hpcflow-new2 0.2.0a227__py3-none-any.whl → 0.2.0a229__py3-none-any.whl

hpcflow/_version.py

@@ -1 +1 @@
-__version__ = "0.2.0a227"
+__version__ = "0.2.0a229"

hpcflow/sdk/cli.py

@@ -190,7 +190,7 @@ def _make_API_CLI(app: BaseApp):
         format, or a YAML/JSON string.
 
         """
-        wk = app.make_workflow(
+        wk_or_sub = app.make_workflow(
             template_file_or_str=template_file_or_str,
             is_string=string,
             template_format=format,
@@ -204,8 +204,12 @@ def _make_API_CLI(app: BaseApp):
             status=status,
             add_submission=add_submission,
         )
-        assert isinstance(wk, Workflow)
-        click.echo(wk.path)
+        if add_submission:
+            assert isinstance(wk_or_sub, Submission)
+            click.echo(wk_or_sub.workflow.path)
+        else:
+            assert isinstance(wk_or_sub, Workflow)
+            click.echo(wk_or_sub.path)
 
     @click.command(name="go")
     @click.argument("template_file_or_str")

hpcflow/sdk/core/actions.py

@@ -3017,6 +3017,7 @@ class Action(JSONLike):
             if all(rule.test(element_iteration=element_iter) for rule in cmd.rules)
         ]
 
+    @TimeIt.decorator
     def get_required_executables(self) -> Iterator[str]:
         """Return executable labels required by this action."""
         for command in self.commands:

hpcflow/sdk/core/commands.py

@@ -11,6 +11,7 @@ from typing import Any, ClassVar, TYPE_CHECKING
 
 import numpy as np
 
+from hpcflow.sdk.log import TimeIt
 from hpcflow.sdk.typing import hydrate
 from hpcflow.sdk.core.element import ElementResources
 from hpcflow.sdk.core.errors import NoCLIFormatMethodError
@@ -416,6 +417,7 @@ class Command(JSONLike):
     def _extract_executable_labels(cls, cmd_str: str) -> Sequence[str]:
         return cls.__EXE_RE.findall(cmd_str)
 
+    @TimeIt.decorator
     def get_required_executables(self) -> Sequence[str]:
         """Return executable labels required by this command."""
         # an executable label might appear in the `command` or `executable` attribute:

hpcflow/sdk/core/workflow.py

@@ -1786,6 +1786,20 @@ class Workflow(AppAware):
         elem: int
         task: int
 
+    @TimeIt.decorator
+    def __get_elements_by_task_idx(
+        self, element_idx_by_task: dict[int, set[int]]
+    ) -> dict[int, dict[int, Element]]:
+        return {
+            task_idx: {
+                idx: element
+                for idx, element in zip(
+                    elem_indices, self.tasks[task_idx].elements[list(elem_indices)]
+                )
+            }
+            for task_idx, elem_indices in element_idx_by_task.items()
+        }
+
     @TimeIt.decorator
     def get_elements_from_IDs(self, id_lst: Iterable[int]) -> list[Element]:
         """Return element objects from a list of IDs."""
@@ -1800,10 +1814,7 @@ class Workflow(AppAware):
             index_paths.append(Workflow._IndexPath1(elem_idx, task.index))
             element_idx_by_task[task.index].add(elem_idx)
 
-        elements_by_task = {
-            task_idx: {idx: self.tasks[task_idx].elements[idx] for idx in elem_idxes}
-            for task_idx, elem_idxes in element_idx_by_task.items()
-        }
+        elements_by_task = self.__get_elements_by_task_idx(element_idx_by_task)
 
         return [elements_by_task[path.task][path.elem] for path in index_paths]
 
@@ -1832,10 +1843,7 @@ class Workflow(AppAware):
             index_paths.append(Workflow._IndexPath2(iter_idx, elem_idx, task.index))
             element_idx_by_task[task.index].add(elem_idx)
 
-        elements_by_task = {
-            task_idx: {idx: self.tasks[task_idx].elements[idx] for idx in elem_idx}
-            for task_idx, elem_idx in element_idx_by_task.items()
-        }
+        elements_by_task = self.__get_elements_by_task_idx(element_idx_by_task)
 
         return [
             elements_by_task[path.task][path.elem].iterations[path.iter]
@@ -3627,7 +3635,8 @@ class Workflow(AppAware):
         if status:
             status.update("Adding new submission: resolving jobscripts...")
 
