for tool in tools:
-                        tool_id = (
-                            ET.ElementTree(
-                                file=os.path.join(tool_path, tool.get("file"))
-                            )
-                            .getroot()
-                            .get("id")
-                        )
+                        tool_id = ET.ElementTree(file=os.path.join(tool_path, tool.get("file"))).getroot().get("id")
                         if tool_id:
                             log.info(
-                                "Installing tool dependencies for "
-                                + tool_id
-                                + " from: "
-                                + tool.get("file")
+                                "Installing tool dependencies for %s from: %s",
+                                tool_id,
+                                tool.get("file"),
                             )
                             _install(tool_client, tool_id)
                 elif root.tag == "tool" and root.get("id"):
                     # Install from single tool file
-                    log.info(
-                        "Tool xml found. Installing "
-                        + root.get("id")
-                        + " dependencies.."
-                    )
+                    log.info("Tool xml found. Installing %s dependencies", root.get("id"))
                     _install(tool_client, root.get("id"))
             else:
                 log.info("YAML tool list found, parsing..")
@@ -106,12 +93,12 @@ def main(argv=None):
                     tool_ids = yaml.safe_load(fh)
                 for tool_id in tool_ids:
                     # Install from yaml file
-                    log.info("Installing " + tool_id + " dependencies..")
+                    log.info("Installing %s dependencies..", tool_id)
                     _install(tool_client, tool_id)
 
     if args.id:
         for tool_id in args.id:  # type: str
-            log.info("Installing " + tool_id + " dependencies..")
+            log.info("Installing %s dependencies..", tool_id)
             _install(tool_client, tool_id.strip())
 
 
diff --git a/src/ephemeris/run_data_managers.py b/src/ephemeris/run_data_managers.py
index dd101662..d89268ff 100644
--- a/src/ephemeris/run_data_managers.py
+++ b/src/ephemeris/run_data_managers.py
@@ -81,11 +81,7 @@ def wait(gi, job_list, log):
                         job_hid=job_hid, **job_details
                     )
                 )
-                log.debug(
-                    "Job {job_hid}: Tool '{tool_id}' stdout: {stdout}".format(
-                        job_hid=job_hid, **job_details
-                    )
-                )
+                log.debug("Job {job_hid}: Tool '{tool_id}' stdout: {stdout}".format(job_hid=job_hid, **job_details))
                 failed_jobs.append(job)
                 finished_jobs.append(job)
             else:
@@ -197,9 +193,7 @@ def data_table_entry_exists(self, data_table_name, entry, column="value"):
         try:
             column_index = data_table_content.get("columns").index(column)
         except IndexError:
-            raise IndexError(
-                'Column "%s" does not exist in %s' % (column, data_table_name)
-            )
+            raise IndexError(f'Column "{column}" does not exist in {data_table_name}')
 
         for field in data_table_content.get("fields"):
             if field[column_index] == entry:
@@ -220,14 +214,10 @@ def input_entries_exist_in_data_tables(self, data_tables, input_dict):
         # Return False as soon as entry is not present
         for data_table in data_tables:
             if value_entry:
-                if not self.data_table_entry_exists(
-                    data_table, value_entry, column="value"
-                ):
+                if not self.data_table_entry_exists(data_table, value_entry, column="value"):
                     return False
             if name_entry:
-                if not self.data_table_entry_exists(
-                    data_table, name_entry, column="name"
-                ):
+                if not self.data_table_entry_exists(data_table, name_entry, column="name"):
                     return False
         # If all checks are passed the entries are present in the database tables.
         return True
@@ -266,15 +256,13 @@ def run_jobs(jobs, skipped_jobs):
             for skipped_job in skipped_jobs:
                 if overwrite:
                     log.info(
-                        "%s already run for %s. Entry will be overwritten."
-                        % (skipped_job["tool_id"], skipped_job["inputs"])
+                        "{} already run for {}. Entry will be overwritten.".format(
+                            skipped_job["tool_id"], skipped_job["inputs"]
+                        )
                     )
                     jobs.append(skipped_job)
                 else:
-                    log.info(
-                        "%s already run for %s. Skipping."
-                        % (skipped_job["tool_id"], skipped_job["inputs"])
-                    )
+                    log.info("{} already run for {}. Skipping.".format(skipped_job["tool_id"], skipped_job["inputs"]))
                     all_skipped_jobs.append(skipped_job)
             for job in jobs:
                 started_job = self.tool_client.run_tool(
@@ -296,10 +284,7 @@ def run_jobs(jobs, skipped_jobs):
             all_succesful_jobs.extend(successful_jobs)
             all_failed_jobs.extend(failed_jobs)
 
