Drop support for retired Python 3.5

Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py

scripts/api/common.py

@@ -1,14 +1,15 @@
 """
 Common methods used by the API sample scripts.
 """
-from __future__ import print_function
 
 import json
 import logging
 import sys
-
-from six.moves.urllib.error import HTTPError
-from six.moves.urllib.request import Request, urlopen
+from urllib.error import HTTPError
+from urllib.request import (
+    Request,
+    urlopen,
+)
 
 log = logging.getLogger(__name__)
 
@@ -92,7 +93,7 @@ def display(api_key, url, return_formatted=True):
             if 'name' in i:
                 print('  name: %s' % i.pop('name'))
             for k, v in i.items():
-                print('  %s: %s' % (k, v))
+                print(f'  {k}: {v}')
         print('')
         print('%d element(s) in collection' % len(r))
     elif type(r) == dict:
@@ -100,7 +101,7 @@ def display(api_key, url, return_formatted=True):
         print('Member Information')
         print('------------------')
         for k, v in r.items():
-            print('%s: %s' % (k, v))
+            print(f'{k}: {v}')
     elif type(r) == str:
         print(r)
     else:
@@ -137,7 +138,7 @@ def submit(api_key, url, data, return_formatted=True):
                 if 'name' in i:
                     print('  name: %s' % i.pop('name'))
                 for k, v in i.items():
-                    print('  %s: %s' % (k, v))
+                    print(f'  {k}: {v}')
             else:
                 print(i)
     else:

scripts/api/copy_hda_to_library_folder.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import sys
 
@@ -9,7 +8,7 @@ usage = "USAGE: copy_hda_to_library_folder.py <base url> <api key> <hda id> <lib
 
 
 def copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, message=''):
-    url = 'http://%s/api/libraries/%s/contents' % (base_url, library_id)
+    url = f'http://{base_url}/api/libraries/{library_id}/contents'
     payload = {
         'folder_id'     : folder_id,
         'create_type'   : 'file',

scripts/api/data_manager_example_execute.py

@@ -3,12 +3,10 @@
 # Very simple example of using the API to run Data Managers
 # Script makes the naive assumption that dbkey==sequence id, which in many cases is not true nor desired
 # *** This script is not recommended for use as-is on a production server ***
-from __future__ import print_function
 
 import optparse
 import time
-
-from six.moves.urllib.parse import urljoin
+from urllib.parse import urljoin
 
 from common import get, post  # noqa: I100,I202
 
@@ -35,7 +33,7 @@ def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_
             for i, dataset_dict in enumerate(outputs):
                 if dataset_is_terminal(dataset_dict['id'], api_key=api_key, galaxy_url=galaxy_url):
                     finished_datasets.append(i)
-            for i in reversed(finished_datasets):
+            for _ in reversed(finished_datasets):
                 outputs.pop(0)
             if wait and outputs:
                 time.sleep(sleep_time)

scripts/api/display.py

@@ -1,10 +1,8 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys
-
-from six.moves.urllib.error import URLError
+from urllib.error import URLError
 
 from common import display  # noqa: I100,I202
 

scripts/api/example_watch_folder.py

@@ -10,7 +10,6 @@ python example_watch_folder.py <api_key> <api_url> /tmp/g_inbox/ /tmp/g_inbox/do
 
 NOTE:  The upload method used requires the data library filesystem upload allow_library_path_paste
 """
-from __future__ import print_function
 
 import os
 import shutil
@@ -65,7 +64,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
                         # Successful upload of dataset, we have the ldda now.  Run the workflow.
                         wf_data = {}
                         wf_data['workflow_id'] = workflow['id']
-                        wf_data['history'] = "%s - %s" % (fname, workflow['name'])
+                        wf_data['history'] = "{} - {}".format(fname, workflow['name'])
                         wf_data['ds_map'] = {}
                         for step_id, ds_in in workflow['inputs'].items():
                             wf_data['ds_map'][step_id] = {'src': 'ld', 'id': ds['id']}

scripts/api/fetch_to_library.py

@@ -12,7 +12,7 @@ def main():
     parser.add_argument('target', metavar='FILE', type=str,
                         help='file describing data library to fetch')
     args = parser.parse_args()
-    with open(args.target, "r") as f:
+    with open(args.target) as f:
         target = yaml.safe_load(f)
 
     histories_url = args.url + "/api/histories"

scripts/api/filter_failed_datasets_from_collection.py

@@ -6,7 +6,6 @@ datasets "(not ok)" and the successfully finished datasets "(ok)".
 Sample call:
 python filter_failed_datasets_from_collection.py <GalaxyUrl> <ApiKey> MySpecialHistory 1234
 """
-from __future__ import print_function
 
 import sys
 

scripts/api/history_create_history.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys

scripts/api/history_delete_history.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys

scripts/api/import_library_dataset_to_history.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys

scripts/api/import_workflows_from_installed_tool_shed_repository.py

@@ -5,7 +5,6 @@ Import one or more exported workflows contained within a specified tool shed rep
 Here is a working example of how to use this script to repair a repository installed into Galaxy.
 python ./import_workflows_from_installed_tool_shed_repository.py -a 22be3b -l http://localhost:8763/ -n workflow_with_tools -o test -r ef45bb64237e -u http://localhost:9009/
 """
-from __future__ import print_function
 
 import argparse
 
@@ -38,7 +37,7 @@ def main(options):
             break
     if tool_shed_repository_id:
         # Get the list of exported workflows contained in the installed repository.
-        url = '%s%s' % (base_galaxy_url, '/api/tool_shed_repositories/%s/exported_workflows' % str(tool_shed_repository_id))
+        url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/exported_workflows' % str(tool_shed_repository_id))
         exported_workflows = display(api_key, url, return_formatted=False)
         if exported_workflows:
             # Import all of the workflows in the list of exported workflows.
@@ -47,7 +46,7 @@ def main(options):
             # data[ 'index' ] = 0
             # and change the url to be ~/import_workflow (singular).  For example,
             # url = '%s%s' % ( base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflow' % str( tool_shed_repository_id ) )
-            url = '%s%s' % (base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflows' % str(tool_shed_repository_id))
+            url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflows' % str(tool_shed_repository_id))
             submit(options.api, url, data)
     else:
         print("Invalid tool_shed / name / owner / changeset_revision.")

scripts/api/install_tool_shed_repositories.py

@@ -35,7 +35,7 @@ def main(options):
         revision_data['tool_shed_url'] = options.tool_shed_url.rstrip('/')
         revision_data['name'] = options.name
         revision_data['owner'] = options.owner
-        revision_url = '%s%s' % (options.local_url.rstrip('/'), '/api/tool_shed_repositories/get_latest_installable_revision')
+        revision_url = '{}{}'.format(options.local_url.rstrip('/'), '/api/tool_shed_repositories/get_latest_installable_revision')
         latest_installable_revision = submit(options.api,
                                              revision_url,
                                              revision_data,
@@ -49,7 +49,7 @@ def main(options):
         data['install_repository_dependencies'] = options.install_repository_dependencies
     if options.install_tool_dependencies:
         data['install_tool_dependencies'] = options.install_tool_dependencies
-    submit(options.api, '%s%s' % (options.local_url.rstrip('/'), '/api/tool_shed_repositories/new/install_repository_revision'), data)
+    submit(options.api, '{}{}'.format(options.local_url.rstrip('/'), '/api/tool_shed_repositories/new/install_repository_revision'), data)
 
 
 if __name__ == '__main__':

scripts/api/library_create_folder.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys

scripts/api/library_create_library.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys

scripts/api/library_upload_dir.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import argparse
 import os
@@ -8,7 +7,7 @@ import sys
 from bioblend import galaxy
 
 
-class Uploader(object):
+class Uploader:
 
     def __init__(self, url, api, library_id, folder_id, should_link,
                  non_local):
@@ -132,7 +131,7 @@ class Uploader(object):
             # So that we can check if it really needs to be uploaded.
             already_uploaded = memo_key in self.memo_path.keys()
             fid = self.memoized_path(basepath, base_folder=self.folder_id)
-            print('[%s/%s] %s/%s uploaded=%s' % (idx + 1, len(all_files), fid, fname, already_uploaded))
+            print('[{}/{}] {}/{} uploaded={}'.format(idx + 1, len(all_files), fid, fname, already_uploaded))
 
             if not already_uploaded:
                 if self.non_local:

scripts/api/library_upload_from_import_dir.py

@@ -3,7 +3,6 @@
 Example usage:
 ./library_upload_from_import_dir.py <key> http://127.0.0.1:8080/api/libraries/dda47097d9189f15/contents Fdda47097d9189f15 auto /Users/EnisAfgan/projects/pprojects/galaxy/lib_upload_dir ?
 """
-from __future__ import print_function
 
 import os
 import sys

scripts/api/load_data_with_metadata.py

@@ -9,7 +9,6 @@ python load_data_with_metadata.py <api_key> <api_url> /data/folder "API Imports"
 
