jobflow 0.1.13__py3-none-any.whl → 0.1.15__py3-none-any.whl

jobflow/_version.py

@@ -1,7 +1,7 @@
-from pkg_resources import DistributionNotFound, get_distribution
+from importlib.metadata import PackageNotFoundError, version
 
 try:
-    __version__ = get_distribution("jobflow").version
-except DistributionNotFound:
+    __version__ = version("jobflow")
+except PackageNotFoundError:  # pragma: no cover
     # package is not installed
     __version__ = ""

jobflow/core/flow.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import logging
 import warnings
 from copy import deepcopy
-from typing import TYPE_CHECKING, Sequence
+from typing import TYPE_CHECKING
 
 from monty.json import MSONable
 
@@ -14,13 +14,13 @@ from jobflow.core.reference import find_and_get_references
 from jobflow.utils import ValueEnum, contains_flow_or_job, suuid
 
 if TYPE_CHECKING:
-    from typing import Any, Callable, Iterator
+    from collections.abc import Iterator, Sequence
+    from typing import Any, Callable
 
     from networkx import DiGraph
 
     from jobflow import Job
 
-__all__ = ["JobOrder", "Flow", "get_flow"]
 
 logger = logging.getLogger(__name__)
 
@@ -166,7 +166,7 @@ class Flow(MSONable):
             raise TypeError(
                 f"Flow can only contain Job or Flow objects, not {type(value).__name__}"
             )
-        jobs = list(self.jobs)
+        jobs = list(self)
         jobs[idx] = value  # type: ignore[index, assignment]
         self.jobs = tuple(jobs)
 
@@ -188,10 +188,10 @@ class Flow(MSONable):
 
     def __sub__(self, other: Flow | Job) -> Flow:
         """Remove a job or subflow from the flow."""
-        if other not in self.jobs:
+        if other not in self:
             raise ValueError(f"{other!r} not found in flow")
         new_flow = deepcopy(self)
-        new_flow.jobs = tuple([job for job in new_flow.jobs if job != other])
+        new_flow.jobs = tuple([job for job in new_flow if job != other])
         return new_flow
 
     def __repr__(self, level: int = 0, prefix: str = "") -> str:
@@ -201,8 +201,8 @@ class Flow(MSONable):
         _prefix = f"{prefix}." if prefix else ""
         job_reprs = "\n".join(
             f"{indent}{_prefix}{i}. "
-            f"{j.__repr__(level + 1, f'{_prefix}{i}') if isinstance(j, Flow) else j}"
-            for i, j in enumerate(self.jobs, 1)
+            f"{jb.__repr__(level + 1, f'{_prefix}{i}') if isinstance(jb, Flow) else jb}"
+            for i, jb in enumerate(self, 1)
         )
         return f"Flow({name=}, {uuid=})\n{job_reprs}"
 
@@ -298,7 +298,7 @@ class Flow(MSONable):
             The uuids of all Jobs in the Flow (including nested Flows).
         """
         uuids: list[str] = []
-        for job in self.jobs:
+        for job in self:
             if isinstance(job, Flow):
                 uuids.extend(job.job_uuids)
             else:
@@ -316,7 +316,7 @@ class Flow(MSONable):
             The uuids of all Jobs and Flows in the Flow (including nested Flows).
         """
         uuids: list[str] = []
-        for job in self.jobs:
+        for job in self:
             if isinstance(job, Flow):
                 uuids.extend(job.all_uuids)
             uuids.append(job.uuid)
@@ -336,7 +336,7 @@ class Flow(MSONable):
 
         import networkx as nx
 
-        graph = nx.compose_all([job.graph for job in self.jobs])
+        graph = nx.compose_all([job.graph for job in self])
 
         for node in graph:
             node_props = graph.nodes[node]
@@ -346,7 +346,7 @@ class Flow(MSONable):
         if self.order == JobOrder.LINEAR:
             # add fake edges between jobs to force linear order
             edges = []
-            for job_a, job_b in nx.utils.pairwise(self.jobs):
+            for job_a, job_b in nx.utils.pairwise(self):
                 if isinstance(job_a, Flow):
                     leaves = [v for v, d in job_a.graph.out_degree() if d == 0]
                 else:
@@ -474,7 +474,7 @@ class Flow(MSONable):
         >>> flow.update_kwargs({"number": 10}, name_filter="add")
         >>> flow.update_kwargs({"number": 10}, function_filter=add)
         """
-        for job in self.jobs:
+        for job in self:
             job.update_kwargs(
                 update,
                 name_filter=name_filter,
@@ -573,7 +573,7 @@ class Flow(MSONable):
         ...     {"number": 10}, class_filter=AddMaker, nested=False
         ... )
         """
-        for job in self.jobs:
+        for job in self:
             job.update_maker_kwargs(
                 update,
                 name_filter=name_filter,
@@ -598,7 +598,7 @@ class Flow(MSONable):
         else:
             self.name += append_str
 
-        for job in self.jobs:
+        for job in self:
             job.append_name(append_str, prepend=prepend)
 
     def update_metadata(
@@ -647,7 +647,7 @@ class Flow(MSONable):
 
         >>> flow.update_metadata({"tag": "addition_job"})
         """
-        for job in self.jobs:
+        for job in self:
             job.update_metadata(
                 update,
                 name_filter=name_filter,
@@ -717,7 +717,7 @@ class Flow(MSONable):
 
