Add pyproject.toml and update import sorting

Author: apontzen

pyproject.toml

@@ -0,0 +1,14 @@
+[build-system]
+requires = ["setuptools"]
+
+[tool.pytest.ini_options]
+testpaths = ['tests']
+addopts = "--tb=short"
+
+[tool.isort]
+profile = "black"
+combine_as_imports = true
+known_first_party = [
+  "tangos",
+]
+sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]

tangos/__init__.py

@@ -9,11 +9,22 @@
 
 import sqlalchemy
 import sqlalchemy.orm.session
-from sqlalchemy import (Boolean, Column, DateTime, Float, ForeignKey, Index,
-                        Integer, String, and_, create_engine, or_, orm)
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    Float,
+    ForeignKey,
+    Index,
+    Integer,
+    String,
+    and_,
+    create_engine,
+    or_,
+    orm,
+)
 from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import (backref, clear_mappers, deferred, relationship,
-                            sessionmaker)
+from sqlalchemy.orm import backref, clear_mappers, deferred, relationship, sessionmaker
 from sqlalchemy.orm.session import Session
 
 from . import core, log, properties

tangos/core/__init__.py

@@ -187,8 +187,11 @@ def close_session():
     if Session is not None:
         Session = None
 
-from .dictionary import (_get_dict_cache_for_session, get_dict_id,
-                         get_or_create_dictionary_item)
+from .dictionary import (
+    _get_dict_cache_for_session,
+    get_dict_id,
+    get_or_create_dictionary_item,
+)
 
 __all__ = ['DictionaryItem',
            'sim_query_from_name_list', 'sim_query_from_args',

tangos/core/halo.py

@@ -353,10 +353,12 @@ def calculate_for_descendants(self, *plist, **kwargs):
         :param nmax: The maximum number of descendants to consider (default 1000)
         :param strategy: The class to use to find the descendants (default relation_finding.MultiHopMajorDescendantsStrategy)
         """
-        from .. import live_calculation
-        from .. import query as db_query
-        from .. import relation_finding
-        from .. import temporary_halolist as thl
+        from .. import (
+            live_calculation,
+            query as db_query,
+            relation_finding,
+            temporary_halolist as thl,
+        )
         from . import Session
 
         nmax = kwargs.get('nmax',1000)

tangos/core/simulation.py

@@ -7,8 +7,7 @@
 from .. import config, input_handlers
 from ..config import DOUBLE_PRECISION, LARGE_BINARY
 from . import Base, creator, data_attribute_mapper
-from .dictionary import (DictionaryItem, get_dict_id,
-                         get_or_create_dictionary_item)
+from .dictionary import DictionaryItem, get_dict_id, get_or_create_dictionary_item
 
 
 class Simulation(Base):

tangos/live_calculation/__init__.py

@@ -12,12 +12,10 @@
 import tangos.core.halo_data
 from tangos.core import extraction_patterns
 from tangos.live_calculation.query_masking import QueryMask
-from tangos.live_calculation.query_multivalue_folding import \
-    QueryMultivalueFolding
+from tangos.live_calculation.query_multivalue_folding import QueryMultivalueFolding
 from tangos.util import consistent_collection
 
-from .. import core
-from .. import temporary_halolist as thl
+from .. import core, temporary_halolist as thl
 
 
 class UnknownValue:

tangos/live_calculation/builtin_functions/__init__.py

@@ -5,8 +5,13 @@
 
 from ... import core
 from ...core import extraction_patterns
-from .. import (BuiltinFunction, FixedInput, FixedNumericInput, LiveProperty,
-                StoredProperty)
+from .. import (
+    BuiltinFunction,
+    FixedInput,
+    FixedNumericInput,
+    LiveProperty,
+    StoredProperty,
+)
 