 NOTE:  The upload method used requires the data library filesystem upload allow_library_path_paste
 """
-from __future__ import print_function
 
 import argparse
 import json

scripts/api/repair_tool_shed_repository.py

@@ -5,7 +5,6 @@ Repair a specified repository revision previously installed into Galaxy.
 Here is a working example of how to use this script to repair a repository installed into Galaxy.
 ./repair_tool_shed_repository.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb
 """
-from __future__ import print_function
 
 import argparse
 
@@ -26,7 +25,7 @@ def main(options):
     base_galaxy_url = options.local_url.rstrip('/')
     base_tool_shed_url = options.tool_shed_url.rstrip('/')
     cleaned_tool_shed_url = clean_url(base_tool_shed_url)
-    installed_tool_shed_repositories_url = '%s/api/%s' % (base_galaxy_url, 'tool_shed_repositories')
+    installed_tool_shed_repositories_url = '{}/api/{}'.format(base_galaxy_url, 'tool_shed_repositories')
     data = {}
     data['tool_shed_url'] = cleaned_tool_shed_url
     data['name'] = options.name
@@ -43,7 +42,7 @@ def main(options):
             tool_shed_repository_id = installed_tool_shed_repository['id']
             break
     if tool_shed_repository_id:
-        url = '%s%s' % (base_galaxy_url, '/api/tool_shed_repositories/%s/repair_repository_revision' % str(tool_shed_repository_id))
+        url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/repair_repository_revision' % str(tool_shed_repository_id))
         submit(options.api, url, data)
     else:
         print("Invalid tool_shed / name / owner / changeset_revision.")

scripts/api/search.py

@@ -1,7 +1,6 @@
 """
 Sample script for Galaxy Search API
 """
-from __future__ import print_function
 
 import json
 import sys
@@ -9,7 +8,7 @@ import sys
 import requests
 
 
-class RemoteGalaxy(object):
+class RemoteGalaxy:
 
     def __init__(self, url, api_key):
         self.url = url

scripts/api/upload_to_history.py

@@ -2,7 +2,6 @@
 """
 Upload a file to the desired history.
 """
-from __future__ import print_function
 
 import json
 import os

scripts/api/workflow_delete.py

@@ -8,7 +8,6 @@ API example script for deleting workflows
 Example calls:
 python workflow_delete.py <api_key> <galaxy_url>/api/workflows/<workflow id> True
 """
-from __future__ import print_function
 
 import os
 import sys

scripts/api/workflow_execute.py

@@ -5,7 +5,6 @@ Example calls:
 python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'Test API History' '38=ldda=0qr350234d2d192f'
 python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f'
 """
-from __future__ import print_function
 
 import os
 import sys

scripts/api/workflow_execute_parameters.py

@@ -9,7 +9,6 @@ Example calls:
 python workflow_execute.py <api_key> <galaxy_url>/api/workflows <workflow_id> 'hist_id=<history_id>' '38=hda=<file_id>' 'param=tool=name=value'
 python workflow_execute_parameters.py <api_key> http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000'
 """
-from __future__ import print_function
 
 import os
 import sys

scripts/api/workflow_import.py

@@ -4,7 +4,6 @@ Import workflows from the command line.
 Example calls:
 python workflow_import.py <api_key> <galaxy_url> '/path/to/workflow/file [--add_to_menu]'
 """
-from __future__ import print_function
 
 import os
 import sys

scripts/api/workflow_import_from_file_rpark.py

@@ -3,7 +3,6 @@
 python rpark_import_workflow_from_file.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows/import 'spp_submodule.ga'
 python rpark_import_workflow_from_file.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows/import 'spp_submodule.ga'
 """
-from __future__ import print_function
 
 import json
 import os

scripts/apply_tags.py

@@ -6,7 +6,7 @@ import time
 from bioblend.galaxy import GalaxyInstance
 
 
-class ApplyTagsHistory(object):
+class ApplyTagsHistory:
 
     @classmethod
     def __init__(self, galaxy_url, galaxy_api_key, history_id=None):

scripts/auth/pam_auth_helper.py

@@ -16,7 +16,7 @@ except ImportError:
 
 
 def handle_timeout(signum, stack):
-    raise IOError("Timed out reading input")
+    raise OSError("Timed out reading input")
 
 
 # set timeout so we don't block on reading stdin
@@ -32,10 +32,10 @@ signal.alarm(0)
 p_auth = pam.pam()
 authenticated = p_auth.authenticate(pam_username, pam_password, service=pam_service)
 if authenticated:
-    log.debug('PAM auth helper: authentication successful for {}'.format(pam_username))
+    log.debug(f'PAM auth helper: authentication successful for {pam_username}')
     sys.stdout.write('True\n')
     sys.exit(0)
 else:
-    log.debug('PAM auth helper: authentication failed for {}'.format(pam_username))
+    log.debug(f'PAM auth helper: authentication failed for {pam_username}')
     sys.stdout.write('False\n')
     sys.exit(1)

scripts/bootstrap_history.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 # Little script to make HISTORY.rst more easy to format properly, lots TODO
 # pull message down and embed, use arg parse, handle multiple, etc...
-from __future__ import print_function
 
 import calendar
 import datetime
@@ -13,6 +12,7 @@ import string
 import sys
 import textwrap
 from collections import OrderedDict
+from urllib.parse import urljoin
 
 try:
     import requests
@@ -22,8 +22,6 @@ try:
     from github import Github
 except ImportError:
     Github = None
-from six import string_types
-from six.moves.urllib.parse import urljoin
 
 log = logging.getLogger(__name__)
 
@@ -31,8 +29,8 @@ PROJECT_DIRECTORY = os.path.join(os.path.dirname(__file__), os.pardir)
 GALAXY_VERSION_FILE = os.path.join(PROJECT_DIRECTORY, "lib", "galaxy", "version.py")
 PROJECT_OWNER = "galaxyproject"
 PROJECT_NAME = "galaxy"
-PROJECT_URL = "https://github.com/%s/%s" % (PROJECT_OWNER, PROJECT_NAME)
-PROJECT_API = "https://api.github.com/repos/%s/%s/" % (PROJECT_OWNER, PROJECT_NAME)
+PROJECT_URL = f"https://github.com/{PROJECT_OWNER}/{PROJECT_NAME}"
+PROJECT_API = f"https://api.github.com/repos/{PROJECT_OWNER}/{PROJECT_NAME}/"
 RELEASES_PATH = os.path.join(PROJECT_DIRECTORY, "doc", "source", "releases")
 RELEASE_DELTA_MONTHS = 4  # Number of months between releases.
 
@@ -332,7 +330,7 @@ def release_issue(argv):
     )
     release_issue_contents = RELEASE_ISSUE_TEMPLATE.safe_substitute(**release_issue_template_params)
     github = _github_client()
-    repo = github.get_repo("%s/%s" % (PROJECT_OWNER, PROJECT_NAME))
+    repo = github.get_repo(f"{PROJECT_OWNER}/{PROJECT_NAME}")
     repo.create_issue(
         title="Publication of Galaxy Release v %s" % release_name,
         body=release_issue_contents,
@@ -430,15 +428,15 @@ def check_blocking_issues(argv):
 
 
 def _pr_to_str(pr):
-    if isinstance(pr, string_types):
+    if isinstance(pr, str):
         return pr
-    return "PR #%s (%s) %s" % (pr.number, pr.title, pr.html_url)
+    return f"PR #{pr.number} ({pr.title}) {pr.html_url}"
 
 
 def _issue_to_str(pr):
-    if isinstance(pr, string_types):
+    if isinstance(pr, str):
         return pr
-    return "Issue #%s (%s) %s" % (pr.number, pr.title, pr.html_url)
+    return f"Issue #{pr.number} ({pr.title}) {pr.html_url}"
 
 
 def _next_version_params(release_name):
@@ -469,13 +467,10 @@ def _release_dates(version):
     return freeze_date, release_date
 
 
-def _get_prs(release_name, state="closed", pr_cache=[]):
+def _get_prs(release_name, state="closed"):
     github = _github_client()
-    repo = github.get_repo("%s/%s" % (PROJECT_OWNER, PROJECT_NAME))
-    add_to_cache = not pr_cache
-    pull_requests = pr_cache or repo.get_pulls(
-        state=state,
-    )
+    repo = github.get_repo(f"{PROJECT_OWNER}/{PROJECT_NAME}")
+    pull_requests = repo.get_pulls(state=state)
     reached_old_prs = False
 
     for pr in pull_requests:
@@ -490,8 +485,6 @@ def _get_prs(release_name, state="closed", pr_cache=[]):
         proper_state = state != "closed" or merged_at
         if not proper_state or not milestone or milestone.title != release_name:
             continue
-        if add_to_cache:
-            pr_cache.append(pr)
         yield pr
 
 
@@ -545,7 +538,7 @@ def main(argv):
     def extend_target(target, line, source=history):
         from_str = ".. %s\n" % target
         if target not in source:
-            raise Exception("Failed to find target [%s] in source [%s]" % (target, source))
+            raise Exception(f"Failed to find target [{target}] in source [{source}]")
         return source.replace(from_str, from_str + line + "\n")
 
     ident = argv[1]
@@ -590,10 +583,10 @@ def main(argv):
         text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL)
         prs_content = extend_target("github_links", text, prs_content)
         if owner:
-            to_doc += "\n(thanks to `@%s <https://github.com/%s>`__)." % (
+            to_doc += "\n(thanks to `@{} <https://github.com/{}>`__).".format(
                 owner, owner,
             )
-        to_doc += "\n`Pull Request {0}`_".format(pull_request)
+        to_doc += f"\n`Pull Request {pull_request}`_"
         labels = None
         if req and 'labels' in req:
             labels = req['labels']
@@ -602,12 +595,12 @@ def main(argv):
         issue = ident[len("issue"):]
         text = ".. _Issue {0}: {1}/issues/{0}".format(issue, PROJECT_URL)
         prs_content = extend_target("github_links", text, prs_content)
-        to_doc += "`Issue {0}`_".format(issue)
+        to_doc += f"`Issue {issue}`_"
     else:
         short_rev = ident[:7]
         text = ".. _{0}: {1}/commit/{0}".format(short_rev, PROJECT_URL)
         prs_content = extend_target("github_links", text, prs_content)
-        to_doc += "{0}_".format(short_rev)
+        to_doc += f"{short_rev}_"
 
     to_doc = wrap(to_doc)
     if text_target is not None:
@@ -626,7 +619,7 @@ def main(argv):
 
 
 def _read_file(path):
-    with open(path, "r") as f:
+    with open(path) as f:
         return f.read()
 
