Merge pull request #1275 from bernt-matthias/topic/22.05

bump galaxy packages to 22.05

planemo/commands/cmd_autoupdate.py

@@ -93,7 +93,7 @@ def cli(ctx, paths, **kwds):  # noqa C901
 
     if any(r.type in {RunnableType.galaxy_tool, RunnableType.directory} for r in runnables):
         # update Galaxy tools
-        for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
+        for tool_path, tool_xml in yield_tool_sources_on_paths(ctx, paths, recursive):
             if tool_path.split("/")[-1] in tools_to_skip:
                 info("Skipping tool %s" % tool_path)
                 continue

planemo/commands/cmd_ci_find_tools.py

@@ -27,7 +27,7 @@ def cli(ctx, paths, **kwds):
     operations over for continuous integration operations.
     """
     tool_paths = []
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(ctx, paths, recursive=True):
+    for tool_path, tool_source in yield_tool_sources_on_paths(ctx, paths, recursive=True):
         if is_tool_load_error(tool_source):
             continue
         tool_paths.append(tool_path)

planemo/commands/cmd_shed_diff.py

@@ -84,7 +84,6 @@ def cli(ctx, paths, **kwds):
     }
 
     def diff(realized_repository):
-
         # We create a temporary redirection from kwds's
         # output to our tempfile. This lets us capture the
         # diff and redirect it to their requested location as

planemo/conda.py

@@ -87,7 +87,7 @@ def collect_conda_targets(ctx, paths, recursive=False, found_tool_callback=None)
         else:
             real_paths.append(path)
 
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(
+    for tool_path, tool_source in yield_tool_sources_on_paths(
         ctx, real_paths, recursive=recursive, exclude_deprecated=True
     ):
         if found_tool_callback:
@@ -132,9 +132,7 @@ def collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=False, found
     """
     conda_target_lists = set()
     tool_paths = collections.defaultdict(list)
-    for (tool_path, tool_source) in yield_tool_sources_on_paths(
-        ctx, paths, recursive=recursive, yield_load_errors=False
-    ):
+    for tool_path, tool_source in yield_tool_sources_on_paths(ctx, paths, recursive=recursive, yield_load_errors=False):
         try:
             if found_tool_callback:
                 found_tool_callback(tool_path)
@@ -153,7 +151,7 @@ def collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=False, found
 
 def tool_source_conda_targets(tool_source):
     """Load CondaTarget object from supplied abstract tool source."""
-    requirements, _ = tool_source.parse_requirements_and_containers()
+    requirements, *_ = tool_source.parse_requirements_and_containers()
     return conda_util.requirements_to_conda_targets(requirements)
 
 

planemo/engine/interface.py

@@ -75,7 +75,7 @@ def test(self, runnables, test_timeout):
         test_cases = [t for tl in map(cases, runnables) for t in tl]
         test_results = self._collect_test_results(test_cases, test_timeout)
         tests = []
-        for (test_case, run_response) in test_results:
+        for test_case, run_response in test_results:
             test_case_data = test_case.structured_test_data(run_response)
             tests.append(test_case_data)
         test_data = {

planemo/galaxy/activity.py

@@ -414,7 +414,6 @@ def _get_metadata(self, history_content_type, content_id):
             raise Exception("Unknown history content type encountered [%s]" % history_content_type)
 
     def collect_outputs(self, ctx, output_directory):
-
         outputs_dict = {}
         # TODO: rather than creating a directory just use
         # Galaxy paths if they are available in this

planemo/galaxy/config.py

@@ -26,8 +26,8 @@
     TYPE_CHECKING,
 )
 
-from galaxy.containers.docker_model import DockerVolume
 from galaxy.tool_util.deps import docker_util
+from galaxy.tool_util.deps.container_volumes import DockerVolume
 from galaxy.util.commands import argv_to_str
 from packaging.version import parse as parse_version
 

planemo/galaxy/workflows.py

@@ -164,7 +164,7 @@ def describe_outputs(runnable, gi=None):
         workflow = _raw_dict(runnable.path)
 
     outputs = []
-    for (order_index, step) in workflow["steps"].items():
+    for order_index, step in workflow["steps"].items():
         optional = False
         if not step.get("tool_id"):
             # One of the parameter types ... need eliminate this guesswork on the Galaxy side
@@ -370,7 +370,6 @@ def _elements_to_test_def(
 
