Merge pull request #464 from satra/sty/black

Style update files with latest release of black

Author: satra

.github/workflows/teststyle.yml

@@ -25,5 +25,5 @@ jobs:
 
     - name: Check Style
       run: |
-        pip install black==19.3b0 codecov
+        pip install black==21.4b2 codecov
         black --check pydra setup.py

.pre-commit-config.yaml

@@ -9,6 +9,6 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 21.4b2
     hooks:
     -   id: black

pydra/engine/boutiques.py

@@ -107,8 +107,8 @@ def _download_spec(self, zenodo_id):
             return zenodo_file
 
     def _prepare_input_spec(self, names_subset=None):
-        """ creating input spec from the zenodo file
-            if name_subset provided, only names from the subset will be used in the spec
+        """creating input spec from the zenodo file
+        if name_subset provided, only names from the subset will be used in the spec
         """
         binputs = self.bosh_spec["inputs"]
         self._input_spec_keys = {}
@@ -148,8 +148,8 @@ def _prepare_input_spec(self, names_subset=None):
         return spec
 
     def _prepare_output_spec(self, names_subset=None):
-        """ creating output spec from the zenodo file
-            if name_subset provided, only names from the subset will be used in the spec
+        """creating output spec from the zenodo file
+        if name_subset provided, only names from the subset will be used in the spec
         """
         boutputs = self.bosh_spec["output-files"]
         fields = []

pydra/engine/core.py

@@ -238,10 +238,10 @@ def errored(self):
 
     @property
     def checksum(self):
-        """ Calculates the unique checksum of the task.
-            Used to create specific directory name for task that are run;
-            and to create nodes checksums needed for graph checkums
-            (before the tasks have inputs etc.)
+        """Calculates the unique checksum of the task.
+        Used to create specific directory name for task that are run;
+        and to create nodes checksums needed for graph checkums
+        (before the tasks have inputs etc.)
         """
         input_hash = self.inputs.hash
         if self.state is None:
@@ -305,9 +305,9 @@ def checksum_states(self, state_index=None):
 
     @property
     def uid(self):
-        """ the unique id number for the task
-            It will be used to create unique names for slurm scripts etc.
-            without a need to run checksum
+        """the unique id number for the task
+        It will be used to create unique names for slurm scripts etc.
+        without a need to run checksum
         """
         return self._uid
 
@@ -334,16 +334,16 @@ def set_state(self, splitter, combiner=None):
     @property
     def output_names(self):
         """Get the names of the outputs from the task's output_spec
-            (not everything has to be generated, see generated_output_names).
+        (not everything has to be generated, see generated_output_names).
         """
         return [f.name for f in attr.fields(make_klass(self.output_spec))]
 
     @property
     def generated_output_names(self):
-        """ Get the names of the outputs generated by the task.
-            If the spec doesn't have generated_output_names method,
-            it uses output_names.
-            The results depends on the input provided to the task
+        """Get the names of the outputs generated by the task.
+        If the spec doesn't have generated_output_names method,
+        it uses output_names.
+        The results depends on the input provided to the task
         """
         output_klass = make_klass(self.output_spec)
         if hasattr(output_klass, "generated_output_names"):
@@ -606,7 +606,7 @@ def get_input_el(self, ind):
             return None, inputs_dict
 
     def pickle_task(self):
-        """ Pickling the tasks with full inputs"""
+        """Pickling the tasks with full inputs"""
         pkl_files = self.cache_dir / "pkl_files"
         pkl_files.mkdir(exist_ok=True, parents=True)
         task_main_path = pkl_files / f"{self.name}_{self.uid}_task.pklz"
@@ -862,10 +862,10 @@ def graph_sorted(self):
 
     @property
     def checksum(self):
-        """ Calculates the unique checksum of the task.
-            Used to create specific directory name for task that are run;
-            and to create nodes checksums needed for graph checkums
-            (before the tasks have inputs etc.)
+        """Calculates the unique checksum of the task.
+        Used to create specific directory name for task that are run;
+        and to create nodes checksums needed for graph checkums
+        (before the tasks have inputs etc.)
         """
         # if checksum is called before run the _graph_checksums is not ready
         if is_workflow(self) and self.inputs._graph_checksums is attr.NOTHING:
@@ -884,8 +884,8 @@ def checksum(self):
         return self._checksum
 
     def _checksum_wf(self, input_hash, with_splitter=False):
-        """ creating hash value for workflows
-            includes connections and splitter if with_splitter is True
+        """creating hash value for workflows
+        includes connections and splitter if with_splitter is True
         """
         connection_hash = hash_function(self._connections)
         hash_list = [input_hash, connection_hash]

pydra/engine/graph.py

@@ -99,9 +99,9 @@ def edges_names(self):
 