 
@@ -637,7 +630,7 @@ def _write_file(path, contents):
 
 def _text_target(pull_request, labels=None):
     pr_number = None
-    if isinstance(pull_request, string_types):
+    if isinstance(pull_request, str):
         pr_number = pull_request
     else:
         pr_number = pull_request.number
@@ -738,7 +731,7 @@ def _releases():
 def _github_client():
     try:
         github_json_path = os.path.expanduser("~/.github.json")
-        with open(github_json_path, "r") as fh:
+        with open(github_json_path) as fh:
             github_json_dict = json.load(fh)
         github = Github(**github_json_dict)
     except Exception:
@@ -764,7 +757,7 @@ def process_sentence(message):
     # Strip tags like [15.07].
     message = re.sub(r"^\s*\[.*\]\s*", r"", message)
     # Link issues and pull requests...
-    issue_url = "https://github.com/%s/%s/issues" % (PROJECT_OWNER, PROJECT_NAME)
+    issue_url = f"https://github.com/{PROJECT_OWNER}/{PROJECT_NAME}/issues"
     message = re.sub(r'#(\d+)', r'`#\1 <%s/\1>`__' % issue_url, message)
     return message
 

scripts/build_toolbox.py

@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import os
 from xml.etree import ElementTree as ET
 
@@ -36,7 +34,7 @@ def getfilenamelist(startdir):
     return filenamelist
 
 
-class ToolBox(object):
+class ToolBox:
     def __init__(self):
         from collections import defaultdict
         self.tools = defaultdict(list)

scripts/check_python.py

@@ -2,20 +2,19 @@
 If the current installed Python version is not supported, prints an error
 message to stderr and returns 1
 """
-from __future__ import print_function
 
 import sys
 
 
 def check_python():
-    if sys.version_info[:2] >= (3, 5):
+    if sys.version_info[:2] >= (3, 6):
         # supported
         return
     else:
         version_string = '.'.join(str(_) for _ in sys.version_info[:3])
         msg = """\
 ERROR: Your Python version is: %s
-Galaxy is currently supported on Python >=3.5 .
+Galaxy is currently supported on Python >=3.6 .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -36,7 +36,6 @@ Email Template Variables:
 
 Author: Lance Parsons (lparsons@princeton.edu)
 """
-from __future__ import print_function
 
 import argparse
 import logging
@@ -134,7 +133,7 @@ def main():
         if os.path.exists(default_template):
             template_file = default_template
         elif os.path.exists(sample_template_file):
-            print("Copying %s to %s" % (sample_template_file, default_template))
+            print(f"Copying {sample_template_file} to {default_template}")
             shutil.copyfile(sample_template_file, default_template)
             template_file = default_template
         else:

scripts/cleanup_datasets/cleanup_datasets.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import argparse
 import logging
@@ -515,7 +514,7 @@ def _purge_folder(folder, app, remove_from_disk, info_only=False):
         app.sa_session.flush()
 
 
-class CleanupDatasetsApplication(object):
+class CleanupDatasetsApplication:
     """Encapsulates the state of a Universe application"""
     def __init__(self, config):
         self.object_store = build_object_store_from_config(config)

scripts/cleanup_datasets/pgcleanup.py

@@ -4,7 +4,6 @@ pgcleanup.py - A script for cleaning up datasets in Galaxy efficiently, by
     bypassing the Galaxy model and operating directly on the database.
     PostgreSQL 9.1 or greater is required.
 """
-from __future__ import print_function
 
 import argparse
 import datetime
@@ -54,7 +53,7 @@ class LevelFormatter(logging.Formatter):
         return logging.Formatter.format(self, record)
 
 
-class Action(object):
+class Action:
     """Base class for all actions.
 
     When writing new actions, the following things happen automatically:
@@ -204,11 +203,11 @@ class Action(object):
 
     def _log_results(self, results, primary_key):
         for primary in sorted(results.keys()):
-            self.log.info('%s: %s' % (primary_key, primary))
+            self.log.info(f'{primary_key}: {primary}')
             for causal, s in zip(self.causals, results[primary]):
                 for r in sorted(s):
                     secondaries = ', '.join('%s: %s' % x for x in zip(causal[1:], r[1:]))
-                    self.log.info('%s %s caused %s' % (causal[0], r[0], secondaries))
+                    self.log.info('{} {} caused {}'.format(causal[0], r[0], secondaries))
 
     def handle_results(self, cur):
         results = {}
@@ -233,7 +232,7 @@ class Action(object):
         pass
 
 
-class RemovesObjects(object):
+class RemovesObjects:
     """Base class for mixins that remove objects from object stores.
     """
     def _init(self):
@@ -280,7 +279,7 @@ class RemovesObjects(object):
 #
 
 
-class PurgesHDAs(object):
+class PurgesHDAs:
     """Avoid repetition in queries that purge HDAs, since they must also delete MetadataFiles and ICDAs.
 
     To use, place ``{purge_hda_dependencies_sql}`` somewhere in your CTEs after a ``purged_hda_ids`` CTE returning HDA
@@ -336,7 +335,7 @@ class PurgesHDAs(object):
         )
 
 
-class RequiresDiskUsageRecalculation(object):
+class RequiresDiskUsageRecalculation:
     """Causes disk usage to be recalculated for affected users.
 
     To use, ensure your query returns a ``recalculate_disk_usage_user_id`` column.
@@ -626,7 +625,7 @@ class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
     )
 
     def _init(self):
-        super(PurgeDeletedUsers, self)._init()
+        super()._init()
         self.__zero_disk_usage_user_ids = set()
         self._register_row_method(self.collect_zero_disk_usage_user_id)
         self._register_post_method(self.zero_disk_usage)
@@ -952,7 +951,7 @@ class PurgeDatasets(RemovesDatasets, Action):
     """
 
 
-class Cleanup(object):
+class Cleanup:
     def __init__(self):
         self.args = None
         self.config = None

scripts/cleanup_datasets/populate_uuid.py

@@ -6,7 +6,6 @@ Populates blank uuid fields in datasets with randomly generated values
 Going forward, these ids will be generated for all new datasets. This
 script fixes datasets that were generated before the change.
 """
-from __future__ import print_function
 
 import argparse
 import os

scripts/communication/communication_server.py

@@ -30,7 +30,6 @@ from datetime import timedelta
 from functools import update_wrapper
 
 import flask.ext.login as flask_login
-import six
 from flask import (
     current_app,
     Flask,
@@ -109,9 +108,9 @@ def crossdomain(origin=None, methods=None, headers=None,
                 automatic_options=True):
     if methods is not None:
         methods = ', '.join(sorted(x.upper() for x in methods))
-    if headers is not None and not isinstance(headers, six.string_types):
+    if headers is not None and not isinstance(headers, str):
         headers = ', '.join(x.upper() for x in headers)
-    if not isinstance(origin, six.string_types):
+    if not isinstance(origin, str):
         origin = ', '.join(origin)
     if isinstance(max_age, timedelta):
         max_age = max_age.total_seconds()
@@ -168,14 +167,14 @@ def static_style():
 
 @socketio.on('event connect', namespace='/chat')
 def event_connect(message):
-    log.info("%s connected" % (current_user.username,))
+    log.info(f"{current_user.username} connected")
 
 
 @socketio.on('event broadcast', namespace='/chat')
 def event_broadcast(message):
     message = sanitize_html(message['data'])
 
-    log.debug("%s broadcast '%s'" % (current_user.username, message))
+    log.debug(f"{current_user.username} broadcast '{message}'")
 
     emit('event response',
         {'data': message, 'user': current_user.username, 'gravatar': hashlib.md5(current_user.email).hexdigest()}, broadcast=True)
@@ -186,7 +185,7 @@ def send_room_message(message):
     data = sanitize_html(message['data'])
     room = sanitize_html(message['room'])
 
-    log.debug("%s sent '%s' to %s" % (current_user.username, message, room))
+    log.debug(f"{current_user.username} sent '{message}' to {room}")
 
     emit('event response room',
         {'data': data, 'user': current_user.username, 'gravatar': hashlib.md5(current_user.email).hexdigest(), 'chatroom': room}, room=room)
@@ -202,7 +201,7 @@ def event_disconnect(message):
 def join(message):
     room = sanitize_html(message['room'])
 
-    log.debug("%s joined %s" % (current_user.username, room))
+    log.debug(f"{current_user.username} joined {room}")
     join_room(room)
 
     emit('event response room',
@@ -213,7 +212,7 @@ def join(message):
 def leave(message):
     room = sanitize_html(message['room'])
 
-    log.debug("%s left %s" % (current_user.username, room))
+    log.debug(f"{current_user.username} left {room}")
     leave_room(room)
 
     emit('event response room',

scripts/config_sample_to_kwalify.py

@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import sys
 
 
@@ -13,7 +11,7 @@ def main():
     except KeyError:
         sample = "config/galaxy.ini.sample"
 
-    for line in open(sample, "r"):
+    for line in open(sample):
         is_app_main = line.startswith('[app:main]')
         if not found_app_main and not is_app_main:
             continue

scripts/db_shell.py

@@ -13,15 +13,12 @@
 # You can also use this script as a library, for instance see https://gist.github.com/1979583
 # TODO: This script overlaps a lot with manage_db.py and create_db.py,
 # these should maybe be refactored to remove duplication.
-from __future__ import print_function
 
 import datetime
 import decimal
 import os.path
 import sys
 
-from six import string_types
-
 # Setup DB scripting environment
 from sqlalchemy import *  # noqa
 from sqlalchemy.orm import *  # noqa
@@ -36,9 +33,6 @@ from galaxy.model import set_datatypes_registry  # More explicit than `*` import
 from galaxy.model.mapping import init
 from galaxy.model.orm.scripts import get_config
 
-if sys.version_info > (3,):
-    long = int
-
 registry = Registry()
 registry.load_datatypes()
 set_datatypes_registry(registry)
@@ -71,7 +65,7 @@ def printquery(statement, bind=None):
                 self, bindparam, within_columns_clause=False,
                 literal_binds=False, **kwargs
         ):
-            return super(LiteralCompiler, self).render_literal_bindparam(
+            return super().render_literal_bindparam(
                 bindparam,
                 within_columns_clause=within_columns_clause,
                 literal_binds=literal_binds,
@@ -88,12 +82,12 @@ def printquery(statement, bind=None):
             of the DBAPI.
 