         >>> flow.update_config({"manager_config": {"_fworker": "myfworker"}})
         """
-        for job in self.jobs:
+        for job in self:
             job.update_config(
                 config,
                 name_filter=name_filter,
@@ -756,8 +756,8 @@ class Flow(MSONable):
                 self.hosts.extend(hosts_uuids)
         else:
             hosts_uuids = [self.uuid]
-        for j in self.jobs:
-            j.add_hosts_uuids(hosts_uuids, prepend=prepend)
+        for job in self:
+            job.add_hosts_uuids(hosts_uuids, prepend=prepend)
 
     def add_jobs(self, jobs: Job | Flow | Sequence[Flow | Job]) -> None:
         """
@@ -794,7 +794,8 @@ class Flow(MSONable):
                     f"current Flow ({self.uuid})"
                 )
             job_ids.add(job.uuid)
-            job.add_hosts_uuids(hosts)
+            if job.host != self.uuid:
+                job.add_hosts_uuids(hosts)
         self._jobs += tuple(jobs)
 
     def remove_jobs(self, indices: int | list[int]):
@@ -810,12 +811,12 @@ class Flow(MSONable):
         """
         if not isinstance(indices, (list, tuple)):
             indices = [indices]
-        if any(i < 0 or i >= len(self.jobs) for i in indices):
+        if any(idx < 0 or idx >= len(self) for idx in indices):
             raise ValueError(
                 "Only indices between 0 and the number of the jobs are accepted"
             )
 
-        new_jobs = tuple(j for i, j in enumerate(self.jobs) if i not in indices)
+        new_jobs = tuple(job for idx, job in enumerate(self) if idx not in indices)
         uuids: set = set()
         for job in new_jobs:
             if isinstance(job, Flow):

jobflow/core/job.py

@@ -13,7 +13,8 @@ from jobflow.core.reference import OnMissing, OutputReference
 from jobflow.utils.uuid import suuid
 
 if typing.TYPE_CHECKING:
-    from typing import Any, Callable, Hashable, Sequence
+    from collections.abc import Hashable, Sequence
+    from typing import Any, Callable
 
     from networkx import DiGraph
     from pydantic import BaseModel
@@ -22,8 +23,6 @@ if typing.TYPE_CHECKING:
 
 logger = logging.getLogger(__name__)
 
-__all__ = ["job", "Job", "Response", "JobConfig", "store_inputs"]
-
 
 @dataclass
 class JobConfig(MSONable):
@@ -560,6 +559,7 @@ class Job(MSONable):
 
         from jobflow import CURRENT_JOB
         from jobflow.core.flow import get_flow
+        from jobflow.core.schemas import JobStoreDocument
 
         index_str = f", {self.index}" if self.index != 1 else ""
         logger.info(f"Starting job - {self.name} ({self.uuid}{index_str})")
@@ -633,15 +633,15 @@ class Job(MSONable):
             ) from err
 
         save = {k: "output" if v is True else v for k, v in self._kwargs.items()}
-        data = {
-            "uuid": self.uuid,
-            "index": self.index,
-            "output": output,
-            "completed_at": datetime.now().isoformat(),
-            "metadata": self.metadata,
-            "hosts": self.hosts,
-            "name": self.name,
-        }
+        data: JobStoreDocument = JobStoreDocument(
+            uuid=self.uuid,
+            index=self.index,
+            output=output,
+            completed_at=datetime.now().isoformat(),
+            metadata=self.metadata,
+            hosts=self.hosts,
+            name=self.name,
+        )
         store.update(data, key=["uuid", "index"], save=save)
 
         CURRENT_JOB.reset()
@@ -1321,6 +1321,7 @@ def prepare_replace(
         store_output_job.index = current_job.index + 1
         store_output_job.metadata = current_job.metadata
         store_output_job.output_schema = current_job.output_schema
+        store_output_job._kwargs = current_job._kwargs
         replace.add_jobs(store_output_job)
 
     elif isinstance(replace, Job):

jobflow/core/maker.py

@@ -12,8 +12,6 @@ if typing.TYPE_CHECKING:
 
     import jobflow
 
-__all__ = ["Maker"]
-
 
 @dataclass
 class Maker(MSONable):

jobflow/core/reference.py

@@ -4,24 +4,18 @@ from __future__ import annotations
 
 import contextlib
 import typing
-from typing import Any, Sequence
+from typing import Any
 
 from monty.json import MontyDecoder, MontyEncoder, MSONable, jsanitize
 from pydantic import BaseModel
-from pydantic.utils import lenient_issubclass
+from pydantic.v1.utils import lenient_issubclass
 
 from jobflow.utils.enum import ValueEnum
 
 if typing.TYPE_CHECKING:
-    import jobflow
+    from collections.abc import Sequence
 
-__all__ = [
-    "OnMissing",
-    "OutputReference",
-    "resolve_references",
-    "find_and_resolve_references",
-    "find_and_get_references",
-]
+    import jobflow
 
 
 class OnMissing(ValueEnum):
@@ -95,14 +89,14 @@ class OutputReference(MSONable):
         uuid: str,
         attributes: tuple[tuple[str, Any], ...] = (),
         output_schema: type[BaseModel] = None,
-    ):
+    ) -> None:
         super().__init__()
         self.uuid = uuid
         self.attributes = attributes
         self.output_schema = output_schema
 
         for attr_type, attr in attributes:
-            if attr_type not in ("a", "i"):
+            if attr_type not in {"a", "i"}:
                 raise ValueError(
                     f"Unrecognised attribute type '{attr_type}' for attribute '{attr}'"
                 )
@@ -165,11 +159,12 @@ class OutputReference(MSONable):
         if on_missing == OnMissing.ERROR and index not in cache[self.uuid]:
             istr = f" ({index})" if index is not None else ""
             raise ValueError(
-                f"Could not resolve reference - {self.uuid}{istr} not in store or cache"
+                f"Could not resolve reference - {self.uuid}{istr} not in store or "
+                f"{index=}, {cache=}"
             )
-        elif on_missing == OnMissing.NONE and index not in cache[self.uuid]:
+        if on_missing == OnMissing.NONE and index not in cache[self.uuid]:
             return None
-        elif on_missing == OnMissing.PASS and index not in cache[self.uuid]:
+        if on_missing == OnMissing.PASS and index not in cache[self.uuid]:
             return self
 
         data = cache[self.uuid][index]
@@ -182,7 +177,11 @@ class OutputReference(MSONable):
 
         for attr_type, attr in self.attributes:
             # i means index else use attribute access
-            data = data[attr] if attr_type == "i" else getattr(data, attr)
+            data = (
+                data[attr]
+                if attr_type == "i" or isinstance(data, dict)
+                else getattr(data, attr)
+            )
 
         return data
 
@@ -206,12 +205,11 @@ class OutputReference(MSONable):
         if inplace:
             self.uuid = uuid
             return self
-        else:
-            from copy import deepcopy
+        from copy import deepcopy
 
