Refactor

pyiron_base/__init__.py

@@ -5,45 +5,45 @@
 from pyiron_base.state import state
 
 # API of the pyiron_base module - in alphabetical order
-from pyiron_base.generic.factory import PyironFactory
-from pyiron_base.generic.flattenedstorage import FlattenedStorage
-from pyiron_base.generic.hdfio import FileHDFio, ProjectHDFio
-from pyiron_base.generic.datacontainer import DataContainer
-from pyiron_base.generic.inputlist import InputList
-from pyiron_base.generic.parameters import GenericParameters
-from pyiron_base.generic.filedata import load_file, FileDataTemplate, FileData
-from pyiron_base.generic.util import Deprecator, deprecate, deprecate_soon, ImportAlarm
-from pyiron_base.job.executable import Executable
-from pyiron_base.job.external import Notebook, load, dump
-from pyiron_base.job.generic import GenericJob
-from pyiron_base.job.interactive import InteractiveBase
-from pyiron_base.job.interactivewrapper import InteractiveWrapper
-from pyiron_base.job.jobstatus import (
+from pyiron_base.interfaces.factory import PyironFactory
+from pyiron_base.storage.flattenedstorage import FlattenedStorage
+from pyiron_base.storage.hdfio import FileHDFio, ProjectHDFio
+from pyiron_base.storage.datacontainer import DataContainer
+from pyiron_base.storage.inputlist import InputList
+from pyiron_base.storage.parameters import GenericParameters
+from pyiron_base.storage.filedata import load_file, FileDataTemplate, FileData
+from pyiron_base.utils.util import Deprecator, deprecate, deprecate_soon, ImportAlarm
+from pyiron_base.jobs.job.extension.executable import Executable
+from pyiron_base.project.external import Notebook, load, dump
+from pyiron_base.jobs.job.generic import GenericJob
+from pyiron_base.jobs.job.interactive import InteractiveBase
+from pyiron_base.jobs.master.interactivewrapper import InteractiveWrapper
+from pyiron_base.jobs.job.extension.jobstatus import (
     JobStatus,
     job_status_successful_lst,
     job_status_finished_lst,
     job_status_lst,
 )
-from pyiron_base.job.jobtype import JOB_CLASS_DICT, JobType, JobTypeChoice
-from pyiron_base.job.template import TemplateJob, PythonTemplateJob
-from pyiron_base.job.factory import JobFactoryCore
-from pyiron_base.master.generic import GenericMaster, get_function_from_string
-from pyiron_base.master.list import ListMaster
-from pyiron_base.master.parallel import ParallelMaster, JobGenerator
-from pyiron_base.master.serial import SerialMasterBase
-from pyiron_base.master.flexible import FlexibleMaster
+from pyiron_base.jobs.job.jobtype import JOB_CLASS_DICT, JobType, JobTypeChoice
+from pyiron_base.jobs.job.template import TemplateJob, PythonTemplateJob
+from pyiron_base.jobs.job.factory import JobFactoryCore
+from pyiron_base.jobs.master.generic import GenericMaster, get_function_from_string
+from pyiron_base.jobs.master.list import ListMaster
+from pyiron_base.jobs.master.parallel import ParallelMaster, JobGenerator
+from pyiron_base.jobs.master.serial import SerialMasterBase
+from pyiron_base.jobs.master.flexible import FlexibleMaster
 from pyiron_base.project.generic import Project, Creator
-from pyiron_base.pyio.parser import Logstatus, extract_data_from_file
-from pyiron_base.server.queuestatus import validate_que_request
+from pyiron_base.utils.parser import Logstatus, extract_data_from_file
+from pyiron_base.jobs.job.extension.server.queuestatus import validate_que_request
 from pyiron_base.state.settings import Settings
 from pyiron_base.state.install import install_dialog
-from pyiron_base.table.datamining import PyironTable, TableJob
-from pyiron_base.generic.object import HasDatabase, HasStorage, PyironObject
+from pyiron_base.jobs.datamining import PyironTable, TableJob
+from pyiron_base.utils.object import HasDatabase, HasStorage, PyironObject
 from pyiron_base.database.performance import get_database_statistics
 from pyiron_base.interfaces.has_groups import HasGroups
 from pyiron_base.interfaces.has_hdf import HasHDF
 
-from pyiron_base.toolkit import Toolkit, BaseTools
+from pyiron_base.jobs.job.toolkit import Toolkit, BaseTools
 
