hpcflow-new2 0.2.0a177__py3-none-any.whl → 0.2.0a178__py3-none-any.whl

hpcflow/_version.py

@@ -1 +1 @@
-__version__ = "0.2.0a177"
+__version__ = "0.2.0a178"

hpcflow/sdk/cli.py

@@ -31,8 +31,13 @@ from hpcflow.sdk.cli_common import (
     zip_path_opt,
     zip_overwrite_opt,
     zip_log_opt,
+    zip_include_execute_opt,
+    zip_include_rechunk_backups_opt,
     unzip_path_opt,
     unzip_log_opt,
+    rechunk_backup_opt,
+    rechunk_chunk_size_opt,
+    rechunk_status_opt,
 )
 from hpcflow.sdk.helper.cli import get_helper_CLI
 from hpcflow.sdk.log import TimeIt
@@ -425,11 +430,28 @@ def _make_workflow_CLI(app):
     @zip_path_opt
     @zip_overwrite_opt
     @zip_log_opt
+    @zip_include_execute_opt
+    @zip_include_rechunk_backups_opt
     @click.pass_context
-    def zip_workflow(ctx, path, overwrite, log):
+    def zip_workflow(
+        ctx,
+        path,
+        overwrite,
+        log,
+        include_execute,
+        include_rechunk_backups,
+    ):
         """Generate a copy of the workflow in the zip file format in the current working
         directory."""
-        click.echo(ctx.obj["workflow"].zip(path=path, overwrite=overwrite, log=log))
+        click.echo(
+            ctx.obj["workflow"].zip(
+                path=path,
+                overwrite=overwrite,
+                log=log,
+                include_execute=include_execute,
+                include_rechunk_backups=include_rechunk_backups,
+            )
+        )
 
     @workflow.command(name="unzip")
     @unzip_path_opt
@@ -440,6 +462,37 @@ def _make_workflow_CLI(app):
         current working directory."""
         click.echo(ctx.obj["workflow"].unzip(path=path, log=log))
 
+    @workflow.command(name="rechunk")
+    @rechunk_backup_opt
+    @rechunk_chunk_size_opt
+    @rechunk_status_opt
+    @click.pass_context
+    def rechunk(ctx, backup, chunk_size, status):
+        """Rechunk metadata/runs and parameters/base arrays."""
+        ctx.obj["workflow"].rechunk(backup=backup, chunk_size=chunk_size, status=status)
+
+    @workflow.command(name="rechunk-runs")
+    @rechunk_backup_opt
+    @rechunk_chunk_size_opt
+    @rechunk_status_opt
+    @click.pass_context
+    def rechunk_runs(ctx, backup, chunk_size, status):
+        """Rechunk the metadata/runs array."""
+        ctx.obj["workflow"].rechunk_runs(
+            backup=backup, chunk_size=chunk_size, status=status
+        )
+
+    @workflow.command(name="rechunk-parameter-base")
+    @rechunk_backup_opt
+    @rechunk_chunk_size_opt
+    @rechunk_status_opt
+    @click.pass_context
+    def rechunk_parameter_base(ctx, backup, chunk_size, status):
+        """Rechunk the parameters/base array."""
+        ctx.obj["workflow"].rechunk_parameter_base(
+            backup=backup, chunk_size=chunk_size, status=status
+        )
+
     workflow.help = workflow.help.format(app_name=app.name)
 
     workflow.add_command(_make_workflow_submission_CLI(app))
@@ -711,8 +764,18 @@ def _make_zip_CLI(app):
     @zip_path_opt
     @zip_overwrite_opt
     @zip_log_opt
+    @zip_include_execute_opt
+    @zip_include_rechunk_backups_opt
     @workflow_ref_type_opt
-    def zip_workflow(workflow_ref, path, overwrite, log, ref_type):
+    def zip_workflow(
+        workflow_ref,
+        path,
+        overwrite,
+        log,
+        include_execute,
+        include_rechunk_backups,
+        ref_type,
+    ):
         """Generate a copy of the specified workflow in the zip file format in the
         current working directory.
 
