fractal-server 2.13.0__py3-none-any.whl → 2.14.0__py3-none-any.whl

{fractal_server-2.13.0.dist-info → fractal_server-2.14.0.dist-info}/RECORD

@@ -1,134 +1,142 @@
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 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/db/__init__.py,sha256=wup2wcOkyOh8Vd0Xm76PZn_naxeMqaL4eF8DHHXTGlI,2889
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 fractal_server/app/models/__init__.py,sha256=xJWiGAwpXmCpnFMC4c_HTqoUCzMOXrakoGLUH_uMvdA,415
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 fractal_server/app/models/linkuserproject.py,sha256=hvaxh3Lkiy2uUCwB8gvn8RorCpvxSSdzWdCS_U1GL7g,315
 fractal_server/app/models/security.py,sha256=mMb_HiwWY74QZrs9xuyno0CVSmk4GYQWk5FxGixr8SU,3860
 fractal_server/app/models/user_settings.py,sha256=Y-ZV-uZAFLZqXxy8c5_Qeh_F7zQuZDWOgLpU6Zs6iqU,1316
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 fractal_server/app/user_settings.py,sha256=OP1yiYKtPadxwM51_Q0hdPk3z90TCN4z1BLpQsXyWiU,1316
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 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
 fractal_server/images/__init__.py,sha256=-_wjoKtSX02P1KjDxDP_EXKvmbONTRmbf7iGVTsyBpM,154
 fractal_server/images/models.py,sha256=jdGKMPi8WlO9Kvns4grIOU5LjujnvwIGjMFMC0wNy08,3501
-fractal_server/images/tools.py,sha256=4kfPAFJJnvg7fM-cL0JMx97Dc1Npva_0ghitEji3JUU,3407
+fractal_server/images/tools.py,sha256=-zFDzRv6cbbRo21OrD0eZY5qWcoMX8dxgEnfyI3tOcg,4140
 fractal_server/logger.py,sha256=5Z3rfsFwl8UysVljTOaaIvt8Pyp6CVH492ez3jE8WAw,5113
 fractal_server/main.py,sha256=FD9KzTTsXTQnTW0z3Hu7y0Nj_oAkBeZEInKDXFd4hjE,4561
 fractal_server/migrations/env.py,sha256=nfyBpMIOT3kny6t-b-tUjyRjZ4k906bb1_wCQ7me1BI,1353
@@ -138,6 +146,7 @@ fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_
 fractal_server/migrations/versions/19eca0dd47a9_user_settings_project_dir.py,sha256=Q1Gj1cJ0UrdLBJ5AXfFK9QpxTtmcv-4Z3NEGDnxOme4,961
 fractal_server/migrations/versions/1eac13a26c83_drop_v1_tables.py,sha256=ok8dl4IkI-dfsyE_NZ8IndjQrnQ_g6CDZo4PwozpIwE,1605
 fractal_server/migrations/versions/316140ff7ee1_remove_usersettings_cache_dir.py,sha256=lANgTox0rz459_yo1Rw7fGCT1qw5sUCUXTLUMc_Bzf8,911
+fractal_server/migrations/versions/47351f8c7ebc_drop_dataset_filters.py,sha256=vePkVm1iUHiPNKLQ3KR7BBLdHruqBdl87j_tUCbMbEA,1414
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
 fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py,sha256=5ROUgcoZOdjf8kMt6cxuvPhzHmV6xaCxvZEbhUEyZM4,3271
@@ -152,19 +161,25 @@ fractal_server/migrations/versions/94a47ea2d3ff_remove_cache_dir_slurm_user_and_
 fractal_server/migrations/versions/97f444d47249_add_applyworkflow_project_dump.py,sha256=eKTZm3EgUgapXBxO0RuHkEfTKic-TZG3ADaMpGLuc0k,1057
 fractal_server/migrations/versions/99ea79d9e5d2_add_dataset_history.py,sha256=0im6TxDr53sKKcjiPgeH4ftVRGnRXZSh2lPbRQ1Ir9w,883
 fractal_server/migrations/versions/9c5ae74c9b98_add_user_settings_table.py,sha256=syONdZNf4-OnAcWIsbzXpYwpXPsXZ4SsmjwVvmVG0PU,2256
+fractal_server/migrations/versions/9db60297b8b2_set_ondelete.py,sha256=F0IdXk8vclViOGKe2SOHO3MsQsqe7SsZRSqz9cXhhrE,7928
 fractal_server/migrations/versions/9fd26a2b0de4_add_workflow_timestamp_created.py,sha256=4l1AHGUsa0ONoJVZlr3fTXw_xbbQ8O7wlD92Az2aRfM,1849
 fractal_server/migrations/versions/a7f4d6137b53_add_workflow_dump_to_applyworkflow.py,sha256=ekDUML7ILpmdoqEclKbEUdyLi4uw9HSG_sTjG2hp_JE,867
