changed all imports to absolute imports

tclose · tclose · commit 5686862b13ac · 2025-03-19T21:08:54.000+11:00
diff --git a/pydra/engine/audit.py b/pydra/engine/audit.py
@@ -38,7 +38,7 @@ def __init__(self, audit_flags, messengers, messenger_args, develop=None):
             If True, the local context.jsonld file is used, otherwise the one from github is used.
 
         """
-        from .helpers import ensure_list
+        from pydra.engine.helpers import ensure_list
 
         self.audit_flags = audit_flags
         self.messengers = ensure_list(messengers)
@@ -97,7 +97,7 @@ def monitor(self):
     def finalize_audit(self, result):
         """End auditing."""
         if self.audit_check(AuditFlag.RESOURCE):
-            from .helpers import gather_runtime_info
+            from pydra.engine.helpers import gather_runtime_info
 
             self.resource_monitor.stop()
             result.runtime = gather_runtime_info(self.resource_monitor.fname)
@@ -184,7 +184,7 @@ def audit_check(self, flag):
 
     def audit_task(self, task: "Task"):
         import subprocess as sp
-        from .helpers import list_fields
+        from pydra.engine.helpers import list_fields
 
         label = task.name
 
diff --git a/pydra/engine/core.py b/pydra/engine/core.py
@@ -20,18 +20,18 @@
 from pydra.engine.specs import TaskDef, WorkflowDef, TaskOutputs, WorkflowOutputs
 from pydra.engine.graph import DiGraph, INPUTS_NODE_NAME, OUTPUTS_NODE_NAME
 from pydra.engine import state
-from .lazy import LazyInField, LazyOutField
+from pydra.engine.lazy import LazyInField, LazyOutField
 from pydra.utils.hash import hash_function, Cache
 from pydra.engine.state import State
-from .node import Node
+from pydra.engine.node import Node
 from datetime import datetime
 from fileformats.core import FileSet
-from .specs import (
+from pydra.engine.specs import (
     RuntimeSpec,
     Result,
     TaskHooks,
 )
-from .helpers import (
+from pydra.engine.helpers import (
     attrs_fields,
     attrs_values,
     fields_values,
@@ -43,7 +43,7 @@
     is_lazy,
     ensure_list,
 )
-from .helpers_file import copy_nested_files, template_update
+from pydra.engine.helpers_file import copy_nested_files, template_update
 from pydra.utils.messenger import AuditFlag
 from pydra.engine.environments import Environment
 
diff --git a/pydra/engine/environments.py b/pydra/engine/environments.py
@@ -1,7 +1,7 @@
 import typing as ty
 import os
 from copy import copy
-from .helpers import execute
+from pydra.engine.helpers import execute
 from pathlib import Path
 import logging
 from fileformats.generic import FileSet
diff --git a/pydra/engine/graph.py b/pydra/engine/graph.py
@@ -6,7 +6,7 @@
 from collections import Counter
 import subprocess as sp
 
-from .helpers import ensure_list
+from pydra.engine.helpers import ensure_list
 
 
 NodeType = ty.TypeVar("NodeType")
@@ -404,7 +404,7 @@ def calculate_max_paths(self):
 
     def create_dotfile_simple(self, outdir, name="graph"):
         """creates a simple dotfile (no nested structure)"""
-        from .core import is_workflow
+        from pydra.engine.core import is_workflow
 
         dotstr = "digraph G {\n"
         for nd in self.nodes:
@@ -503,7 +503,7 @@ def create_dotfile_nested(self, outdir, name="graph"):
         return dotfile
 
     def _create_dotfile_single_graph(self, nodes, edges):
-        from .core import is_workflow
+        from pydra.engine.core import is_workflow
 
         wf_asnd = {}
         dotstr = ""
diff --git a/pydra/engine/helpers.py b/pydra/engine/helpers.py
@@ -20,8 +20,8 @@
 
 
 if ty.TYPE_CHECKING:
-    from .specs import TaskDef, Result, WorkflowOutputs, WorkflowDef
-    from .core import Task
+    from pydra.engine.specs import TaskDef, Result, WorkflowOutputs, WorkflowDef
+    from pydra.engine.core import Task
     from pydra.design.base import Field
     from pydra.engine.lazy import LazyField
 
@@ -41,7 +41,7 @@ def plot_workflow(
     lazy: ty.Sequence[str] | ty.Set[str] = (),
 ):
     """creating a graph - dotfile and optionally exporting to other formats"""
-    from .core import Workflow
+    from pydra.engine.core import Workflow
 
     # Create output directory
     out_dir.mkdir(parents=True, exist_ok=True)
@@ -117,7 +117,7 @@ def fields_dict(definition: "type[TaskDef] | TaskDef") -> dict[str, "Field"]:
     return {f.name: f for f in list_fields(definition)}
 
 
-# from .specs import MultiInputFile, MultiInputObj, MultiOutputObj, MultiOutputFile
+# from pydra.engine.specs import MultiInputFile, MultiInputObj, MultiOutputObj, MultiOutputFile
 
 
 def from_list_if_single(obj: ty.Any) -> ty.Any:
@@ -252,7 +252,7 @@ def copyfile_workflow(
     wf_path: os.PathLike, outputs: "WorkflowOutputs"
 ) -> "WorkflowOutputs":
     """if file in the wf results, the file will be copied to the workflow directory"""
-    from .helpers_file import copy_nested_files
+    from pydra.engine.helpers_file import copy_nested_files
 
     for field in attrs_fields(outputs):
         value = getattr(outputs, field.name)
@@ -278,7 +278,7 @@ def gather_runtime_info(fname):
         A runtime object containing the collected information.
 
