hpcflow-new2 0.2.0a207__py3-none-any.whl → 0.2.0a208__py3-none-any.whl

hpcflow/_version.py

@@ -1 +1 @@
-__version__ = "0.2.0a207"
+__version__ = "0.2.0a208"

hpcflow/data/scripts/main_script_test_hdf5_in_obj_group.py

@@ -0,0 +1,12 @@
+import h5py  # type: ignore[import-untyped]
+
+
+def main_script_test_hdf5_in_obj_group(_input_files):
+    # read inputs
+    with h5py.File(_input_files["hdf5"], mode="r") as fh:
+        all_a = [p1c_dat.attrs["a"].item() for p1c_dat in fh["p1c"].values()]
+
+    # process
+    p2 = sum(all_a) + 100
+
+    return {"p2": p2}

hpcflow/sdk/core/actions.py

@@ -988,7 +988,7 @@ class ElementActionRun(AppAware):
                 try:
                     assert isinstance(v, ParameterValue)
                     v.dump_to_HDF5_group(grp_k)
-                except AttributeError:
+                except AssertionError:
                     # probably an element group (i.e. v is a list of `ParameterValue`
                     # objects):
                     assert isinstance(v, list)

hpcflow/sdk/core/element.py

@@ -66,10 +66,11 @@ class _ElementPrefixedParameter(AppAware):
 
     def __getattr__(self, name: str) -> ElementParameter | Mapping[str, ElementParameter]:
         if name not in self.prefixed_names_unlabelled:
-            raise ValueError(
-                f"No {self._prefix} named {name!r}. Available {self._prefix} are: "
-                f"{self.prefixed_names_unlabelled_str}."
-            )
+            if names_str := self.prefixed_names_unlabelled_str:
+                msg_info = f"Available {self._prefix} are: {names_str}."
+            else:
+                msg_info = f"There are no {self._prefix} available."
+            raise ValueError(f"No {self._prefix} named {name!r}. {msg_info}")
 
         if labels := self.prefixed_names_unlabelled.get(name):
             # is multiple; return a dict of `ElementParameter`s

hpcflow/sdk/core/errors.py

@@ -14,7 +14,7 @@ if TYPE_CHECKING:
     from .object_list import WorkflowLoopList
     from .parameters import InputSource, ValueSequence, SchemaInput
     from .types import ScriptData
-    from .task import WorkflowTask
+    from .task import WorkflowTask, Task
 
 
 class InputValueDuplicateSequenceAddress(ValueError):
@@ -94,10 +94,12 @@ class MissingInputs(Exception):
 
     # TODO: add links to doc pages for common user-exceptions?
 
-    def __init__(self, missing_inputs: Iterable[str]) -> None:
+    def __init__(self, task: Task, missing_inputs: Iterable[str]) -> None:
         self.missing_inputs = tuple(missing_inputs)
         missing_str = ", ".join(map(repr, missing_inputs))
-        super().__init__(f"The following inputs have no sources: {missing_str}.")
+        super().__init__(
+            f"Task {task.name}: the following inputs have no sources: {missing_str}."
+        )
 
 
 class UnrequiredInputSources(ValueError):

hpcflow/sdk/core/parameters.py

@@ -43,7 +43,7 @@ if TYPE_CHECKING:
     from collections.abc import Iterable, Iterator, Mapping
     from typing import Any, ClassVar, Literal
     from typing_extensions import Self, TypeAlias
-    from h5py import Group  # type: ignore
+    from h5py import Group as HDF5Group  # type: ignore
     from numpy.typing import NDArray
     from ..app import BaseApp
     from ..typing import ParamSource
@@ -116,21 +116,21 @@ class ParameterValue:
         """
         raise NotImplementedError
 
-    def dump_to_HDF5_group(self, group: Group):
+    def dump_to_HDF5_group(self, group: HDF5Group):
         """
         Write this parameter value to an HDF5 group.
         """
         raise NotImplementedError
 
     @classmethod
-    def dump_element_group_to_HDF5_group(cls, objs: list[ParameterValue], group: Group):
+    def dump_element_group_to_HDF5_group(cls, objs: list[Self], group: HDF5Group):
         """
         Write a list (from an element group) of parameter values to an HDF5 group.
         """
         raise NotImplementedError
 