-        log.info(
-            "Running data managers that populate the following source data tables: %s"
-            % self.source_tables
-        )
+        log.info("Running data managers that populate the following source data tables: %s" % self.source_tables)
         run_jobs(self.fetch_jobs, self.skipped_fetch_jobs)
         log.info("Running data managers that index sequences.")
         run_jobs(self.index_jobs, self.skipped_index_jobs)
@@ -308,9 +293,7 @@ def run_jobs(jobs, skipped_jobs):
         log.info("Successful jobs: %i " % len(all_succesful_jobs))
         log.info("Skipped jobs: %i " % len(all_skipped_jobs))
         log.info("Failed jobs: %i " % len(all_failed_jobs))
-        InstallResults = namedtuple(
-            "InstallResults", ["successful_jobs", "failed_jobs", "skipped_jobs"]
-        )
+        InstallResults = namedtuple("InstallResults", ["successful_jobs", "failed_jobs", "skipped_jobs"])
         return InstallResults(
             successful_jobs=all_succesful_jobs,
             failed_jobs=all_failed_jobs,
diff --git a/src/ephemeris/set_library_permissions.py b/src/ephemeris/set_library_permissions.py
index bd198bb0..23492877 100644
--- a/src/ephemeris/set_library_permissions.py
+++ b/src/ephemeris/set_library_permissions.py
@@ -43,9 +43,7 @@ def set_permissions(gi, library_id, role_ids, auto):
     )
     if auto:
         for current in range(total):
-            log.debug(
-                "Processing dataset %d of %d, ID=%s", current, total, datasets[current]
-            )
+            log.debug("Processing dataset %d of %d, ID=%s", current, total, datasets[current])
             gi.libraries.set_dataset_permissions(
                 dataset_id=datasets[current],
                 access_in=role_ids,
@@ -80,12 +78,10 @@ def _parser():
     parser = argparse.ArgumentParser(
         parents=[parent],
         formatter_class=HideUnderscoresHelpFormatter,
-        description="Populate the Galaxy data library with data."
+        description="Populate the Galaxy data library with data.",
     )
     parser.add_argument("library", help="Specify the data library ID")
-    parser.add_argument(
-        "--roles", nargs="+", help="Specify a list of comma separated role IDs"
-    )
+    parser.add_argument("--roles", nargs="+", help="Specify a list of comma separated role IDs")
     parser.add_argument(
         "-y",
         "--yes",
@@ -106,15 +102,11 @@ def _parser():
 def main(argv=None):
     args = _parser().parse_args(argv)
     if args.user and args.password:
-        gi = galaxy.GalaxyInstance(
-            url=args.galaxy, email=args.user, password=args.password
-        )
+        gi = galaxy.GalaxyInstance(url=args.galaxy, email=args.user, password=args.password)
     elif args.api_key:
         gi = galaxy.GalaxyInstance(url=args.galaxy, key=args.api_key)
     else:
-        sys.exit(
-            "Please specify either a valid Galaxy username/password or an API key."
-        )
+        sys.exit("Please specify either a valid Galaxy username/password or an API key.")
 
     if args.verbose:
         log.basicConfig(level=log.DEBUG)
@@ -126,9 +118,7 @@ def main(argv=None):
     if args.roles and args.library:
         args.roles = [r.strip() for r in args.roles.split(",")]
     else:
-        sys.exit(
-            "Specify library ID (--library myLibraryID) and (list of) role(s) (--roles roleId1,roleId2)"
-        )
+        sys.exit("Specify library ID (--library myLibraryID) and (list of) role(s) (--roles roleId1,roleId2)")
     set_permissions(gi, library_id=args.library, role_ids=args.roles, auto=args.yes)
     log.info(
         "\nThis script uses bioblend to update ALL permissions of ALL datasets in a"
diff --git a/src/ephemeris/setup_data_libraries.py b/src/ephemeris/setup_data_libraries.py
index e8066694..68225fe4 100644
--- a/src/ephemeris/setup_data_libraries.py
+++ b/src/ephemeris/setup_data_libraries.py
@@ -18,9 +18,7 @@
 def create_legacy(gi, desc):
     destination = desc["destination"]
     if destination["type"] != "library":
-        raise Exception(
-            "Only libraries may be created with pre-18.05 Galaxies using this script."
-        )
+        raise Exception("Only libraries may be created with pre-18.05 Galaxies using this script.")
     library_name = destination.get("name")
     library_description = destination.get("description")
     library_synopsis = destination.get("synopsis")
@@ -42,9 +40,7 @@ def create_legacy(gi, desc):
         print("Library already exists! id: " + str(lib_id))
         folder_id = gi.libraries.show_library(lib_id)["root_folder_id"]
     else:
-        lib = gi.libraries.create_library(
-            library_name, library_description, library_synopsis
-        )
+        lib = gi.libraries.create_library(library_name, library_description, library_synopsis)
         lib_id = lib["id"]
         folder_id = lib["root_folder_id"]
 
@@ -64,21 +60,15 @@ def populate_items(base_folder_id, has_items):
                 if rmt_folder_list:
                     folder_id = rmt_folder_list[0]["id"]
                 else:
-                    folder = gi.libraries.create_folder(
-                        lib_id, name, description, base_folder_id=base_folder_id
-                    )
+                    folder = gi.libraries.create_folder(lib_id, name, description, base_folder_id=base_folder_id)
                     folder_id = folder[0]["id"]
             for item in has_items["items"]:
                 populate_items(folder_id, item)
         else:
             src = has_items["src"]
             if src != "url":
-                raise Exception(
-                    "For pre-18.05 Galaxies only support URLs src items are supported."
-                )
-            rmt_library_files = gi.folders.show_folder(base_folder_id, contents=True)[
-                "folder_contents"
-            ]
+                raise Exception("For pre-18.05 Galaxies only support URLs src items are supported.")
+            rmt_library_files = gi.folders.show_folder(base_folder_id, contents=True)["folder_contents"]
             file_names = []
             for item in rmt_library_files:
                 if item["type"] == "file":
@@ -163,9 +153,7 @@ def normalize_items(has_items):
 
     if training:
         destination["name"] = destination.get("name", "Training Data")
-        destination["description"] = destination.get(
-            "description", "Data pulled from online archives."
-        )
+        destination["description"] = destination.get("description", "Data pulled from online archives.")
     else:
         destination["name"] = destination.get("name", "New Data Library")
         destination["description"] = destination.get("description", "")
@@ -191,17 +179,10 @@ def normalize_items(has_items):
                         job_ids.append(subjob["id"])
 
         while True:
-            job_states = [
-                jc.get_state(job) in ("ok", "error", "deleted") for job in job_ids
-            ]
+            job_states = [jc.get_state(job) in ("ok", "error", "deleted") for job in job_ids]
             log.debug(
                 "Job states: %s"
-                % ",".join(
-                    [
-                        "%s=%s" % (job_id, job_state)
-                        for (job_id, job_state) in zip(job_ids, job_states)
-                    ]
-                )
+                % ",".join([f"{job_id}={job_state}" for (job_id, job_state) in zip(job_ids, job_states)])
             )
 
             if all(job_states):
@@ -217,7 +198,7 @@ def _parser():
     parser = argparse.ArgumentParser(
         parents=[parent],
         formatter_class=HideUnderscoresHelpFormatter,
-        description="Populate the Galaxy data library with data."
+        description="Populate the Galaxy data library with data.",
     )
     parser.add_argument("-i", "--infile", required=True, type=argparse.FileType("r"))
     parser.add_argument(
@@ -238,15 +219,11 @@ def _parser():
 def main(argv=None):
     args = _parser().parse_args(argv)
     if args.user and args.password:
-        gi = galaxy.GalaxyInstance(
-            url=args.galaxy, email=args.user, password=args.password
-        )
+        gi = galaxy.GalaxyInstance(url=args.galaxy, email=args.user, password=args.password)
     elif args.api_key:
         gi = galaxy.GalaxyInstance(url=args.galaxy, key=args.api_key)
     else:
-        sys.exit(
-            "Please specify either a valid Galaxy username/password or an API key."
-        )
+        sys.exit("Please specify either a valid Galaxy username/password or an API key.")
 