+fractal_server/migrations/versions/af1ef1c83c9b_add_accounting_tables.py,sha256=BftudWuSGvKGBzIL5AMb3yWkgTAuaKPBGsYcOzp_gLQ,1899
 fractal_server/migrations/versions/af8673379a5c_drop_old_filter_columns.py,sha256=9sLd0F7nO5chHHm7RZ4wBA-9bvWomS-av_odKwODADM,1551
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 fractal_server/migrations/versions/d256a7379ab8_taskgroup_activity_and_venv_info_to_.py,sha256=HN3_Pk8G81SzdYjg4K1RZAyjKSlsZGvcYE2nWOUbwxQ,3861
 fractal_server/migrations/versions/d4fe3708d309_make_applyworkflow_workflow_dump_non_.py,sha256=6cHEZFuTXiQg9yu32Y3RH1XAl71av141WQ6UMbiITIg,949
 fractal_server/migrations/versions/da2cb2ac4255_user_group_viewer_paths.py,sha256=yGWSA2HIHUybcVy66xBITk08opV2DFYSCIIrulaUZhI,901
 fractal_server/migrations/versions/db09233ad13a_split_filters_and_keep_old_columns.py,sha256=NumyjvciIjgShLZcmpDvh3ggJxnc-W1kc7vofrpcNOs,2906
 fractal_server/migrations/versions/e75cac726012_make_applyworkflow_start_timestamp_not_.py,sha256=lOggSvzGWqQvnxxFuSM6W50Ui49R918A-uBuiZJ0pNM,963
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 fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py,sha256=jilQW3QIqYQ4Q6hCnUiG7UtNMpA41ujqrB3tPFiPM1Q,1221
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 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
+fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py,sha256=TDWCaIoM0Q4SpRWmR9zr_rdp3lJXhCfBPTMhtrP5xYE,3950
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=lNy4IX1I4We6VoWa4Bz4fUPuApLMSoejpyE6I3jDZeM,22869
+fractal_server/ssh/_fabric.py,sha256=jF7Nny0r3_PL1WjM1Zlw1I73Uqerx-mTaDWQlOaOpa0,23324
 fractal_server/string_tools.py,sha256=niViRrrZAOo0y6pEFI9L_eUYS1PoOiQZUBtngiLc2_k,1877
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
@@ -172,30 +187,30 @@ fractal_server/tasks/utils.py,sha256=V7dj8o2AnoHhGSTYlqJHcRFhCIpmOrMOUhtiE_DvRVA
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/tasks/v2/local/__init__.py,sha256=9RVItnS7OyLsJOuJjWMCicaky4ASUPQEYD4SzDs0hOE,141
 fractal_server/tasks/v2/local/_utils.py,sha256=EvhmVwYjqaNyDCUMEsTWYOUXLgEwR1xr6bu32apCEI8,2491
-fractal_server/tasks/v2/local/collect.py,sha256=gtntegkilH-zdZpMQaSWYA3DuUqKRAlsoYhs-iJLEKc,12194
+fractal_server/tasks/v2/local/collect.py,sha256=-ScW8Vm0cguwEDQarNAaZFtai0jFFVBrIaVgo2G9KCE,12204
 fractal_server/tasks/v2/local/deactivate.py,sha256=94s_RDND8aR5Y8RxFrRx61rZBMPGqOmFnBFLVKK1HVY,10038
 fractal_server/tasks/v2/local/reactivate.py,sha256=eBgFgq5xVKNr4DIDX7QU8xXerhwMrPaHDJ1wTth7aQc,6191
 fractal_server/tasks/v2/ssh/__init__.py,sha256=aSQbVi6Ummt9QzcSLWNmSqYjfdxrn9ROmqgH6bDpI7k,135
 fractal_server/tasks/v2/ssh/_utils.py,sha256=LjaEYVUJDChilu3YuhxuGWYRNnVJ_zqNE9SDHdRTIHY,2824
-fractal_server/tasks/v2/ssh/collect.py,sha256=-wqqGMapjD1hQz1vphwXmZaD4qzziMetc6lV6fckDO4,13552
+fractal_server/tasks/v2/ssh/collect.py,sha256=gGFdKTawfi3xyUuslyB-QoNNtc7SXx23a7K7wNH8HhM,13562
 fractal_server/tasks/v2/ssh/deactivate.py,sha256=EAVH2HtyvmIFXqUwsGYhlJcAcVh_MvIOaKDY8AyBODw,11400
 fractal_server/tasks/v2/ssh/reactivate.py,sha256=8Rnbbny7TjMEAHhboqfgxBVZZK5UNNmh4Ud-0y3jaVM,7970
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
-fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=Gpk2io8u9YaflFUlQu2NgkDQw5AA4m4AOVG1sB4yrHQ,1822
+fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=Md2LPt3BJ7IfN0USF2uivl4rP8OwbzJOUepGAr_Cicg,1836
 fractal_server/tasks/v2/templates/3_pip_freeze.sh,sha256=JldREScEBI4cD_qjfX4UK7V4aI-FnX9ZvVNxgpSOBFc,168
-fractal_server/tasks/v2/templates/4_pip_show.sh,sha256=84NGHlg6JIbrQktgGKyfGsggPFzy6RBJuOmIpPUhsrw,1747
+fractal_server/tasks/v2/templates/4_pip_show.sh,sha256=qm1vPy6AkKhWDjCJGXS8LqCLYO3KsAyRK325ZsFcF6U,1747
 fractal_server/tasks/v2/templates/5_get_venv_size_and_file_number.sh,sha256=q-6ZUvA6w6FDVEoSd9O63LaJ9tKZc7qAFH72SGPrd_k,284
 fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh,sha256=A2y8RngEjAcRhG-_owA6P7tAdrS_AszFuGXnaeMV8u0,1122
-fractal_server/tasks/v2/utils_background.py,sha256=6wM7Z6zedsR8oVGwrJ-HN2Hj1b7BgmaSBdvuB_r9hI8,4246
-fractal_server/tasks/v2/utils_database.py,sha256=iLbwkxMxTCgpyKe1JQzdfIR3zBfxohgmLwSdGps1AUo,1274
+fractal_server/tasks/v2/utils_background.py,sha256=FKJvtz1YuFLXV1TuoSeebWA0uDWsQIUxpFqWtKSJigc,3423
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 fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
 fractal_server/tasks/v2/utils_python_interpreter.py,sha256=5_wrlrTqXyo1YuLZvAW9hrSoh5MyLOzdPVUlUwM7uDQ,955
-fractal_server/tasks/v2/utils_templates.py,sha256=07TZpJ0Mh_A4lXVXrrH2o1VLFFGwxeRumA6DdgMgCWk,2947
+fractal_server/tasks/v2/utils_templates.py,sha256=Kc_nSzdlV6KIsO0CQSPs1w70zLyENPqJeTQEFiz4bOg,3124
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=PMwrxWFxRTQRl1b9h-NRIbFGPKqpH_hXnkAT3NfZdpY,3571
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
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-fractal_server-2.13.0.dist-info/METADATA,sha256=YY5WVT35OWNC2Ilx_EIBFAIfd7KXo5xZjDEVfe04R-E,4548
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-fractal_server-2.13.0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.13.0.dist-info/RECORD,,
+fractal_server-2.14.0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.14.0.dist-info/METADATA,sha256=rbNZVkwzYDYoAd4gozu4v5w4oOdWKv75wCav4EKOWCI,4560
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+fractal_server-2.14.0.dist-info/RECORD,,

{fractal_server-2.13.0.dist-info → fractal_server-2.14.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.0
+Generator: poetry-core 2.1.0
 Root-Is-Purelib: true
 Tag: py3-none-any

fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py

@@ -1,126 +0,0 @@
-import os
-import threading
-import time
-import traceback
-from itertools import count
-
-from ......logger import set_logger
-from fractal_server.app.runner.exceptions import JobExecutionError
-
-logger = set_logger(__name__)
-
-
-class FractalSlurmSSHWaitThread(threading.Thread):
-    """
-    Thread that monitors a pool of SLURM jobs
-
-    This class is a custom re-implementation of the waiting thread class from:
-
-    > clusterfutures <https://github.com/sampsyo/clusterfutures>
-    > Original Copyright
-    > Copyright 2021 Adrian Sampson <asampson@cs.washington.edu>
-    > License: MIT
-
-    Attributes:
-        shutdown_file:
-        shutdown_callback:
-        slurm_poll_interval:
-        jobs_finished_callback:
-        active_job_ids:
-        shutdown:
-        lock:
-    """
-
-    shutdown_file: str
-    shutdown_callback: callable
-    slurm_poll_interval = 30
-    jobs_finished_callback: callable
-    active_job_ids: list[str]
-    shutdown: bool