@@ -721,7 +784,15 @@ def _make_zip_CLI(app):
         """
         workflow_path = app._resolve_workflow_reference(workflow_ref, ref_type)
         wk = app.Workflow(workflow_path)
-        click.echo(wk.zip(path=path, overwrite=overwrite, log=log))
+        click.echo(
+            wk.zip(
+                path=path,
+                overwrite=overwrite,
+                log=log,
+                include_execute=include_execute,
+                include_rechunk_backups=include_rechunk_backups,
+            )
+        )
 
     return zip_workflow
 
@@ -760,6 +831,27 @@ def _make_cancel_CLI(app):
     return cancel
 
 
+def _make_rechunk_CLI(app):
+    @click.command(name="rechunk")
+    @click.argument("workflow_ref")
+    @workflow_ref_type_opt
+    @rechunk_backup_opt
+    @rechunk_chunk_size_opt
+    @rechunk_status_opt
+    def rechunk(workflow_ref, ref_type, backup, chunk_size, status):
+        """Rechunk metadata/runs and parameters/base arrays.
+
+        WORKFLOW_REF is the local ID (that provided by the `show` command}) or the
+        workflow path.
+
+        """
+        workflow_path = app._resolve_workflow_reference(workflow_ref, ref_type)
+        wk = app.Workflow(workflow_path)
+        wk.rechunk(backup=backup, chunk_size=chunk_size, status=status)
+
+    return rechunk
+
+
 def _make_open_CLI(app):
     @click.group(name="open")
     def open_file():
@@ -1129,6 +1221,7 @@ def make_cli(app):
     new_CLI.add_command(_make_cancel_CLI(app))
     new_CLI.add_command(_make_zip_CLI(app))
     new_CLI.add_command(_make_unzip_CLI(app))
+    new_CLI.add_command(_make_rechunk_CLI(app))
     for cli_cmd in _make_API_CLI(app):
         new_CLI.add_command(cli_cmd)
 

hpcflow/sdk/cli_common.py

@@ -141,6 +141,8 @@ zip_overwrite_opt = click.option(
     help="If set, any existing file will be overwritten.",
 )
 zip_log_opt = click.option("--log", help="Path to a log file to use during zipping.")
+zip_include_execute_opt = click.option("--include-execute", is_flag=True)
+zip_include_rechunk_backups_opt = click.option("--include-rechunk-backups", is_flag=True)
 unzip_path_opt = click.option(
     "--path",
     default=".",
@@ -151,3 +153,23 @@ unzip_path_opt = click.option(
     ),
 )
 unzip_log_opt = click.option("--log", help="Path to a log file to use during unzipping.")
+rechunk_backup_opt = click.option(
+    "--backup/--no-backup",
+    default=True,
+    help=("First copy a backup of the array to a directory ending in `.bak`."),
+)
+rechunk_chunk_size_opt = click.option(
+    "--chunk-size",
+    type=click.INT,
+    default=None,
+    help=(
+        "New chunk size (array items per chunk). If unset (as by default), the array "
+        "will be rechunked to a single chunk array (i.e with a chunk size equal to the "
+        "array's shape)."
+    ),
+)
+rechunk_status_opt = click.option(
+    "--status/--no-status",
+    default=True,
+    help="If True, display a live status to track rechunking progress.",
+)

hpcflow/sdk/core/workflow.py

@@ -1696,7 +1696,14 @@ class Workflow:
 
         return wk
 
-    def zip(self, path=".", log=None, overwrite=False) -> str:
+    def zip(
+        self,
+        path=".",
+        log=None,
+        overwrite=False,
+        include_execute=False,
+        include_rechunk_backups=False,
+    ) -> str:
         """
         Parameters
         ----------
@@ -1705,7 +1712,13 @@ class Workflow:
             directory, the zip file will be created within this directory. Otherwise,
             this path is assumed to be the full file path to the new zip file.
         """
-        return self._store.zip(path=path, log=log, overwrite=overwrite)
+        return self._store.zip(
+            path=path,
+            log=log,
+            overwrite=overwrite,
+            include_execute=include_execute,
+            include_rechunk_backups=include_rechunk_backups,
+        )
 
     def unzip(self, path=".", log=None) -> str:
         """
@@ -2943,6 +2956,34 @@ class Workflow:
                     final_runs[loop_name].append(final[0])
         return dict(final_runs)
 