     @classmethod
-    def save_from_HDF5_group(cls, group: Group, param_id: int, workflow: Workflow):
+    def save_from_HDF5_group(cls, group: HDF5Group, param_id: int, workflow: Workflow):
         """
         Extract a parameter value from an HDF5 group.
         """

hpcflow/sdk/core/task.py

@@ -2217,7 +2217,7 @@ class WorkflowTask(AppAware):
             self.__enforce_some_sanity(sources_by_task, element_set)
 
         if missing:
-            raise MissingInputs(missing)
+            raise MissingInputs(self.template, missing)
         return padded_elem_iters
 
     def __enforce_some_sanity(

hpcflow/sdk/core/test_utils.py

@@ -13,8 +13,8 @@ from hpcflow.sdk.typing import hydrate
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Mapping
-    from typing_extensions import TypeAlias
-    from h5py import Group as HDFSGroup  # type: ignore
+    from typing_extensions import TypeAlias, Self
+    from h5py import Group as HDF5Group  # type: ignore
     from .actions import Action
     from .element import ElementGroup
     from .loop import Loop
@@ -272,7 +272,7 @@ class P1_sub_parameter_cls(ParameterValue):
     def prepare_JSON_dump(self) -> dict[str, Any]:
         return {"e": self.e}
 
-    def dump_to_HDF5_group(self, group: HDFSGroup):
+    def dump_to_HDF5_group(self, group: HDF5Group):
         group.attrs["e"] = self.e
 
 
@@ -376,7 +376,7 @@ class P1_parameter_cls(ParameterValue):
         sub_param_js = self.sub_param.prepare_JSON_dump() if self.sub_param else None
         return {"a": self.a, "d": self.d, "sub_param": sub_param_js}
 
-    def dump_to_HDF5_group(self, group: HDFSGroup):
+    def dump_to_HDF5_group(self, group: HDF5Group):
         group.attrs["a"] = self.a
         if self.d is not None:
             group.attrs["d"] = self.d
@@ -384,13 +384,28 @@ class P1_parameter_cls(ParameterValue):
             sub_group = group.create_group("sub_param")
             self.sub_param.dump_to_HDF5_group(sub_group)
 
+    @classmethod
+    def dump_element_group_to_HDF5_group(self, objs: list[Self], group: HDF5Group):
+        """
+        Write a list (from an element group) of parameter values to an HDF5 group.
+        """
+
+        for obj_idx, p1_obj in enumerate(objs):
+            grp_i = group.create_group(f"{obj_idx}")
+            grp_i.attrs["a"] = p1_obj.a
+            if p1_obj.d is not None:
+                group.attrs["d"] = p1_obj.d
+            if p1_obj.sub_param:
+                sub_group = grp_i.create_group("sub_param")
+                p1_obj.sub_param.dump_to_HDF5_group(sub_group)
+
     @classmethod
     def save_from_JSON(cls, data: dict, param_id: int | list[int], workflow: Workflow):
         obj = cls(**data)  # TODO: pass sub-param
         workflow.set_parameter_value(param_id=param_id, value=obj, commit=True)
 
     @classmethod
-    def save_from_HDF5_group(cls, group: HDFSGroup, param_id: int, workflow: Workflow):
+    def save_from_HDF5_group(cls, group: HDF5Group, param_id: int, workflow: Workflow):
         a = group.attrs["a"].item()
         if "d" in group.attrs:
             d = group.attrs["d"].item()

hpcflow/tests/scripts/test_main_scripts.py

@@ -458,6 +458,50 @@ def test_script_hdf5_in_obj(null_config, tmp_path: Path, combine_scripts: bool):
     assert p2.value == a_val + 100
 