-    _lock: threading.Lock
-
-    def __init__(self, callback: callable, interval=1):
-        """
-        Init method
-
-        This method is executed on the main thread.
-        """
-        threading.Thread.__init__(self, daemon=True)
-        self.callback = callback
-        self.interval = interval
-        self._lock = threading.Lock()
-        self.shutdown = False
-        self.active_job_ids = []
-
-    def wait(self, *, job_id: str):
-        """
-        Add a a new job to the set of jobs being waited for.
-
-        This method is executed on the main thread.
-        """
-        if self.shutdown:
-            error_msg = "Cannot call `wait` method after executor shutdown."
-            logger.warning(error_msg)
-            raise JobExecutionError(info=error_msg)
-        with self._lock:
-            self.active_job_ids.append(job_id)
-
-    def check_shutdown(self):
-        """
-        Check whether the shutdown file exists
-
-        This method is executed on the waiting thread.
-        """
-        if os.path.exists(self.shutdown_file):
-            logger.info(
-                f"Detected executor-shutdown file {self.shutdown_file}"
-            )
-            self.shutdown = True
-
-    def check_jobs(self):
-        """
-        Check whether some jobs are over, and call callback.
-
-        This method is executed on the waiting thread.
-        """
-        try:
-            if self.active_job_ids == []:
-                return
-            finished_jobs = self.jobs_finished_callback(self.active_job_ids)
-            if finished_jobs == set(self.active_job_ids):
-                self.callback(self.active_job_ids)
-                self.active_job_ids = []
-
-        except Exception:
-            # If anything goes wrong, print an exception without re-raising
-            traceback.print_exc()
-
-    def run(self):
-        """
-        Run forever (until a shutdown takes place) and trigger callback
-
-        This method is executed on the waiting thread.
-
-        Note that `shutdown_callback` only takes care of cleaning up the
-        FractalSlurmExecutor variables, and then the `return` here is enough
-        to fully clean up the `FractalFileWaitThread` object.
-        """
-
-        # FIXME SSH: are those try/except below needed?
-
-        skip = max(self.slurm_poll_interval // self.interval, 1)
-        for ind in count():
-            self.check_shutdown()
-            if self.shutdown:
-                try:
-                    self.shutdown_callback()
-                except Exception:  # nosec
-                    pass
-                return
-            if ind % skip == 0:
-                with self._lock:
-                    try:
-                        self.check_jobs()
-                    except Exception:  # nosec
-                        pass
-            time.sleep(self.interval)

fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py

@@ -1,116 +0,0 @@
-import uuid
-from pathlib import Path
-from typing import Optional
-
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    SlurmConfig,
-)
-
-
-class SlurmJob:
-    """
-    Collect information related to a FractalSlurmSSHExecutor job
-
-    This includes three groups of attributes:
-
-    1. Attributes related to the (possibly multi-task) SLURM job, e.g.