+    def rechunk_runs(
+        self,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        self._store.rechunk_runs(chunk_size=chunk_size, backup=backup, status=status)
+
+    def rechunk_parameter_base(
+        self,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        self._store.rechunk_parameter_base(
+            chunk_size=chunk_size, backup=backup, status=status
+        )
+
+    def rechunk(
+        self,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        """Rechunk metadata/runs and parameters/base arrays."""
+        self.rechunk_runs(chunk_size=chunk_size, backup=backup, status=status)
+        self.rechunk_parameter_base(chunk_size=chunk_size, backup=backup, status=status)
+
 
 @dataclass
 class WorkflowBlueprint:

hpcflow/sdk/persistence/zarr.py

@@ -5,6 +5,8 @@ from contextlib import contextmanager
 from dataclasses import dataclass
 from datetime import datetime
 from pathlib import Path
+import shutil
+import time
 from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple, Union
 
 import numpy as np
@@ -1152,7 +1154,14 @@ class ZarrPersistentStore(PersistentStore):
         with self.using_resource("attrs", action="read") as attrs:
             return attrs["name"]
 
-    def zip(self, path=".", log=None, overwrite=False):
+    def zip(
+        self,
+        path=".",
+        log=None,
+        overwrite=False,
+        include_execute=False,
+        include_rechunk_backups=False,
+    ):
         """
         Parameters
         ----------
@@ -1188,16 +1197,120 @@ class ZarrPersistentStore(PersistentStore):
             add_pw_to="target_options",
         )
         dst_zarr_store = zarr.storage.FSStore(url="", fs=zfs)
+        excludes = []
+        if not include_execute:
+            excludes.append("execute")
+        if not include_rechunk_backups:
+            excludes.append("runs.bak")
+            excludes.append("base.bak")
+
         zarr.convenience.copy_store(
             src_zarr_store,
             dst_zarr_store,
-            excludes="execute",
+            excludes=excludes or None,
             log=log,
         )
         del zfs  # ZipFileSystem remains open for instance lifetime
         status.stop()
         return dst_path
 
+    def _rechunk_arr(
+        self,
+        arr,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        arr_path = Path(self.workflow.path) / arr.path
+        arr_name = arr.path.split("/")[-1]
+
+        if status:
+            console = Console()
+            status = console.status("Rechunking...")
+            status.start()
+        backup_time = None
+
+        if backup:
+            if status:
+                status.update("Backing up...")
+            backup_path = arr_path.with_suffix(".bak")
+            if backup_path.is_dir():
+                pass
+            else:
+                tic = time.perf_counter()
+                shutil.copytree(arr_path, backup_path)
+                toc = time.perf_counter()
+                backup_time = toc - tic
+
+        tic = time.perf_counter()
+        arr_rc_path = arr_path.with_suffix(".rechunked")
+        arr = zarr.open(arr_path)
+        if status:
+            status.update("Creating new array...")
+        arr_rc = zarr.create(
+            store=arr_rc_path,
+            shape=arr.shape,
+            chunks=arr.shape if chunk_size is None else chunk_size,
+            dtype=object,
+            object_codec=MsgPack(),
+        )
+        if status:
+            status.update("Copying data...")
+        data = np.empty(shape=arr.shape, dtype=object)
+        bad_data = []
+        for idx in range(len(arr)):
+            try:
+                data[idx] = arr[idx]
+            except RuntimeError:
+                # blosc decompression errors
+                bad_data.append(idx)
+                pass
+        arr_rc[:] = data
+
+        arr_rc.attrs.put(arr.attrs.asdict())
+
+        if status:
+            status.update("Deleting old array...")
+        shutil.rmtree(arr_path)
+
+        if status:
+            status.update("Moving new array into place...")
+        shutil.move(arr_rc_path, arr_path)
+
+        toc = time.perf_counter()
+        rechunk_time = toc - tic
+
+        if status:
+            status.stop()
+
+        if backup_time:
+            print(f"Time to backup {arr_name}: {backup_time:.1f} s")
+
+        print(f"Time to rechunk and move {arr_name}: {rechunk_time:.1f} s")
+
+        if bad_data:
+            print(f"Bad data at {arr_name} indices: {bad_data}.")
+
+        return arr_rc
+
+    def rechunk_parameter_base(
+        self,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        arr = self._get_parameter_base_array()
+        return self._rechunk_arr(arr, chunk_size, backup, status)
+
+    def rechunk_runs(
+        self,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        arr = self._get_EARs_arr()
+        return self._rechunk_arr(arr, chunk_size, backup, status)
+
 
