Merge pull request #230 from pynbody/python-3.12

Add python 3.12 to test matrix

Author: apontzen

.github/workflows/build-test.yaml

@@ -13,10 +13,16 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.9, "3.10", "3.11", "3.12"]
         sqlalchemy-version: ["1.4", "2.0"]
-        numpy-version: ["1.18", "1.22"]
+        numpy-version: ["1.22", "1.26"]
         TANGOS_TESTING_DB_BACKEND: [sqlite, mysql+pymysql, postgresql+psycopg2]
+        exclude:
+          - python-version: "3.12"
+            sqlalchemy-version: "1.4"
+          - python-version: "3.12"
+            numpy-version: "1.22"
+
     runs-on: ${{ matrix.os }}
     env:
       C: gcc-10
@@ -55,10 +61,10 @@ jobs:
     - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install numpy~=${{ matrix.numpy-version}} scipy "matplotlib<3.3.0" pytest h5py pip webtest pyquery sphinx pygments pandas sqlalchemy~=${{ matrix.sqlalchemy-version}} cython pyramid ipython pyramid_mako PyMySQL[rsa] psycopg2-binary
+        python -m pip install numpy~=${{ matrix.numpy-version}} sqlalchemy~=${{ matrix.sqlalchemy-version}}
     - name: Build and install tangos
       run: |
-        python setup.py develop
+        pip install -e .[test,rmdbs]
     - name: Check that tangos can import without pynbody
       run: |
          python -c "import tangos"

setup.py

@@ -72,6 +72,7 @@ def get_version(rel_path):
           "Programming Language :: Python :: 3.9",
           "Programming Language :: Python :: 3.10",
           "Programming Language :: Python :: 3.11",
+          "Programming Language :: Python :: 3.12",
           "License :: OSI Approved :: BSD License",
       ],
       author="Andrew Pontzen",
@@ -100,5 +101,9 @@ def get_version(rel_path):
       tests_require=tests_require,
       test_suite="tests",
       long_description=long_description,
-      long_description_content_type='text/markdown'
+      long_description_content_type='text/markdown',
+      extras_require={'test': tests_require,
+                      'rmdbs': ['PyMySQL[rsa]',
+                                'psycopg2-binary']
+                      }
       )

tangos/core/halo_data/link.py

@@ -16,13 +16,13 @@ class HaloLink(Base):
 
     halo_from = relationship(SimulationObjectBase, primaryjoin=halo_from_id == SimulationObjectBase.id,
                              backref=backref('links', cascade_backrefs=False,
-                                             lazy='dynamic',
+                                             lazy='dynamic', viewonly=True,
                                              primaryjoin=halo_from_id == SimulationObjectBase.id),
                              cascade='')
 
     halo_to = relationship(SimulationObjectBase, primaryjoin=(halo_to_id == SimulationObjectBase.id),
                            backref=backref('reverse_links', cascade_backrefs=False,
-                                           lazy='dynamic',
+                                           lazy='dynamic', viewonly=True,
                                            primaryjoin=halo_to_id == SimulationObjectBase.id),
                            cascade='')
 

tangos/core/halo_data/property.py

@@ -15,7 +15,7 @@ class HaloProperty(Base):
     # n.b. backref defined below
     halo = relationship(SimulationObjectBase, cascade='',
                         backref=backref('all_properties',overlaps='properties,deprecated_properties',
-                                        cascade_backrefs=False),
+                                        cascade_backrefs=False, viewonly=True),
                         overlaps='properties,deprecated_properties')
 
     data_float = Column(DOUBLE_PRECISION)
@@ -27,8 +27,10 @@ class HaloProperty(Base):
 
     deprecated = Column(Boolean, default=False, nullable=False)
 