     if args.verbose:
         log.basicConfig(level=log.DEBUG)
diff --git a/src/ephemeris/shed_tools.py b/src/ephemeris/shed_tools.py
index 9754c03d..8807fc07 100644
--- a/src/ephemeris/shed_tools.py
+++ b/src/ephemeris/shed_tools.py
@@ -136,9 +136,7 @@ def installed_repositories(self) -> List[InstallRepoDict]:
             get_all_tools=True,
         ).tool_list.get("tools")
 
-    def filter_installed_repos(
-        self, repos: Iterable[InstallRepoDict], check_revision: bool = True
-    ) -> FilterResults:
+    def filter_installed_repos(self, repos: Iterable[InstallRepoDict], check_revision: bool = True) -> FilterResults:
         """This filters a list of repositories"""
         not_installed_repos: List[InstallRepoDict] = []
         already_installed_repos: List[InstallRepoDict] = []
@@ -185,11 +183,7 @@ def install_repositories(
             for key in repo.keys():
                 if key not in VALID_KEYS and key != "revisions":
                     if log:
-                        log.warning(
-                            "'{0}' not a valid key. Will be skipped during parsing".format(
-                                key
-                            )
-                        )
+                        log.warning(f"'{key}' not a valid key. Will be skipped during parsing")
 
         # Start by flattening the repo list per revision
         flattened_repos = flatten_repo_info(repositories)
@@ -221,9 +215,7 @@ def install_repositories(
         for skipped_repo in filtered_repos.already_installed_repos:
             counter += 1
             if log:
-                log_repository_install_skip(
-                    skipped_repo, counter, total_num_repositories, log
-                )
+                log_repository_install_skip(skipped_repo, counter, total_num_repositories, log)
             skipped_repositories.append(skipped_repo)
 
         # Install repos
@@ -248,36 +240,25 @@ def install_repositories(
         # Log results
         if log:
             log.info(
-                "Installed repositories ({0}): {1}".format(
+                "Installed repositories ({}): {}".format(
                     len(installed_repositories),
-                    [
-                        (t["name"], t.get("changeset_revision"))
-                        for t in installed_repositories
-                    ],
+                    [(t["name"], t.get("changeset_revision")) for t in installed_repositories],
                 )
             )
             log.info(
-                "Skipped repositories ({0}): {1}".format(
+                "Skipped repositories ({}): {}".format(
                     len(skipped_repositories),
-                    [
-                        (t["name"], t.get("changeset_revision"))
-                        for t in skipped_repositories
-                    ],
+                    [(t["name"], t.get("changeset_revision")) for t in skipped_repositories],
                 )
             )
             log.info(
-                "Errored repositories ({0}): {1}".format(
+                "Errored repositories ({}): {}".format(
                     len(errored_repositories),
-                    [
-                        (t["name"], t.get("changeset_revision", ""))
-                        for t in errored_repositories
-                    ],
+                    [(t["name"], t.get("changeset_revision", "")) for t in errored_repositories],
                 )
             )
             log.info("All repositories have been installed.")
-            log.info(
-                "Total run time: {0}".format(dt.datetime.now() - installation_start)
-            )
+            log.info(f"Total run time: {dt.datetime.now() - installation_start}")
         return InstallResults(
             installed_repositories=installed_repositories,
             skipped_repositories=skipped_repositories,
@@ -288,20 +269,16 @@ def update_repositories(self, repositories=None, log=None, **kwargs):
         if not repositories:  # Repositories None or empty list
             repositories = self.installed_repositories()
         else:
-            filtered_repos = self.filter_installed_repos(
-                repositories, check_revision=False
-            )
+            filtered_repos = self.filter_installed_repos(repositories, check_revision=False)
             if filtered_repos.not_installed_repos:
                 if log:
                     log.warning(
-                        "The following tools are not installed and will not be upgraded: {0}".format(
+                        "The following tools are not installed and will not be upgraded: {}".format(
                             filtered_repos.not_installed_repos
                         )
                     )
             repositories = filtered_repos.already_installed_repos
-        return self.install_repositories(
-            repositories, force_latest_revision=True, log=log, **kwargs
-        )
+        return self.install_repositories(repositories, force_latest_revision=True, log=log, **kwargs)
 
     def test_tools(
         self,
@@ -329,26 +306,20 @@ def test_tools(
 
         installed_tools = []
         for target_repository in target_repositories:
-            repo_tools = tools_for_repository(
-                self.gi, target_repository, all_tools=test_all_versions
-            )
+            repo_tools = tools_for_repository(self.gi, target_repository, all_tools=test_all_versions)
             installed_tools.extend(repo_tools)
 
         all_test_results = []
         galaxy_interactor = self._get_interactor(test_user, test_user_api_key)
         if client_test_config_path is not None:
-            with open(client_test_config_path, "r") as f:
+            with open(client_test_config_path) as f:
                 client_test_config_dict = yaml.full_load(f)
-            client_test_config = DictClientTestConfig(
-                client_test_config_dict.get("tools")
-            )
+            client_test_config = DictClientTestConfig(client_test_config_dict.get("tools"))
         else:
             client_test_config = None
 
         if test_history_name:
-            for history in self.gi.histories.get_histories(
-                name=test_history_name, deleted=False
-            ):
+            for history in self.gi.histories.get_histories(name=test_history_name, deleted=False):
                 test_history = history["id"]
                 log.debug(
                     "Using existing history with id '%s', last updated: %s",
@@ -357,9 +328,7 @@ def test_tools(
                 )
                 break
             else:
-                test_history = galaxy_interactor.new_history(
-                    history_name=test_history_name
-                )
+                test_history = galaxy_interactor.new_history(history_name=test_history_name)
         else:
             test_history = galaxy_interactor.new_history()
 
