Rename PointCloud -> PointCloudDataFrame on spatial branch (#3104)

Merge in `main` and rename `PointCloud` -> `PointCloudDataFrame` --------- Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: Paul Hoffman <mojaveazure@users.noreply.github.com> Co-authored-by: Aaron Wolen <aaron@wolen.com> Co-authored-by: nguyenv <vivian@tiledb.com>
single-cell-data · Oct 1, 2024 · 3fc7a34 · 3fc7a34
1 parent 45937a1
commit 3fc7a34
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diff --git a/.github/workflows/python-ci-packaging.yml b/.github/workflows/python-ci-packaging.yml
@@ -65,7 +65,7 @@ jobs:
           apt-get install --yes cmake git python-is-python3 python3 python3-pip python3-venv unzip wget
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0 # for setuptools-scm
+          fetch-depth: 0  # for setuptools-scm
       - name: Configure Git
         run: |
           # This is a permissions quirk due to running Git as root inside of a Docker container
@@ -76,7 +76,7 @@ jobs:
         run: |
           mkdir -p external
           # Please do not edit manually -- let scripts/update-tiledb-version.py update this
-          wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.1/tiledb-linux-x86_64-2.26.1-db1cee4.tar.gz
+          wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.2/tiledb-linux-x86_64-2.26.2-30fc114.tar.gz
           tar -C external -xzf tiledb-linux-x86_64-*.tar.gz
           ls external/lib/
           echo "LD_LIBRARY_PATH=$(pwd)/external/lib" >> $GITHUB_ENV
@@ -101,7 +101,7 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse 'setuptools>=70.1' wheel
           ./venv-soma/bin/pip list
       - name: Build wheel
         run: |
@@ -164,15 +164,15 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0 # for setuptools-scm
+          fetch-depth: 0  # for setuptools-scm
       - name: Check if System Integrity Protection (SIP) is enabled
         run: csrutil status
       - name: Install pre-built libtiledb
         if: ${{ matrix.TILEDB_EXISTS == 'yes' }}
         run: |
           mkdir -p external
           # Please do not edit manually -- let scripts/update-tiledb-version.py update this
-          wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.1/tiledb-macos-x86_64-2.26.1-db1cee4.tar.gz
+          wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.2/tiledb-macos-x86_64-2.26.2-30fc114.tar.gz
           tar -C external -xzf tiledb-macos-x86_64-*.tar.gz
           ls external/lib/
           echo "DYLD_LIBRARY_PATH=$(pwd)/external/lib" >> $GITHUB_ENV
@@ -201,7 +201,7 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel 'setuptools>=70.1'
           ./venv-soma/bin/pip list
       - name: Build wheel
         run: |
@@ -257,17 +257,17 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0 # for setuptools-scm
+          fetch-depth: 0  # for setuptools-scm
       - name: Install pre-built libtiledb
         run: |
           mkdir -p external
           if [ `uname -s` == "Darwin" ];
           then
             # Please do not edit manually -- let scripts/update-tiledb-version.py update this
-            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.1/tiledb-macos-x86_64-2.26.1-db1cee4.tar.gz
+            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.2/tiledb-macos-x86_64-2.26.2-30fc114.tar.gz
           else
             # Please do not edit manually -- let scripts/update-tiledb-version.py update this
-            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.1/tiledb-linux-x86_64-2.26.1-db1cee4.tar.gz
+            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.26.2/tiledb-linux-x86_64-2.26.2-30fc114.tar.gz
           fi
           tar -C external -xzf tiledb-*.tar.gz
           ls external/lib/
@@ -302,7 +302,7 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel 'setuptools>=70.1'
           ./venv-soma/bin/pip list
       - name: Install TileDB-SOMA-Py with setuptools and --libtiledbsoma
         run: |
@@ -359,13 +359,13 @@ jobs:
       - uses: actions/checkout@v4
         with:
           path: TileDB-SOMA
-          fetch-depth: 0 # for setuptools-scm
+          fetch-depth: 0  # for setuptools-scm
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install dependencies
-        run: pip install --prefer-binary pybind11 wheel
+        run: pip install --prefer-binary pybind11 'setuptools>=70.1' wheel
       - name: Build source tarball (sdist)
         run: |
           cd TileDB-SOMA/apis/python