             """
-            if isinstance(value, string_types):
+            if isinstance(value, str):
                 value = value.replace("'", "''")
                 return "'%s'" % value
             elif value is None:
                 return "NULL"
-            elif isinstance(value, (float, int, long)):
+            elif isinstance(value, (float, int)):
                 return repr(value)
             elif isinstance(value, decimal.Decimal):
                 return str(value)

scripts/docker_swarm_manager.py

@@ -2,7 +2,6 @@
 """
 Docker Swarm mode management
 """
-from __future__ import absolute_import, print_function
 
 import argparse
 import errno
@@ -58,7 +57,7 @@ SWARM_MANAGER_CONF_DEFAULTS = {
 log = logging.getLogger(__name__)
 
 
-class SwarmManager(object):
+class SwarmManager:
 
     def __init__(self, conf, docker_interface):
         self._conf = conf
@@ -93,7 +92,7 @@ class SwarmManager(object):
             p = subprocess.Popen(raw_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True, shell=True)
             stdout, stderr = p.communicate()
             if p.returncode not in allowed_returncodes:
-                msg = "error running '%s': returned %s" % (raw_cmd, p.returncode)
+                msg = f"error running '{raw_cmd}': returned {p.returncode}"
                 if attempt < command_retries + 1:
                     msg += ', waiting %s seconds' % self._conf.command_retry_wait
                     time.sleep(self._conf.command_retry_wait)
@@ -172,10 +171,10 @@ class SwarmManager(object):
         node_task_ids = [t.id for nt in [n.tasks for n in nodes] for t in nt]
         envs = {}
         for service in services:
-            envs[service.id] = ['%s=%s' % (k, service.env.get(k, 'unset')) for k in self._conf.log_environment_variables]
+            envs[service.id] = ['{}={}'.format(k, service.env.get(k, 'unset')) for k in self._conf.log_environment_variables]
         log.info('%s nodes, %s services (%s terminal)', len(nodes), len(services), len(terminal))
         if terminal:
-            service_strs = ['%s (state: %s)' % (s.name, s.state) for s in terminal]
+            service_strs = [f'{s.name} (state: {s.state})' for s in terminal]
             log.info('terminal services: %s', ', '.join(service_strs) or 'none')
         for service in services:
             unassigned_tasks = [t for t in service.tasks if t.id not in node_task_ids]
@@ -291,7 +290,7 @@ class SwarmManager(object):
         return ready
 
 
-class SwarmState(object):
+class SwarmState:
 
     def __init__(self, conf, interface_conf):
         self._conf = conf
@@ -558,7 +557,7 @@ def _load_xdg_environment():
 def _swarm_manager_pidfile(conf):
     try:
         os.makedirs(os.path.dirname(conf['pid_file']))
-    except (IOError, OSError) as exc:
+    except OSError as exc:
         if exc.errno != errno.EEXIST:
             raise
     return daemon.pidfile.PIDLockFile(conf['pid_file'])

scripts/drmaa_external_runner.py

@@ -5,7 +5,6 @@ Submit a DRMAA job given a user id and a job template file (in JSON format)
 defining any or all of the following: args, remoteCommand, outputPath,
 errorPath, nativeSpecification, name, email, project
 """
-from __future__ import print_function
 
 import errno
 import json
@@ -118,7 +117,7 @@ def main():
     # then the pbs cluster_files_directory does not need to
     # be readable by all users
     json_file_exists(json_filename)
-    with open(json_filename, 'r') as f:
+    with open(json_filename) as f:
         data = json.load(f)
     set_user(userid, assign_all_groups)
     # Added to disable LSF generated messages that would interfer with this

scripts/edam_mapping.py

@@ -11,8 +11,6 @@ run from the Galaxy root.
 
  % python script/edam_mapping.py > edam_mapping.tsv
 """
-from __future__ import absolute_import
-from __future__ import print_function
 
 import os
 import sys
@@ -59,4 +57,4 @@ for ext, edam_format in sorted(datatypes_registry.edam_formats.items()):
     edam_info = format_info[edam_format]
     edam_label = edam_info["label"]
     edam_definition = edam_info["definition"]
-    print("%s\t%s\t%s\t%s" % (ext, edam_format, edam_label, edam_definition))
+    print(f"{ext}\t{edam_format}\t{edam_label}\t{edam_definition}")

scripts/extract_dataset_part.py

@@ -30,7 +30,7 @@ def __main__():
     if not os.path.isfile(file_path):
         # Nothing to do - some splitters don't write a JSON file
         sys.exit(0)
-    data = json.load(open(file_path, 'r'))
+    data = json.load(open(file_path))
     try:
         class_name_parts = data['class_name'].split('.')
         module_name = '.'.join(class_name_parts[:-1])

scripts/extract_toolbox_sections.py

@@ -65,7 +65,7 @@ def main():
             hastoolboxpos = True
 
         if (not (hastags and hastoolboxpos)):
-            original = open(toolconffile, 'r')
+            original = open(toolconffile)
             contents = original.readlines()
             original.close()
 
@@ -124,7 +124,7 @@ def getfnl(startdir):
                 try:
                     doc = ET.parse(fullfn)
                 except Exception as e:
-                    raise Exception("Oops, bad XML in '%s': %s" % (fullfn, e))
+                    raise Exception(f"Oops, bad XML in '{fullfn}': {e}")
                 rootelement = doc.getroot()
                 # here we check if this xml file actually is a tool conf xml!
                 if rootelement.tag == 'tool':

scripts/fetch_eggs.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 from os import pardir
 from os.path import (

scripts/galaxy-main

@@ -29,10 +29,9 @@ import signal
 import sys
 import threading
 from argparse import ArgumentParser
+from configparser import ConfigParser
 from logging.config import fileConfig
 
-from six.moves.configparser import ConfigParser
-
 try:
     from daemonize import Daemonize
 except ImportError:

scripts/get_platforms.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import os
 import sys

scripts/get_uwsgi_args.py

@@ -1,11 +1,7 @@
-from __future__ import print_function
-
 import os
+import shlex
 import sys
 
-from six import string_types
-from six.moves import shlex_quote
-
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 
 from galaxy.util.path import get_ext
@@ -49,13 +45,13 @@ def __add_arg(args, arg, value):
     if isinstance(value, bool):
         if value is True:
             args.append(optarg)
-    elif isinstance(value, string_types):
+    elif isinstance(value, str):
         # the = in --optarg=value is usually, but not always, optional
         if value.startswith('='):
-            args.append(shlex_quote(optarg + value))
+            args.append(shlex.quote(optarg + value))
         else:
             args.append(optarg)
-            args.append(shlex_quote(value))
+            args.append(shlex.quote(value))
     else:
         [__add_arg(args, arg, v) for v in value]
 
@@ -91,8 +87,8 @@ def _get_uwsgi_args(cliargs, kwargs):
         'threads': '4',
         'buffer-size': '16384',  # https://github.com/galaxyproject/galaxy/issues/1530
         'http': 'localhost:{port}'.format(port=DEFAULT_PORTS[cliargs.app]),
-        'static-map': ('/static={here}/static'.format(here=os.getcwd()),
-                       '/favicon.ico={here}/static/favicon.ico'.format(here=os.getcwd())),
+        'static-map': (f'/static={os.getcwd()}/static',
+                       f'/favicon.ico={os.getcwd()}/static/favicon.ico'),
         'die-on-term': True,
         'enable-threads': True,
         'hook-master-start': ('unix_signal:2 gracefully_kill_them_all',
@@ -106,7 +102,7 @@ def _get_uwsgi_args(cliargs, kwargs):
         if cliargs.app in ["tool_shed"]:
             __add_arg(args, 'module', 'tool_shed.webapp.buildapp:uwsgi_app()')
         else:
-            __add_arg(args, 'module', 'galaxy.webapps.{app}.buildapp:uwsgi_app()'.format(app=cliargs.app))
+            __add_arg(args, 'module', f'galaxy.webapps.{cliargs.app}.buildapp:uwsgi_app()')
     # only include virtualenv if it's set/exists, otherwise this breaks conda-env'd Galaxy
     if not __arg_set('virtualenv', uwsgi_kwargs) and ('VIRTUAL_ENV' in os.environ or os.path.exists('.venv')):
         __add_arg(args, 'virtualenv', os.environ.get('VIRTUAL_ENV', '.venv'))
@@ -118,9 +114,9 @@ def _get_uwsgi_args(cliargs, kwargs):
         # route: ^/static/scripts/bundled/ http:127.0.0.1:8081
         if hmr_server.lower() in ['1', 'true', 'default']:
             hmr_server = "http:127.0.0.1:8081"
-        __add_arg(args, 'route', '^/static/dist/ {hmr_server}'.format(hmr_server=hmr_server))
+        __add_arg(args, 'route', f'^/static/dist/ {hmr_server}')
     # We always want to append client/src/assets as static-safe.
-    __add_arg(args, 'static-safe', '{here}/client/src/assets'.format(here=os.getcwd()))
+    __add_arg(args, 'static-safe', f'{os.getcwd()}/client/src/assets')
 