 Project.register_tools("base", BaseTools)
 
@@ -55,7 +55,7 @@
 
 # Internal init
 from ._version import get_versions
-from pyiron_base.generic.jedi import fix_ipython_autocomplete
+from pyiron_base.utils.jedi import fix_ipython_autocomplete
 
 # Set version of pyiron_base
 __version__ = get_versions()["version"]

pyiron_base/cli/ls.py

@@ -9,7 +9,7 @@
 import re
 import sys
 import pandas as pd
-import pyiron_base.job.jobstatus
+import pyiron_base.jobs.job.extension.jobstatus
 from pyiron_base import Project
 
 __author__ = "Marvin Poul"
@@ -72,10 +72,10 @@ def register(parser):
         "-s",
         "--status",
         nargs="+",
-        choices=pyiron_base.job.jobstatus.job_status_lst,
+        choices=pyiron_base.jobs.job.extension.jobstatus.job_status_lst,
         metavar="status",
         help="job status must be one of the given, one of {}".format(
-            ", ".join(pyiron_base.job.jobstatus.job_status_lst)
+            ", ".join(pyiron_base.jobs.job.extension.jobstatus.job_status_lst)
         ),
     )
     filter.add_argument(

pyiron_base/cli/rm.py

@@ -5,7 +5,7 @@
 """
 
 import os
-from pyiron_base import Project
+from pyiron_base.project.generic import Project
 
 __author__ = "Marvin Poul"
 __copyright__ = (

pyiron_base/cli/wrapper.py

@@ -4,7 +4,7 @@
 Run a job from hdf5.
 """
 
-from pyiron_base.job.wrapper import job_wrapper_function
+from pyiron_base.jobs.job.wrapper import job_wrapper_function
 
 
 def register(parser):

pyiron_base/database/filetable.py

@@ -4,7 +4,7 @@
 import datetime
 import h5io
 from pyfileindex import PyFileIndex
-from pyiron_base.generic.util import Singleton
+from pyiron_base.utils.util import Singleton
 from pyiron_base.database.generic import IsDatabase
 
 

pyiron_base/database/generic.py

@@ -13,7 +13,7 @@
 import time
 import os
 from datetime import datetime
-from pyiron_base.generic.util import deprecate
+from pyiron_base.utils.util import deprecate
 import pandas
 from sqlalchemy import (
     create_engine,

pyiron_base/database/manager.py

@@ -7,7 +7,7 @@
 
 from urllib.parse import quote_plus
 from pyiron_base.state.logger import logger
-from pyiron_base.generic.util import Singleton
+from pyiron_base.utils.util import Singleton
 from pyiron_base.state.settings import settings as s
 from pyiron_base.database.generic import DatabaseAccess
 import os

pyiron_base/interfaces/has_hdf.py

@@ -3,7 +3,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 """Interface for classes to serialize to HDF5."""
 
-from pyiron_base.generic.hdfio import ProjectHDFio
+from pyiron_base.storage.hdfio import ProjectHDFio
 
 from abc import ABC, abstractmethod
 

pyiron_base/table/datamining.py → pyiron_base/jobs/datamining.py

@@ -14,11 +14,10 @@
 from tqdm.auto import tqdm
 import types
 
-from pyiron_base.job.generic import GenericJob
-from pyiron_base.generic.datacontainer import DataContainer
-from pyiron_base.generic.hdfio import FileHDFio
+from pyiron_base.jobs.job.generic import GenericJob
+from pyiron_base.storage.hdfio import FileHDFio
 from pyiron_base.interfaces.has_groups import HasGroups
-from pyiron_base.master.generic import get_function_from_string
+from pyiron_base.jobs.master.generic import get_function_from_string
 
