galaxyproject · jmchilton · Jun 23, 2025 · Jun 21, 2025 · Jun 21, 2025 · Jun 21, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.12.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.9
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
diff --git a/Makefile b/Makefile
@@ -73,7 +73,9 @@ lint: ## check style using tox and flake8 for Python 2 and Python 3
 test: ## run tests with the default Python (faster than tox)
 	$(IN_VENV) pytest $(TESTS)
 
-format: ## format Python code with black
+format: ## format Python code with ruff, black and isort
+	$(IN_VENV) ruff format planemo tests
+	$(IN_VENV) isort planemo tests
 	$(IN_VENV) black planemo tests
 
 quick-test: ## run quickest tests with the default Python

diff --git a/planemo/commands/cmd_share_test.py b/planemo/commands/cmd_share_test.py
@@ -9,7 +9,7 @@
 from planemo.cli import command_function
 from planemo.io import info
 
-PLANEMO_TEST_VIEWER_URL_TEMPLATE = "http://galaxyproject.github.io/planemo/tool_test_viewer.html" "?test_data_url=%s"
+PLANEMO_TEST_VIEWER_URL_TEMPLATE = "http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=%s"
 
 
 @click.command("share_test")

diff --git a/planemo/commands/cmd_shed_diff.py b/planemo/commands/cmd_shed_diff.py
@@ -35,7 +35,7 @@
 @click.option(
     "--raw",
     is_flag=True,
-    help="Do not attempt smart diff of XML to filter out attributes " "populated by the Tool Shed.",
+    help="Do not attempt smart diff of XML to filter out attributes populated by the Tool Shed.",
 )
 @options.report_xunit()
 @command_function

diff --git a/planemo/commands/cmd_shed_init.py b/planemo/commands/cmd_shed_init.py
@@ -16,7 +16,7 @@
 @click.option(
     "--from_workflow",
     type=click.Path(exists=True, file_okay=True, resolve_path=True),
-    help=("Attempt to generate repository dependencies from specified " "workflow."),
+    help=("Attempt to generate repository dependencies from specified workflow."),
 )
 @click.option("--description", help="Specify repository description for .shed.yml.")
 @click.option("--long_description", help="Specify repository long_description for .shed.yml.")

diff --git a/planemo/commands/cmd_shed_lint.py b/planemo/commands/cmd_shed_lint.py
@@ -26,8 +26,7 @@
     is_flag=True,
     default=False,
     help=(
-        "Ensure .shed.yml files contain enough metadata for each repository "
-        "to allow automated creation and/or updates."
+        "Ensure .shed.yml files contain enough metadata for each repository to allow automated creation and/or updates."
     ),
 )
 @click.option(

diff --git a/planemo/commands/cmd_shed_upload.py b/planemo/commands/cmd_shed_upload.py
@@ -28,7 +28,7 @@
 )
 @click.option(
     "--tar",
-    help="Specify a pre-existing tar file instead of automatically building " "one as part of this command.",
+    help="Specify a pre-existing tar file instead of automatically building one as part of this command.",
     type=tar_path,
     default=None,
 )

diff --git a/planemo/cwl/run.py b/planemo/cwl/run.py
@@ -34,7 +34,7 @@
 if TYPE_CHECKING:
     from planemo.cli import PlanemoCliContext
 
-JSON_PARSE_ERROR_MESSAGE = "Failed to parse JSON from cwltool output [%s] " "in file [%s]. cwltool logs [%s]."
+JSON_PARSE_ERROR_MESSAGE = "Failed to parse JSON from cwltool output [%s] in file [%s]. cwltool logs [%s]."
 