-        cache = ObjectCache.build(self, elements=True, iterations=True, runs=True)
+        with self._store.cache_ctx():
+            cache = ObjectCache.build(self, elements=True, iterations=True, runs=True)
 
         sub_obj: Submission = self._app.Submission(
             index=new_idx,
@@ -3719,7 +3728,7 @@ class Workflow(AppAware):
 
         """
         with self._app.config.cached_config():
-            with self.cached_merged_parameters():
+            with self.cached_merged_parameters(), self._store.cache_ctx():
                 js, element_deps = self._resolve_singular_jobscripts(
                     cache, tasks, force_array
                 )

hpcflow/sdk/demo/cli.py

@@ -29,6 +29,7 @@ from hpcflow.sdk.cli_common import (
     make_status_opt,
     add_sub_opt,
 )
+from hpcflow.sdk.submission.submission import Submission
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
@@ -133,7 +134,7 @@ def get_demo_workflow_CLI(app: BaseApp):
         status: bool = True,
         add_submission: bool = False,
     ):
-        wk = app.make_demo_workflow(
+        wk_or_sub = app.make_demo_workflow(
             workflow_name=workflow_name,
             template_format=format,
             path=path,
@@ -146,8 +147,12 @@ def get_demo_workflow_CLI(app: BaseApp):
             status=status,
             add_submission=add_submission,
         )
-        assert isinstance(wk, Workflow)
-        click.echo(wk.path)
+        if add_submission:
+            assert isinstance(wk_or_sub, Submission)
+            click.echo(wk_or_sub.workflow.path)
+        else:
+            assert isinstance(wk_or_sub, Workflow)
+            click.echo(wk_or_sub.path)
 
     @demo_workflow.command("go")
     @click.argument("workflow_name")

hpcflow/tests/unit/test_cli.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 import pytest
 
 from click.testing import CliRunner
@@ -143,3 +144,27 @@ def test_cli_click_exit_code_non_zero(tmp_path):
     )
     assert result.exit_code == 2
     assert error_file.is_file()
+
+
+def test_cli_make_demo_workflow(new_null_config, tmp_path):
+    """Check the demo workflow directory is generated."""
+    runner = CliRunner()
+    result = runner.invoke(
+        hf.cli, args=f'demo-workflow make workflow_1 --path "{str(tmp_path)}"'
+    )
+    assert result.exit_code == 0
+    assert Path(result.stdout_bytes.decode().strip()).is_dir()
+
+
+def test_cli_make_demo_workflow_add_sub(new_null_config, tmp_path):
+    """Check the demo workflow directory is generated, and a submission is added."""
+    runner = CliRunner()
+    result = runner.invoke(
+        hf.cli,
+        args=f'demo-workflow make workflow_1 --path "{str(tmp_path)}" --add-submission',
+    )
+    assert result.exit_code == 0
+    wk_path = Path(result.stdout_bytes.decode().strip())
+    assert wk_path.is_dir()
+    wk = hf.Workflow(wk_path)
+    assert len(wk.submissions) == 1

{hpcflow_new2-0.2.0a227.dist-info → hpcflow_new2-0.2.0a229.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hpcflow-new2
-Version: 0.2.0a227
+Version: 0.2.0a229
 Summary: Computational workflow management
 License: MPL-2.0
 Author: aplowman