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,7 +18,7 @@ repos:
         # Pandas 2.x types (e.g. `pd.Series[Any]`). See `_types.py` or https://github.com/single-cell-data/TileDB-SOMA/issues/2839
         # for more info.
         - "pandas-stubs>=2"
-        - "somacore==1.0.18"
+        - "somacore==1.0.19"
         - types-setuptools
       args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"]
       pass_filenames: false
diff --git a/apis/python/notebooks/tutorial_spatial.ipynb b/apis/python/notebooks/tutorial_spatial.ipynb
@@ -197,7 +197,7 @@
       "\n",
       "/home/julia/Software/TileDB-Inc/TileDB-SOMA/apis/python/src/tiledbsoma/_multiscale_image.py:151: UserWarning: Support for spatial types is experimental. Changes to both the API and data storage may not be backwards compatible.\n",
       "  warnings.warn(SPATIAL_DISCLAIMER)\n",
-      "/home/julia/Software/TileDB-Inc/TileDB-SOMA/apis/python/src/tiledbsoma/_point_cloud.py:116: UserWarning: Support for spatial types is experimental. Changes to both the API and data storage may not be backwards compatible.\n",
+      "/home/julia/Software/TileDB-Inc/TileDB-SOMA/apis/python/src/tiledbsoma/_point_cloud_dataframe.py:116: UserWarning: Support for spatial types is experimental. Changes to both the API and data storage may not be backwards compatible.\n",
       "  warnings.warn(SPATIAL_DISCLAIMER)\n"
      ]
     }
@@ -591,7 +591,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x7f3c3cd20cd0>"
+       "<matplotlib.image.AxesImage at 0x7fd55f5d9710>"
       ]
      },
      "execution_count": 20,
@@ -1065,7 +1065,7 @@
     {
      "data": {
       "text/plain": [
-       "<somacore.coordinates.IdentityTransform at 0x7f3c5f839510>"
+       "<somacore.coordinates.IdentityTransform at 0x7fd55cc1a550>"
       ]
      },
      "execution_count": 28,
@@ -1086,7 +1086,7 @@
     {
      "data": {
       "text/plain": [
-       "<somacore.coordinates.ScaleTransform at 0x7f3c3ce66e90>"
+       "<somacore.coordinates.ScaleTransform at 0x7fd53a107950>"
       ]
      },
      "execution_count": 29,
@@ -1100,23 +1100,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 31,
    "id": "8fa549eb-598d-4a0c-9ab9-dd1bfac4199b",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<somacore.coordinates.IdentityTransform at 0x7f3c5f884fd0>"
+       "<somacore.coordinates.IdentityTransform at 0x7fd55f637610>"
       ]
      },
-     "execution_count": 30,
+     "execution_count": 31,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "scene.get_transform_to_point_cloud(\"loc\")"
+    "scene.get_transform_to_point_cloud_dataframe(\"loc\")"
    ]
   },
   {
@@ -1133,7 +1133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 32,
    "id": "18751a3c-0e29-4e00-ba58-3529e7164f6c",
    "metadata": {},
    "outputs": [],
@@ -1145,7 +1145,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 33,
    "id": "02d18d4b-0caf-4fd5-ab6f-a0c8b2122069",
    "metadata": {},
    "outputs": [
@@ -1155,10 +1155,10 @@
        "SpatialRead(data=<pyarrow.Tensor>\n",
        "type: uint8\n",
        "shape: (753, 853, 3)\n",
-       "strides: (2559, 3, 1), data_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), output_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), coordinate_transform=<somacore.coordinates.AffineTransform object at 0x7f3c6223ca50>)"
+       "strides: (2559, 3, 1), data_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), output_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), coordinate_transform=<somacore.coordinates.AffineTransform object at 0x7fd55f640310>)"
       ]
      },
-     "execution_count": 32,
+     "execution_count": 33,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1178,17 +1178,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 34,
    "id": "e136c1b9-3b7f-44ed-aa20-e2abdb1868e1",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "SpatialRead(data=<tiledbsoma._read_iters.TableReadIter object at 0x7f3c3ce090d0>, data_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), output_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), coordinate_transform=<somacore.coordinates.IdentityTransform object at 0x7f3c5f83b490>)"
+       "SpatialRead(data=<tiledbsoma._read_iters.TableReadIter object at 0x7fd55cbdf850>, data_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), output_coordinate_space=CoordinateSpace(axes=(Axis(name='x', unit='pixels'), Axis(name='y', unit='pixels'))), coordinate_transform=<somacore.coordinates.IdentityTransform object at 0x7fd55cbedc10>)"
       ]
      },
-     "execution_count": 33,
+     "execution_count": 34,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1200,7 +1200,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 35,
    "id": "53554033-a469-4126-88a3-bd9cec9fd78f",
    "metadata": {},
    "outputs": [
@@ -1380,7 +1380,7 @@
        "[928 rows x 7 columns]"
       ]
      },
-     "execution_count": 34,
+     "execution_count": 35,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1392,7 +1392,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 36,
    "id": "34a51b21-2d77-47c2-a3e1-bf159cd1b001",
    "metadata": {},
    "outputs": [
@@ -1404,7 +1404,7 @@
        "       [ 0.00000000e+00,  0.00000000e+00,  1.00000000e+00]])"
       ]
      },
-     "execution_count": 35,
+     "execution_count": 36,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1416,7 +1416,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 37,
    "id": "c7c22f26-613c-44d9-9ce9-7abc64b377f9",
    "metadata": {},
    "outputs": [],
@@ -1429,7 +1429,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": 38,
    "id": "021cf9b5-9880-4857-8164-326dc26d8b6d",
    "metadata": {},
    "outputs": [],
@@ -1449,7 +1449,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 39,
    "id": "1a67bc46-f768-4a16-8324-828c5a38bd57",
    "metadata": {},
    "outputs": [