 class ZarrZipPersistentStore(ZarrPersistentStore):
     """A store designed mainly as an archive format that can be uploaded to data
@@ -1257,3 +1370,12 @@ class ZarrZipPersistentStore(ZarrPersistentStore):
     def delete_no_confirm(self) -> None:
         # `ZipFileSystem.rm()` does not seem to be implemented.
         raise NotImplementedError()
+
+    def _rechunk_arr(
+        self,
+        arr,
+        chunk_size: Optional[int] = None,
+        backup: Optional[bool] = True,
+        status: Optional[bool] = True,
+    ):
+        raise NotImplementedError

hpcflow/tests/unit/test_persistence.py

@@ -1,4 +1,6 @@
-from importlib import resources
+from pathlib import Path
+import numpy as np
+import zarr
 import pytest
 from hpcflow.sdk.core.test_utils import make_test_data_YAML_workflow
 from hpcflow.sdk.persistence.base import StoreEAR, StoreElement, StoreElementIter
@@ -239,3 +241,118 @@ def test_make_zarr_store_no_compressor(null_config, tmp_path):
         store="zarr",
         store_kwargs={"compressor": None},
     )
+
+
+@pytest.mark.integration
+def test_zarr_rechunk_data_equivalent(null_config, tmp_path):
+    t1 = hf.Task(
+        schema=hf.task_schemas.test_t1_conditional_OS,
+        inputs={"p1": 101},
+        repeats=3,
+    )
+    wk = hf.Workflow.from_template_data(
+        tasks=[t1],
+        template_name="test_run_rechunk",
+        workflow_name="test_run_rechunk",
+        path=tmp_path,
+    )
+    wk.submit(wait=True, status=False, add_to_known=False)
+    wk.rechunk_runs(backup=True, status=False, chunk_size=None)  # None -> one chunk
+
+    arr = wk._store._get_EARs_arr()
+    assert arr.chunks == arr.shape
+
+    bak_path = (Path(wk.path) / arr.path).with_suffix(".bak")
+    arr_bak = zarr.open(bak_path)
+
+    assert arr_bak.chunks == (1,)
+
+    # check backup and new runs data are equal:
+    assert np.all(arr[:] == arr_bak[:])
+
+    # check attributes are equal:
+    assert arr.attrs.asdict() == arr_bak.attrs.asdict()
+
+
+@pytest.mark.integration
+def test_zarr_rechunk_data_equivalent_custom_chunk_size(null_config, tmp_path):
+    t1 = hf.Task(
+        schema=hf.task_schemas.test_t1_conditional_OS,
+        inputs={"p1": 101},
+        repeats=3,
+    )
+    wk = hf.Workflow.from_template_data(
+        tasks=[t1],
+        template_name="test_run_rechunk",
+        workflow_name="test_run_rechunk",
+        path=tmp_path,
+    )
+    wk.submit(wait=True, status=False, add_to_known=False)