-            new_reference = deepcopy(self)
-            new_reference.uuid = uuid
-            return new_reference
+        new_reference = deepcopy(self)
+        new_reference.uuid = uuid
+        return new_reference
 
     def __getitem__(self, item) -> OutputReference:
         """Index the reference."""
@@ -269,7 +267,7 @@ class OutputReference(MSONable):
         """Return a hash of the reference."""
         return hash(str(self))
 
-    def __eq__(self, other: Any) -> bool:
+    def __eq__(self, other: object) -> bool:
         """Test for equality against another reference."""
         if isinstance(other, OutputReference):
             return (
@@ -291,7 +289,7 @@ class OutputReference(MSONable):
         """Serialize the reference as a dict."""
         schema = self.output_schema
         schema_dict = MontyEncoder().default(schema) if schema is not None else None
-        data = {
+        return {
             "@module": self.__class__.__module__,
             "@class": type(self).__name__,
             "@version": None,
@@ -299,7 +297,6 @@ class OutputReference(MSONable):
             "attributes": self.attributes,
             "output_schema": schema_dict,
         }
-        return data
 
 
 def resolve_references(
@@ -382,7 +379,7 @@ def find_and_get_references(arg: Any) -> tuple[OutputReference, ...]:
         # if the argument is a reference then stop there
         return (arg,)
 
-    elif isinstance(arg, (float, int, str, bool)):
+    if isinstance(arg, (float, int, str, bool)):
         # argument is a primitive, we won't find a reference here
         return ()
 
@@ -438,7 +435,7 @@ def find_and_resolve_references(
         # if the argument is a reference then stop there
         return arg.resolve(store, cache=cache, on_missing=on_missing)
 
-    elif isinstance(arg, (float, int, str, bool)):
+    if isinstance(arg, (float, int, str, bool)):
         # argument is a primitive, we won't find a reference here
         return arg
 
@@ -503,7 +500,7 @@ def validate_schema_access(
         raise AttributeError(f"{schema.__name__} does not have attribute '{item}'.")
 
     subschema = None
-    item_type = schema.__fields__[item].outer_type_
+    item_type = schema.model_fields[item].annotation
     if lenient_issubclass(item_type, BaseModel):
         subschema = item_type
 

jobflow/core/schemas.py

@@ -0,0 +1,34 @@
+"""A Pydantic model for Jobstore document."""
+
+from typing import Any
+
+from pydantic import BaseModel, Field
+
+
+class JobStoreDocument(BaseModel):
+    """A Pydantic model for Jobstore document."""
+
+    uuid: str = Field(
+        None, description="An unique identifier for the job. Generated automatically."
+    )
+    index: int = Field(
+        None,
+        description="The index of the job (number of times the job has been replaced).",
+    )
+    output: Any = Field(
+        None,
+        description="This is a reference to the future job output.",
+    )
+    completed_at: str = Field(None, description="The time the job was completed.")
+    metadata: dict = Field(
+        None,
+        description="Metadata information supplied by the user.",
+    )
+    hosts: list[str] = Field(
+        None,
+        description="The list of UUIDs of the hosts containing the job.",
+    )
+    name: str = Field(
+        None,
+        description="The name of the job.",
+    )

jobflow/core/state.py

@@ -15,12 +15,8 @@ import typing
 from monty.design_patterns import singleton
 
 if typing.TYPE_CHECKING:
-    pass
-
     import jobflow
 
-__all__ = ["CURRENT_JOB"]
-
 
 @singleton
 class State:

jobflow/core/store.py

@@ -11,17 +11,19 @@ from jobflow.core.reference import OnMissing
 from jobflow.utils.find import get_root_locations
 
 if typing.TYPE_CHECKING:
+    from collections.abc import Iterator
     from enum import Enum
     from pathlib import Path
-    from typing import Any, Dict, Iterator, List, Optional, Type, Union
+    from typing import Any, Optional, Union
 
     from maggma.core import Sort
 
-    obj_type = Union[str, Enum, Type[MSONable], List[Union[Enum, str, Type[MSONable]]]]
-    save_type = Optional[Dict[str, obj_type]]
-    load_type = Union[bool, Dict[str, Union[bool, obj_type]]]
+    from jobflow.core.schemas import JobStoreDocument
+
+    obj_type = Union[str, Enum, type[MSONable], list[Union[Enum, str, type[MSONable]]]]
+    save_type = Optional[dict[str, obj_type]]
+    load_type = Union[bool, dict[str, Union[bool, obj_type]]]
 
-__all__ = ["JobStore"]
 
 T = typing.TypeVar("T", bound="JobStore")
 
@@ -249,12 +251,11 @@ class JobStore(Store):
         docs = self.query(
             criteria=criteria, properties=properties, load=load, sort=sort, limit=1
         )
-        d = next(docs, None)
-        return d
+        return next(docs, None)
 
     def update(
         self,
-        docs: list[dict] | dict,
+        docs: list[dict] | dict | JobStoreDocument | list[JobStoreDocument],
         key: list | str = None,
         save: bool | save_type = None,
     ):
@@ -264,7 +265,7 @@ class JobStore(Store):
         Parameters
         ----------
         docs
-            The document or list of documents to update.
+            The Pydantic document or list of Pydantic documents to update.
         key
             Field name(s) to determine uniqueness for a document, can be a list of
             multiple fields, a single field, or None if the Store's key field is to
@@ -495,7 +496,7 @@ class JobStore(Store):
         #       this could be fixed but will require more complicated logic just to
         #       catch a very unlikely event.
 