 
 def _job_inputs_template_from_invocation(invocation_id, galaxy_url, galaxy_api_key):
-
     user_gi = gi(url=galaxy_url, key=galaxy_api_key)
     invocation = user_gi.invocations.show_invocation(invocation_id)
     template = {}

planemo/reports/allure.py

@@ -52,7 +52,6 @@ def process(self, structured_data, file_modication_datetime=None):
         plugin_manager.unregister(plugin=self.logger)
 
     def process_test_case(self, test_case, file_modication_datetime=None):
-
         with self.lifecycle.schedule_test_case() as test_result:
             test_index = test_case["id"]
             test_data = test_case.get("data") or {}

planemo/shed/__init__.py

@@ -963,7 +963,7 @@ def __init__(self, repo_pairs, description=None):
     def __str__(self):
         contents = '<repositories description="%s">' % self.description
         line_template = '  <repository owner="%s" name="%s" />\n'
-        for (owner, name) in self.repo_pairs:
+        for owner, name in self.repo_pairs:
             contents += line_template % (owner, name)
         contents += "</repositories>"
         return contents
@@ -1021,7 +1021,7 @@ def _realize_to(self, ctx, directory, name, multiple, **kwds):
                 continue
             realized_file.realize_to(directory)
 
-        for (name, contents) in config.get("_files", {}).items():
+        for name, contents in config.get("_files", {}).items():
             path = os.path.join(directory, name)
             with open(path, "w") as f:
                 f.write(contents)

planemo/shed_lint.py

@@ -121,7 +121,7 @@ def lint_repository(ctx, realized_repository, **kwds):
 
 def lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args):
     path = realized_repository.path
-    for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive=True):
+    for tool_path, tool_source in yield_tool_sources(ctx, path, recursive=True):
         original_path = tool_path.replace(path, realized_repository.real_path)
         info("+Linting tool %s" % original_path)
         if handle_tool_load_error(tool_path, tool_source):

planemo/tool_lint.py

@@ -36,7 +36,7 @@ def lint_tools_on_path(ctx, paths, lint_args, **kwds):
     assert_tools = kwds.get("assert_tools", True)
     recursive = kwds.get("recursive", False)
     exit_codes = []
-    for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
+    for tool_path, tool_xml in yield_tool_sources_on_paths(ctx, paths, recursive):
         if handle_tool_load_error(tool_path, tool_xml):
             exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
             continue

planemo/tools.py

@@ -56,7 +56,7 @@ def yield_tool_sources_on_paths(
 ) -> Iterator[Tuple[str, Union[ToolSource, object]]]:
     """Walk paths and yield ToolSource objects discovered."""
     for path in paths:
-        for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive, yield_load_errors):
+        for tool_path, tool_source in yield_tool_sources(ctx, path, recursive, yield_load_errors):
             if exclude_deprecated and "deprecated" in tool_path:
                 continue
             yield (tool_path, tool_source)
@@ -71,7 +71,7 @@ def yield_tool_sources(
         recursive,
         register_load_errors=True,
     )
-    for (tool_path, tool_source) in tools:
+    for tool_path, tool_source in tools:
         if is_tool_load_error(tool_source):
             if yield_load_errors:
                 yield (tool_path, tool_source)

requirements.txt

@@ -3,9 +3,8 @@ bioblend>=1.0.0
 click!=8.0.2
 cwltool>=1.0.20191225192155
 ephemeris>=0.10.3
-galaxy-containers<22.5
-galaxy-tool-util>=21.1.1,<22.5
-galaxy-util>=20.5.0,<22.5
+galaxy-tool-util>=22.5.dev2,<23.0
+galaxy-util[template]>=22.5.dev2,<23.0
 glob2
 gxformat2>=0.14.0
 h5py

tests/data/data_manager/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py

@@ -373,7 +373,6 @@ def _stream_fasta_to_file(fasta_stream, target_directory, sequence_id, close_str
     fasta_base_filename = "%s.fa" % sequence_id
     fasta_filename = os.path.join(target_directory, fasta_base_filename)
     with open(fasta_filename, "wb+") as fasta_writer:
-
         if isinstance(fasta_stream, list) and len(fasta_stream) == 1:
             fasta_stream = fasta_stream[0]