Import implementation of ExperimentAxisQuery. (#78)

As discussed in #76,
the full implementation of `ExperientAxisQuery` should be provided by
the base SOMA implementation since it does not vary from storage engine
to storage engine. This copies most of the implementation from the
existing TileDB version, with some reorganization to make the main
query class a little smaller:

- Pulls more of the caching-specific behavior of join IDs into the
  `_JoinIDCache` class.
- Pulls more indexing-related work into the `_AxisIndexer` class.
  - Makes formerly-public `AxisIndexer` private.
    (If this should be public this can be easily reverted.)
  - Renames methods to `by_[axis]`.
  - Separates out index caching logic from main methods.
- Uses an `_Axis` enum internally for axis selection.
- Shortens `AxisQueryResult` name.
- Make `_read` and `_AxisQueryResult` internal-only.

pyproject.toml

@@ -14,7 +14,9 @@ dependencies = [
   "anndata",
   "attrs>=22.1",
   "numpy>=1.21",
+  "pandas",
   "pyarrow",
+  "scipy",
   "typing-extensions",
 ]
 requires-python = "~=3.7"
@@ -43,5 +45,5 @@ single_line_exclusions = ["typing", "typing_extensions"]
 
 [[tool.mypy.overrides]]
 # These dependencies do not currently have canonical type stubs.
-module = ["anndata", "pyarrow"]
+module = ["anndata", "pandas", "pyarrow", "scipy"]
 ignore_missing_imports = true

python-spec/requirements-py3.10.txt

@@ -1,4 +1,13 @@
+anndata==0.8.0
 attrs==22.2.0
+h5py==3.7.0
+natsort==8.2.0
 numpy==1.24.1
+packaging==23.0
+pandas==1.5.2
 pyarrow==10.0.1
+python-dateutil==2.8.2
+pytz==2022.7
+scipy==1.10.0
+six==1.16.0
 typing_extensions==4.4.0

python-spec/requirements-py3.7-lint.txt

@@ -1,8 +1,19 @@
+anndata==0.8.0
 attrs==22.2.0
+h5py==3.7.0
+importlib-metadata==6.0.0
 mypy==0.991
 mypy-extensions==0.4.3
+natsort==8.2.0
 numpy==1.21.6
+packaging==23.0
+pandas==1.3.5
 pyarrow==10.0.1
+python-dateutil==2.8.2
+pytz==2022.7
+scipy==1.7.3
+six==1.16.0
 tomli==2.0.1
 typed-ast==1.5.4
 typing_extensions==4.4.0
+zipp==3.11.0

python-spec/requirements-py3.7.txt

@@ -1,4 +1,15 @@
+anndata==0.8.0
 attrs==22.2.0
+h5py==3.7.0
+importlib-metadata==6.0.0
+natsort==8.2.0
 numpy==1.21.6
+packaging==23.0
+pandas==1.3.5
 pyarrow==10.0.1
+python-dateutil==2.8.2
+pytz==2022.7
+scipy==1.7.3
+six==1.16.0
 typing_extensions==4.4.0
+zipp==3.11.0

python-spec/requirements-py3.8.txt

@@ -1,4 +1,13 @@
+anndata==0.8.0
 attrs==22.2.0
+h5py==3.7.0
+natsort==8.2.0
 numpy==1.24.1
+packaging==23.0
+pandas==1.5.2
 pyarrow==10.0.1
+python-dateutil==2.8.2
+pytz==2022.7
+scipy==1.10.0
+six==1.16.0
 typing_extensions==4.4.0

python-spec/requirements-py3.9.txt

@@ -1,4 +1,13 @@
+anndata==0.8.0
 attrs==22.2.0
+h5py==3.7.0
+natsort==8.2.0
 numpy==1.24.1
+packaging==23.0
+pandas==1.5.2
 pyarrow==10.0.1
+python-dateutil==2.8.2
+pytz==2022.7
+scipy==1.10.0
+six==1.16.0
 typing_extensions==4.4.0

python-spec/src/somacore/__init__.py

@@ -9,6 +9,7 @@
 from somacore import ephemeral
 from somacore import options
 from somacore.query import axis
+from somacore.query import query
 
 try:
     # This trips up mypy since it's a generated file:
@@ -37,6 +38,7 @@
 ResultOrder = options.ResultOrder
 
 AxisQuery = axis.AxisQuery
+ExperimentAxisQuery = query.ExperimentAxisQuery
 
 __all__ = (
     "SOMAObject",

python-spec/src/somacore/composed.py

@@ -1,7 +1,5 @@
 """Implementations of the composed SOMA data types."""
 
-from typing import Optional
-
 from typing_extensions import Final
 
 from somacore import _wrap
@@ -76,13 +74,15 @@ def axis_query(
         self,
         measurement_name: str,
         *,
-        obs_query: Optional[axis.AxisQuery] = None,
-        var_query: Optional[axis.AxisQuery] = None,
-    ) -> query.ExperimentAxisQuery:
+        obs_query: axis.AxisQuery = axis.AxisQuery(),
+        var_query: axis.AxisQuery = axis.AxisQuery(),
+    ) -> "query.ExperimentAxisQuery":
         """Creates an axis query over this experiment.
 
         See :class:`query.ExperimentAxisQuery` for details on usage.
         """
-        raise NotImplementedError()
+        return query.ExperimentAxisQuery(
+            self, measurement_name, obs_query=obs_query, var_query=var_query
+        )
 
     soma_type: Final = "SOMAExperiment"