 
 class CwlToolRunResponse(SuccessfulRunResponse):

diff --git a/planemo/galaxy/activity.py b/planemo/galaxy/activity.py
@@ -575,7 +575,7 @@ def get_output(self, output_id):
     def download_output_to(self, ctx, dataset_details, output_directory, filename=None):
         extension = dataset_details["file_ext"]
         if filename is None:
-            local_filename = f'{sanitize_filename(dataset_details.get("cwl_file_name") or dataset_details.get("name"))}__{dataset_details["uuid"]}.{extension}'
+            local_filename = f"{sanitize_filename(dataset_details.get('cwl_file_name') or dataset_details.get('name'))}__{dataset_details['uuid']}.{extension}"
         else:
             local_filename = f"{filename}.{extension}"
         destination = os.path.join(output_directory, local_filename)

diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -413,7 +413,7 @@ def config_join(*args):
                 tool_data_table_config_path=",".join(tool_data_tables) if tool_data_tables else None,
                 data_manager_config_file=",".join(data_manager_config_paths)
                 or None,  # without 'or None' may raise IOError in galaxy (see #946)
-                integrated_tool_panel_config=("${temp_directory}/" "integrated_tool_panel_conf.xml"),
+                integrated_tool_panel_config=("${temp_directory}/integrated_tool_panel_conf.xml"),
                 migrated_tools_config=empty_tool_conf,
                 test_data_dir=test_data_dir,  # TODO: make gx respect this
                 shed_data_manager_config_file=shed_data_manager_config_file,

diff --git a/planemo/galaxy/distro_tools.py b/planemo/galaxy/distro_tools.py
@@ -41,12 +41,10 @@
     "__DATA_FETCH__": "${model_tools_path}/data_fetch.xml",
     "__IMPORT_HISTORY__": "${model_tools_path}/imp_exp/imp_history_from_archive.xml",
     "__EXPORT_HISTORY__": "${model_tools_path}/imp_exp/exp_history_to_archive.xml",
-    "__UNZIP_COLLECTION__": "${model_tools_path}/unzip_collection.xml",
     "__ZIP_COLLECTION__": "${model_tools_path}/zip_collection.xml",
     "__FILTER_FAILED_DATASETS__": "${model_tools_path}/filter_failed_collection.xml",
     "__FILTER_EMPTY_DATASETS__": "${model_tools_path}/filter_empty_collection.xml",
     "__FLATTEN__": "${model_tools_path}/flatten_collection.xml",
-    "__SORTLIST__": "${model_tools_path}/sort_collection_list.xml",
     "__MERGE_COLLECTION__": "${model_tools_path}/merge_collection.xml",
     "__RELABEL_FROM_FILE__": "${model_tools_path}/relabel_from_file.xml",
     "__FILTER_FROM_FILE__": "${model_tools_path}/filter_from_file.xml",

diff --git a/planemo/galaxy/invocations/api.py b/planemo/galaxy/invocations/api.py
@@ -45,7 +45,6 @@ class Job(TypedDict, total=False):
 
 
 class InvocationApi(Protocol):
-
     def get_invocation(self, invocation_id: str) -> Invocation: ...
 
     def get_invocation_summary(self, invocation_id: str, state: Optional[str] = None) -> InvocationJobsSummary: ...
@@ -56,7 +55,6 @@ def get_job(self, job_id: str, full_details: bool = False) -> Job: ...
 
 
 class BioblendInvocationApi(InvocationApi):
-
     def __init__(self, ctx, user_gi):
         self._ctx = ctx
         self._user_gi = user_gi

diff --git a/planemo/galaxy/invocations/polling.py b/planemo/galaxy/invocations/polling.py
@@ -15,12 +15,10 @@
 
 
 class PollingTracker(Protocol):
-
     def sleep(self) -> None: ...
 
 
 class PollingTrackerImpl(PollingTracker):
-
     def __init__(self, polling_backoff: int, timeout=None):
         self.polling_backoff = polling_backoff
         self.timeout = timeout

diff --git a/planemo/galaxy/invocations/progress.py b/planemo/galaxy/invocations/progress.py
@@ -44,7 +44,6 @@ class InvocationJobsSummary(TypedDict, total=False):
 
 
 class WorkflowProgress(Progress):
-
     _jobs_task: TaskID
     _steps_task: TaskID
     _subworkflows_task: Optional[TaskID] = None
@@ -339,7 +338,6 @@ def running_count(job_summary: InvocationJobsSummary) -> int:
 
 
 class WorkflowProgressDisplay(Live):
-
     def __init__(
         self,
         invocation_id: str,

diff --git a/planemo/galaxy/invocations/simulations.py b/planemo/galaxy/invocations/simulations.py
@@ -32,7 +32,6 @@ def tick_when_active(self) -> None: ...
 