     for arg in DEFAULT_ARGS['_all_'] + DEFAULT_ARGS[cliargs.app]:
         if not __arg_set(arg, uwsgi_kwargs):

scripts/grt/export.py

@@ -4,7 +4,6 @@
 See doc/source/admin/grt.rst for more detailed usage information.
 """
 import argparse
-import io
 import json
 import logging
 import os
@@ -47,7 +46,7 @@ def _init(args):
 
 def kw_metrics(job):
     return {
-        '%s_%s' % (metric.plugin, metric.metric_name): metric.metric_value
+        f'{metric.plugin}_{metric.metric_name}': metric.metric_value
         for metric in job.metrics
     }
 
@@ -100,7 +99,7 @@ def main(argv):
     REPORT_BASE = os.path.join(REPORT_DIR, REPORT_IDENTIFIER)
 
     if os.path.exists(CHECK_POINT_FILE):
-        with open(CHECK_POINT_FILE, 'r') as handle:
+        with open(CHECK_POINT_FILE) as handle:
             last_job_sent = int(handle.read())
     else:
         last_job_sent = -1
@@ -133,7 +132,7 @@ def main(argv):
         if end_job_id - last_job_sent > args.max_records:
             end_job_id = last_job_sent + args.max_records
 
-    annotate('endpoint_end', 'Processing jobs (%s, %s]' % (last_job_sent, end_job_id))
+    annotate('endpoint_end', f'Processing jobs ({last_job_sent}, {end_job_id}]')
 
     # Remember the last job sent.
     if end_job_id == last_job_sent:
@@ -146,8 +145,8 @@ def main(argv):
     blacklisted_tools = config['sanitization']['tools']
 
     annotate('export_jobs_start', 'Exporting Jobs')
-    with io.open(REPORT_BASE + '.jobs.tsv', 'w', encoding='utf-8') as handle_job:
-        handle_job.write(u'\t'.join(('id', 'tool_id', 'tool_version', 'state', 'create_time')) + '\n')
+    with open(REPORT_BASE + '.jobs.tsv', 'w', encoding='utf-8') as handle_job:
+        handle_job.write('\t'.join(('id', 'tool_id', 'tool_version', 'state', 'create_time')) + '\n')
         for offset_start in range(last_job_sent, end_job_id, args.batch_size):
             logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
             for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
@@ -178,8 +177,8 @@ def main(argv):
     annotate('export_jobs_end')
 
     annotate('export_datasets_start', 'Exporting Datasets')
-    with io.open(REPORT_BASE + '.datasets.tsv', 'w', encoding='utf-8') as handle_datasets:
-        handle_datasets.write(u'\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
+    with open(REPORT_BASE + '.datasets.tsv', 'w', encoding='utf-8') as handle_datasets:
+        handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
         for offset_start in range(last_job_sent, end_job_id, args.batch_size):
             logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
 
@@ -258,8 +257,8 @@ def main(argv):
     annotate('export_datasets_end')
 
     annotate('export_metric_num_start', 'Exporting Metrics (Numeric)')
-    with io.open(REPORT_BASE + '.metric_num.tsv', 'w', encoding='utf-8') as handle_metric_num:
-        handle_metric_num.write(u'\t'.join(('job_id', 'plugin', 'name', 'value')) + '\n')
+    with open(REPORT_BASE + '.metric_num.tsv', 'w', encoding='utf-8') as handle_metric_num:
+        handle_metric_num.write('\t'.join(('job_id', 'plugin', 'name', 'value')) + '\n')
         for offset_start in range(last_job_sent, end_job_id, args.batch_size):
             logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
             for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \

scripts/grt/upload.py

@@ -43,7 +43,7 @@ def main(argv):
 
     # Contact the server and check auth details.
     headers = {
-        'AUTHORIZATION': '%s:%s' % (GRT_INSTANCE_ID, GRT_API_KEY)
+        'AUTHORIZATION': f'{GRT_INSTANCE_ID}:{GRT_API_KEY}'
     }
     r = requests.post(GRT_URL + 'api/whoami', headers=headers)
     data = r.json()

scripts/helper.py

@@ -4,7 +4,6 @@ A command line helper for common operations performed by Galaxy maintainers.
 Encodes and decodes IDs, returns Dataset IDs if provided an HDA or LDDA id,
 returns the disk path of a dataset.
 """
-from __future__ import print_function
 
 import argparse
 import os
@@ -30,10 +29,10 @@ helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
 model = galaxy.config.init_models_from_config(config)
 
 if args.encode_id:
-    print('Encoded "%s": %s' % (args.encode_id, helper.encode_id(args.encode_id)))
+    print('Encoded "{}": {}'.format(args.encode_id, helper.encode_id(args.encode_id)))
 
 if args.decode_id:
-    print('Decoded "%s": %s' % (args.decode_id, helper.decode_id(args.decode_id)))
+    print('Decoded "{}": {}'.format(args.decode_id, helper.decode_id(args.decode_id)))
 
 if args.hda_id:
     try:
@@ -41,7 +40,7 @@ if args.hda_id:
     except Exception:
         hda_id = int(helper.decode_id(args.hda_id))
     hda = model.context.current.query(model.HistoryDatasetAssociation).get(hda_id)
-    print('HDA "%s" is Dataset "%s" at: %s' % (hda.id, hda.dataset.id, hda.file_name))
+    print(f'HDA "{hda.id}" is Dataset "{hda.dataset.id}" at: {hda.file_name}')
 
 if args.ldda_id:
     try:
@@ -49,4 +48,4 @@ if args.ldda_id:
     except Exception:
         ldda_id = int(helper.decode_id(args.ldda_id))
     ldda = model.context.current.query(model.HistoryDatasetAssociation).get(ldda_id)
-    print('LDDA "%s" is Dataset "%s" at: %s' % (ldda.id, ldda.dataset.id, ldda.file_name))
+    print(f'LDDA "{ldda.id}" is Dataset "{ldda.dataset.id}" at: {ldda.file_name}')

scripts/loc_files/create_all_fasta_loc.py

@@ -23,7 +23,6 @@ usage: %prog [options]
    -a, --append=a: Append to existing all_fasta.loc file rather than create new
    -p, --sample-text=p: Copy over text from all_fasta.loc.sample file (false if set to append)
 """
-from __future__ import print_function
 
 import optparse
 import os
@@ -197,7 +196,7 @@ def __main__():
     if len(options.fasta_exts) == 1:
         print('with the extension %s.' % ', '.join(fasta_exts[:-1]))
     else:
-        print('with the extension %s or %s.' % (', '.join(fasta_exts[:-1]), fasta_exts[-1]))
+        print('with the extension {} or {}.'.format(', '.join(fasta_exts[:-1]), fasta_exts[-1]))
     print('\nSkipping the following:\n\t%s' % '\n\t'.join(exemptions))
 
     # get column names
@@ -217,7 +216,7 @@ def __main__():
             if cols:
                 col_values = [col.strip() for col in cols.split(',')]
     if not col_values or not loc_path:
-        raise Exception('No columns can be found for this data table (%s) in %s' % (options.data_table, options.data_table_xml))
+        raise Exception(f'No columns can be found for this data table ({options.data_table}) in {options.data_table_xml}')
 
     # get all fasta paths under genome directory
     fasta_locs = {}
@@ -225,7 +224,7 @@ def __main__():
     genome_subdirs = [dr for dr in os.listdir(options.genome_dir) if dr not in exemptions]
     for genome_subdir in genome_subdirs:
         possible_names = [genome_subdir]
-        possible_names.extend(['%s%s' % (genome_subdir, _) for _ in variants])
+        possible_names.extend([f'{genome_subdir}{_}' for _ in variants])
         # get paths to all fasta files
         for path_to_look_in in paths_to_look_in:
             for dirpath, dirnames, filenames in os.walk(path_to_look_in % genome_subdir):
@@ -238,17 +237,17 @@ def __main__():
                                 name = DBKEY_DESCRIPTION_MAP[genome_subdir]
                             else:
                                 try:
-                                    name = '%s %s' % (DBKEY_DESCRIPTION_MAP[genome_subdir], VARIANT_MAP[fasta_base.replace(genome_subdir, '')])
+                                    name = '{} {}'.format(DBKEY_DESCRIPTION_MAP[genome_subdir], VARIANT_MAP[fasta_base.replace(genome_subdir, '')])
                                 except KeyError:
-                                    name = '%s %s' % (DBKEY_DESCRIPTION_MAP[genome_subdir], fasta_base.replace(genome_subdir, ''))
+                                    name = '{} {}'.format(DBKEY_DESCRIPTION_MAP[genome_subdir], fasta_base.replace(genome_subdir, ''))
                             fasta_locs[fasta_base] = {'value': fasta_base, 'dbkey': genome_subdir, 'name': name, 'path': os.path.join(dirpath, fn)}
                         else:
                             unmatching_fasta_paths.append(os.path.join(dirpath, fn))
         # remove redundant fasta files
         for k, v in variant_exclusions.items():
-            leave_in = '%s%s' % (genome_subdir, k)
+            leave_in = f'{genome_subdir}{k}'
             if leave_in in fasta_locs:
-                to_remove = ['%s%s' % (genome_subdir, _) for _ in v]
+                to_remove = [f'{genome_subdir}{_}' for _ in v]
                 for tr in to_remove:
                     if tr in fasta_locs:
                         del fasta_locs[tr]