@@ -401,21 +370,9 @@ def test_tools(
                     json.dump(report_obj, f)
                 if log:
                     log.info("Report written to '%s'", os.path.abspath(test_json))
-                    log.info(
-                        "Passed tool tests ({0}): {1}".format(
-                            n_passed, [t for t in tests_passed]
-                        )
-                    )
-                    log.info(
-                        "Failed tool tests ({0}): {1}".format(
-                            n_failed, [t[0] for t in test_exceptions]
-                        )
-                    )
-                    log.info(
-                        "Total tool test time: {0}".format(
-                            dt.datetime.now() - tool_test_start
-                        )
-                    )
+                    log.info(f"Passed tool tests ({n_passed}): {[t for t in tests_passed]}")
+                    log.info(f"Failed tool tests ({n_failed}): {[t[0] for t in test_exceptions]}")
+                    log.info(f"Total tool test time: {dt.datetime.now() - tool_test_start}")
 
     def _get_interactor(self, test_user, test_user_api_key):
         if test_user_api_key is None:
@@ -458,9 +415,7 @@ def _test_tool(
         if tool_version:
             label_base += "/" + str(tool_version)
         try:
-            tool_test_dicts = galaxy_interactor.get_tool_tests(
-                tool_id, tool_version=tool_version
-            )
+            tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
         except Exception as e:
             if log:
                 log.warning(
@@ -469,9 +424,7 @@ def _test_tool(
                     exc_info=True,
                 )
             test_exceptions.append((label_base, e))
-            Results = namedtuple(
-                "Results", ["tool_test_results", "tests_passed", "test_exceptions"]
-            )
+            Results = namedtuple("Results", ["tool_test_results", "tests_passed", "test_exceptions"])
             return Results(
                 tool_test_results=tool_test_results,
                 tests_passed=tests_passed,
@@ -516,10 +469,7 @@ def register(job_data):
             executor.submit(run_test, test_index, test_id)
 
     def install_repository_revision(self, repository: InstallRepoDict, log):
-        default_err_msg = (
-            "All repositories that you are attempting to install "
-            "have been previously installed."
-        )
+        default_err_msg = "All repositories that you are attempting to install " "have been previously installed."
         start = dt.datetime.now()
         try:
             response = self.tool_shed_client.install_repository_revision(
@@ -541,23 +491,18 @@ def install_repository_revision(self, repository: InstallRepoDict, log):
                 #  installed, possibly because the selected repository has
                 #  already been installed.'}
                 if log:
-                    log.debug(
-                        "\tRepository {0} is already installed.".format(
-                            repository["name"]
-                        )
-                    )
+                    log.debug("\tRepository {} is already installed.".format(repository["name"]))
             if log:
-                log_repository_install_success(
-                    repository=repository, start=start, log=log
-                )
+                log_repository_install_success(repository=repository, start=start, log=log)
             return "installed"
         except (ConnectionError, requests.exceptions.ConnectionError) as e:
             if default_err_msg in unicodify(e):
                 # THIS SHOULD NOT HAPPEN DUE TO THE CHECKS EARLIER
                 if log:
                     log.debug(
-                        "\tRepository %s already installed (at revision %s)"
-                        % (repository["name"], repository["changeset_revision"])
+                        "\tRepository {} already installed (at revision {})".format(
+                            repository["name"], repository["changeset_revision"]
+                        )
                     )
                 return "skipped"
             elif "504" in unicodify(e) or "Connection aborted" in unicodify(e):
@@ -566,25 +511,27 @@ def install_repository_revision(self, repository: InstallRepoDict, log):
                         "Timeout during install of %s, extending wait to 1h",
                         repository["name"],
                     )
-                success = self.wait_for_install(
-                    repository=repository, log=log, timeout=3600
-                )
+                success = self.wait_for_install(repository=repository, log=log, timeout=3600)
                 if success:
                     if log:
-                        log_repository_install_success(
-                            repository=repository, start=start, log=log
-                        )
+                        log_repository_install_success(repository=repository, start=start, log=log)
                     return "installed"
                 else:
                     if log:
                         log_repository_install_error(
-                            repository=repository, start=start, msg=getattr(e, "body", unicodify(e)), log=log
+                            repository=repository,
+                            start=start,
+                            msg=getattr(e, "body", unicodify(e)),
+                            log=log,
                         )
                     return "error"
             else:
                 if log:
                     log_repository_install_error(
-                        repository=repository, start=start, msg=getattr(e, "body", unicodify(e)), log=log
+                        repository=repository,
+                        start=start,
+                        msg=getattr(e, "body", unicodify(e)),
+                        log=log,
                     )
                 return "error"
 