-        if isinstance(which, int) or which in ("last", "first"):
+        if isinstance(which, int) or which in {"last", "first"}:
             sort = -1 if which == "last" else 1
 
             criteria: dict[str, Any] = {"uuid": uuid}
@@ -521,28 +522,27 @@ class JobStore(Store):
             return find_and_resolve_references(
                 result["output"], self, cache=cache, on_missing=on_missing
             )
-        else:
-            results = list(
-                self.query(
-                    criteria={"uuid": uuid},
-                    properties=["output"],
-                    sort={"index": 1},
-                    load=load,
-                )
+        results = list(
+            self.query(
+                criteria={"uuid": uuid},
+                properties=["output"],
+                sort={"index": 1},
+                load=load,
             )
+        )
 
-            if len(results) == 0:
-                raise ValueError(f"UUID: {uuid} has no outputs.")
+        if len(results) == 0:
+            raise ValueError(f"UUID: {uuid} has no outputs.")
 
-            results = [r["output"] for r in results]
+        results = [r["output"] for r in results]
 
-            refs = find_and_get_references(results)
-            if any(ref.uuid == uuid for ref in refs):
-                raise RuntimeError("Reference cycle detected - aborting.")
+        refs = find_and_get_references(results)
+        if any(ref.uuid == uuid for ref in refs):
+            raise RuntimeError("Reference cycle detected - aborting.")
 
-            return find_and_resolve_references(
-                results, self, cache=cache, on_missing=on_missing
-            )
+        return find_and_resolve_references(
+            results, self, cache=cache, on_missing=on_missing
+        )
 
     @classmethod
     def from_file(cls: type[T], db_file: str | Path, **kwargs) -> T:
@@ -661,6 +661,10 @@ class JobStore(Store):
 
         all_stores = {s.__name__: s for s in all_subclasses(maggma.stores.Store)}
 
+        # add ssh tunnel support
+        tunnel = maggma.stores.ssh_tunnel.SSHTunnel
+        all_stores[tunnel.__name__] = tunnel
+
         docs_store_info = spec["docs_store"]
         docs_store = _construct_store(docs_store_info, all_stores)
 
@@ -760,7 +764,7 @@ def _filter_blobs(
 
     new_blobs = []
     new_locations = []
-    for _store_name, store_load in load.items():
+    for store_load in load.values():
         for blob, location in zip(blob_infos, locations):
             if store_load is True:
                 new_blobs.append(blob)

jobflow/managers/fireworks.py

@@ -7,11 +7,10 @@ import typing
 from fireworks import FiretaskBase, Firework, FWAction, Workflow, explicit_serialize
 
 if typing.TYPE_CHECKING:
-    from typing import Sequence
+    from collections.abc import Sequence
 
     import jobflow
-
-__all__ = ["flow_to_workflow", "job_to_firework", "JobFiretask"]
+    from jobflow.core.job import Job
 
 
 def flow_to_workflow(
@@ -148,7 +147,6 @@ class JobFiretask(FiretaskBase):
     def run_task(self, fw_spec):
         """Run the job and handle any dynamic firework submissions."""
         from jobflow import SETTINGS, initialize_logger
-        from jobflow.core.job import Job
 
         job: Job = self.get("job")
         store = self.get("store")
@@ -192,11 +190,10 @@ class JobFiretask(FiretaskBase):
             else:
                 detours = [detour_wf]
 
-        fwa = FWAction(
+        return FWAction(
             stored_data=response.stored_data,
             detours=detours,
             additions=additions,
             defuse_workflow=response.stop_jobflow,
             defuse_children=response.stop_children,
         )
-        return fwa

jobflow/managers/local.py

@@ -6,12 +6,10 @@ import logging
 import typing
 
 if typing.TYPE_CHECKING:
-    pass
+    from pathlib import Path
 
     import jobflow
 
-__all__ = ["run_locally"]
-
 logger = logging.getLogger(__name__)
 
 
@@ -20,6 +18,7 @@ def run_locally(
     log: bool = True,
     store: jobflow.JobStore = None,
     create_folders: bool = False,
+    root_dir: str | Path | None = None,
     ensure_success: bool = False,
     allow_external_references: bool = False,
 ) -> dict[str, dict[int, jobflow.Response]]:
@@ -28,25 +27,29 @@ def run_locally(
 
     Parameters
     ----------
-    flow
+    flow : Flow | Job | list[Job]
         A job or flow.
-    log
+    log : bool
         Whether to print log messages.
-    store
+    store : JobStore
         A job store. If a job store is not specified then
         :obj:`JobflowSettings.JOB_STORE` will be used. By default this is a maggma
         ``MemoryStore`` but can be customised by setting the jobflow configuration file.
-    create_folders
+    create_folders : bool
         Whether to run each job in a new folder.
-    ensure_success
+    root_dir : str | Path | None
+        The root directory to run the jobs in or where to create new subfolders if
+            ``create_folders`` is True. If None then the current working
+            directory will be used.
+    ensure_success : bool
         Raise an error if the flow was not executed successfully.
-    allow_external_references
+    allow_external_references : bool
         If False all the references to other outputs should be from other Jobs
         of the Flow.
 