scripts/metagenomics/convert_title.py

@@ -3,7 +3,6 @@
 convert nt and wgs data (fasta format) to giNumber_seqLen
 run formatdb in the command line: gunzip -c nt.gz |formatdb -i stdin -p F -n "nt.chunk" -v 2000
 """
-from __future__ import print_function
 
 import sys
 

scripts/microbes/create_bacteria_loc_file.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-from __future__ import print_function
 
 import os
 import sys
@@ -21,7 +20,7 @@ def __main__():
         for file in files:
             if file[-5:] == ".info":
                 tmp_dict = {}
-                info_file = open(os.path.join(this_base_dir, file), 'r')
+                info_file = open(os.path.join(this_base_dir, file))
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
@@ -48,26 +47,26 @@ def __main__():
             continue
         if 'build' in org:
             build = org['build']
-            print("ORG\t%s\t%s\t%s\t%s\t%s\t%s\tUCSC" % (build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
+            print("ORG\t{}\t{}\t{}\t{}\t{}\t{}\tUCSC".format(build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
         else:
-            print("ORG\t%s\t%s\t%s\t%s\t%s\t%s\tNone" % (build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
+            print("ORG\t{}\t{}\t{}\t{}\t{}\t{}\tNone".format(build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
 
         for chr in org['chrs']:
             chr = org['chrs'][chr]
-            print("CHR\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr['refseq']))
+            print("CHR\t{}\t{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr['refseq']))
             for feature in ['CDS', 'tRNA', 'rRNA']:
-                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join(org['base_dir'], "%s.%s.bed" % (chr['chromosome'], feature))))
+                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join(org['base_dir'], "{}.{}.bed".format(chr['chromosome'], feature))))
             # FASTA
-            print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])))
+            print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])))
             # GeneMark
             if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])):
-                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])))
+                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])))
             # GenMarkHMM
             if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])):
-                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])))
+                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])))
             # Glimmer3
             if os.path.exists(os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])):
-                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])))
+                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])))
 
 
 if __name__ == "__main__":

scripts/microbes/create_bacteria_table.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-from __future__ import print_function
 
 import os
 import sys
@@ -21,7 +20,7 @@ def __main__():
         for file in files:
             if file[-5:] == ".info":
                 tmp_dict = {}
-                info_file = open(os.path.join(this_base_dir, file), 'r')
+                info_file = open(os.path.join(this_base_dir, file))
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:

scripts/microbes/create_nib_seq_loc_file.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-from __future__ import print_function
 
 import os
 import sys
@@ -30,7 +29,7 @@ def __main__():
         for file in files:
             if file[-5:] == ".info":
                 tmp_dict = {}
-                info_file = open(os.path.join(this_base_dir, file), 'r')
+                info_file = open(os.path.join(this_base_dir, file))
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
@@ -68,7 +67,7 @@ def __main__():
             print("Skipping", build)
             # continue
 
-        loc_out.write("seq %s %s\n" % (build, seq_path))
+        loc_out.write(f"seq {build} {seq_path}\n")
 
         # Print org info
 
@@ -79,7 +78,7 @@ def __main__():
             nib_out_file = os.path.join(seq_path, "%s.nib " % chr['chromosome'])
             # create nibs using faToNib binary
             # TODO: when bx supports writing nib, use it here instead
-            command = "faToNib %s %s" % (fasta_file, nib_out_file)
+            command = f"faToNib {fasta_file} {nib_out_file}"
             os.system(command)
 
     loc_out.close()

scripts/microbes/get_builds_lengths.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-from __future__ import print_function
 
 import os
 import sys
@@ -21,7 +20,7 @@ def __main__():
         for file in files:
             if file[-5:] == ".info":
                 tmp_dict = {}
-                info_file = open(os.path.join(this_base_dir, file), 'r')
+                info_file = open(os.path.join(this_base_dir, file))
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
@@ -53,8 +52,8 @@ def __main__():
         chrs = []
         for chrom in org['chrs']:
             chrom = org['chrs'][chrom]
-            chrs.append("%s=%s" % (chrom['chromosome'], chrom['length']))
-        print("%s\t%s\t%s" % (build, org['name'], ",".join(chrs)))
+            chrs.append("{}={}".format(chrom['chromosome'], chrom['length']))
+        print("{}\t{}\t{}".format(build, org['name'], ",".join(chrs)))
 
 
 if __name__ == "__main__":

scripts/microbes/harvest_bacteria.py

@@ -4,19 +4,18 @@
 # Harvest Bacteria
 # Connects to NCBI's Microbial Genome Projects website and scrapes it for information.
 # Downloads and converts annotations for each Genome
-from __future__ import print_function
 
 import os
 import sys
 import time
 from ftplib import FTP
+from urllib.request import urlretrieve
 
 import requests
 try:
     from bs4 import BeautifulSoup
 except ImportError:
     raise Exception("BeautifulSoup4 library not found, please install it, e.g. with 'pip install BeautifulSoup4'")
-from six.moves.urllib.request import urlretrieve
 
 from util import (  # noqa: I202
     get_bed_from_genbank,
@@ -52,7 +51,7 @@ def iter_genome_projects(url="http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?vie
 
         group = fields[3].split(">")[-1]
 
-        info_url = "%s%s" % (info_url_base, org_num)
+        info_url = f"{info_url_base}{org_num}"
 
         org_genbank = fields[7].split("\">")[-1].split("<")[0].split(".")[0]
         org_refseq = fields[8].split("\">")[-1].split("<")[0].split(".")[0]
@@ -74,7 +73,7 @@ def get_chroms_by_project_id(org_num, base_url="http://www.ncbi.nlm.nih.gov/entr
     html = None
     while html_count < 500 and html is None:
         html_count += 1
-        url = "%s%s" % (base_url, org_num)
+        url = f"{base_url}{org_num}"
         try:
             html = requests.get(url).text
         except Exception:
@@ -116,11 +115,11 @@ def get_ftp_contents(ftp_url):
 def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
     for file_type, items in desired_ftp_files.items():
         ext = items['ext']
-        ftp_filename = "%s.%s" % (refseq, ext)
-        target_filename = os.path.join(org_dir, "%s.%s" % (refseq, ext))
+        ftp_filename = f"{refseq}.{ext}"
+        target_filename = os.path.join(org_dir, f"{refseq}.{ext}")
         if ftp_filename in ftp_contents:
             url_count = 0
-            url = "%s/%s" % (ftp_url, ftp_filename)
+            url = f"{ftp_url}/{ftp_filename}"
             results = None
             while url_count < 500 and results is None:
                 url_count += 1
@@ -152,7 +151,7 @@ def process_FASTA(filename, org_num, refseq):
 
     # Create Chrom Info File:
     chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), 'wb+')
-    chrom_info_file.write("chromosome=%s\nname=%s\nlength=%s\norganism=%s\n" % (refseq, chr_name, len(fasta), org_num))
+    chrom_info_file.write("chromosome={}\nname={}\nlength={}\norganism={}\n".format(refseq, chr_name, len(fasta), org_num))
     try:
         chrom_info_file.write("gi=%s\n" % accesions['gi'])
     except Exception:
@@ -172,7 +171,7 @@ def process_Genbank(filename, org_num, refseq):
     # extracts 'CDS', 'tRNA', 'rRNA' features from genbank file
     features = get_bed_from_genbank(filename, refseq, ['CDS', 'tRNA', 'rRNA'])
     for feature, values in features.items():
-        feature_file = open(os.path.join(os.path.split(filename)[0], "%s.%s.bed" % (refseq, feature)), 'wb+')
+        feature_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.{feature}.bed"), 'wb+')
         feature_file.write('\n'.join(values))
         feature_file.close()
     print("Genbank extraction finished for chrom:", refseq, "file:", filename)
@@ -225,7 +224,7 @@ def __main__():
     except Exception:
         print("path '%s' seems to already exist" % base_dir)
 
-    for org_num, name, chroms, kingdom, group, org_genbank, org_refseq, info_url, ftp_url in iter_genome_projects():
+    for org_num, name, chroms, kingdom, group, _, _, info_url, ftp_url in iter_genome_projects():
         if chroms is None:
             continue  # No chrom information, we can't really do anything with this organism
         # Create org directory, if exists, assume it is done and complete --> skip it

scripts/microbes/ncbi_to_ucsc.py

@@ -3,15 +3,13 @@
 Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable.
 Uses UCSC Archaea DSN.
 """
-from __future__ import print_function
 
 import os
 import sys
 from shutil import move
+from urllib.request import urlopen
 from xml.etree import ElementTree
 
-from six.moves.urllib.request import urlopen
-
 
 def __main__():
     base_dir = os.path.join(os.getcwd(), "bacteria")
@@ -26,7 +24,7 @@ def __main__():
         for file in files:
             if file[-5:] == ".info":
                 tmp_dict = {}
-                info_file = open(os.path.join(this_base_dir, file), 'r')
+                info_file = open(os.path.join(this_base_dir, file))
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:

scripts/microbes/util.py

@@ -7,7 +7,7 @@ assert sys.version_info[:2] >= (2, 4)
 