 
+@pytest.mark.integration
+@pytest.mark.skipif("hf.run_time_info.is_frozen")
+@pytest.mark.parametrize("combine_scripts", [False, True])
+def test_script_hdf5_in_obj_group(null_config, tmp_path: Path, combine_scripts: bool):
+    s0 = hf.TaskSchema(
+        objective="define_p1c",
+        inputs=[hf.SchemaInput(parameter=hf.Parameter("p1c"))],
+    )
+    s1 = hf.TaskSchema(
+        objective="t1",
+        inputs=[hf.SchemaInput(parameter=hf.Parameter("p1c"), group="my_group")],
+        outputs=[hf.SchemaOutput(parameter=hf.Parameter("p2"))],
+        actions=[
+            hf.Action(
+                script="<<script:main_script_test_hdf5_in_obj_group.py>>",
+                script_data_in="hdf5",
+                script_data_out="direct",
+                script_exe="python_script",
+                environments=[hf.ActionEnvironment(environment="python_env")],
+                requires_dir=True,
+            )
+        ],
+        parameter_class_modules=["hpcflow.sdk.core.test_utils"],
+    )
+    a_vals = (1, 2)
+    t0 = hf.Task(
+        schema=s0,
+        sequences=[hf.ValueSequence(path="inputs.p1c", values=[P1(a=i) for i in a_vals])],
+        groups=[hf.ElementGroup("my_group")],
+    )
+    t1 = hf.Task(schema=s1)
+    wk = hf.Workflow.from_template_data(
+        tasks=[t0, t1],
+        template_name="main_script_test",
+        path=tmp_path,
+        resources={"any": {"combine_scripts": combine_scripts}},
+    )
+    wk.submit(wait=True, add_to_known=False, status=False)
+
+    p2 = wk.tasks[1].elements[0].outputs.p2
+    assert isinstance(p2, hf.ElementParameter)
+    assert p2.value == sum(a_vals) + 100
+
+
 @pytest.mark.integration
 @pytest.mark.skipif("hf.run_time_info.is_frozen")
 @pytest.mark.parametrize("combine_scripts", [False, True])

{hpcflow_new2-0.2.0a207.dist-info → hpcflow_new2-0.2.0a208.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hpcflow-new2
-Version: 0.2.0a207
+Version: 0.2.0a208
 Summary: Computational workflow management
 License: MPL-2.0
 Author: aplowman