     Returns
     -------
-    Dict[str, Dict[int, Response]]
+    dict[str, dict[int, Response]]
         The responses of the jobs, as a dict of ``{uuid: {index: response}}``.
     """
     from collections import defaultdict
@@ -63,6 +66,9 @@ def run_locally(
     if store is None:
         store = SETTINGS.JOB_STORE
 
+    root_dir = Path.cwd() if root_dir is None else Path(root_dir).resolve()
+    root_dir.mkdir(exist_ok=True)
+
     store.connect()
 
     if log:
@@ -75,13 +81,11 @@ def run_locally(
     responses: dict[str, dict[int, jobflow.Response]] = defaultdict(dict)
     stop_jobflow = False
 
-    root_dir = Path.cwd()
-
     def _run_job(job: jobflow.Job, parents):
         nonlocal stop_jobflow
 
         if stop_jobflow:
-            return False
+            return None, True
 
         if len(set(parents).intersection(stopped_parents)) > 0:
             # stop children has been called for one of the jobs' parents
@@ -89,14 +93,14 @@ def run_locally(
                 f"{job.name} is a child of a job with stop_children=True, skipping..."
             )
             stopped_parents.add(job.uuid)
-            return
+            return None, False
 
         if (
             len(set(parents).intersection(errored)) > 0
             and job.config.on_missing_references == OnMissing.ERROR
         ):
             errored.add(job.uuid)
-            return
+            return None, False
 
         try:
             response = job.run(store=store)
@@ -105,7 +109,7 @@ def run_locally(
 
             logger.info(f"{job.name} failed with exception:\n{traceback.format_exc()}")
             errored.add(job.uuid)
-            return
+            return None, False
 
         responses[job.uuid][job.index] = response
 
@@ -117,21 +121,24 @@ def run_locally(
 
         if response.stop_jobflow:
             stop_jobflow = True
-            return False
+            return None, True
 
+        diversion_responses = []
         if response.replace is not None:
             # first run any restarts
-            _run(response.replace)
+            diversion_responses.append(_run(response.replace))
 
         if response.detour is not None:
             # next any detours
-            _run(response.detour)
+            diversion_responses.append(_run(response.detour))
 
         if response.addition is not None:
             # finally any additions
-            _run(response.addition)
+            diversion_responses.append(_run(response.addition))
 
-        return response
+        if not all(diversion_responses):
+            return None, False
+        return response, False
 
     def _get_job_dir():
         if create_folders:
@@ -139,19 +146,20 @@ def run_locally(
             job_dir = root_dir / f"job_{time_now}-{randint(10000, 99999)}"
             job_dir.mkdir()
             return job_dir
-        else:
-            return root_dir
+        return root_dir
 
     def _run(root_flow):
-        job: jobflow.Job
+        encountered_bad_response = False
         for job, parents in root_flow.iterflow():
             job_dir = _get_job_dir()
             with cd(job_dir):
-                response = _run_job(job, parents)
-            if response is False:
+                response, jobflow_stopped = _run_job(job, parents)
+
+            encountered_bad_response = encountered_bad_response or response is None
+            if jobflow_stopped is True:
                 return False
 
-        return response is not None
+        return not encountered_bad_response
 
     logger.info("Started executing jobs locally")
     finished_successfully = _run(flow)

jobflow/settings.py

@@ -1,17 +1,17 @@
 """Settings for jobflow."""
 
+import warnings
 from collections import defaultdict
 from pathlib import Path
 
 from maggma.stores import MemoryStore
-from pydantic import BaseSettings, Field, root_validator
+from pydantic import Field, model_validator
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from jobflow import JobStore
 
 DEFAULT_CONFIG_FILE_PATH = Path("~/.jobflow.yaml").expanduser().as_posix()
 
-__all__ = ["JobflowSettings"]
-
 
 def _default_additional_store():
     """Create a default MemoryStore and connect it.
@@ -117,13 +117,10 @@ class JobflowSettings(BaseSettings):
         "%Y-%m-%d-%H-%M-%S-%f",
         description="Date stamp format used to create directories",
     )
+    model_config = SettingsConfigDict(env_prefix="jobflow_")
 
-    class Config:
-        """Pydantic config settings."""
-
-        env_prefix = "jobflow_"
-
-    @root_validator(pre=True)
+    @model_validator(mode="before")
+    @classmethod
     def load_default_settings(cls, values):
         """
         Load settings from file or environment variables.
@@ -136,10 +133,21 @@ class JobflowSettings(BaseSettings):
         from monty.serialization import loadfn
 
         config_file_path: str = values.get("CONFIG_FILE", DEFAULT_CONFIG_FILE_PATH)
-
         new_values = {}
         if Path(config_file_path).exists():
-            new_values.update(loadfn(config_file_path))
+            if Path(config_file_path).stat().st_size == 0:
+                warnings.warn(
+                    f"An empty JobFlow config file was located at {config_file_path}"
+                )
+            else:
+                try:
+                    new_values.update(loadfn(config_file_path))
+                except ValueError:
+                    raise ValueError(
+                        f"A JobFlow configuration file was located at "
+                        f"{config_file_path} but a problem was "
+                        f"encountered while parsing it."
+                    ) from None
 
         store = new_values.get("JOB_STORE")
         if isinstance(store, str):

jobflow/utils/dict_mods.py

@@ -21,9 +21,6 @@ if typing.TYPE_CHECKING:
     from typing import Any
 
 
-__all__ = ["DictMods", "apply_mod"]
-
-
 class DictMods:
     """
     Class to define mongo-like modifications on a dict.

jobflow/utils/enum.py

@@ -2,8 +2,6 @@
 
 from enum import Enum
 
-__all__ = ["ValueEnum"]
-
 
 class ValueEnum(Enum):
     """Enum that serializes to string as the value and can be compared against a str."""
@@ -16,8 +14,7 @@ class ValueEnum(Enum):
         """Compare to another enum for equality."""
         if type(self) == type(other) and self.value == other.value:
             return True
-        else:
-            return str(self.value) == str(other)
+        return str(self.value) == str(other)
 
     def __hash__(self):
         """Get a hash of the enum."""

