[pre-commit.ci] pre-commit autoupdate (#618)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 22.12.0 → 23.1.0](psf/black@22.12.0...23.1.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
     -   id: black
 -   repo: https://github.com/codespell-project/codespell

pydra/__init__.py

@@ -23,7 +23,6 @@
 
 
 def check_latest_version():
-
     import etelemetry
 
     return etelemetry.check_available_version("nipype/pydra", __version__, lgr=logger)

pydra/engine/core.py

@@ -696,7 +696,7 @@ def done(self):
 
     def _combined_output(self, return_inputs=False):
         combined_results = []
-        for (gr, ind_l) in self.state.final_combined_ind_mapping.items():
+        for gr, ind_l in self.state.final_combined_ind_mapping.items():
             combined_results_gr = []
             for ind in ind_l:
                 result = load_result(self.checksum_states(ind), self.cache_locations)
@@ -1253,7 +1253,7 @@ def create_dotfile(self, type="simple", export=None, name=None, output_dir=None)
             for task in self.graph.nodes:
                 self.create_connections(task, detailed=True)
             # adding wf outputs
-            for (wf_out, lf) in self._connections:
+            for wf_out, lf in self._connections:
                 self.graph.add_edges_description((self.name, wf_out, lf.name, lf.field))
             dotfile = self.graph.create_dotfile_detailed(outdir=outdir, name=name)
         else:

pydra/engine/graph.py

@@ -85,7 +85,7 @@ def edges(self, edges):
         """Add edges to the graph (nodes should be already set)."""
         if edges:
             edges = ensure_list(edges)
-            for (nd_out, nd_in) in edges:
+            for nd_out, nd_in in edges:
                 if nd_out not in self.nodes or nd_in not in self.nodes:
                     raise Exception(
                         f"edge {(nd_out, nd_in)} can't be added to the graph"
@@ -131,7 +131,7 @@ def _create_connections(self):
             self.predecessors[nd.name] = []
             self.successors[nd.name] = []
 
-        for (nd_out, nd_in) in self.edges:
+        for nd_out, nd_in in self.edges:
             self.predecessors[nd_in.name].append(nd_out)
             self.successors[nd_out.name].append(nd_in)
 
@@ -148,7 +148,7 @@ def add_nodes(self, new_nodes):
     def add_edges(self, new_edges):
         """Add new edges and sort the new graph."""
         self.edges = self._edges + ensure_list(new_edges)
-        for (nd_out, nd_in) in ensure_list(new_edges):
+        for nd_out, nd_in in ensure_list(new_edges):
             self.predecessors[nd_in.name].append(nd_out)
             self.successors[nd_out.name].append(nd_in)
         if self._sorted_nodes is not None:

pydra/engine/helpers_state.py

@@ -237,7 +237,7 @@ def remove_inp_from_splitter_rpn(splitter_rpn, inputs_to_remove):
     stack_inp = []
     stack_sgn = []
     from_last_sign = []
-    for (ii, el) in enumerate(splitter_rpn_copy):
+    for ii, el in enumerate(splitter_rpn_copy):
         # element is a sign
         if el == "." or el == "*":
             stack_sgn.append((ii, el))
@@ -589,7 +589,7 @@ def combine_final_groups(combiner, groups, groups_stack, keys):
     gr_final = list(gr_final)
     map_gr_nr = {nr: i for (i, nr) in enumerate(sorted(gr_final))}
     groups_final_map = {}
-    for (inp, gr) in groups_final.items():
+    for inp, gr in groups_final.items():
         if isinstance(gr, int):
             groups_final_map[inp] = map_gr_nr[gr]
         elif isinstance(gr, list):

pydra/engine/task.py

@@ -654,7 +654,6 @@ def _check_inputs(self):
                 or "pydra.engine.specs.File" in str(fld.type)
                 or "pydra.engine.specs.Directory" in str(fld.type)
             ):
-
                 if fld.name == "image":
                     continue
                 file = Path(getattr(self.inputs, fld.name))

pydra/engine/tests/test_shelltask.py

@@ -3251,6 +3251,7 @@ def test_shell_cmd_outputspec_8d(tmpdir, plugin, results_function):
     """
     customised output_spec, adding Directory to the output named by input spec
     """
+
     # For /tmp/some_dict/test this function returns "/test"
     def get_lowest_directory(directory_path):
         return str(directory_path).replace(str(Path(directory_path).parents[0]), "")
@@ -4395,7 +4396,8 @@ def test_shell_cmd_non_existing_outputs_1(tmpdir):
 
 def test_shell_cmd_non_existing_outputs_2(tmpdir):
     """Checking that non existing output files do not return a phantom path,
-    but return NOTHING instead. This test has one existing and one non existing output file."""
+    but return NOTHING instead. This test has one existing and one non existing output file.
+    """
     input_spec = SpecInfo(
         name="Input",
         fields=[
@@ -4460,7 +4462,8 @@ def test_shell_cmd_non_existing_outputs_2(tmpdir):
 
 def test_shell_cmd_non_existing_outputs_3(tmpdir):
     """Checking that non existing output files do not return a phantom path,
-    but return NOTHING instead. This test has an existing mandatory output and another non existing output file."""
+    but return NOTHING instead. This test has an existing mandatory output and another non existing output file.
+    """
     input_spec = SpecInfo(
         name="Input",
         fields=[
@@ -4886,7 +4889,6 @@ def formatter_1(in1, in2):
 
 @no_win
 def test_shellcommand_error_msg(tmpdir):
-
     script_path = Path(tmpdir) / "script.sh"
 
     with open(script_path, "w") as f:

pydra/engine/workers.py

@@ -758,7 +758,6 @@ async def submit_array_job(self, sargs, tasks_to_run, error_file):
         self.output_by_jobid[jobid] = (rc, stdout, stderr)
 
         for task_pkl, ind, rerun in tasks_to_run:
-
             self.jobid_by_task_uid[Path(task_pkl).parent.name] = jobid
 
         if error_file:
@@ -813,7 +812,6 @@ async def _submit_job(
                     await asyncio.sleep(self.poll_delay)
 
     async def _poll_job(self, jobid, cache_dir):
-
         cmd = (f"qstat", "-j", jobid)
         logger.debug(f"Polling job {jobid}")
         rc, stdout, stderr = await read_and_display_async(*cmd, hide_display=True)