diff --git a/apis/python/pyproject.toml b/apis/python/pyproject.toml
@@ -1,8 +1,7 @@
 [build-system]
 requires = [
     "pybind11[global]>=2.10.0",
-    "setuptools>=65.5.1",
-    "wheel>=0.37.1",
+    "setuptools>=70.1",  # `setuptools.command.bdist_wheel`
     "cmake>=3.21",
 ]
 build-backend = "setuptools.build_meta"

diff --git a/apis/python/setup.py b/apis/python/setup.py
@@ -21,8 +21,8 @@
 import sys
 from typing import Optional
 
+import setuptools.command.bdist_wheel
 import setuptools.command.build_ext
-import wheel.bdist_wheel
 
 try:
     from pybind11.setup_helpers import Pybind11Extension
@@ -219,7 +219,7 @@ def run(self):
         super().run()
 
 
-class bdist_wheel(wheel.bdist_wheel.bdist_wheel):
+class bdist_wheel(setuptools.command.bdist_wheel.bdist_wheel):
     def run(self):
         find_or_build_package_data(self)
         super().run()
@@ -307,9 +307,9 @@ def run(self):
                 "src/tiledbsoma/soma_array.cc",
                 "src/tiledbsoma/soma_object.cc",
                 "src/tiledbsoma/soma_dataframe.cc",
+                "src/tiledbsoma/soma_point_cloud_dataframe.cc",
                 "src/tiledbsoma/soma_dense_ndarray.cc",
                 "src/tiledbsoma/soma_sparse_ndarray.cc",
-                "src/tiledbsoma/soma_point_cloud.cc",
                 "src/tiledbsoma/soma_group.cc",
                 "src/tiledbsoma/soma_collection.cc",
                 "src/tiledbsoma/pytiledbsoma.cc",
@@ -336,7 +336,7 @@ def run(self):
         "scanpy>=1.9.2",
         "scipy",
         # Note: the somacore version is in .pre-commit-config.yaml too
-        "somacore==1.0.18",
+        "somacore==1.0.19",
         "tiledb~=0.32.0",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],

diff --git a/apis/python/src/tiledbsoma/__init__.py b/apis/python/src/tiledbsoma/__init__.py
@@ -187,11 +187,9 @@ def _new_shape_feature_flag_enabled() -> bool:
 from ._indexer import IntIndexer, tiledbsoma_build_index
 from ._measurement import Measurement
 from ._multiscale_image import MultiscaleImage
-from ._point_cloud import PointCloud
+from ._point_cloud_dataframe import PointCloudDataFrame
 from ._geometry_dataframe import GeometryDataFrame
 from ._sparse_nd_array import SparseNDArray, SparseNDArrayRead
-from ._point_cloud import PointCloud
-from ._geometry_dataframe import GeometryDataFrame
 from ._scene import Scene
 from .options import SOMATileDBContext, TileDBCreateOptions, TileDBWriteOptions
 from .pytiledbsoma import (
@@ -229,7 +227,7 @@ def _new_shape_feature_flag_enabled() -> bool:
     "MultiscaleImage",
     "NotCreateableError",
     "open",
-    "PointCloud",
+    "PointCloudDataFrame",
     "ResultOrder",
     "Scene",
     "show_package_versions",

diff --git a/apis/python/src/tiledbsoma/_constants.py b/apis/python/src/tiledbsoma/_constants.py
@@ -8,15 +8,12 @@
 
 SOMA_JOINID = "soma_joinid"
 SOMA_GEOMETRY = "soma_geometry"
+SOMA_COORDINATE_SPACE_METADATA_KEY = "soma_coordinate_space"
+SOMA_MULTISCALE_IMAGE_SCHEMA = "soma_multiscale_image_schema"
 SOMA_OBJECT_TYPE_METADATA_KEY = "soma_object_type"
 SOMA_ENCODING_VERSION_METADATA_KEY = "soma_encoding_version"
-SOMA_ENCODING_VERSION = "1"
-
+SOMA_ENCODING_VERSION = "1.1.0"
 
-# Spatial specific constants
-SOMA_GEOMETRY = "soma_geometry"
-SOMA_COORDINATE_SPACE_METADATA_KEY = "soma_coordinate_space"
-SOMA_MULTISCALE_IMAGE_SCHEMA = "soma_multiscale_image_schema"
 SPATIAL_DISCLAIMER = (
     "Support for spatial types is experimental. Changes to both the API and data "
     "storage may not be backwards compatible."