 
 @BuiltinFunction.register

tangos/live_calculation/builtin_functions/search.py

@@ -1,9 +1,14 @@
 import numpy as np
 
-from ... import core, relation_finding
-from ... import temporary_halolist as thl
-from .. import (BuiltinFunction, FixedInput, FixedNumericInput,
-                MultiCalculation, ReturnInputHalos, StoredProperty)
+from ... import core, relation_finding, temporary_halolist as thl
+from .. import (
+    BuiltinFunction,
+    FixedInput,
+    FixedNumericInput,
+    MultiCalculation,
+    ReturnInputHalos,
+    StoredProperty,
+)
 
 
 def _find_progenitor_or_descendant(source_halos, property_proxy, property_criterion, strategy):

tangos/live_calculation/parser.py

@@ -5,8 +5,15 @@
 
 _parsing_lock = threading.Lock() # pyparsing is NOT thread safe
 
-from . import (Calculation, FixedInput, FixedNumericInput, Link, LiveProperty,
-               MultiCalculation, StoredProperty)
+from . import (
+    Calculation,
+    FixedInput,
+    FixedNumericInput,
+    Link,
+    LiveProperty,
+    MultiCalculation,
+    StoredProperty,
+)
 
 
 def pack_args(for_function):

tangos/parallel_tasks/pynbody_server/__init__.py

@@ -12,9 +12,12 @@
 from ..async_message import AsyncProcessedMessage
 from ..message import ExceptionMessage, Message
 from . import snapshot_queue, transfer_array
-from .snapshot_queue import (ConfirmLoadPynbodySnapshot,
-                             ReleasePynbodySnapshot,
-                             RequestLoadPynbodySnapshot, _server_queue)
+from .snapshot_queue import (
+    ConfirmLoadPynbodySnapshot,
+    ReleasePynbodySnapshot,
+    RequestLoadPynbodySnapshot,
+    _server_queue,
+)
 
 
 class ReturnPynbodyArray(Message):

tangos/query.py

@@ -1,8 +1,7 @@
 from sqlalchemy import and_
 
 from tangos import Base, Creator, get_default_session
-from tangos.core import (HaloProperty, Simulation, SimulationObjectBase,
-                         TimeStep)
+from tangos.core import HaloProperty, Simulation, SimulationObjectBase, TimeStep
 
 
 def all_simulations(session=None):

tangos/relation_finding/__init__.py

@@ -1,8 +1,9 @@
 from .multi_hop import MultiHopStrategy
-from .multi_hop_variants import (MultiHopAllProgenitorsStrategy,
-                                 MultiHopMajorDescendantsStrategy,
-                                 MultiHopMajorProgenitorsStrategy,
-                                 MultiHopMostRecentMergerStrategy)
+from .multi_hop_variants import (
+    MultiHopAllProgenitorsStrategy,
+    MultiHopMajorDescendantsStrategy,
+    MultiHopMajorProgenitorsStrategy,
+    MultiHopMostRecentMergerStrategy,
+)
 from .multi_source import MultiSourceMultiHopStrategy
-from .one_hop import (HopMajorDescendantStrategy, HopMajorProgenitorStrategy,
-                      HopStrategy)
+from .one_hop import HopMajorDescendantStrategy, HopMajorProgenitorStrategy, HopStrategy

tangos/relation_finding/tree.py

@@ -5,9 +5,13 @@
 from sqlalchemy.orm import object_session
 
 from .. import core, live_calculation, temporary_halolist
-from ..config import (mergertree_max_hops, mergertree_max_nhalos,
-                      mergertree_min_fractional_NDM,
-                      mergertree_min_fractional_weight, mergertree_timeout)
+from ..config import (
+    mergertree_max_hops,
+    mergertree_max_nhalos,
+    mergertree_min_fractional_NDM,
+    mergertree_min_fractional_weight,
+    mergertree_timeout,
+)
 from ..log import logger
 from . import MultiHopAllProgenitorsStrategy
 

tangos/testing/db_diff.py

@@ -2,8 +2,7 @@
 import numpy.testing as npt
 from sqlalchemy.orm import Session, joinedload, object_session, undefer
 
-from .. import (all_simulations, config, core, get_object, get_simulation,
-                get_timestep)
+from .. import all_simulations, config, core, get_object, get_simulation, get_timestep
 from ..log import logger
 