     """
-    from .specs import Runtime
+    from pydra.engine.specs import Runtime
 
     runtime = Runtime(rss_peak_gb=None, vms_peak_gb=None, cpu_peak_percent=None)
 
@@ -526,7 +526,7 @@ def load_and_run(task_pkl: Path, rerun: bool = False) -> Path:
         The path to the pickled result file
     """
 
-    from .specs import Result
+    from pydra.engine.specs import Result
 
     try:
         task: Task[DefType] = load_task(task_pkl=task_pkl)
diff --git a/pydra/engine/helpers_state.py b/pydra/engine/helpers_state.py
@@ -4,7 +4,7 @@
 from copy import deepcopy
 import logging
 import typing as ty
-from .helpers import ensure_list, attrs_values
+from pydra.engine.helpers import ensure_list, attrs_values
 
 logger = logging.getLogger("pydra")
 
diff --git a/pydra/engine/lazy.py b/pydra/engine/lazy.py
@@ -4,12 +4,12 @@
 from typing import Self
 from pydra.utils.typing import StateArray
 from pydra.utils.hash import hash_single
-from . import node
+from pydra.engine import node
 
 if ty.TYPE_CHECKING:
-    from .submitter import DiGraph, NodeExecution
-    from .core import Task, Workflow
-    from .specs import TaskDef
+    from pydra.engine.submitter import DiGraph, NodeExecution
+    from pydra.engine.core import Task, Workflow
+    from pydra.engine.specs import TaskDef
 
 
 T = ty.TypeVar("T")
@@ -73,7 +73,9 @@ def split(self) -> Self:
         """ "Splits" the lazy field over an array of nodes by replacing the sequence type
         of the lazy field with StateArray to signify that it will be "split" across
         """
-        from ..utils.typing import TypeParser  # pylint: disable=import-outside-toplevel
+        from pydra.utils.typing import (
+            TypeParser,
+        )  # pylint: disable=import-outside-toplevel
 
         # Modify the type of the lazy field to include the split across a state-array
         inner_type, prev_split_depth = TypeParser.strip_splits(self._type)
diff --git a/pydra/engine/node.py b/pydra/engine/node.py
@@ -2,7 +2,7 @@
 from copy import deepcopy
 from enum import Enum
 import attrs
-from . import lazy
+from pydra.engine import lazy
 from pydra.engine.helpers import (
     attrs_values,
     is_lazy,
@@ -11,8 +11,8 @@
 from pydra.engine.state import State
 
 if ty.TYPE_CHECKING:
-    from .core import Workflow
-    from .environments import Environment
+    from pydra.engine.core import Workflow
+    from pydra.engine.environments import Environment
     from pydra.engine.specs import TaskDef, TaskOutputs, TaskHooks
 
 
diff --git a/pydra/engine/specs.py b/pydra/engine/specs.py
@@ -20,7 +20,7 @@
 from pydra.utils.messenger import AuditFlag, Messenger
 from pydra.utils.typing import is_optional, optional_type
 from pydra.utils.hash import register_serializer, hash_single
-from .helpers import (
+from pydra.engine.helpers import (
     attrs_fields,
     attrs_values,
     is_lazy,
@@ -31,9 +31,9 @@
     fields_in_formatter,
     state_array_support,
 )
-from .helpers_file import template_update, template_update_single
-from . import helpers_state as hlpst
-from . import lazy
+from pydra.engine.helpers_file import template_update, template_update_single
+from pydra.engine import helpers_state as hlpst
+from pydra.engine import lazy
 from pydra.utils.hash import hash_function, Cache
 from pydra.utils.typing import (
     StateArray,
diff --git a/pydra/engine/state.py b/pydra/engine/state.py
@@ -4,8 +4,8 @@
 import itertools
 from functools import reduce
 import typing as ty
-from . import helpers_state as hlpst
-from .helpers import ensure_list
+from pydra.engine import helpers_state as hlpst
+from pydra.engine.helpers import ensure_list
 from pydra.utils.typing import StateArray, TypeParser
 
 op = {".": zip, "*": itertools.product}
diff --git a/pydra/engine/submitter.py b/pydra/engine/submitter.py
@@ -12,30 +12,30 @@
 from datetime import datetime
 from collections import defaultdict
 import attrs
-from .workers import Worker, WORKERS
-from .graph import DiGraph
-from .helpers import (
+from pydra.engine.workers import Worker, WORKERS
+from pydra.engine.graph import DiGraph
+from pydra.engine.helpers import (
     get_open_loop,
     list_fields,
     attrs_values,
 )
 from pydra.utils.hash import PersistentCache
 from pydra.engine.lazy import LazyField
-from .audit import Audit
-from .core import Task
+from pydra.engine.audit import Audit
+from pydra.engine.core import Task
 from pydra.utils.messenger import AuditFlag, Messenger
 from pydra.utils import default_run_cache_dir
 from pydra.design import workflow
-from .state import State
+from pydra.engine.state import State
 import logging
 