@@ -601,15 +548,8 @@ def wait_for_install(self, repository, log=None, timeout=3600):
         owner = repository["owner"]
         changeset_revision = repository["changeset_revision"]
         installed_repos = self.tool_shed_client.get_repositories()
-        filtered_repos = [
-            r for r in installed_repos if r["name"] == name and r["owner"] == owner
-        ]
-        assert (
-            filtered_repos
-        ), "Repository '%s' from owner '%s' not in list of repositories." % (
-            name,
-            owner,
-        )
+        filtered_repos = [r for r in installed_repos if r["name"] == name and r["owner"] == owner]
+        assert filtered_repos, f"Repository '{name}' from owner '{owner}' not in list of repositories."
         # Check if exact repository revision in filtered_repos
         installing_repo_id = None
         for repo in filtered_repos:
@@ -618,11 +558,7 @@ def wait_for_install(self, repository, log=None, timeout=3600):
                 break
         else:
             # Galaxy may have decided to install a newer repository revision. We now try to guess which repository that is.
-            non_terminal = [
-                r
-                for r in filtered_repos
-                if r["status"] in NON_TERMINAL_REPOSITORY_STATES
-            ]
+            non_terminal = [r for r in filtered_repos if r["status"] in NON_TERMINAL_REPOSITORY_STATES]
             if len(non_terminal) == 1:
                 # Unambiguous, we wait for this repo
                 installing_repo_id = non_terminal[0]["id"]
@@ -633,15 +569,11 @@ def wait_for_install(self, repository, log=None, timeout=3600):
                 # Raise an exception and continue with the remaining repos.
                 msg = "Could not track repository for name '%s', owner '%s', revision '%s'. "
                 msg += "Please uninstall all non-terminal repositories and ensure revision '%s' is installable."
-                raise AssertionError(
-                    msg % (name, owner, changeset_revision, changeset_revision)
-                )
+                raise AssertionError(msg % (name, owner, changeset_revision, changeset_revision))
         start = dt.datetime.now()
         while (dt.datetime.now() - start) < dt.timedelta(seconds=timeout):
             try:
-                installed_repo = self.tool_shed_client.show_repository(
-                    installing_repo_id
-                )
+                installed_repo = self.tool_shed_client.show_repository(installing_repo_id)
                 status = installed_repo["status"]
                 if status == "Installed":
                     return True
@@ -650,10 +582,7 @@ def wait_for_install(self, repository, log=None, timeout=3600):
                 elif status in NON_TERMINAL_REPOSITORY_STATES:
                     time.sleep(10)
                 else:
-                    raise AssertionError(
-                        "Repository name '%s', owner '%s' in unknown status '%s'"
-                        % (name, owner, status)
-                    )
+                    raise AssertionError(f"Repository name '{name}', owner '{owner}' in unknown status '{status}'")
             except ConnectionError as e:
                 if log:
                     log.warning("Failed to get repositories list: %s", unicodify(e))
@@ -667,9 +596,7 @@ def log_repository_install_error(repository, start, msg, log):
     """
     end = dt.datetime.now()
     log.error(
-        "\t* Error installing a repository (after %s seconds)! Name: %s,"
-        "owner: %s, "
-        "revision: %s, error: %s",
+        "\t* Error installing a repository (after %s seconds)! Name: %s," "owner: %s, " "revision: %s, error: %s",
         str(end - start),
         repository.get("name", ""),
         repository.get("owner", ""),
@@ -685,14 +612,15 @@ def log_repository_install_success(repository, start, log):
     """
     end = dt.datetime.now()
     log.debug(
-        "\trepository %s installed successfully (in %s) at revision %s"
-        % (repository["name"], str(end - start), repository["changeset_revision"])
+        "\trepository {} installed successfully (in {}) at revision {}".format(
+            repository["name"], str(end - start), repository["changeset_revision"]
+        )
     )
 
 
 def log_repository_install_skip(repository, counter, total_num_repositories, log):
     log.debug(
-        "({0}/{1}) repository {2} already installed at revision {3}. Skipping.".format(
+        "({}/{}) repository {} already installed at revision {}. Skipping.".format(
             counter,
             total_num_repositories,
             repository["name"],
@@ -702,17 +630,19 @@ def log_repository_install_skip(repository, counter, total_num_repositories, log
 
 
 def log_repository_install_start(
-    repository: InstallRepoDict, counter, total_num_repositories, installation_start, log
+    repository: InstallRepoDict,
+    counter,
+    total_num_repositories,
+    installation_start,
+    log,
 ):
     log.debug(
-        '(%s/%s) Installing repository %s from %s to section "%s" at revision %s (TRT: %s)'
-        % (
+        '({}/{}) Installing repository {} from {} to section "{}" at revision {} (TRT: {})'.format(
             counter,
             total_num_repositories,
             repository["name"],
             repository["owner"],
-            repository.get("tool_panel_section_id")
-            or repository.get("tool_panel_section_label"),
+            repository.get("tool_panel_section_id") or repository.get("tool_panel_section_label"),
             repository.get("changeset_revision"),
             dt.datetime.now() - installation_start,
         )
@@ -745,9 +675,7 @@ def main(argv=None):
     disable_external_library_logging()
     args = parser().parse_args(argv)
     log = setup_global_logger(name=__name__, log_file=args.log_file)
-    gi = get_galaxy_connection(
-        args, file=args.tool_list_file, log=log, login_required=True
-    )
+    gi = get_galaxy_connection(args, file=args.tool_list_file, log=log, login_required=True)
     install_repository_manager = InstallRepositoryManager(gi)
 
     repos = args_to_repos(args)
@@ -761,13 +689,9 @@ def main(argv=None):
     kwargs = dict(
         default_install_tool_dependencies=tool_list.get("install_tool_dependencies")
         or getattr(args, "install_tool_dependencies", False),
-        default_install_repository_dependencies=tool_list.get(
-            "install_repository_dependencies"
-        )
+        default_install_repository_dependencies=tool_list.get("install_repository_dependencies")
         or getattr(args, "install_repository_dependencies", False),
-        default_install_resolver_dependencies=tool_list.get(
-            "install_resolver_dependencies"
-        )
+        default_install_resolver_dependencies=tool_list.get("install_resolver_dependencies")
         or getattr(args, "install_resolver_dependencies", False),
     )
 
@@ -775,9 +699,7 @@ def main(argv=None):
     # Or do testing if the action is `test`
     install_results = None
     if args.action == "update":
-        install_results = install_repository_manager.update_repositories(
-            repositories=repos, log=log, **kwargs
-        )
+        install_results = install_repository_manager.update_repositories(repositories=repos, log=log, **kwargs)
     elif args.action == "install":
         install_results = install_repository_manager.install_repositories(
             repos, log=log, force_latest_revision=args.force_latest_revision, **kwargs
@@ -795,9 +717,7 @@ def main(argv=None):
             client_test_config_path=args.client_test_config,
         )
     else:
-        raise NotImplementedError(
-            "This point in the code should not be reached. Please contact the developers."
-        )
+        raise NotImplementedError("This point in the code should not be reached. Please contact the developers.")
 