{hpcflow_new2-0.2.0a227.dist-info → hpcflow_new2-0.2.0a229.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=Jgo3POaN0i9GWVRAfP7uEOtWUMY-0Fis95oTeRaSmHQ,26
+hpcflow/_version.py,sha256=N1YPfrQRLSWxAxps9EY74f8NTNfrZeI0hAp1gPseh58,26
 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
@@ -65,7 +65,7 @@ hpcflow/data/workflows/workflow_1.yaml,sha256=lF7Re2SVc_5gQk5AwB0gXaq-n-T5ia4su3
 hpcflow/examples.ipynb,sha256=cLKp4QsxwwMXRanDnfWY9kqsV23q6G4raOpu6IZXnMw,28553
 hpcflow/sdk/__init__.py,sha256=BEbIz8adCAX06ZmvEcquEu29PmQDvVP1I1qn_q78dYc,6289
 hpcflow/sdk/app.py,sha256=UWnpxdEqVD07VE-Rr23xhVHesF3zZI6ryLJ1-yXKp7M,146820
-hpcflow/sdk/cli.py,sha256=qMFACsIA32gD2oLC8_FD9JjFYgidCoGxOH-L3qM2xx0,45818
+hpcflow/sdk/cli.py,sha256=982MaA8xbrQr3AGniHoahiZkmgQccE-DJ2ykwV21EFc,45989
 hpcflow/sdk/cli_common.py,sha256=MO0TbC280JdZTLnxSV15wE7PDNx83sotpJsyAN1E2F4,10458
 hpcflow/sdk/config/__init__.py,sha256=pkufl_CXm_Kswk1x7LTavuplWjUbUCitK0AJ2E60gwM,137
 hpcflow/sdk/config/callbacks.py,sha256=cuW31ZW0YTOi5K5P-NYHuiK1YLsglMEH3c_u6mddVE8,8078
@@ -75,11 +75,11 @@ 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=zLsCmeKW8dmRZ-6MEkO8M4kboFxldASLu0IdCwGU-uk,118467
+hpcflow/sdk/core/actions.py,sha256=ZoM-2L9qPc52fi26YBDwKHr1axPqhSI_89lRPsmnokM,118489
 hpcflow/sdk/core/app_aware.py,sha256=SnQCix09IHhqPAHBpbdhQAf3wDKvO6n6ym4XJ8vrv1s,569
 hpcflow/sdk/core/cache.py,sha256=6b0emvJGP-yf5UxKmEY_s4_gdyUfaNaXafq-qQaoBfU,8174
 hpcflow/sdk/core/command_files.py,sha256=LcrK7wjQnxmTDUrsC0Xgbjsy1NGodf62LrrTSNAAxxE,24942
-hpcflow/sdk/core/commands.py,sha256=vFyZ9Cv_tvGqSGtVEnAHAeXA-HAxWoF0nmf1e0bFCvs,15993
+hpcflow/sdk/core/commands.py,sha256=mm4FVTpkjVXxfCOlyHcfEPy2DrBkhPaOaq0gk5ExvKA,16050
 hpcflow/sdk/core/element.py,sha256=pPRezx0HATKH55qEstXp1xOG4S8oGLVnJ3sQcEmLsXo,68152
 hpcflow/sdk/core/enums.py,sha256=scp7b7gbFSefu1bks2M2u6amq6G_lB_j_h8U_TPM4bU,5316
 hpcflow/sdk/core/environment.py,sha256=m0Qp4Y1XcPJ1yPrdHp6RJv9_H61nA9Qo2ZJV_-wGne8,7959
@@ -99,7 +99,7 @@ hpcflow/sdk/core/test_utils.py,sha256=UXe8P-1b_6Pn6vdgJfMVsTGJdVI65TZ2mSUgWHlVnn
 hpcflow/sdk/core/types.py,sha256=kqVXpiH8qwOVVBAw6GFvUQVdNYLEv7qIbgEkgfK0DO8,13021
 hpcflow/sdk/core/utils.py,sha256=EFflyTr6Ju8v0AfZYQuFnJm-hNjtx0XbnFuccM7cV-k,36950
 hpcflow/sdk/core/validation.py,sha256=4-0g5z3CgjFLQ2FCM0p0mjvNqHYuLhIqvQR_kpM0tsU,1838
-hpcflow/sdk/core/workflow.py,sha256=aM4JTfaIhtDA3dOeNC4ThTA1L7_EGOyBOPMcvf6KjC8,183779
+hpcflow/sdk/core/workflow.py,sha256=qZdQm0AxcV9XhZ2WrzqZNkPOTyWh9ifsZmoYMasH_q0,184085
 hpcflow/sdk/core/zarr_io.py,sha256=i6WqkFXe-q1sJGTCYAbsNRXRrdkxZy6NRahTcuZPuX4,5906