 logger = logging.getLogger("pydra.submitter")
 
 if ty.TYPE_CHECKING:
-    from .node import Node
-    from .specs import WorkflowDef, TaskDef, TaskOutputs, TaskHooks, Result
-    from .core import Workflow
-    from .environments import Environment
+    from pydra.engine.node import Node
+    from pydra.engine.specs import WorkflowDef, TaskDef, TaskOutputs, TaskHooks, Result
+    from pydra.engine.core import Workflow
+    from pydra.engine.environments import Environment
 
 
 DefType = ty.TypeVar("DefType", bound="TaskDef")
@@ -107,7 +107,7 @@ def __init__(
         if worker is None:
             worker = "debug"
 
-        from . import check_latest_version
+        from pydra.engine import check_latest_version
 
         if Task._etelemetry_version_data is None:
             Task._etelemetry_version_data = check_latest_version()
@@ -258,24 +258,24 @@ def Split(
             environment=environment,
             hooks=hooks,
         )
-        try:
-            self.run_start_time = datetime.now()
-            if self.worker.is_async:  # Only workflow tasks can be async
-                self.loop.run_until_complete(self.worker.run_async(task, rerun=rerun))
-            else:
-                self.worker.run(task, rerun=rerun)
-        except Exception as e:
-            msg = (
-                f"Full crash report for {type(task_def).__name__!r} task is here: "
-                + str(task.output_dir / "_error.pklz")
-            )
-            if raise_errors:
-                e.add_note(msg)
-                raise e
-            else:
-                logger.error("\nTask execution failed\n%s", msg)
-        finally:
-            self.run_start_time = None
+        # try:
+        self.run_start_time = datetime.now()
+        if self.worker.is_async:  # Only workflow tasks can be async
+            self.loop.run_until_complete(self.worker.run_async(task, rerun=rerun))
+        else:
+            self.worker.run(task, rerun=rerun)
+        # except Exception as e:
+        #     msg = (
+        #         f"Full crash report for {type(task_def).__name__!r} task is here: "
+        #         + str(task.output_dir / "_error.pklz")
+        #     )
+        #     if raise_errors:
+        #         e.add_note(msg)
+        #         raise e
+        #     else:
+        #         logger.error("\nTask execution failed\n%s", msg)
+        # finally:
+        #     self.run_start_time = None
         PersistentCache().clean_up()
         result = task.result()
         if result is None:
diff --git a/pydra/engine/task.py b/pydra/engine/task.py
@@ -44,18 +44,18 @@
 import attrs
 import json
 from pathlib import Path
-from .core import Task
+from pydra.engine.core import Task
 from pydra.utils.messenger import AuditFlag
-from .specs import (
+from pydra.engine.specs import (
     PythonDef,
     ShellDef,
     attrs_fields,
 )
-from .helpers import (
+from pydra.engine.helpers import (
     attrs_values,
 )
 from pydra.engine.helpers_file import is_local_file
-from .environments import Native
+from pydra.engine.environments import Native
 
 
 class PythonTask(Task):
diff --git a/pydra/engine/tests/test_shelltask.py b/pydra/engine/tests/test_shelltask.py
@@ -22,9 +22,7 @@
     StateArray,
 )
 from .utils import run_no_submitter, run_submitter, no_win, get_output_names
-import sys
 import platform
-import pytest
 
 if sys.platform.startswith("win"):
     pytest.skip("SLURM not available in windows", allow_module_level=True)
diff --git a/pydra/engine/workers.py b/pydra/engine/workers.py
@@ -12,9 +12,9 @@
 from shutil import copyfile, which
 import cloudpickle as cp
 import concurrent.futures as cf
-from .core import Task
-from .specs import TaskDef
-from .helpers import (
+from pydra.engine.core import Task
+from pydra.engine.specs import TaskDef
+from pydra.engine.helpers import (
     get_available_cpus,
     read_and_display_async,
     save,
@@ -27,7 +27,7 @@
 logger = logging.getLogger("pydra.worker")
 
 if ty.TYPE_CHECKING:
-    from .specs import Result
+    from pydra.engine.specs import Result
 
 DefType = ty.TypeVar("DefType", bound="TaskDef")
 
diff --git a/pydra/utils/hash.py b/pydra/utils/hash.py
@@ -26,8 +26,7 @@
 from fileformats.core.fileset import FileSet, MockMixin
 from fileformats.generic import FsObject
 import fileformats.core.exceptions
-from . import user_cache_dir, add_exc_note
-from .misc import in_stdlib
+from pydra.utils.misc import in_stdlib, user_cache_dir, add_exc_note
 
 logger = logging.getLogger("pydra")
 