     # Run tests on the install results if required.
     if install_results and args.test or args.test_existing:
diff --git a/src/ephemeris/shed_tools_args.py b/src/ephemeris/shed_tools_args.py
index db51904a..18ec43cb 100644
--- a/src/ephemeris/shed_tools_args.py
+++ b/src/ephemeris/shed_tools_args.py
@@ -42,8 +42,7 @@ def parser():
     # SUBPARSERS
     install_command_parser = subparsers.add_parser(
         "install",
-        help="This installs tools in Galaxy from the Tool Shed."
-        "Use shed-tools install --help for more information",
+        help="This installs tools in Galaxy from the Tool Shed." "Use shed-tools install --help for more information",
         formatter_class=HideUnderscoresHelpFormatter,
         parents=[common_arguments],
     )
@@ -57,8 +56,7 @@ def parser():
 
     test_command_parser = subparsers.add_parser(
         "test",
-        help="This tests the supplied list of tools in Galaxy. "
-        "Use shed-tools test --help for more information",
+        help="This tests the supplied list of tools in Galaxy. " "Use shed-tools test --help for more information",
         formatter_class=HideUnderscoresHelpFormatter,
         parents=[common_arguments],
     )
@@ -91,13 +89,11 @@ def parser():
         )
         command_parser.add_argument(
             "--name",
-            help="The name of the tool to install (only applicable "
-            "if the tools file is not provided).",
+            help="The name of the tool to install (only applicable " "if the tools file is not provided).",
         )
         command_parser.add_argument(
             "--owner",
-            help="The owner of the tool to install (only applicable "
-            "if the tools file is not provided).",
+            help="The owner of the tool to install (only applicable " "if the tools file is not provided).",
         )
         command_parser.add_argument(
             "--revisions",
@@ -295,8 +291,7 @@ def parser():
         "--client-test-config",
         "--client_test_config",
         dest="client_test_config",
-        help="Annotate expectations about tools in client testing YAML "
-        "configuration file.",
+        help="Annotate expectations about tools in client testing YAML " "configuration file.",
     )
 
     return shed_parser
diff --git a/src/ephemeris/shed_tools_methods.py b/src/ephemeris/shed_tools_methods.py
index 0995afb2..b1429726 100644
--- a/src/ephemeris/shed_tools_methods.py
+++ b/src/ephemeris/shed_tools_methods.py
@@ -31,9 +31,7 @@ def complete_repo_information(
     default_install_resolver_dependencies: bool,
     force_latest_revision,
 ) -> "InstallRepoDict":
-    tool["tool_shed_url"] = format_tool_shed_url(
-        tool.get("tool_shed_url") or default_toolshed_url
-    )
+    tool["tool_shed_url"] = format_tool_shed_url(tool.get("tool_shed_url") or default_toolshed_url)
     tool = get_changeset_revisions(tool, force_latest_revision=force_latest_revision)
     repo: "InstallRepoDict" = dict(
         name=tool["name"],
@@ -44,8 +42,7 @@ def complete_repo_information(
         or default_install_repository_dependencies,
         install_resolver_dependencies=tool.get("install_resolver_dependencies")
         or default_install_resolver_dependencies,
-        install_tool_dependencies=tool.get("install_tool_dependencies")
-        or default_install_tool_dependencies,
+        install_tool_dependencies=tool.get("install_tool_dependencies") or default_install_tool_dependencies,
     )
     # We need those values. Throw a KeyError when not present
     tool_panel_section_label = tool.get("tool_panel_section_label")
@@ -66,9 +63,7 @@ def format_tool_shed_url(tool_shed_url: str) -> str:
     return formatted_tool_shed_url
 
 
-def get_changeset_revisions(
-    repository: "InstallRepoDict", force_latest_revision: bool = False
-):
+def get_changeset_revisions(repository: "InstallRepoDict", force_latest_revision: bool = False):
     """
     Select the correct changeset revision for a repository,
     and make sure the repository exists
@@ -83,9 +78,7 @@ def get_changeset_revisions(
             repository["name"], repository["owner"]
         )
         if not installable_revisions:  #
-            raise LookupError(
-                "Repo does not exist in tool shed: {0}".format(repository)
-            )
+            raise LookupError(f"Repo does not exist in tool shed: {repository}")
         repository["changeset_revision"] = installable_revisions[-1]
 
     return repository
diff --git a/src/ephemeris/sleep.py b/src/ephemeris/sleep.py
index 0b78b9a4..aa3912b4 100755
--- a/src/ephemeris/sleep.py
+++ b/src/ephemeris/sleep.py
@@ -22,14 +22,10 @@
 DEFAULT_SLEEP_WAIT = 1
 MESSAGE_KEY_NOT_YET_VALID = "[%02d] Provided key not (yet) valid... %s\n"
 MESSAGE_INVALID_JSON = "[%02d] No valid json returned... %s\n"
-MESSAGE_FETCHING_USER = (
-    "[%02d] Connection error fetching user details, exiting with error code. %s\n"
-)
+MESSAGE_FETCHING_USER = "[%02d] Connection error fetching user details, exiting with error code. %s\n"
 MESSAGE_KEY_NOT_YET_ADMIN = "[%02d] Provided key not (yet) admin... %s\n"
 MESSAGE_GALAXY_NOT_YET_UP = "[%02d] Galaxy not up yet... %s\n"
-MESSAGE_TIMEOUT = (
-    "Failed to contact Galaxy within timeout (%s), exiting with error code.\n"
-)
+MESSAGE_TIMEOUT = "Failed to contact Galaxy within timeout (%s), exiting with error code.\n"
 
 
 def _parser():
@@ -48,13 +44,17 @@ def _parser():
         help="Galaxy startup timeout in seconds. The default value of 0 waits forever",
     )
     parser.add_argument(
-        "-a", "--api-key", "--api_key", dest="api_key", help="Sleep until key becomes available."
+        "-a",
+        "--api-key",
+        "--api_key",
+        dest="api_key",
+        help="Sleep until key becomes available.",
     )
     parser.add_argument("--ensure-admin", "--ensure_admin", default=False, action="store_true")
     return parser
 