 
 # genbank_to_bed
-class Region(object):
+class Region:
     def __init__(self):
         self.qualifiers = {}
         self.start = None
@@ -37,7 +37,7 @@ class Region(object):
                     self.end = end
 
 
-class GenBankFeatureParser(object):
+class GenBankFeatureParser:
     """Parses Features from Single Locus GenBank file"""
     def __init__(self, fh, features_list=[]):
         self.fh = fh
@@ -90,9 +90,9 @@ class GenBankFeatureParser(object):
                     else:
                         # continuation of multi-line qualifier content
                         if last_feature_name.lower() in ['translation']:
-                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "%s%s" % (self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
+                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{}{}".format(self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
                         else:
-                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "%s %s" % (self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
+                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{} {}".format(self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
 
     def get_features_by_type(self, feature_type):
         if feature_type not in self.features:
@@ -117,7 +117,7 @@ def get_bed_from_genbank(gb_file, chrom, feature_list):
             if not name:
                 name = "unknown"
 
-            features[feature_type].append("%s\t%s\t%s\t%s\t%s\t%s" % (chrom, feature.start, feature.end, name, 0, feature.strand))  # append new bed field here
+            features[feature_type].append("{}\t{}\t{}\t{}\t{}\t{}".format(chrom, feature.start, feature.end, name, 0, feature.strand))  # append new bed field here
     return features
 
 

scripts/objectstore/copy_files_to_irods.py

@@ -75,7 +75,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
     db_connection_info = None
 
     if start_dataset_id > end_dataset_id:
-        print("Error: start_dataset_id {} cannot be larger than end_dataset_id {}".format(start_dataset_id, end_dataset_id))
+        print(f"Error: start_dataset_id {start_dataset_id} cannot be larger than end_dataset_id {end_dataset_id}")
         return
 
     # read object_store_info file
@@ -135,7 +135,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
 
             object_store_path = object_store_info.get(object_store_id)
             if object_store_path is None:
-                print("Error: object_store_info_file does not have a value for {}".format(object_store_id))
+                print(f"Error: object_store_info_file does not have a value for {object_store_id}")
                 raise Exception
 
             irods_resc = get_irods_resource(conn, objectid, object_store_id, irods_info)
@@ -155,7 +155,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                 # Add disk file to collection
                 options = {kw.REG_CHKSUM_KW : '', kw.RESC_NAME_KW: irods_resc}
                 session.data_objects.put(disk_file_path, irods_file_path, **options)
-                print("Copied disk file {} to irods {}".format(disk_file_path, irods_file_path))
+                print(f"Copied disk file {disk_file_path} to irods {irods_file_path}")
 
                 if os.path.isdir(disk_folder_path):
                     disk_folder_path_all_files = disk_folder_path + "/*"
@@ -165,7 +165,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
 
                     iput_command = "iput -R " + irods_resc + " -rk " + disk_folder_path_all_files + " " + irods_folder_collection_path
                     subprocess.call(iput_command, shell=True)
-                    print("Copied disk folder {} to irods {}".format(disk_folder_path, irods_folder_collection_path))
+                    print(f"Copied disk folder {disk_folder_path} to irods {irods_folder_collection_path}")
 
             if copy_or_checksum == "checksum":
                 # Calculate disk file checksum. Then get the file checksum from irods and compare it with the calculated disk file checksum
@@ -177,7 +177,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                     # obj.checksum is prepended with 'sha2:'. Remove that so we can compare it to disk file checksum
                     irods_file_checksum = obj.checksum[5:]
                     if irods_file_checksum != disk_file_checksum:
-                        print("Error: irods file checksum {} does not match disk file checksum {} for irods file {} and disk file {}".format(irods_file_checksum, disk_file_checksum, irods_file_path, disk_file_path))
+                        print(f"Error: irods file checksum {irods_file_checksum} does not match disk file checksum {disk_file_checksum} for irods file {irods_file_path} and disk file {disk_file_path}")
                         continue
                 except (DataObjectDoesNotExist, CollectionDoesNotExist) as e:
                     print(e)
@@ -207,7 +207,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                                 # obj.checksum is prepended with 'sha2:'. Remove that so we can compare it to disk file checksum
                                 an_irods_file_checksum = obj.checksum[5:]
                                 if an_irods_file_checksum != a_disk_file_checksum:
-                                    print("Error: irods file checksum {} does not match disk file checksum {} for irods file {} and disk file {}".format(an_irods_file_checksum, a_disk_file_checksum, an_irods_file_path, a_disk_file_path))
+                                    print(f"Error: irods file checksum {an_irods_file_checksum} does not match disk file checksum {a_disk_file_checksum} for irods file {an_irods_file_path} and disk file {a_disk_file_path}")
                                     continue
                             except (DataObjectDoesNotExist, CollectionDoesNotExist) as e:
                                 print(e)
@@ -217,7 +217,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                                 continue
 
                     # Delete file on disk
-                    print("Removing directory {}".format(disk_folder_path))
+                    print(f"Removing directory {disk_folder_path}")
                     shutil.rmtree(disk_folder_path)
 
                 # Update object store id
@@ -231,7 +231,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                 update_cursor.close()
 
                 # Delete file on disk
-                print("Removing file {}".format(disk_file_path))
+                print(f"Removing file {disk_file_path}")
                 os.remove(disk_file_path)
 
     except Exception as e:
@@ -261,12 +261,12 @@ def get_irods_resource(conn, objectid, object_store_id, irods_info):
         read_cursor.execute(last_accessed_sql_statement, args)
         row = read_cursor.fetchone()
         if row is None:
-            print("Could not find the last access time for dataset with id {}. Returning the default resc {}.".format(objectid, irods_resc))
+            print(f"Could not find the last access time for dataset with id {objectid}. Returning the default resc {irods_resc}.")
             return irods_resc
 
         dataset_id = row[0]
         if int(dataset_id) != objectid:
-            print("The returned dataset id {} does not match the passed in datsetid {}. Returning the default resc {}.".format(dataset_id, objectid, irods_resc))
+            print(f"The returned dataset id {dataset_id} does not match the passed in datsetid {objectid}. Returning the default resc {irods_resc}.")
             return irods_resc
 
         max_create_time = row[1]
@@ -274,10 +274,10 @@ def get_irods_resource(conn, objectid, object_store_id, irods_info):
         max_create_time_dt = max_create_time.replace(tzinfo=None)
         # If the last time a dataset was accessed was prior to a cuttoff date, use the tape resource. Otherwise, use the regular (non-tape) resource
         if max_create_time_dt < irods_tape_resc_cuttoff_dt:
-            print("The last time dataset with id {} was accessed {} is prior to tape resource cuttoff {}. Using tape resource in irods.".format(objectid, max_create_time_dt, irods_tape_resc_cuttoff_dt))
+            print(f"The last time dataset with id {objectid} was accessed {max_create_time_dt} is prior to tape resource cuttoff {irods_tape_resc_cuttoff_dt}. Using tape resource in irods.")
             return irods_tape_resc
 
-        print("The last time dataset with id {} was accessed {} is after the tape resource cuttoff {}. Using regular (non-tape) resource in irods.".format(objectid, max_create_time_dt, irods_tape_resc_cuttoff_dt))
+        print(f"The last time dataset with id {objectid} was accessed {max_create_time_dt} is after the tape resource cuttoff {irods_tape_resc_cuttoff_dt}. Using regular (non-tape) resource in irods.")
         return irods_resc
 
     except Exception as e:
@@ -287,7 +287,7 @@ def get_irods_resource(conn, objectid, object_store_id, irods_info):
 
 
 def get_file_checksum(disk_file_path):
-    checksum_cmd = "shasum -a 256 {} | xxd -r -p | base64".format(disk_file_path)
+    checksum_cmd = f"shasum -a 256 {disk_file_path} | xxd -r -p | base64"
     disk_file_checksum = subprocess.check_output(checksum_cmd, shell=True)
     # remove '\n' from the end of disk_file_checksum
     disk_file_checksum_len = len(disk_file_checksum)

scripts/paster.py

@@ -4,7 +4,6 @@ Bootstrap the Galaxy framework.
 This should not be called directly!  Use the run.sh script in Galaxy's
 top level directly.
 """
-from __future__ import absolute_import
 
 import os
 import sys

scripts/plugin_staging.py

@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import glob
 import os
 import shutil
@@ -25,7 +23,7 @@ def stage_static(f):
         else:
             shutil.copy(src, dest)
     except Exception:
-        print("Error copying '%s' to '%s'" % (src, dest))
+        print(f"Error copying '{src}' to '{dest}'")
         raise
 
 

scripts/runtime_stats.py

@@ -29,7 +29,6 @@ Examples
 # 2 days:
 % ./runtime_stats.py -c galaxy.ini --like -m $((2 * 60)) -M $((2 * 24 * 60 * 60)) 'tophat2'
 """
-from __future__ import print_function
 
 import argparse
 import os
@@ -136,7 +135,7 @@ def query(tool_id=None, user=None, like=None, source='metrics',
 
     connect_arg_str = ''
     for k, v in connect_args.items():
-        connect_arg_str += '%s=%s' % (k, v)
+        connect_arg_str += f'{k}={v}'
 
     pc = psycopg2.connect(connect_arg_str)
     cur = pc.cursor()
@@ -149,7 +148,7 @@ def query(tool_id=None, user=None, like=None, source='metrics',
                 field = 'username'
             else:
                 field = 'email'
-            sql = 'SELECT id FROM galaxy_user WHERE %s = %s' % (field, '%s')
+            sql = 'SELECT id FROM galaxy_user WHERE {} = {}'.format(field, '%s')
             cur.execute(sql, (user,))
             if debug:
                 print('Executed:')

scripts/set_dataset_sizes.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import argparse
 import os

scripts/set_user_disk_usage.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import argparse
 import os

scripts/slideshow/build_slideshow.py

@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import os
 import string
 import sys
@@ -7,7 +5,7 @@ import sys
 