{hpcflow_new2-0.2.0a207.dist-info → hpcflow_new2-0.2.0a208.dist-info}/RECORD

@@ -1,7 +1,7 @@
 hpcflow/__init__.py,sha256=WIETuRHeOp2SqUqHUzpjQ-lk9acbYv-6aWOhZPRdlhs,64
 hpcflow/__pyinstaller/__init__.py,sha256=YOzBlPSck6slucv6lJM9K80JtsJWxXRL00cv6tRj3oc,98
 hpcflow/__pyinstaller/hook-hpcflow.py,sha256=P2b-8QdQqkSS7cJB6CB3CudUuJ9iZzTh2fQF4hNdCa4,1118
-hpcflow/_version.py,sha256=KznvFP2-RqfaLYFjGRIq-cjLHrJRFJuxyroYBl__DWs,26
+hpcflow/_version.py,sha256=vL0IzortUjskEsZDLgY-9fJufiwBTmivGzqqjcD05aw,26
 hpcflow/app.py,sha256=gl2viVS65PbpDhUp2DARaYHFDqDWQjuoyB3ikrCNRW4,1367
 hpcflow/cli.py,sha256=G2J3D9v6MnMWOWMMWK6UEKLn_6wnV9lT_qygEBBxg-I,66
 hpcflow/data/demo_data_manifest/__init__.py,sha256=Hsq0jT8EXM13wu1MpGy5FQgyuz56ygep4VWOnulFn50,41
@@ -37,6 +37,7 @@ hpcflow/data/scripts/main_script_test_direct_in_group_one_fail_direct_out_3.py,s
 hpcflow/data/scripts/main_script_test_direct_sub_param_in_direct_out.py,sha256=pQ-BD1FmqTIHeCaAakCr1M61cWb1Fjinzr1qA3HX3ik,131
 hpcflow/data/scripts/main_script_test_hdf5_in_obj.py,sha256=WMRuzwkU4WFLrmUGD0999IowHY1y7cLeS2iuR2R7Dqo,265
 hpcflow/data/scripts/main_script_test_hdf5_in_obj_2.py,sha256=SCDkTctGAaHAOWxijVNs59SVsL6YiaIttNN43noPpis,255
+hpcflow/data/scripts/main_script_test_hdf5_in_obj_group.py,sha256=ACIHdsp6Q7-TsE2P0uiaFhSy9E92PGoRqDE8mnpbmOQ,318
 hpcflow/data/scripts/main_script_test_hdf5_out_obj.py,sha256=nV_U5DA2xAeV1z9TLyIOUu3rfI2AZSFteFSbGVHQnFE,299
 hpcflow/data/scripts/main_script_test_json_and_direct_in_json_out.py,sha256=Y1kpKu59DbjqKW2i4QcmfHzdXYmiAEvNzqIqBU_Z4fg,336
 hpcflow/data/scripts/main_script_test_json_in_json_and_direct_out.py,sha256=jjiceG1d6saMWOYZIHfK1pJIWhwyNRAQeZgy49NC5LU,374
@@ -73,27 +74,27 @@ hpcflow/sdk/config/config_file.py,sha256=wfDjozV9lXTnaxQoe-z-1Y7dtO0N4o1kgEwKtrL
 hpcflow/sdk/config/errors.py,sha256=Ft0e0rqIh9NoxWu3R8RSHel2fLONrXrgmFdNGZ_nOac,8341
 hpcflow/sdk/config/types.py,sha256=hw8latN2PqgGB_cOcD2pmgf5hSE7Dl94xLGKosydpCo,3935
 hpcflow/sdk/core/__init__.py,sha256=uxvGIUmzvFvylxFL4OGoKHs8GABHHPFaki-Xyc7Nquk,861
-hpcflow/sdk/core/actions.py,sha256=jSnOCJFe9_gL0JFE73Q6tLJnQeqfkit9526xry4fFLY,118219
+hpcflow/sdk/core/actions.py,sha256=379uJT_fScwa-n_aEGd-DlXzZpFLFWkctxnMa-u4Y0U,118219
 hpcflow/sdk/core/app_aware.py,sha256=A5L9U_wcf9eleuDj1vxZMai1Fk7FLNdMjzA-ay1hHeE,568
 hpcflow/sdk/core/cache.py,sha256=FNOaZzZmtcoFwByR39kI65XdbO6i6qpYup9qrwUN-YM,8172
 hpcflow/sdk/core/command_files.py,sha256=9YbQuOfa0HrAZcAtgH8_k3oJRfRVRpv5QtZ9Uag9W2I,24961
 hpcflow/sdk/core/commands.py,sha256=vFyZ9Cv_tvGqSGtVEnAHAeXA-HAxWoF0nmf1e0bFCvs,15993
-hpcflow/sdk/core/element.py,sha256=n2_val24HFwIGiVm1xikVOXbTQ69neO8YzRWZ48VYaQ,68295
+hpcflow/sdk/core/element.py,sha256=VVk-lt03kN-vk38jhuzTV8GcPKWKyziXS2gbDA9mTBQ,68412
 hpcflow/sdk/core/enums.py,sha256=b0Zd35AdEEfQYWIO0IHc---hqcWyQ3HC35vGWbzB7sA,4386
 hpcflow/sdk/core/environment.py,sha256=vvHJhdI8Jeae20AGvbp0DY-Wm7efNFlAkkcLESKljFQ,7955
-hpcflow/sdk/core/errors.py,sha256=E5UZrarHi5_adxGs7v_MfKugu8blXdRSHK71WbdzCUE,28724
+hpcflow/sdk/core/errors.py,sha256=5Bjk1w8FdVP4X7oFCNtzxJ_q4uaSZfQausZkWvYMkS4,28782
 hpcflow/sdk/core/execute.py,sha256=Gc2SauA4QNA1W4Gi2FYoKoqkoJtGg57cgn1p87WNCIs,7221
 hpcflow/sdk/core/json_like.py,sha256=f3Q1lxebn79nHIIQ2iRw9MbIDByGmdnlGp4yW39p-9g,29479
 hpcflow/sdk/core/loop.py,sha256=1GRUerSIAQ30KDi1-0M5gNiwzslSnmTTshLYUHwIMn0,50083