 
-class SleepCondition(object):
+class SleepCondition:
     def __init__(self):
         self.sleep = True
 
@@ -72,18 +72,15 @@ def galaxy_wait(
 ):
     """Pass user_key to ensure it works before returning."""
     if verbose:
-        sys.stdout.write(
-            "calling galaxy_wait with timeout=%s ensure_admin=%s\n\n\n"
-            % (timeout, ensure_admin)
-        )
+        sys.stdout.write(f"calling galaxy_wait with timeout={timeout} ensure_admin={ensure_admin}\n\n\n")
         sys.stdout.flush()
 
     version_url = galaxy_url + "/api/version"
     if api_key:
         # adding the key to the URL will ensure Galaxy returns invalid responses until
         # the key is available.
-        version_url = "%s?key=%s" % (version_url, api_key)
-        current_user_url = "%s/api/users/current?key=%s" % (galaxy_url, api_key)
+        version_url = f"{version_url}?key={api_key}"
+        current_user_url = f"{galaxy_url}/api/users/current?key={api_key}"
     else:
         assert not ensure_admin
 
@@ -99,24 +96,18 @@ def galaxy_wait(
                 result = requests.get(version_url)
                 if result.status_code == 403:
                     if verbose:
-                        sys.stdout.write(
-                            MESSAGE_KEY_NOT_YET_VALID % (count, result.__str__())
-                        )
+                        sys.stdout.write(MESSAGE_KEY_NOT_YET_VALID % (count, result.__str__()))
                         sys.stdout.flush()
                 else:
                     try:
                         result = result.json()
                         if verbose:
-                            sys.stdout.write(
-                                "Galaxy Version: %s\n" % result["version_major"]
-                            )
+                            sys.stdout.write("Galaxy Version: %s\n" % result["version_major"])
                             sys.stdout.flush()
                         version_obtained = True
                     except ValueError:
                         if verbose:
-                            sys.stdout.write(
-                                MESSAGE_INVALID_JSON % (count, result.__str__())
-                            )
+                            sys.stdout.write(MESSAGE_INVALID_JSON % (count, result.__str__()))
                             sys.stdout.flush()
 
             if version_obtained:
@@ -124,9 +115,7 @@ def galaxy_wait(
                     result = requests.get(current_user_url)
                     if result.status_code != 200:
                         if verbose:
-                            sys.stdout.write(
-                                MESSAGE_FETCHING_USER % (count, result.__str__())
-                            )
+                            sys.stdout.write(MESSAGE_FETCHING_USER % (count, result.__str__()))
                             sys.stdout.flush()
                             return False
 
@@ -139,17 +128,13 @@ def galaxy_wait(
                         break
                     else:
                         if verbose:
-                            sys.stdout.write(
-                                MESSAGE_KEY_NOT_YET_ADMIN % (count, result.__str__())
-                            )
+                            sys.stdout.write(MESSAGE_KEY_NOT_YET_ADMIN % (count, result.__str__()))
                             sys.stdout.flush()
                 else:
                     break
         except requests.exceptions.ConnectionError as e:
             if verbose:
-                sys.stdout.write(
-                    MESSAGE_GALAXY_NOT_YET_UP % (count, unicodify(e)[:100])
-                )
+                sys.stdout.write(MESSAGE_GALAXY_NOT_YET_UP % (count, unicodify(e)[:100]))
                 sys.stdout.flush()
         count += 1
 
diff --git a/src/ephemeris/workflow_install.py b/src/ephemeris/workflow_install.py
index ab573250..2e670f76 100644
--- a/src/ephemeris/workflow_install.py
+++ b/src/ephemeris/workflow_install.py
@@ -16,11 +16,9 @@ def import_workflow(gi, path, publish_wf=False):
     Given a connection to a Galaxy Instance (gi) and a path to a Galaxy workflow file,
     this function will import the worklfow into Galaxy.
     """
-    with open(path, "r") as wf_file:
+    with open(path) as wf_file:
         import_uuid = json.load(wf_file).get("uuid")
-    existing_uuids = [
-        d.get("latest_workflow_uuid") for d in gi.workflows.get_workflows()
-    ]
+    existing_uuids = [d.get("latest_workflow_uuid") for d in gi.workflows.get_workflows()]
     if import_uuid not in existing_uuids:
         gi.workflows.import_workflow_from_local_path(path, publish=publish_wf)
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 3f2a4c30..0ff220f5 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -5,9 +5,7 @@
 from galaxy.tool_util.verify.interactor import GalaxyInteractorApi
 from galaxy_test.driver.driver_util import GalaxyTestDriver
 
-GalaxyContainer = namedtuple(
-    "GalaxyContainer", ["url", "gi", "password", "username", "api_key"]
-)
+GalaxyContainer = namedtuple("GalaxyContainer", ["url", "gi", "password", "username", "api_key"])
 
 
 @pytest.fixture(scope="class")
@@ -42,9 +40,7 @@ def start_container(tmpdir_factory):
     port = server_wrapper.port
     prefix = server_wrapper.prefix or ""
     url = f"http://{host}:{port}{prefix.rstrip('/')}/"
-    interactor = GalaxyInteractorApi(
-        galaxy_url=url, master_api_key="123456789", test_user="test@bx.psu.edu"
-    )
+    interactor = GalaxyInteractorApi(galaxy_url=url, master_api_key="123456789", test_user="test@bx.psu.edu")
     gi = GalaxyInstance(url, key=interactor.api_key, password="testpass")
     try:
         yield GalaxyContainer(
diff --git a/tests/test_run_data_managers.py b/tests/test_run_data_managers.py
index 4e9ee824..d12f5272 100644
--- a/tests/test_run_data_managers.py
+++ b/tests/test_run_data_managers.py
@@ -14,7 +14,7 @@
 AUTH_BY = "key"
 