+    wk.rechunk_runs(backup=True, status=False, chunk_size=2)
+
+    arr = wk._store._get_EARs_arr()
+    assert arr.chunks == (2,)
+
+    bak_path = (Path(wk.path) / arr.path).with_suffix(".bak")
+    arr_bak = zarr.open(bak_path)
+
+    assert arr_bak.chunks == (1,)
+
+    # check backup and new runs data are equal:
+    assert np.all(arr[:] == arr_bak[:])
+
+
+@pytest.mark.integration
+def test_zarr_rechunk_data_no_backup_load_runs(null_config, tmp_path):
+    t1 = hf.Task(
+        schema=hf.task_schemas.test_t1_conditional_OS,
+        inputs={"p1": 101},
+        repeats=3,
+    )
+    wk = hf.Workflow.from_template_data(
+        tasks=[t1],
+        template_name="test_run_rechunk",
+        workflow_name="test_run_rechunk",
+        path=tmp_path,
+    )
+    wk.submit(wait=True, status=False, add_to_known=False)
+    wk.rechunk_runs(backup=False, status=False)
+
+    arr = wk._store._get_EARs_arr()
+
+    bak_path = (Path(wk.path) / arr.path).with_suffix(".bak")
+    assert not bak_path.is_file()
+
+    # check we can load runs:
+    runs = wk._store._get_persistent_EARs(id_lst=list(range(wk.num_EARs)))
+    run_ID = []
+    for i in runs.values():
+        run_ID.append(i.id_)
+
+
+@pytest.mark.integration
+def test_zarr_rechunk_data_no_backup_load_parameter_base(null_config, tmp_path):
+    t1 = hf.Task(
+        schema=hf.task_schemas.test_t1_conditional_OS,
+        inputs={"p1": 101},
+        repeats=3,
+    )
+    wk = hf.Workflow.from_template_data(
+        tasks=[t1],
+        template_name="test_run_rechunk",
+        workflow_name="test_run_rechunk",
+        path=tmp_path,
+    )
+    wk.submit(wait=True, status=False, add_to_known=False)
+    wk.rechunk_parameter_base(backup=False, status=False)
+
+    arr = wk._store._get_parameter_base_array()
+
+    bak_path = (Path(wk.path) / arr.path).with_suffix(".bak")
+    assert not bak_path.is_file()
+
+    # check we can load parameters:
+    params = wk.get_all_parameters()
+    param_IDs = []
+    for i in params:
+        param_IDs.append(i.id_)

hpcflow_new2-0.2.0a178.dist-info/LICENSE

@@ -0,0 +1,375 @@
+© Copyright 2024 hpcflow developers
+
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

{hpcflow_new2-0.2.0a177.dist-info → hpcflow_new2-0.2.0a178.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hpcflow-new2
-Version: 0.2.0a177
+Version: 0.2.0a178
 Summary: Computational workflow management
 License: MIT
 Author: aplowman