 SCRIPTS_DIRECTORY = os.path.dirname(__file__)
 TEMPLATE_PATH = os.path.join(SCRIPTS_DIRECTORY, "slideshow_template.html")
-TEMPLATE = string.Template(open(TEMPLATE_PATH, "r").read())
+TEMPLATE = string.Template(open(TEMPLATE_PATH).read())
 
 
 def main(argv=None):
@@ -16,7 +14,7 @@ def main(argv=None):
     title = argv[1]
     markdown_source = argv[2]
     output = os.path.splitext(markdown_source)[0] + '.html'
-    with open(markdown_source, "r") as s:
+    with open(markdown_source) as s:
         content = s.read()
     html = TEMPLATE.safe_substitute(**{
         'title': title,

scripts/summarize_timings.py

@@ -1,5 +1,4 @@
 """Script to parse timings out of a Galaxy log and summarize."""
-from __future__ import print_function
 
 import re
 from argparse import ArgumentParser
@@ -24,7 +23,7 @@ def main(argv=None):
     pattern_str = args.pattern
     filter_pattern = re.compile(pattern_str) if pattern_str is not None else None
     times = []
-    for line in open(args.file, "r"):
+    for line in open(args.file):
         if filter_pattern and not filter_pattern.search(line):
             continue
 

scripts/tool_shed/api/common.py

@@ -1,12 +1,8 @@
-from __future__ import print_function
-
 import json
 import os
 import sys
-
-import six
-from six.moves.urllib.error import HTTPError
-from six.moves.urllib.request import (
+from urllib.error import HTTPError
+from urllib.request import (
     build_opener,
     HTTPRedirectHandler,
     install_opener,
@@ -94,7 +90,7 @@ def display(url, api_key=None, return_formatted=True):
         # Only return the first 1K of errors.
         print(e.read(1024))
         sys.exit(1)
-    if isinstance(r, six.text_type):
+    if isinstance(r, str):
         print('error: %s' % r)
         return None
     if not return_formatted:
@@ -111,7 +107,7 @@ def display(url, api_key=None, return_formatted=True):
             if 'name' in i:
                 print('  name: %s' % i.pop('name'))
             for k, v in i.items():
-                print('  %s: %s' % (k, v))
+                print(f'  {k}: {v}')
         print()
         print('%d element(s) in collection' % len(r))
     elif isinstance(r, dict):
@@ -119,7 +115,7 @@ def display(url, api_key=None, return_formatted=True):
         print('Member Information')
         print('------------------')
         for k, v in r.items():
-            print('%s: %s' % (k, v))
+            print(f'{k}: {v}')
     else:
         print('response is unknown type: %s' % type(r))
 
@@ -133,7 +129,7 @@ def get(url, api_key=None):
         sys.exit("URL did not return JSON data")
 
 
-def get_api_url(base, parts=[], params=None):
+def get_api_url(base, parts, params=None):
     """Compose and return a URL for the Tool Shed API."""
     if 'api' in parts and parts.index('api') != 0:
         parts.pop(parts.index('api'))
@@ -271,7 +267,7 @@ def submit(url, data, api_key=None, return_formatted=True):
                 if 'name' in i:
                     print('  name: %s' % i.pop('name'))
                 for k, v in i.items():
-                    print('  %s: %s' % (k, v))
+                    print(f'  {k}: {v}')
             else:
                 print(i)
     else:

scripts/tool_shed/api/create_categories.py

@@ -17,7 +17,6 @@ available in the test public Tool Shed and create each of them in a local develo
 
 ./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009
 """
-from __future__ import print_function
 
 import argparse
 

scripts/tool_shed/api/create_users.py

@@ -18,7 +18,6 @@ are available in the test public Tool Shed and create each of them in a local de
 
 ./create_users.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009
 """
-from __future__ import print_function
 
 import argparse
 

scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py

@@ -1,11 +1,10 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import optparse
 import os
 import sys
+from configparser import ConfigParser
 
-from six.moves.configparser import ConfigParser
 from sqlalchemy.exc import OperationalError, ProgrammingError
 
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
@@ -99,7 +98,7 @@ def get_local_tool_shed_url(config_parser):
         if config_parser.has_option('server:main', 'port'):
             port = config_parser.get('server:main', 'port')
     host = '127.0.0.1'
-    print('http://%s:%s' % (host, port))
+    print(f'http://{host}:{port}')
     return 0
 
 
@@ -115,7 +114,7 @@ def main(args):
         return check_db(config_parser)
     elif args.method == 'admin_user_info':
         (username, email, password) = admin_user_info()
-        print('%s__SEP__%s__SEP__%s' % (username, email, password))
+        print(f'{username}__SEP__{email}__SEP__{password}')
         return 0
     elif args.method == 'get_url':
         return get_local_tool_shed_url(config_parser)

scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py

@@ -1,12 +1,10 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import logging
 import optparse
 import os
 import sys
-
-from six.moves.configparser import ConfigParser
+from configparser import ConfigParser
 
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
 sys.path.insert(1, os.path.join(os.path.dirname(__file__)))
@@ -24,7 +22,7 @@ from bootstrap_util import admin_user_info  # noqa: I100,I201
 log = logging.getLogger(__name__)
 
 
-class BootstrapApplication(object):
+class BootstrapApplication:
     """
     Creates a basic Tool Shed application in order to discover the database connection and use SQL
     to create a user and API key.

scripts/tool_shed/build_ts_whoosh_index.py

@@ -10,7 +10,6 @@ Make sure you adjust your Toolshed config to:
 
 This script expects the Tool Shed's runtime virtualenv to be active.
 """
-from __future__ import print_function
 
 import argparse
 import logging

scripts/tool_shed/deprecate_repositories_without_metadata.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
+import configparser
 import logging
 import os
 import string
@@ -12,7 +12,6 @@ from optparse import OptionParser
 from time import strftime
 
 import sqlalchemy as sa
-from six.moves import configparser
 from sqlalchemy import and_, distinct, false, not_
 
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib'))
@@ -92,7 +91,7 @@ def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
     body += '\n'.join(build_citable_url(url, repository) for repository in repositories_deprecated)
     try:
         galaxy_send_mail(from_address, email, subject, body, app.config)
-        print("# An email has been sent to %s, the owner of %s." % (owner, ', '.join(repository.name for repository in repositories_deprecated)))
+        print("# An email has been sent to {}, the owner of {}.".format(owner, ', '.join(repository.name for repository in repositories_deprecated)))
         return True
     except Exception as e:
         print("# An error occurred attempting to send email: %s" % e)
@@ -130,10 +129,10 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
             .filter(app.model.Repository.table.c.id == repository_id).one()
         owner = repository.user
         if info_only:
-            print('# Repository %s owned by %s would have been deprecated, but info_only was set.' % (repository.name, repository.user.username))
+            print(f'# Repository {repository.name} owned by {repository.user.username} would have been deprecated, but info_only was set.')
         else:
             if verbose:
-                print('# Deprecating repository %s owned by %s.' % (repository.name, owner.username))
+                print(f'# Deprecating repository {repository.name} owned by {owner.username}.')
             if owner.username not in repositories_by_owner:
                 repositories_by_owner[owner.username] = dict(owner=owner, repositories=[])
             repositories_by_owner[owner.username]['repositories'].append(repository)
@@ -152,7 +151,7 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
     print("####################################################################################")
 
 
-class DeprecateRepositoriesApplication(object):
+class DeprecateRepositoriesApplication:
     """Encapsulates the state of a Universe application"""
     def __init__(self, config):
         if config.database_connection is False:

scripts/tools/maf/check_loc_file.py

@@ -1,7 +1,6 @@
 # Dan Blankenberg
 # This script checks maf_index.loc file for inconsistencies between what is listed as available and what is really available.
 # Make sure that required dependencies (e.g. galaxy_root/lib) are included in your PYTHONPATH
-from __future__ import print_function
 
 import sys
 

scripts/tools/re_escape_output.py

@@ -21,7 +21,7 @@ def __main__():
             suffix = 're_match_multiline'
         else:
             suffix = 're_match'
-        output = open("%s.%s" % (args[0], suffix), 'wb')
+        output = open("{}.{}".format(args[0], suffix), 'wb')
     if options.multiline:
         lines = [re.escape(input.read())]
     else:

scripts/update_shed_config_path.py

@@ -1,10 +1,8 @@
-from __future__ import print_function
-
 import argparse
 import os
 import sys
+from configparser import ConfigParser
 
-from six.moves.configparser import SafeConfigParser
 from sqlalchemy import create_engine, MetaData
 from sqlalchemy.orm import scoped_session, sessionmaker
 
@@ -27,7 +25,7 @@ def main(opts, session, model):
 
 
 def create_database(config_file):
-    parser = SafeConfigParser()
+    parser = ConfigParser()
     parser.read(config_file)
     # Determine which database connection to use.
     database_connection = parser.get('app:main', 'install_database_connection')