 
-class TestRunDataManagers(object):
+class TestRunDataManagers:
     """This class tests run-data-managers"""
 
     def test_install_data_managers(self, start_container):
@@ -43,9 +43,7 @@ def test_run_data_managers(self, start_container):
             )
         else:
             argv.extend(["-a", container.api_key])
-        argv.extend(
-            ["-g", container.url, "--config", "tests/run_data_managers.yaml.test"]
-        )
+        argv.extend(["-g", container.url, "--config", "tests/run_data_managers.yaml.test"])
         sys.argv = argv
         run_data_managers.main()
 
diff --git a/tests/test_setup_data_libraries_cli.py b/tests/test_setup_data_libraries_cli.py
index cc0ab25a..12f19b5e 100644
--- a/tests/test_setup_data_libraries_cli.py
+++ b/tests/test_setup_data_libraries_cli.py
@@ -5,9 +5,7 @@
 from ephemeris.setup_data_libraries import main as setup_data_libraries_cli
 
 LIBRARY_DATA_EXAMPLE = pathlib.Path(__file__).parent / "library_data_example.yaml"
-LIBRARY_DATA_LEGACY_EXAMPLE = (
-    pathlib.Path(__file__).parent / "library_data_example_legacy.yaml"
-)
+LIBRARY_DATA_LEGACY_EXAMPLE = pathlib.Path(__file__).parent / "library_data_example_legacy.yaml"
 
 
 def test_setup_data_libraries_with_username_and_password(
diff --git a/tests/test_shed_tools.py b/tests/test_shed_tools.py
index 90d80042..459f84c3 100644
--- a/tests/test_shed_tools.py
+++ b/tests/test_shed_tools.py
@@ -16,7 +16,7 @@
 # The start_container fixture has the "class" scope.
 
 
-class TestMiscellaneous(object):
+class TestMiscellaneous:
     """This class is for miscellaneous tests that can use the same galaxy container"""
 
     def test_invalid_keys_in_repo_list(self, caplog, start_container):
@@ -34,10 +34,7 @@ def test_invalid_keys_in_repo_list(self, caplog, start_container):
             ],
             log=logging.getLogger(),
         )
-        assert (
-            "'sesame_ouvre_toi' not a valid key. Will be skipped during parsing"
-            in caplog.text
-        )
+        assert "'sesame_ouvre_toi' not a valid key. Will be skipped during parsing" in caplog.text
 
     @pytest.mark.parametrize("parallel_tests", [1, 2])
     def test_tool_tests(self, caplog, start_container, parallel_tests):
diff --git a/tests/test_shed_tools_cli.py b/tests/test_shed_tools_cli.py
index 64da4ad2..88780bff 100644
--- a/tests/test_shed_tools_cli.py
+++ b/tests/test_shed_tools_cli.py
@@ -31,9 +31,7 @@ def install_old_cdhit(start_container: GalaxyContainer):
 
 def get_tool_list(start_container: GalaxyContainer, *extra_args):
     with tempfile.NamedTemporaryFile(mode="r") as tool_list_file:
-        get_tool_list_cli(
-            ["-g", start_container.url, "-o", tool_list_file.name, *extra_args]
-        )
+        get_tool_list_cli(["-g", start_container.url, "-o", tool_list_file.name, *extra_args])
         return tool_list_file.read()
 
 
diff --git a/tests/test_shed_tools_methods.py b/tests/test_shed_tools_methods.py
index 76cc018f..5ec8e9a1 100644
--- a/tests/test_shed_tools_methods.py
+++ b/tests/test_shed_tools_methods.py
@@ -11,9 +11,7 @@ def test_flatten_repo_info():
             tool_panel_section_label="NGS: Alignment",
             revisions=["1", "2"],
         ),
-        dict(
-            name="bowtie2", owner="devteam", tool_panel_section_label="NGS: Alignment"
-        ),
+        dict(name="bowtie2", owner="devteam", tool_panel_section_label="NGS: Alignment"),
     ]
     flattened_repos = flatten_repo_info(test_repositories)
     assert flattened_repos == [
@@ -29,7 +27,5 @@ def test_flatten_repo_info():
             tool_panel_section_label="NGS: Alignment",
             changeset_revision="2",
         ),
-        dict(
-            name="bowtie2", owner="devteam", tool_panel_section_label="NGS: Alignment"
-        ),
+        dict(name="bowtie2", owner="devteam", tool_panel_section_label="NGS: Alignment"),
     ]
diff --git a/tox.ini b/tox.ini
index 6a8c85bd..9afd6851 100644
--- a/tox.ini
+++ b/tox.ini
@@ -5,9 +5,16 @@ source_dir = src/ephemeris
 test_dir = tests
 
 [testenv:py38-lint]
-commands = flake8 {[tox]source_dir} {[tox]test_dir}
+commands =
+  black --check {[tox]source_dir} {[tox]test_dir}
+  isort --check-only {[tox]source_dir} {[tox]test_dir}
+  ruff {[tox]source_dir} {[tox]test_dir}
+  flake8 {[tox]source_dir} {[tox]test_dir}
 skip_install = True
 deps =
+    black
+    isort
+    ruff
     flake8
     flake8-import-order
 
@@ -23,3 +30,11 @@ commands =
     # This is needed for codacy to understand which files have coverage testing
     # Unfortunately this has to run in the tox env to have access to envsitepackagesdir
     sed -i 's|{envsitepackagesdir}|src|' coverage.xml
+
+[testenv:mypy]
+commands =
+  mypy -p ephemeris
+deps =
+  mypy
+  types-PyYAML
+  types-requests