jobflow/utils/find.py

@@ -5,17 +5,11 @@ from __future__ import annotations
 import typing
 
 if typing.TYPE_CHECKING:
-    from typing import Any, Hashable
+    from collections.abc import Hashable
+    from typing import Any
 
     from monty.json import MSONable
 
-__all__ = [
-    "find_key",
-    "find_key_value",
-    "update_in_dictionary",
-    "contains_flow_or_job",
-]
-
 
 def find_key(
     d: dict[Hashable, Any] | list[Any],
@@ -78,10 +72,8 @@ def find_key(
             if (
                 inspect.isclass(key)
                 and issubclass(key, MSONable)
-                and "@module" in obj
-                and obj["@module"] == key.__module__
-                and "@class" in obj
-                and obj["@class"] == key.__name__
+                and obj.get("@module") == key.__module__
+                and obj.get("@class") == key.__name__
             ):
                 found_items.add(path)
                 found = True
@@ -209,7 +201,7 @@ def contains_flow_or_job(obj: Any) -> bool:
         # if the argument is an flow or job then stop there
         return True
 
-    elif isinstance(obj, (float, int, str, bool)):
+    if isinstance(obj, (float, int, str, bool)):
         # argument is a primitive, we won't find an flow or job here
         return False
 

jobflow/utils/graph.py

@@ -8,19 +8,15 @@ import networkx as nx
 from monty.dev import requires
 
 try:
-    import matplotlib
+    import matplotlib as mpl
 except ImportError:
-    matplotlib = None
+    mpl = None
 
 import typing
 
 if typing.TYPE_CHECKING:
-    pass
-
     import jobflow
 
-__all__ = ["itergraph", "draw_graph", "to_pydot", "to_mermaid"]
-
 
 def itergraph(graph: nx.DiGraph):
     """
@@ -56,7 +52,7 @@ def itergraph(graph: nx.DiGraph):
         yield from nx.topological_sort(subgraph)
 
 
-@requires(matplotlib, "matplotlib must be installed to plot flow graphs.")
+@requires(mpl, "matplotlib must be installed to plot flow graphs.")
 def draw_graph(
     graph: nx.DiGraph,
     layout_function: typing.Callable = None,
@@ -155,20 +151,20 @@ def to_pydot(flow: jobflow.Flow):
     nx_graph = flow.graph
     pydot_graph = pydot.Dot(f'"{flow.name}"', graph_type="digraph")
 
-    for n, nodedata in nx_graph.nodes(data=True):
-        str_nodedata = {k: str(v) for k, v in nodedata.items()}
-        p = pydot.Node(str(n), **str_nodedata)
+    for n, node_data in nx_graph.nodes(data=True):
+        str_node_data = {k: str(v) for k, v in node_data.items()}
+        p = pydot.Node(str(n), **str_node_data)
         pydot_graph.add_node(p)
 
-    for u, v, edgedata in nx_graph.edges(data=True):
-        str_edgedata = {k: str(v) for k, v in edgedata.items()}
-        edge = pydot.Edge(str(u), str(v), label=str_edgedata["properties"])
+    for u, v, edge_data in nx_graph.edges(data=True):
+        str_edge_data = {k: str(v) for k, v in edge_data.items()}
+        edge = pydot.Edge(str(u), str(v), label=str_edge_data["properties"])
         pydot_graph.add_edge(edge)
 
     def add_cluster(nested_flow, outer_graph):
         cluster = pydot.Cluster(nested_flow.uuid)
         cluster.set_label(nested_flow.name)
-        for job in nested_flow.jobs:
+        for job in nested_flow:
             if isinstance(job, Flow):
                 add_cluster(job, cluster)
             else:
@@ -236,7 +232,7 @@ def to_mermaid(flow: jobflow.Flow | jobflow.Job, show_flow_boxes: bool = False)
     def add_subgraph(nested_flow, indent_level=1):
         prefix = "    " * indent_level
 
-        for job in nested_flow.jobs:
+        for job in nested_flow:
             if isinstance(job, Flow):
                 if show_flow_boxes:
                     lines.append(f"{prefix}subgraph {job.uuid} [{job.name}]")

jobflow/utils/log.py

@@ -2,8 +2,6 @@
 
 import logging
 
-__all__ = ["initialize_logger"]
-
 
 def initialize_logger(level: int = logging.INFO) -> logging.Logger:
     """Initialize the default logger.