     @property
     def nodes_details(self):
-        """ dictionary with details of the nodes
-            for each task, there are inputs/outputs and connections
-            (with input/output fields names)
+        """dictionary with details of the nodes
+        for each task, there are inputs/outputs and connections
+        (with input/output fields names)
         """
         # removing repeated fields from inputs and outputs
         for el in self._nodes_details.values():
@@ -156,7 +156,7 @@ def add_edges(self, new_edges):
             self.sorting(presorted=self.sorted_nodes + [])
 
     def add_edges_description(self, new_edge_details):
-        """ adding detailed description of the connections, filling _nodes_details"""
+        """adding detailed description of the connections, filling _nodes_details"""
         in_nd, in_fld, out_nd, out_fld = new_edge_details
         for key in [in_nd, out_nd]:
             self._nodes_details.setdefault(
@@ -309,7 +309,7 @@ def _checking_successors_nodes(self, node, remove=True):
             return True
 
     def remove_successors_nodes(self, node):
-        """ Removing all the nodes that follow the node"""
+        """Removing all the nodes that follow the node"""
         self._successors_all = []
         self._checking_successors_nodes(node=node, remove=False)
         self.remove_nodes_connections(nodes=node)
@@ -352,7 +352,7 @@ def calculate_max_paths(self):
             self._checking_path(node_name=nm, first_name=nm)
 
     def create_dotfile_simple(self, outdir, name="graph"):
-        """ creates a simple dotfile (no nested structure)"""
+        """creates a simple dotfile (no nested structure)"""
         from .core import is_workflow
 
         dotstr = "digraph G {\n"
@@ -384,7 +384,7 @@ def create_dotfile_simple(self, outdir, name="graph"):
         return dotfile
 
     def create_dotfile_detailed(self, outdir, name="graph_det"):
-        """ creates a detailed dotfile (detailed connections - input/output fields,
+        """creates a detailed dotfile (detailed connections - input/output fields,
         but no nested structure)
         """
         dotstr = "digraph structs {\n"
@@ -492,7 +492,7 @@ def _create_dotfile_single_graph(self, nodes, edges):
         return dotstr
 
     def export_graph(self, dotfile, ext="png"):
-        """ exporting dotfile to other format, equires the dot command"""
+        """exporting dotfile to other format, equires the dot command"""
         available_ext = [
             "bmp",
             "canon",

pydra/engine/helpers.py

@@ -159,7 +159,7 @@ def save(task_path: Path, result=None, task=None, name_prefix=None):
 
 
 def copyfile_workflow(wf_path, result):
-    """ if file in the wf results, the file will be copied to the workflow directory"""
+    """if file in the wf results, the file will be copied to the workflow directory"""
     for field in attr_fields(result.output):
         value = getattr(result.output, field.name)
         # if the field is a path or it can contain a path _copyfile_single_value is run
@@ -175,7 +175,7 @@ def copyfile_workflow(wf_path, result):
 
 
 def _copyfile_single_value(wf_path, value):
-    """ checking a single value for files that need to be copied to the wf dir"""
+    """checking a single value for files that need to be copied to the wf dir"""
     if isinstance(value, (tuple, list)):
         return [_copyfile_single_value(wf_path, val) for val in value]
     elif isinstance(value, dict):
@@ -369,7 +369,7 @@ def custom_validator(instance, attribute, value):
 
 
 def _type_validator(instance, attribute, value, tp, cont_type):
-    """ creating a customized type validator,
+    """creating a customized type validator,
     uses validator.deep_iterable/mapping if the field is a container
     (i.e. ty.List or ty.Dict),
     it also tries to guess when the value is a list due to the splitter
@@ -421,9 +421,9 @@ def _types_updates(tp_list, name):
 
 
 def _single_type_update(tp, name, simplify=False):
-    """ updating a single type with other related types - e.g. adding bytes for str
-        if simplify is True, than changing typing.List to list etc.
-        (assuming that I validate only one depth, so have to simplify at some point)
+    """updating a single type with other related types - e.g. adding bytes for str
+    if simplify is True, than changing typing.List to list etc.
+    (assuming that I validate only one depth, so have to simplify at some point)
     """
     if isinstance(tp, type) or tp in [File, Directory]:
         if tp is str:
@@ -456,7 +456,7 @@ def _single_type_update(tp, name, simplify=False):
 
 
 def _check_special_type(tp, name):
-    """checking if the type is a container: ty.List, ty.Dict or ty.Union """
+    """checking if the type is a container: ty.List, ty.Dict or ty.Union"""
     if sys.version_info.minor >= 8:
         return ty.get_origin(tp), ty.get_args(tp)
     else:
@@ -477,7 +477,7 @@ def _check_special_type(tp, name):
 
 
 def _allowed_values_validator(instance, attribute, value):
-    """ checking if the values is in allowed_values"""
+    """checking if the values is in allowed_values"""
     allowed = attribute.metadata["allowed_values"]
     if value is attr.NOTHING:
         pass
@@ -769,9 +769,9 @@ def load_and_run(
     task_pkl, ind=None, rerun=False, submitter=None, plugin=None, **kwargs
 ):
     """
-     loading a task from a pickle file, settings proper input
-     and running the task
-     """
+    loading a task from a pickle file, settings proper input
+    and running the task
+    """
     try:
         task = load_task(task_pkl=task_pkl, ind=ind)
     except Exception as excinfo:
@@ -813,7 +813,7 @@ async def load_and_run_async(task_pkl, ind=None, submitter=None, rerun=False, **
 