 hpcflow/sdk/core/loop_cache.py,sha256=C0t9UpvHFdTmw3bViZ2wccjZWtkbSbN9APvcwzBSREg,10801
 hpcflow/sdk/core/object_list.py,sha256=eX6jcJNlXcbiu3LMnU6kGOkBeUB9WUh9vrGsv97DInk,29906
-hpcflow/sdk/core/parameters.py,sha256=qN_Lg8nleKOJutt3JiifNCnT5TvALi8D9eWFbRVz3r4,97812
+hpcflow/sdk/core/parameters.py,sha256=fljEF6pfzPcLqTonDPC5q7OWPS31ib8Fc9DWQMK1rhw,97827
 hpcflow/sdk/core/rule.py,sha256=LiNyKp09a6TRGJvtiB1CcNqgyAIuPhuSW2RVfDWf5FE,6274
 hpcflow/sdk/core/run_dir_files.py,sha256=yh49BSlswqqyr97x5nDT87qu2MlOLMu7Arzl_B-fxy0,2061
 hpcflow/sdk/core/skip_reason.py,sha256=xPm8bd8sbPpiZ3sx9ZeW0jxgRQ0TBokSv0XIJKrEW2Y,113
-hpcflow/sdk/core/task.py,sha256=irMSVwfqUJYq6dYtoozGoKK3TKyic4im5XQb2N9i4Zw,142577
+hpcflow/sdk/core/task.py,sha256=0aqkwP-idjD5OYU-TLzVtjTdIVotb6ayAEzGGjM6sm0,142592
 hpcflow/sdk/core/task_schema.py,sha256=Aw13WNLutU_nIJknC9noJyEFkpxMLz3cN7ojIMgwZqI,38843
-hpcflow/sdk/core/test_utils.py,sha256=7AWsJhJScYVzgx2edUkn1jTog1fKL54S6w_BERTEDpE,13172
+hpcflow/sdk/core/test_utils.py,sha256=UXe8P-1b_6Pn6vdgJfMVsTGJdVI65TZ2mSUgWHlVnnc,13766
 hpcflow/sdk/core/types.py,sha256=y07Z6xbagPy45P4FfSu-Sv6q2Caeo9886L5JjWYaEOg,13030
 hpcflow/sdk/core/utils.py,sha256=P3JBrPS9ZM0sKrrihxaQScdFVX6ePSYQB5Rfbboo8CM,36316
 hpcflow/sdk/core/validation.py,sha256=PtM-3j5_mzp79DObgsWeJOZjOOJPKqkwWgeyDAVuAf0,1926
@@ -161,7 +162,7 @@ hpcflow/tests/schedulers/direct_linux/test_direct_linux_submission.py,sha256=pgH
 hpcflow/tests/schedulers/sge/test_sge_submission.py,sha256=NKO2wBR9AOW8chEBW2nZ9OyDMa_8xZWDw16gtg5g-C8,1107
 hpcflow/tests/schedulers/slurm/test_slurm_submission.py,sha256=Hcok40_hWb68T0hFzODcmzXr10M6WavLD3qiyzjcNOI,493
 hpcflow/tests/scripts/test_input_file_generators.py,sha256=zyM_0AXFDCHMO75GC3we__z4KeqcF5s7MFw2MJfeDec,9960
-hpcflow/tests/scripts/test_main_scripts.py,sha256=T_jKsD323RJJ1x8OaCr2XH_Y4cALX229yAybnDHZa9U,46295
+hpcflow/tests/scripts/test_main_scripts.py,sha256=qj4tg5s9Ii-n9b0bbWHAAGeXIoCPBZDhEMYH9LoAmbk,47911
 hpcflow/tests/scripts/test_non_snippet_script.py,sha256=XFn34lLxd8iL03a4OIY9pbT5NWbjswDcjp2jaQF2ICU,1304
 hpcflow/tests/scripts/test_ouput_file_parsers.py,sha256=gB6W1stp5TdoRjupbvt6_Ufs1TsOQwTUS5oHif4P3c8,12092
 hpcflow/tests/shells/wsl/test_wsl_submission.py,sha256=L9TChOSwLKGIcHrfNno843SNpNWopgHY7Ptc_HzMEtA,1069
@@ -215,8 +216,8 @@ hpcflow/tests/workflows/test_submission.py,sha256=SUbBUbD8C8LSulrI7aETkzP9RqED48
 hpcflow/tests/workflows/test_workflows.py,sha256=9z3rtXjA5iMOp4C0q4TkD_9kLzwourCY-obpeOtnNt0,18927
 hpcflow/tests/workflows/test_zip.py,sha256=MzEwsIAYV_1A3bD0XRo23zUwUKVzkkmNd8_cil6YdWQ,578
 hpcflow/viz_demo.ipynb,sha256=6D9uBbWK3oMfbaf93Tnv5riFPtW-2miUTWNr9kGcnd4,228913
-hpcflow_new2-0.2.0a207.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
-hpcflow_new2-0.2.0a207.dist-info/METADATA,sha256=zhJ-9B36m2gRh-tUh8wCKfHzerHXdc3v_reUMAH0q1g,2671
-hpcflow_new2-0.2.0a207.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-hpcflow_new2-0.2.0a207.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
-hpcflow_new2-0.2.0a207.dist-info/RECORD,,
+hpcflow_new2-0.2.0a208.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
+hpcflow_new2-0.2.0a208.dist-info/METADATA,sha256=bFA3B3L4JMaPEyabyXQgyxcoOmt7Wp9qZEN2gwmFva0,2671
+hpcflow_new2-0.2.0a208.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+hpcflow_new2-0.2.0a208.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
+hpcflow_new2-0.2.0a208.dist-info/RECORD,,