{jobflow-0.1.13.dist-info → jobflow-0.1.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: jobflow
-Version: 0.1.13
+Version: 0.1.15
 Summary: jobflow is a library for writing computational workflows
 Author-email: Alex Ganose <alexganose@gmail.com>
 License: modified BSD
@@ -9,64 +9,67 @@ Project-URL: repository, https://github.com/materialsproject/jobflow
 Project-URL: documentation, https://materialsproject.github.io/jobflow/
 Project-URL: changelog, https://github.com/materialsproject/jobflow/blob/main/CHANGELOG.md
 Keywords: high-throughput,workflow
-Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Information Technology
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: System Administrators
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Database :: Front-Ends
 Classifier: Topic :: Other/Nonlisted Topic
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: PyYAML
-Requires-Dist: maggma >=0.38.1
-Requires-Dist: monty >=2021.5.9
+Requires-Dist: maggma >=0.57.0
+Requires-Dist: monty >=2023.9.25
 Requires-Dist: networkx
-Requires-Dist: pydantic
+Requires-Dist: pydantic-settings >=2.0.3
+Requires-Dist: pydantic >=2.0.1
 Requires-Dist: pydash
 Provides-Extra: dev
 Requires-Dist: pre-commit >=2.12.1 ; extra == 'dev'
 Provides-Extra: docs
-Requires-Dist: autodoc-pydantic ==1.9.0 ; extra == 'docs'
-Requires-Dist: furo ==2023.7.26 ; extra == 'docs'
-Requires-Dist: ipython ==8.14.0 ; extra == 'docs'
+Requires-Dist: autodoc-pydantic ==2.0.1 ; extra == 'docs'
+Requires-Dist: furo ==2023.9.10 ; extra == 'docs'
+Requires-Dist: ipython ==8.18.1 ; extra == 'docs'
 Requires-Dist: myst-parser ==2.0.0 ; extra == 'docs'
-Requires-Dist: nbsphinx ==0.9.2 ; extra == 'docs'
+Requires-Dist: nbsphinx ==0.9.3 ; extra == 'docs'
 Requires-Dist: sphinx-copybutton ==0.5.2 ; extra == 'docs'
-Requires-Dist: sphinx ==7.1.2 ; extra == 'docs'
+Requires-Dist: sphinx ==7.2.6 ; extra == 'docs'
 Provides-Extra: fireworks
 Requires-Dist: FireWorks ; extra == 'fireworks'
 Provides-Extra: strict
 Requires-Dist: FireWorks ==2.0.3 ; extra == 'strict'
 Requires-Dist: PyYAML ==6.0.1 ; extra == 'strict'
-Requires-Dist: maggma ==0.53.0 ; extra == 'strict'
-Requires-Dist: matplotlib ==3.7.2 ; extra == 'strict'
-Requires-Dist: monty ==2023.8.8 ; extra == 'strict'
-Requires-Dist: moto ==4.1.14 ; extra == 'strict'
-Requires-Dist: networkx ==3.1 ; extra == 'strict'
-Requires-Dist: pydantic ==1.10.9 ; extra == 'strict'
+Requires-Dist: maggma ==0.58.0 ; extra == 'strict'
+Requires-Dist: matplotlib ==3.8.2 ; extra == 'strict'
+Requires-Dist: monty ==2023.11.3 ; extra == 'strict'
+Requires-Dist: moto ==4.2.11 ; extra == 'strict'
+Requires-Dist: networkx ==3.2.1 ; extra == 'strict'
+Requires-Dist: pydantic-settings ==2.1.0 ; extra == 'strict'
+Requires-Dist: pydantic ==2.5.2 ; extra == 'strict'
 Requires-Dist: pydash ==7.0.6 ; extra == 'strict'
 Requires-Dist: pydot ==1.4.2 ; extra == 'strict'
-Requires-Dist: typing-extensions ==4.7.1 ; extra == 'strict'
+Requires-Dist: typing-extensions ==4.8.0 ; extra == 'strict'
 Provides-Extra: tests
+Requires-Dist: moto ==4.2.11 ; extra == 'tests'
 Requires-Dist: pytest-cov ==4.1.0 ; extra == 'tests'
-Requires-Dist: pytest ==7.4.0 ; extra == 'tests'
+Requires-Dist: pytest ==7.4.3 ; extra == 'tests'
 Provides-Extra: vis
 Requires-Dist: matplotlib ; extra == 'vis'
 Requires-Dist: pydot ; extra == 'vis'
 
 # jobflow
 
-<a href="https://github.com/materialsproject/jobflow/actions?query=workflow%3Atesting"><img alt="code coverage" src="https://img.shields.io/github/actions/workflow/status/materialsproject/jobflow/testing.yml?branch=main&label=tests"></a>
-<a href="https://codecov.io/gh/materialsproject/jobflow/"><img alt="code coverage" src="https://img.shields.io/codecov/c/gh/materialsproject/jobflow/main"></a>
-<a href="https://pypi.org/project/jobflow"><img alt="pypi version" src="https://img.shields.io/pypi/v/jobflow?color=blue"></a>
-<img alt="supported python versions" src="https://img.shields.io/pypi/pyversions/jobflow">
+[![tests](https://img.shields.io/github/actions/workflow/status/materialsproject/jobflow/testing.yml?branch=main&label=tests)](https://github.com/materialsproject/jobflow/actions?query=workflow%3Atesting)
+[![code coverage](https://img.shields.io/codecov/c/gh/materialsproject/jobflow/main)](https://codecov.io/gh/materialsproject/jobflow/)
+[![pypi version](https://img.shields.io/pypi/v/jobflow?color=blue)](https://pypi.org/project/jobflow/)
+![supported python versions](https://img.shields.io/pypi/pyversions/jobflow)
 
 [Documentation](https://materialsproject.github.io/jobflow/) | [PyPI](https://pypi.org/project/jobflow/) | [GitHub](https://github.com/materialsproject/jobflow)
 
@@ -139,7 +142,7 @@ the jobs is determined automatically and can be visualised using the flow graph.
 