 hpcflow/sdk/data/__init__.py,sha256=-YzROirohSKU2UGYj5vkCe_J2KejbzhIjUXNaJwKHLk,568
 hpcflow/sdk/data/config_file_schema.yaml,sha256=7i3z_m3GBRtLyB4c7qPngnlQWqcIq1CyCcOysDyq4es,791
@@ -110,7 +110,7 @@ hpcflow/sdk/data/parameters_spec_schema.yaml,sha256=Wj7CvG7Ul1nZDtBca-oxeFH_aSZk
 hpcflow/sdk/data/task_schema_spec_schema.yaml,sha256=6NROg7x-493bdvRwvY4M71R7POT-tNnmROkEsnnoL4k,93
 hpcflow/sdk/data/workflow_spec_schema.yaml,sha256=GsagSNksSYIPEJpjpkXd8rWpru7-77tQNxpzCt8aTWE,430
 hpcflow/sdk/demo/__init__.py,sha256=8mgXFcEpn817_vO6L785GW268JUBrZt69bTCGszgvf0,28
-hpcflow/sdk/demo/cli.py,sha256=Esc2E5wUR3ExB1_CfMGX4JqVxIeLQVOPEN5WKTWVpQI,6576
+hpcflow/sdk/demo/cli.py,sha256=mEncltwW4KeybiMxhvL1cl4k7uFzyca8TRzyEMziZx0,6804
 hpcflow/sdk/helper/__init__.py,sha256=HPbnZlvgC9xJKpXyjrBuEXGMIfkLfblD_RBefBLJOFc,29
 hpcflow/sdk/helper/cli.py,sha256=s26xfwzmgjh778nIfjEozqbvs2XvKPoNaHSi_2vr01U,4026
 hpcflow/sdk/helper/helper.py,sha256=T45BEwhPgTlwvqDNbT4Us4UVmdRKRoszIMt8a9B69kE,9475
@@ -171,7 +171,7 @@ hpcflow/tests/unit/test_action.py,sha256=3fSQy0euZwu3CH8xl7nG9vWV1arKiFEHpO8vZNC
 hpcflow/tests/unit/test_action_rule.py,sha256=h7CPBXdHMoHZLqMnYn7EAMEyUsK5KduB4XiJV-N3WAY,729
 hpcflow/tests/unit/test_app.py,sha256=j_FeS6nMU5W2qftNZBQ-HbpBiNzKYLPsaOFSMInvEKw,4200
 hpcflow/tests/unit/test_cache.py,sha256=pSv2sxBpHYlUjVc_PLhbciykGMOOcXF6-C39fPLEbWM,1368
-hpcflow/tests/unit/test_cli.py,sha256=Ypn0k-QXeoeLK77bKGvylqhWgf_khukmNPh4OwG-_zs,4544
+hpcflow/tests/unit/test_cli.py,sha256=LbOcFPglkjWc6NDt8r3gi0mvXQ2sVXp6WiX8fDaVUMc,5426
 hpcflow/tests/unit/test_command.py,sha256=oooZPOYM62j4IHIAgR5kKhY0_cYaCVqFtuH8buGnlYo,23182
 hpcflow/tests/unit/test_config.py,sha256=__rJADdEIia1lA2eSoT40IVw-7ArZSA86PDCQiWP7_M,6182
 hpcflow/tests/unit/test_config_file.py,sha256=H0jXqPDEz4KKJ-VcnhpY9Xf_iVxFZr9eOvKvGRzmHCU,4599
@@ -218,8 +218,8 @@ 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_new2-0.2.0a227.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
-hpcflow_new2-0.2.0a227.dist-info/METADATA,sha256=Q7I7tq_F1uXnwwuKuvhGjdBbBs-AujyfsWgJ4KZ_NFg,2663
-hpcflow_new2-0.2.0a227.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-hpcflow_new2-0.2.0a227.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
-hpcflow_new2-0.2.0a227.dist-info/RECORD,,
+hpcflow_new2-0.2.0a229.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
+hpcflow_new2-0.2.0a229.dist-info/METADATA,sha256=-5FqegeQRZ9QG__KPPlPn0sqUvd-QcDvP5Y1gMeW0TE,2663
+hpcflow_new2-0.2.0a229.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+hpcflow_new2-0.2.0a229.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
+hpcflow_new2-0.2.0a229.dist-info/RECORD,,