 
 __author__ = "Uday Gajera, Jan Janssen, Joerg Neugebauer"

pyiron_base/generic/dynamic.py → pyiron_base/jobs/dynamic.py

@@ -67,7 +67,7 @@ def _get_script(cp):
 
 
 def _init_constructor_dynamic(class_name, module, input_dict):
-    from pyiron_base.job.executable import Executable
+    from pyiron_base.jobs.job.extension.executable import Executable
 
     def __init__(self, project, job_name):
         super(self.__class__, self).__init__(project, job_name)
@@ -84,7 +84,7 @@ def __init__(self, project, job_name):
 
 def class_constructor(cp):
     if "templates" in cp:
-        from pyiron_base.job.script import ScriptJob
+        from pyiron_base.jobs.script import ScriptJob
 
         class_name = os.path.basename(cp)
         script_path = os.path.join(cp, "script.py")
@@ -101,7 +101,7 @@ def class_constructor(cp):
             },
         )
     elif "dynamic" in cp:
-        from pyiron_base.job.template import TemplateJob
+        from pyiron_base.jobs.job.template import TemplateJob
 
         class_name = os.path.basename(cp)
         input_dict = _load_input(path=cp)

pyiron_base/job/core.py → pyiron_base/jobs/job/core.py

@@ -13,8 +13,8 @@
 import warnings
 
 from pyiron_base.interfaces.has_groups import HasGroups
-from pyiron_base.generic.hdfio import ProjectHDFio
-from pyiron_base.job.util import (
+from pyiron_base.storage.hdfio import ProjectHDFio
+from pyiron_base.jobs.job.util import (
     _get_project_for_copy,
     _copy_database_entry,
     _copy_to_delete_existing,

pyiron_base/job/executable.py → pyiron_base/jobs/job/extension/executable.py

@@ -3,7 +3,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import os
-from pyiron_base.generic.object import HasStorage
+from pyiron_base.utils.object import HasStorage
 from pyiron_base.state import state
 
 """

pyiron_base/server/generic.py → pyiron_base/jobs/job/extension/server/generic.py

@@ -8,7 +8,7 @@
 from collections import OrderedDict
 import numbers
 from pyiron_base.state import state
-from pyiron_base.server.runmode import Runmode
+from pyiron_base.jobs.job.extension.server.runmode import Runmode
 import socket
 
 __author__ = "Jan Janssen"

pyiron_base/server/queuestatus.py → pyiron_base/jobs/job/extension/server/queuestatus.py

@@ -8,8 +8,8 @@
 import pandas
 import time
 from pyiron_base.state import state
-from pyiron_base.generic.util import static_isinstance
-from pyiron_base.job.jobstatus import job_status_finished_lst
+from pyiron_base.utils.util import static_isinstance
+from pyiron_base.jobs.job.extension.jobstatus import job_status_finished_lst
 
 __author__ = "Jan Janssen"
 __copyright__ = (
@@ -121,7 +121,7 @@ def queue_delete_job(item):
     Delete a job from the queuing system
 
     Args:
-        item (int, pyiron_base.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
+        item (int, pyiron_base.jobs.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
 
     Returns:
         str: Output from the queuing system as string - optimized for the Sun grid engine
@@ -138,7 +138,7 @@ def queue_enable_reservation(item):
     Enable a reservation for a particular job within the queuing system
 
     Args:
-        item (int, pyiron_base.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
+        item (int, pyiron_base.jobs.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
 
     Returns:
         str: Output from the queuing system as string - optimized for the Sun grid engine
@@ -160,7 +160,7 @@ def wait_for_job(job, interval_in_s=5, max_iterations=100):
     Sleep until the job is finished but maximum interval_in_s * max_iterations seconds.
 
     Args:
-        job (pyiron_base.job.generic.GenericJob): Job to wait for
+        job (pyiron_base.job.utils.GenericJob): Job to wait for
         interval_in_s (int): interval when the job status is queried from the database - default 5 sec.
         max_iterations (int): maximum number of iterations - default 100
 
@@ -312,15 +312,17 @@ def validate_que_request(item):
     Internal function to convert the job_ID or hamiltonian to the queuing system ID.
 
     Args:
-        item (int, pyiron_base.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
+        item (int, pyiron_base.jobs.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
 
     Returns:
         int: queuing system ID
     """
 
     if isinstance(item, int):
         que_id = item
-    elif static_isinstance(item.__class__, "pyiron_base.master.generic.GenericMaster"):
+    elif static_isinstance(
+        item.__class__, "pyiron_base.jobs.master.generic.GenericMaster"
+    ):
         if item.server.queue_id:
             que_id = item.server.queue_id
         else:
@@ -331,12 +333,12 @@ def validate_que_request(item):
             que_id = [queue_id for queue_id in queue_id_lst if queue_id is not None]
             if len(que_id) == 0:
                 raise ValueError("This job does not have a queue ID.")
-    elif static_isinstance(item.__class__, "pyiron_base.job.generic.GenericJob"):
+    elif static_isinstance(item.__class__, "pyiron_base.jobs.job.generic.GenericJob"):
         if item.server.queue_id:
             que_id = item.server.queue_id
         else:
             raise ValueError("This job does not have a queue ID.")
-    elif static_isinstance(item.__class__, "pyiron_base.job.core.JobCore"):
+    elif static_isinstance(item.__class__, "pyiron_base.jobs.job.core.JobCore"):
         if "server" in item.project_hdf5.list_nodes():
             server_hdf_dict = item.project_hdf5["server"]
             if "qid" in server_hdf_dict.keys():