-       submission-file path.
-    2. Attributes related to single tasks, e.g. the paths of their input/output
-       pickle files.
-    3. SLURM configuration options, encoded in a SlurmConfig object.
-
-    Note: A SlurmJob object is generally defined as a multi-task job. Jobs
-    coming from the `map` method must have `single_task_submission=False` (even
-    if `num_tasks_tot=1`), while jobs coming from `submit` must have it set to
-    `True`.
-
-    Attributes:
-        num_tasks_tot:
-            Total number of tasks to be executed as part of this SLURM job.
-        single_task_submission:
-            This must be `True` for jobs submitted as part of the `submit`
-            method, and `False` for jobs coming from the `map` method.
-        slurm_file_prefix:
-            Prefix for SLURM-job related files (submission script and SLURM
-            stdout/stderr); this is also needed in the
-            `_copy_files_from_remote_to_local` method.
-        wftask_file_prefixes:
-            Prefix for files that are created as part of the functions
-            submitted for execution on the `FractalSlurmSSHExecutor`; this is
-            needed in the `_copy_files_from_remote_to_local` method, and also
-            to construct the names of per-task input/output pickle files.
-        wftask_subfolder_name:
-            Name of the per-task subfolder (e.g. `7_task_name`).
-        slurm_script:
-            Path of SLURM submission script.
-        slurm_stdout:
-            Path of SLURM stdout file; if this includes `"%j"`, then this
-            string will be replaced by the SLURM job ID upon `sbatch`
-            submission.
-        slurm_stderr:
-            Path of SLURM stderr file; see `slurm_stdout` concerning `"%j"`.
-        workerids:
-            IDs that enter in the per-task input/output pickle files (one per
-            task).
-        input_pickle_files:
-            Input pickle files (one per task).
-        output_pickle_files:
-            Output pickle files (one per task).
-        slurm_config:
-            `SlurmConfig` object.
-    """
-
-    # Job-related attributes
-    num_tasks_tot: int
-    single_task_submission: bool
-    slurm_file_prefix: str
-    slurm_script_local: Path
-    slurm_script_remote: Path
-    slurm_stdout_local: Path
-    slurm_stdout_remote: Path
-    slurm_stderr_local: Path
-    slurm_stderr_remote: Path
-
-    # Per-task attributes
-    wftask_subfolder_name: str
-    workerids: tuple[str, ...]
-    wftask_file_prefixes: tuple[str, ...]
-    input_pickle_files_local: tuple[Path, ...]
-    input_pickle_files_remote: tuple[Path, ...]
-    output_pickle_files_local: tuple[Path, ...]
-    output_pickle_files_remote: tuple[Path, ...]
-
-    # Slurm configuration
-    slurm_config: SlurmConfig
-
-    def __init__(
-        self,
-        num_tasks_tot: int,
-        slurm_config: SlurmConfig,
-        slurm_file_prefix: Optional[str] = None,
-        wftask_file_prefixes: Optional[tuple[str, ...]] = None,
-        single_task_submission: bool = False,
-    ):
-        if single_task_submission and num_tasks_tot > 1:
-            raise ValueError(
-                "Trying to initialize SlurmJob with"
-                f"{single_task_submission=} and {num_tasks_tot=}."
-            )
-        self.num_tasks_tot = num_tasks_tot
-        self.single_task_submission = single_task_submission
-        self.slurm_file_prefix = slurm_file_prefix or "default_slurm_prefix"
-        if wftask_file_prefixes is None:
-            self.wftask_file_prefixes = tuple(
-                "default_wftask_prefix" for i in range(self.num_tasks_tot)
-            )
-        else:
-            self.wftask_file_prefixes = wftask_file_prefixes
-        self.workerids = tuple(uuid.uuid4() for i in range(self.num_tasks_tot))
-        self.slurm_config = slurm_config
-
-    def get_clean_output_pickle_files(self) -> tuple[str, ...]:
-        """
-        Transform all pathlib.Path objects in self.output_pickle_files to
-        strings
-        """
-        return tuple(str(f.as_posix()) for f in self.output_pickle_files_local)