 ## Installation
 
-The jobflow is a Python 3.8+ library and can be installed using pip.
+`jobflow` is a Python 3.9+ library and can be installed using `pip`.
 
 ```bash
 pip install jobflow

jobflow-0.1.15.dist-info/RECORD

@@ -0,0 +1,27 @@
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+jobflow/_version.py,sha256=Ym07PBD7sAmpqVpX8tuzWma3P_Hv6KXbDKXWkw8OwaI,205
+jobflow/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+jobflow/settings.py,sha256=e_8QwC05MUkDRenAutnqg8eAy7pQ-firtmCob7BKA3g,5474
+jobflow/core/__init__.py,sha256=3sx5t1Gysejc4c_fPrhvCjPUg0p_384Zko8ms2c_NnY,98
+jobflow/core/flow.py,sha256=c_rG9lzOQ00ckzN40gDHLm5CCvFlAeVE75kKLvvdJ2U,28879
+jobflow/core/job.py,sha256=bPZMcmiW-Qqs-qNnlypbwZCgS_IN9kM0sybYw3koXOw,46466
+jobflow/core/maker.py,sha256=DKfFXe91v9rRFtgUrm8FMiEcLArmb6jnK7nysuDdZts,11185
+jobflow/core/reference.py,sha256=x6RXt-yxbQHoea2gb5SR4GWBVD1U2LaNwPxUGPdvGZo,16252
+jobflow/core/schemas.py,sha256=Oi5-PnZpI8S9jSY7Q4f8H7xUybbRZDXlgugeVewVsrA,968
+jobflow/core/state.py,sha256=IGJTtmpotDKEcgDEnsT5x20ZeyvQT68Mr3teTjkgYnM,709
+jobflow/core/store.py,sha256=Bdm92-NqCPpID183DV9F9pMnG9PQLMpFOKUJkbzccNo,26982
+jobflow/managers/__init__.py,sha256=KkA5cVDe2os2_2aTa8eiB9SnkGLZNybcci-Lo4tbaWM,55
+jobflow/managers/fireworks.py,sha256=5IKDkE-dppvbhDWTfJKCMmqvxg50zBgCqm6qUqsVZtc,6654
+jobflow/managers/local.py,sha256=J2GHodXMqryME0EfccJTGgbjXuuwUmtrVA9RnCkDcy8,5355
+jobflow/utils/__init__.py,sha256=meuvfuk05U594rx4YB6BoBnoQxBMjCA2hKX3TSfZsB8,328
+jobflow/utils/dict_mods.py,sha256=g50aMw-mK3RjXp_hHJBR9xUaWRYXoqqmPTMCPDDluz4,6052
+jobflow/utils/enum.py,sha256=rFDdqQr-844Vzj9G9vuzPTWAJG60pQVNzgjyugkNwtc,713
+jobflow/utils/find.py,sha256=Qaxh0TxQtXznK4Wy72klLFfFB3NUfUI4TF6-NEAzxcU,6162
+jobflow/utils/graph.py,sha256=CNZNlUPmkVKio7m9Y3nifM9BbXe8vtvFHuXRwJu84R0,6562
+jobflow/utils/log.py,sha256=tIMpsI4JTlkpxjBZfWqZ0qkEkIxk1-RBasz8JhDcF7E,692
+jobflow/utils/uuid.py,sha256=lVgo8e8gUB7HLSR0H_9uZH-OPkVBaOT39atAnNKYAaI,268
+jobflow-0.1.15.dist-info/LICENSE,sha256=jUEiENfZNQZh9RE9ixtUWgVkLRD85ScZ6iv1WREf19w,2418
+jobflow-0.1.15.dist-info/METADATA,sha256=hFAXrVdF_OJfoi33zxO1DeIbMT9Ky-DJpy5xsES0fMY,9050
+jobflow-0.1.15.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+jobflow-0.1.15.dist-info/top_level.txt,sha256=IanNooU88OupQPDrWnT0rbL3E27P2wEy7Jsfx9_j8zc,8
+jobflow-0.1.15.dist-info/RECORD,,

{jobflow-0.1.13.dist-info → jobflow-0.1.15.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.1)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

jobflow-0.1.13.dist-info/RECORD

@@ -1,26 +0,0 @@
-jobflow/__init__.py,sha256=l7o10BaqEQWw5aZziWRg40PsIAgQ4lrlluXs9hIv2mg,570
-jobflow/_version.py,sha256=ERuIgO0lzbMrVMSXNAE55GxFc5JHDdf1CW7GtoXJ67Q,206
-jobflow/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-jobflow/settings.py,sha256=JHyTq9AOzMjSN5ohpLeooMLM0ddO2nPMuHuOyH62X6E,4908
-jobflow/core/__init__.py,sha256=3sx5t1Gysejc4c_fPrhvCjPUg0p_384Zko8ms2c_NnY,98
-jobflow/core/flow.py,sha256=LqIzSFa3NuLCJLIj7LJeF4WaeR5fya0w24v3fGsR6IM,28907
-jobflow/core/job.py,sha256=15Y3VW8CiDdBN6YxuSk78HvxGnKKW2OSTLVE3AHdtAY,46376
-jobflow/core/maker.py,sha256=cdEH7JE-LOyenibj_6y6N0y1bFe0_xbphTz8toigzzI,11206
-jobflow/core/reference.py,sha256=i9vnM13Ax7_J-RXmXQuYTnacCsc6pNpbCPxI59RU3O0,16287
-jobflow/core/state.py,sha256=qhmrxZ-dWFQV1QZH-FcMAEajYl-Zxue5x8d8xQQO0r0,746
-jobflow/core/store.py,sha256=6pveNBfiBYN6Zpp-PM3GfNWWzH187aVfJ6pyrbQ0j-M,26852
-jobflow/managers/__init__.py,sha256=KkA5cVDe2os2_2aTa8eiB9SnkGLZNybcci-Lo4tbaWM,55
-jobflow/managers/fireworks.py,sha256=VEXsu2bghScl7fH7LQ-FbZOFLeFRCFRu_SRusmmHZ9A,6733
-jobflow/managers/local.py,sha256=rIqYYkF-HEmO2qc5sSbIhkSIA5zlpkH0sRV0mQAt348,4593
-jobflow/utils/__init__.py,sha256=meuvfuk05U594rx4YB6BoBnoQxBMjCA2hKX3TSfZsB8,328
-jobflow/utils/dict_mods.py,sha256=bJmHB-JHtwBwEpWroO1YaOac_AvCItoQ6GBWlWdDMtk,6090
-jobflow/utils/enum.py,sha256=mt8z0D2Nu2oQxZ1vXi6VTqorOMseRptSCjsgMNSvvOE,756
-jobflow/utils/find.py,sha256=dGnXKJ_VDmWKxMBtJo_Dnb9jd3JVcPu7HasZsd6-jmI,6307
-jobflow/utils/graph.py,sha256=61k0bA_MCqlkVtJ2ldwpH6Tx2cwXrE_NWveouh6zwTk,6646
-jobflow/utils/log.py,sha256=dNIOvhApCtW7z1OamLlUmg6TL4mDXOQ0yFQxD8AM0Lk,725
-jobflow/utils/uuid.py,sha256=lVgo8e8gUB7HLSR0H_9uZH-OPkVBaOT39atAnNKYAaI,268
-jobflow-0.1.13.dist-info/LICENSE,sha256=jUEiENfZNQZh9RE9ixtUWgVkLRD85ScZ6iv1WREf19w,2418
-jobflow-0.1.13.dist-info/METADATA,sha256=Aye0TI6H8FgmQgvSmTLXIUFPxwJ3p7D_z1DwCUbRuAM,8976
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-jobflow-0.1.13.dist-info/top_level.txt,sha256=IanNooU88OupQPDrWnT0rbL3E27P2wEy7Jsfx9_j8zc,8
-jobflow-0.1.13.dist-info/RECORD,,