 

tangos/tools/__init__.py

@@ -63,7 +63,17 @@ def add_tools(cls, subparse):
         for c in cls.__subclasses__():
             c.add_tools(subparse)
 
-from . import (add_simulation, ahf_merger_tree_importer, changa_bh_importer,
-               consistent_trees_importer, crosslink, db_importer,
-               merger_tree_patcher, property_deleter, property_importer,
-               property_writer, subfind_merger_tree_importer, timestep_thinner)
+from . import (
+    add_simulation,
+    ahf_merger_tree_importer,
+    changa_bh_importer,
+    consistent_trees_importer,
+    crosslink,
+    db_importer,
+    merger_tree_patcher,
+    property_deleter,
+    property_importer,
+    property_writer,
+    subfind_merger_tree_importer,
+    timestep_thinner,
+)

tangos/tools/add_simulation.py

@@ -2,8 +2,7 @@
 
 import numpy as np
 
-from .. import config, core
-from .. import parallel_tasks as pt
+from .. import config, core, parallel_tasks as pt
 from ..core import Simulation, TimeStep
 from ..log import logger
 

tangos/tools/db_importer.py

@@ -10,8 +10,14 @@
 
 from tangos import Base, Creator, DictionaryItem, core
 from tangos.config import DB_IMPORT_CHUNK_SIZE
-from tangos.core import (HaloLink, HaloProperty, Simulation,
-                         SimulationObjectBase, SimulationProperty, TimeStep)
+from tangos.core import (
+    HaloLink,
+    HaloProperty,
+    Simulation,
+    SimulationObjectBase,
+    SimulationProperty,
+    TimeStep,
+)
 
 from . import GenericTangosTool
 
@@ -326,8 +332,7 @@ def _drop_or_create_indexes(connection, mode='drop', verbose=False):
 
 
 def _dedup_temp_dictionary_items(connection, dict_table):
-    from sqlalchemy import (Column, bindparam, delete, func, select, text,
-                            update)
+    from sqlalchemy import Column, bindparam, delete, func, select, text, update
 
     updater_expressions = _updates_for_all_columns_referencing_dictionary_id()
 

tangos/tracking.py

@@ -4,8 +4,12 @@
 import tangos.parallel_tasks as parallel_tasks
 
 from . import query
-from .core import (HaloLink, SimulationObjectBase, TrackData,
-                   get_or_create_dictionary_item)
+from .core import (
+    HaloLink,
+    SimulationObjectBase,
+    TrackData,
+    get_or_create_dictionary_item,
+)
 
 
 def generate_tracker_halo_link_if_not_present(halo_1, halo_2, dict_obj=None, weight=1.0):

tangos/web/views/halo_data.py

@@ -12,8 +12,11 @@
 from pyramid.view import view_config
 
 from ... import core
-from ...config import (webview_cache_time, webview_default_image_format,
-                       webview_plots_dpi)
+from ...config import (
+    webview_cache_time,
+    webview_default_image_format,
+    webview_plots_dpi,
+)
 from ...log import logger
 from ...util.cache_dict import CacheDict
 from . import halo_from_request, simulation_from_request, timestep_from_request

tests/test_old_database_update.py

@@ -2,8 +2,7 @@
 
 import tangos
 import tangos.testing.simulation_generator
-from tangos import parallel_tasks as pt
-from tangos import testing
+from tangos import parallel_tasks as pt, testing
 
 
 def setup_module():

tests/test_parallel_tasks.py

@@ -5,8 +5,7 @@
 
 import tangos
 import tangos.testing.simulation_generator
-from tangos import parallel_tasks as pt
-from tangos import testing
+from tangos import parallel_tasks as pt, testing
 from tangos.log import logger
 from tangos.parallel_tasks import testing as pt_testing
 

tests/test_simulation_adder.py

@@ -3,9 +3,7 @@
 from pytest import fixture
 
 import tangos as db
-from tangos import input_handlers, log
-from tangos import parallel_tasks as pt
-from tangos import testing, tools
+from tangos import input_handlers, log, parallel_tasks as pt, testing, tools
 from tangos.input_handlers import output_testing
 from tangos.tools import add_simulation