{hpcflow_new2-0.2.0a177.dist-info → hpcflow_new2-0.2.0a178.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=SeMopsPkhCyd9gqIrzwFNRj3ZlkUlUYl-74QYz61mo4,1089
-hpcflow/_version.py,sha256=c6sVLAvL-ZtlEF_CBbI6lCJoA-qh3KPMN5Smq6FFaPk,26
+hpcflow/_version.py,sha256=Aly54M0zR3W7D8mDCqLBInigz_HpeKNFLimAxo_N7ng,26
 hpcflow/app.py,sha256=d-kgfnZNlqlCi2H8bK26714brD_u3ibN3FaEZgjF9aA,1332
 hpcflow/cli.py,sha256=G2J3D9v6MnMWOWMMWK6UEKLn_6wnV9lT_qygEBBxg-I,66
 hpcflow/data/demo_data_manifest/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -36,8 +36,8 @@ hpcflow/data/workflows/workflow_1.yaml,sha256=lF7Re2SVc_5gQk5AwB0gXaq-n-T5ia4su3
 hpcflow/examples.ipynb,sha256=cLKp4QsxwwMXRanDnfWY9kqsV23q6G4raOpu6IZXnMw,28553
 hpcflow/sdk/__init__.py,sha256=SdzVm7dydLv2kmr2tqrH14Gf1GEAEhsEuAuqiGBLHhM,5700
 hpcflow/sdk/app.py,sha256=lS9sl6YEbB02LZbltlgs8neokZNmxfl4aT46-2UuDTQ,96661
-hpcflow/sdk/cli.py,sha256=uIzF2YEFQFxmJNFwZM_OZWpzgJK0BnqNY3zwa9sfVzM,35028
-hpcflow/sdk/cli_common.py,sha256=kDSIe90mxD37lQqvIXDyRauLtTRRnNueSljcRPF_w0M,4738
+hpcflow/sdk/cli.py,sha256=t2p4xxo7yaxO8jZZPcgz1xusjmiOwbqvGtP-2y0Jp8A,37715
+hpcflow/sdk/cli_common.py,sha256=ZtJkol29G-Sztuhl013RqRdS3eOWsCCuh6aKfh7A6jY,5540
 hpcflow/sdk/config/__init__.py,sha256=qJrrxcAN4f1u_RyTtXgz-xlTLwNafE9v0VEMP1x6-bU,70
 hpcflow/sdk/config/callbacks.py,sha256=7z0rFX7ULUTAo24IJr6kLzPmZCgmkaQ8P5e-AfYTcY8,5339
 hpcflow/sdk/config/cli.py,sha256=PsmqrC21GAXx_-UHWVgqg-3luVe4r_MG0HjFRv2Yy1Y,10638
@@ -65,7 +65,7 @@ hpcflow/sdk/core/task_schema.py,sha256=TipXzC2guu9zilv0En-rHt6lUCTSIj5faI4lVWQdU
 hpcflow/sdk/core/test_utils.py,sha256=IhCLvRzDuG4hVNGeGulGKfZEgg7Ow-vgiEqewzMiaZ4,9762
 hpcflow/sdk/core/utils.py,sha256=cpwfoHgbHanZQXmVZRN3VRW8X-zZxb1I6T0v2tWgBK0,25811
 hpcflow/sdk/core/validation.py,sha256=KBKiy5DdfGiGmMaB0HdKTY0V972u5dJzvkYkX0_KtCo,518
-hpcflow/sdk/core/workflow.py,sha256=ziKn1cA4s_eHKPMzyKfHF4bVNF7bfho4dko5qtyZKjU,113111
+hpcflow/sdk/core/workflow.py,sha256=8Xl74KrSXJ5TE5J42w5zLF1Wi-ofALZ0rVlhRDzHAeM,114306
 hpcflow/sdk/core/zarr_io.py,sha256=V_Zm6uSiuaCbXyHFJUO74K1pAr4Zqrj3aLCBjohCwvs,5724
 hpcflow/sdk/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 hpcflow/sdk/data/config_file_schema.yaml,sha256=7i3z_m3GBRtLyB4c7qPngnlQWqcIq1CyCcOysDyq4es,791
@@ -88,7 +88,7 @@ hpcflow/sdk/persistence/json.py,sha256=55F4Txa50I9HzfETPqwo6gAOBRaoewMHGR3V4-2Fi
 hpcflow/sdk/persistence/pending.py,sha256=XktGkRpJmlyjceOiDY0GEL2xRl6k-gbjt057LmEj5oc,25656