pyiron_base/job/factory.py → pyiron_base/jobs/job/factory.py

@@ -6,17 +6,17 @@
 """
 
 from pyiron_base.project.generic import Project
-from pyiron_base.generic.factory import PyironFactory
+from pyiron_base.interfaces.factory import PyironFactory
 from abc import ABC, abstractmethod
-from pyiron_base.job.jobtype import JobType
-from pyiron_base.job.generic import GenericJob
+from pyiron_base.jobs.job.jobtype import JobType
+from pyiron_base.jobs.job.generic import GenericJob
 from typing import Type, Dict, List, Union
 
-from pyiron_base.master.flexible import FlexibleMaster
-from pyiron_base.job.script import ScriptJob
-from pyiron_base.master.serial import SerialMasterBase
-from pyiron_base.table.datamining import TableJob
-from pyiron_base.generic.hdfio import ProjectHDFio
+from pyiron_base.jobs.master.flexible import FlexibleMaster
+from pyiron_base.jobs.script import ScriptJob
+from pyiron_base.jobs.master.serial import SerialMasterBase
+from pyiron_base.jobs.datamining import TableJob
+from pyiron_base.storage.hdfio import ProjectHDFio
 from pyiron_base.state import state
 
 __author__ = "Liam Huber, Jan Janssen"

pyiron_base/job/generic.py → pyiron_base/jobs/job/generic.py

@@ -9,15 +9,15 @@
 import os
 import posixpath
 import h5io
-from pyiron_base.job.jobtype import JobType
+from pyiron_base.jobs.job.jobtype import JobType
 import signal
 import warnings
 
 from pyiron_base.state import state
-from pyiron_base.job.executable import Executable
-from pyiron_base.job.jobstatus import JobStatus
-from pyiron_base.job.core import JobCore
-from pyiron_base.job.runfunction import (
+from pyiron_base.jobs.job.extension.executable import Executable
+from pyiron_base.jobs.job.extension.jobstatus import JobStatus
+from pyiron_base.jobs.job.core import JobCore
+from pyiron_base.jobs.job.runfunction import (
     run_job_with_parameter_repair,
     run_job_with_status_initialized,
     run_job_with_status_created,
@@ -36,14 +36,14 @@
     run_job_with_runmode_queue,
     execute_job_with_external_executable,
 )
-from pyiron_base.job.util import (
+from pyiron_base.jobs.job.util import (
     _copy_restart_files,
     _kill_child,
     _job_store_before_copy,
     _job_reload_after_copy,
 )
-from pyiron_base.generic.util import static_isinstance, deprecate
-from pyiron_base.server.generic import Server
+from pyiron_base.utils.util import static_isinstance, deprecate
+from pyiron_base.jobs.job.extension.server.generic import Server
 from pyiron_base.database.filetable import FileTable
 
 __author__ = "Joerg Neugebauer, Jan Janssen"
@@ -527,7 +527,7 @@ def _internal_copy_to(
 
         # Reload object from HDF5 file
         if not static_isinstance(
-            obj=project.__class__, obj_type="pyiron_base.job.core.JobCore"
+            obj=project.__class__, obj_type="pyiron_base.jobs.job.core.JobCore"
         ):
             _job_reload_after_copy(
                 job=new_job_core, delete_file_after_copy=delete_file_after_copy

pyiron_base/job/interactive.py → pyiron_base/jobs/job/interactive.py

@@ -6,8 +6,8 @@
 """
 
 import numpy as np
-from pyiron_base.job.generic import GenericJob
-from pyiron_base.job.jobtype import JobType
+from pyiron_base.jobs.job.generic import GenericJob
+from pyiron_base.jobs.job.jobtype import JobType
 
 __author__ = "Osamu Waseda, Jan Janssen"
 __copyright__ = (