 
 class StateWithDuration(Ticks):
-
     def __init__(self, state: str, duration: int):
         self.after = 0
         self.state = state
@@ -98,7 +97,6 @@ def active_jobs(self) -> List[Job]:
 
 
 class Invocation(HasState):
-
     def __init__(self, steps: List[InvocationStep], after: int, states: List[StateWithDuration]):
         self.id = str(uuid4())[:8]
         self.steps = steps

diff --git a/planemo/galaxy/run.py b/planemo/galaxy/run.py
@@ -44,7 +44,7 @@
 )
 
 
-CACHED_VIRTUAL_ENV_COMMAND = "if [ -d .venv ]; " "then GALAXY_VIRTUAL_ENV=.venv; " "else GALAXY_VIRTUAL_ENV=%s; fi"
+CACHED_VIRTUAL_ENV_COMMAND = "if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=%s; fi"
 UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
 
 

diff --git a/planemo/galaxy/test/actions.py b/planemo/galaxy/test/actions.py
@@ -22,20 +22,20 @@
 from . import structures as test_structures
 
 NO_XUNIT_REPORT_MESSAGE = (
-    "Cannot locate xUnit report [%s] for tests - " "required to build planemo report and summarize " "tests."
+    "Cannot locate xUnit report [%s] for tests - required to build planemo report and summarize tests."
 )
 NO_JSON_REPORT_MESSAGE = (
-    "Cannot locate JSON report [%s] for tests - " "required to build planemo report and summarize " "tests."
+    "Cannot locate JSON report [%s] for tests - required to build planemo report and summarize tests."
 )
 REPORT_NOT_CHANGED = (
-    "Galaxy failed to update test report [%s] for tests - " "required to build planemo report and summarize " "tests."
+    "Galaxy failed to update test report [%s] for tests - required to build planemo report and summarize tests."
 )
 NO_TESTS_MESSAGE = "No tests were executed - see Galaxy output for details."
 ALL_TESTS_PASSED_MESSAGE = "All %d test(s) executed passed."
 PROBLEM_COUNT_MESSAGE = (
-    "There were problems with %d test(s) - out of %d " "test(s) executed. See %s for detailed breakdown."
+    "There were problems with %d test(s) - out of %d test(s) executed. See %s for detailed breakdown."
 )
-GENERIC_PROBLEMS_MESSAGE = "One or more tests failed. See %s for detailed " "breakdown."
+GENERIC_PROBLEMS_MESSAGE = "One or more tests failed. See %s for detailed breakdown."
 GENERIC_TESTS_PASSED_MESSAGE = "No failing tests encountered."
 TEST_DATA_UPDATED_MESSAGE = "Test data were updated and tests were rerun."
 TEST_DATA_NOT_UPDATED_MESSAGE = "%s Therefore, no test data were updated." % ALL_TESTS_PASSED_MESSAGE

diff --git a/planemo/github_util.py b/planemo/github_util.py
@@ -27,7 +27,7 @@
 
 GH_VERSION = "1.5.0"
 
-NO_GITHUB_DEP_ERROR = "Cannot use github functionality - " "PyGithub library not available."
+NO_GITHUB_DEP_ERROR = "Cannot use github functionality - PyGithub library not available."
 FAILED_TO_DOWNLOAD_GH = "No gh executable available and it could not be installed."
 DEFAULT_REMOTE_NAME = "planemo-remote"
 SLEEP_BEFORE_RELEASE = int(os.environ.get("PLANEMO_SLEEP_BEFORE_RELEASE", 60))
-Original file line number
+Diff line change
@@ Expand Up / @@ -44,7 +44,7 @@ @@
     )
-    CACHED_VIRTUAL_ENV_COMMAND = "if [ -d .venv ]; " "then GALAXY_VIRTUAL_ENV=.venv; " "else GALAXY_VIRTUAL_ENV=%s; fi"
+    CACHED_VIRTUAL_ENV_COMMAND = "if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=%s; fi"
     UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
@@ Expand Down @@