 hpcflow/sdk/persistence/store_resource.py,sha256=oEyocRqa8Uym-57UFosrwate-Xw9O7i2FM82TxHc4m0,4307
 hpcflow/sdk/persistence/utils.py,sha256=yQT6gS-Ipj2N6grtlV5d0czxxKE0CaeqAkXA1247XGo,1522
-hpcflow/sdk/persistence/zarr.py,sha256=otZbR17O3ZNIot7uVAP1UdWs_L0PHS682LuWk3z1_1g,45708
+hpcflow/sdk/persistence/zarr.py,sha256=PSZCOZiNeTcNdxg__dxyrOllPaEBnOLZF1nw0Zzp154,49147
 hpcflow/sdk/runtime.py,sha256=_in5ojiy9R8fD1ZNbdE6PDmZx6kSaiG9WPB6kVBFE7k,9217
 hpcflow/sdk/submission/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 hpcflow/sdk/submission/jobscript.py,sha256=Z9NUzkIcmoFw-XAtG8FdLpO2LtMt3czk1v1BnbM1eZw,44678
@@ -134,7 +134,7 @@ hpcflow/tests/unit/test_json_like.py,sha256=aGCiGfT-tNiFu3yzW6d_T-oDc5QLwSUgq3pN
 hpcflow/tests/unit/test_loop.py,sha256=GNKMGAXP0AaB7fl1TShluyh-PoG7O96X7SGUg6vnK6Y,45149
 hpcflow/tests/unit/test_object_list.py,sha256=nDpbRpCu4XqoYxKMr1_QmDS1s2_6nQOpIEBRHSAXoVg,3049
 hpcflow/tests/unit/test_parameter.py,sha256=39CVido_NJGX-Xj9NDSlazpGzWqMG4zp0GmIKwzO7lI,6659
-hpcflow/tests/unit/test_persistence.py,sha256=DPXFiuY2v8vj0zZ7299nf-KtgYT8LhHI52fq7UPoa6Y,8128
+hpcflow/tests/unit/test_persistence.py,sha256=6NfYzqDHLlTiv3OIcTfIkWusL748cjYi-i4Be9Uo02M,11519
 hpcflow/tests/unit/test_resources.py,sha256=2RRFIn5brKyD1UNmkmnvyjPZowa-dokQd0EuCEeo7so,7799
 hpcflow/tests/unit/test_run.py,sha256=uvG2BbVOD0JJAJCbdh0MMRJME8tVzOm7H4PTLzPLWZY,2613
 hpcflow/tests/unit/test_runtime.py,sha256=HjHPTS3UkX1LcwheFgpp4px_VlRis8KAE2HoeqxRbA8,322
@@ -151,7 +151,8 @@ hpcflow/tests/unit/test_workflow_template.py,sha256=fF7LNveMwCledgncNCRfD9Nd9dL9
 hpcflow/tests/workflows/test_jobscript.py,sha256=9sp1o0g72JZbv2QlOl5v7wCZEFjotxiIKGNUxVaFgaA,724
 hpcflow/tests/workflows/test_workflows.py,sha256=xai6FRtGqG4lStJk6KmsqPUSuvqs9FrsBOxMVALshIs,13400
 hpcflow/viz_demo.ipynb,sha256=1QdnVsk72vihv2L6hOGyk318uEa22ZSgGxQCa7hW2oo,6238
-hpcflow_new2-0.2.0a177.dist-info/METADATA,sha256=I1tkrIUSwRwNsKxjcTy7lrpcOhZp9Z3HUGV_Wdoo9qw,2466
-hpcflow_new2-0.2.0a177.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-hpcflow_new2-0.2.0a177.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
-hpcflow_new2-0.2.0a177.dist-info/RECORD,,
+hpcflow_new2-0.2.0a178.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
+hpcflow_new2-0.2.0a178.dist-info/METADATA,sha256=tSf_ZfRDd8QHkfe2y0Aqt_eLn8T9WE34D-D1Cl7sfSg,2466
+hpcflow_new2-0.2.0a178.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+hpcflow_new2-0.2.0a178.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
+hpcflow_new2-0.2.0a178.dist-info/RECORD,,