-    creator = relationship(creator.Creator, backref=backref(
-        'properties', cascade_backrefs=False, lazy='dynamic'), cascade='save-update')
+    creator = relationship(creator.Creator,
+                           backref=backref('properties', cascade_backrefs=False,
+                                           lazy='dynamic', viewonly=True),
+                           cascade='save-update')
     creator_id = Column(Integer, ForeignKey('creators.id'))
 
     def __init__(self, halo, name, data):

tangos/properties/__init__.py

@@ -1,15 +1,15 @@
 import functools
 import importlib
 import os
+import sys
 import warnings
+from importlib.metadata import entry_points
 
 import numpy as np
-import pkg_resources
-
-from tangos.util import timing_monitor
 
 from .. import input_handlers, parallel_tasks
 from ..log import logger
+from ..util import timing_monitor
 
 
 class PropertyCalculationMetaClass(type):
@@ -569,6 +569,12 @@ def instantiate_class(simulation, property_name, silent_fail=False):
     else:
         return instance[0]
 
+def _get_entry_points():
+    if sys.version_info >= (3, 10):
+        return entry_points(group='tangos.property_modules')
+    else:
+        return entry_points().get('tangos.property_modules', [])
+
 def _import_configured_property_modules():
     if "PYTEST_CURRENT_TEST" in os.environ:
         warnings.warn("Not importing external property modules during testing", ImportWarning)
@@ -582,7 +588,7 @@ def _import_configured_property_modules():
         except ImportError:
             warnings.warn("Failed to import requested property module %r. Some properties may be unavailable."%pm,
                           ImportWarning)
-    for module in pkg_resources.iter_entry_points('tangos.property_modules'):
+    for module in _get_entry_points():
         module.load()
 
 _import_configured_property_modules()

tangos/testing/db_diff.py

@@ -104,12 +104,14 @@ def compare_timestep(self, ts):
 
 
     def _joined_links_load(self, parent):
-        return object_session(parent).query(core.HaloLink).with_parent(parent, type(parent).all_links).\
-            options(joinedload(core.HaloLink.halo_to))
+        return (object_session(parent).query(core.HaloLink).where(
+            core.HaloLink.halo_from_id == parent.id
+        ).options(joinedload(core.HaloLink.halo_to)))
 
     def _joined_properties_load(self, parent):
-        return object_session(parent).query(core.HaloProperty).with_parent(parent, type(parent).all_properties).\
-            options(undefer("*")).options(joinedload(core.HaloProperty.name))
+        return object_session(parent).query(core.HaloProperty).where(
+            core.HaloProperty.halo_id == parent.id
+        ).options(undefer("*")).options(joinedload(core.HaloProperty.name))
 
     def compare_object(self, obj):
         obj1 = get_object(obj, self.session1)

tangos/tools/consistent_trees_importer.py

@@ -113,7 +113,7 @@ def store_ids(self, ts, id_to_tree_id):
         props = []
         for o in objs.values():
             if isinstance(o, PhantomHalo):
-                tree_id = id_to_tree_id.get(-o.finder_id, None)
+                tree_id = id_to_tree_id.get(-int(o.finder_id), None)
             else:
                 tree_id = id_to_tree_id.get(o.finder_id, None)
             if tree_id is not None:

tests/test_consistent_trees.py

@@ -20,7 +20,7 @@ def _create_dummy_simsnap():
     f['pos'].units="Mpc"
     f['vel'] = np.zeros((2097152, 3)).view(pynbody.array.SimArray)
     f['vel'].units = "km s^-1"
-    f['mass'] = np.zeros(2097152).view(pynbody.array.SimArray)
+    f['mass'] = np.ones(2097152).view(pynbody.array.SimArray)
     f['mass'].units="Msol"
     f.properties['boxsize'] = pynbody.units.Unit("50 Mpc")
     return f

tests/test_stat_files.py

@@ -140,7 +140,7 @@ def test_import_properties_is_only_numeric_or_array():
 
     property = importer._create_property(db_name, halo, np.array([42.0, 42.0, 42.0]))
     assert property.data_is_array() == True
-    assert property.data.dtype == np.floating
+    assert np.issubdtype(property.data.dtype, np.floating)
     npt.assert_allclose(property.data, np.array([42.0, 42.0, 42.0]))
 
     # Importing a string should fail