 
 def load_task(task_pkl, ind=None):
-    """ loading a task from a pickle file, settings proper input for the specific ind"""
+    """loading a task from a pickle file, settings proper input for the specific ind"""
     if isinstance(task_pkl, str):
         task_pkl = Path(task_pkl)
     task = cp.loads(task_pkl.read_bytes())
@@ -863,7 +863,7 @@ def position_sort(args):
 
 
 def argstr_formatting(argstr, inputs, value_updates=None):
-    """ formatting argstr that have form {field_name},
+    """formatting argstr that have form {field_name},
     using values from inputs and updating with value_update if provided
     """
     inputs_dict = attr.asdict(inputs)

pydra/engine/helpers_file.py

@@ -741,7 +741,7 @@ def is_local_file(f):
 
 
 def is_existing_file(value):
-    """ checking if an object is an existing file"""
+    """checking if an object is an existing file"""
     if isinstance(value, str) and value == "":
         return False
     try:

pydra/engine/helpers_state.py

@@ -307,7 +307,7 @@ def rpn2splitter(splitter_rpn):
 
 
 def add_name_combiner(combiner, name):
-    """ adding a node's name to each field from the combiner"""
+    """adding a node's name to each field from the combiner"""
     combiner_changed = []
     for comb in combiner:
         if "." not in comb:
@@ -318,7 +318,7 @@ def add_name_combiner(combiner, name):
 
 
 def add_name_splitter(splitter, name):
-    """ adding a node's name to each field from the splitter"""
+    """adding a node's name to each field from the splitter"""
     if isinstance(splitter, str):
         return _add_name([splitter], name)[0]
     elif isinstance(splitter, list):
@@ -329,7 +329,7 @@ def add_name_splitter(splitter, name):
 
 
 def _add_name(mlist, name):
-    """ adding anem to each element from the list"""
+    """adding anem to each element from the list"""
     for i, elem in enumerate(mlist):
         if isinstance(elem, str):
             if "." in elem or elem.startswith("_"):
@@ -371,7 +371,7 @@ def iter_splits(iterable, keys):
 
 
 def input_shape(inp, cont_dim=1):
-    """Get input shape, depends on the container dimension, if not specify it is assumed to be 1 """
+    """Get input shape, depends on the container dimension, if not specify it is assumed to be 1"""
     # TODO: have to be changed for inner splitter (sometimes different length)
     cont_dim -= 1
     shape = [len(inp)]
@@ -536,7 +536,7 @@ def splits(splitter_rpn, inputs, inner_inputs=None, cont_dim=None):
 def _single_op_splits(
     op_single, inputs, inner_inputs, previous_states_ind, cont_dim=None
 ):
-    """ splits function if splitter is a singleton"""
+    """splits function if splitter is a singleton"""
     if op_single.startswith("_"):
         return (previous_states_ind[op_single][0], previous_states_ind[op_single][1])
     if cont_dim is None:
@@ -562,8 +562,8 @@ def _single_op_splits(
 
 
 def splits_groups(splitter_rpn, combiner=None, inner_inputs=None):
-    """ splits inputs to groups (axes) and creates stacks for these groups
-        This is used to specify which input can be combined.
+    """splits inputs to groups (axes) and creates stacks for these groups
+    This is used to specify which input can be combined.
     """
     if not splitter_rpn:
         return [], {}, [], []
@@ -696,7 +696,7 @@ def splits_groups(splitter_rpn, combiner=None, inner_inputs=None):
 
 
 def _single_op_splits_groups(op_single, combiner, inner_inputs, groups):
-    """ splits_groups function if splitter is a singleton"""
+    """splits_groups function if splitter is a singleton"""
     if op_single in inner_inputs:
         # TODO: have to be changed if differ length
         # TODO: i think I don't want to add here from left part

pydra/engine/specs.py

@@ -476,9 +476,9 @@ def collect_additional_outputs(self, inputs, output_dir, outputs):
         return additional_out
 
     def generated_output_names(self, inputs, output_dir):
-        """ Returns a list of all outputs that will be generated by the task.
-            Takes into account the task input and the requires list for the output fields.
-            TODO: should be in all Output specs?
+        """Returns a list of all outputs that will be generated by the task.
+        Takes into account the task input and the requires list for the output fields.
+        TODO: should be in all Output specs?
         """
         # checking the input (if all mandatory fields are provided, etc.)
         inputs.check_fields_input_spec()
@@ -575,8 +575,8 @@ def _field_metadata(self, fld, inputs, output_dir, outputs=None):
             raise Exception("(_field_metadata) is not a current valid metadata key.")
 
     def _check_requires(self, fld, inputs):
-        """ checking if all fields from the requires and template are set in the input
-            if requires is a list of list, checking if at least one list has all elements set
+        """checking if all fields from the requires and template are set in the input
+        if requires is a list of list, checking if at least one list has all elements set
         """
         from .helpers import ensure_list