[python] Revert "Add Windows support for the Python API"

.github/workflows/python-ci-full.yml

@@ -20,7 +20,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-12, windows-2019]
+        # TODO: restore Windows build once we have C++/libtiledbsoma integration supported there
+        os: [ubuntu-22.04, macos-12]
+        # os: [ubuntu-22.04, macos-12, windows-2019]
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         include:
           - runs-on: ubuntu-22.04
@@ -35,6 +37,7 @@ jobs:
       python_version: ${{ matrix.python-version }}
       cc: ${{ matrix.cc }}
       cxx: ${{ matrix.cxx }}
+      is_mac: ${{ contains(matrix.os, 'macos') }}
       report_codecov: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9' }}
       run_lint: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9' }}
     secrets: inherit

.github/workflows/python-ci-minimal.yml

@@ -8,14 +8,10 @@ name: TileDB-SOMA Python CI (Minimal)
 # To test the full matrix on a working branch, invoke ./python-ci-full.yml from
 #   https://github.com/single-cell-data/TileDB-SOMA/actions/workflows/python-ci-full.yml
 on:
-  pull_request:
-    branches:
-      - main
-      - 'release-*'
+  push:
     paths-ignore:
       - 'apis/r/**'
-  workflow_dispatch:
-
+
 jobs:
   build:
     strategy:
@@ -24,20 +20,19 @@ jobs:
         os: [ubuntu-22.04, macos-12]
         python-version: ['3.10', '3.7']
         include:
-          - os: ubuntu-22.04
+          - runs-on: ubuntu-22.04
             cc: gcc-11
             cxx: g++-11
-          - os: macos-12
+          - runs-on: macos-12
             cc: clang
             cxx: clang++
-          - os: windows-2019
-            python-version: '3.10'
     uses: ./.github/workflows/python-ci-single.yml
     with:
       os: ${{ matrix.os }}
       python_version: ${{ matrix.python-version }}
       cc: ${{ matrix.cc }}
       cxx: ${{ matrix.cxx }}
+      is_mac: ${{ contains(matrix.os, 'macos') }}
       report_codecov: ${{ matrix.python-version == '3.10' }}
       run_lint: ${{ matrix.python-version == '3.10' }}
     secrets: inherit

.github/workflows/python-ci-single.yml

@@ -14,22 +14,26 @@ on:
         required: true
         type: string
       cc:
-        required: false
+        required: true
         type: string
       cxx:
-        required: false
+        required: true
         type: string
       report_codecov:
         required: true
         type: boolean
+      is_mac:
+        required: false
+        type: boolean
+        default: false
       run_lint:
         required: false
         type: boolean
         default: false
 
 jobs:
   lint:
-    if: inputs.run_lint
+    if: ${{ inputs.run_lint }}
     runs-on: ${{ inputs.os }}
     steps:
     - name: Checkout TileDB-SOMA
@@ -52,7 +56,6 @@ jobs:
       run: python -m pip -v install pre-commit && pre-commit run -a -v
 
     - name: Check C++ Format
-      shell: bash
       run: ./scripts/run-clang-format.sh . clang-format 0 $(find libtiledbsoma -name "*.cc" -or -name "*.h")
 
   build:
@@ -69,7 +72,7 @@ jobs:
       if: ${{ inputs.os == 'macos-12' }}
       run: sysctl -a | grep cpu
     - name: Select XCode version
-      if: startsWith(inputs.os, 'macos')
+      if: inputs.is_mac
       uses: maxim-lobanov/setup-xcode@v1
       with:
         # Pending https://github.com/actions/runner-images/issues/6350
@@ -123,14 +126,12 @@ jobs:
       run: ctest --output-on-failure --test-dir build/libtiledbsoma -C Release --verbose
 
     - name: Run pytests for C++
-      shell: bash
       # Setting PYTHONPATH ensures the tests load the in-tree source code unde apis/python/src
       # instead of copy we `pip install`ed to site-packages above. That's needed for the code
       # coverage analysis to work.
       run: PYTHONPATH=$(pwd)/apis/python/src python -m pytest --cov=apis/python/src --cov-report=xml libtiledbsoma/test -v --durations=20
 
     - name: Run pytests for Python
-      shell: bash
       # Setting PYTHONPATH ensures the tests load the in-tree source code unde apis/python/src
       # instead of copy we `pip install`ed to site-packages above. That's needed for the code
       # coverage analysis to work.

.gitignore

@@ -1,5 +1,4 @@
 .vscode*
-.vs
 *.swp
 dist/*
 **/venv

apis/python/setup.py

@@ -61,9 +61,13 @@
 
 if libtiledbsoma_dir is None:
     scripts_dir = this_dir / "dist_links" / "scripts"
-    scripts_dir = scripts_dir.resolve()
 
-    libtiledbsoma_dir = scripts_dir.parent / "dist"
+    if scripts_dir.is_symlink():
+        # in git source tree
+        libtiledbsoma_dir = this_dir.parent.parent / "dist"
+    else:
+        # in extracted sdist, with libtiledbsoma copied into dist_links/
+        libtiledbsoma_dir = this_dir / "dist_links" / "dist"
 else:
     libtiledbsoma_dir = pathlib.Path(libtiledbsoma_dir)
 
@@ -147,10 +151,7 @@ def find_or_build_package_data(setuptools_cmd):
         # cause that cache to fall out of sync.
         #
         # See `.github/workflows/python-ci-single.yml` for configuration.
-        if os.name == "nt":
-            subprocess.run(["pwsh.exe", "./bld.ps1"], cwd=scripts_dir, check=True)
-        else:
-            subprocess.run(["./bld"], cwd=scripts_dir, check=True)
+        subprocess.run(["./bld"], cwd=scripts_dir)
         lib_dir = libtiledbsoma_exists()
         assert lib_dir, "error when building libtiledbsoma from source"
 
@@ -197,13 +198,10 @@ def run(self):
     str(libtiledbsoma_dir / "lib"),
     str(tiledb_dir / "lib"),
 ]
-
-CXX_FLAGS = []
-
-if os.name != "nt":
-    CXX_FLAGS.append(f'-Wl,-rpath,{str(libtiledbsoma_dir / "lib")}')
-    CXX_FLAGS.append(f'-Wl,-rpath,{str(tiledb_dir / "lib")}')
-
+CXX_FLAGS = [
+    f'-Wl,-rpath,{str(libtiledbsoma_dir / "lib")}',
+    f'-Wl,-rpath,{str(tiledb_dir / "lib")}',
+]
 if sys.platform == "darwin":
     CXX_FLAGS.append("-mmacosx-version-min=10.14")
 
@@ -227,7 +225,7 @@ def run(self):
 setuptools.setup(
     name="tiledbsoma",
     description="Python API for efficient storage and retrieval of single-cell data using TileDB",
-    long_description=open("README.md", encoding="utf-8").read(),
+    long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
     author="TileDB, Inc.",
     author_email="help@tiledb.io",
@@ -244,7 +242,6 @@ def run(self):
         "Operating System :: Unix",
         "Operating System :: POSIX :: Linux",
         "Operating System :: MacOS :: MacOS X",
-        "Operating System :: Microsoft :: Windows",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
@@ -261,10 +258,9 @@ def run(self):
             ["src/tiledbsoma/pytiledbsoma.cc"],
             include_dirs=INC_DIRS,
             library_dirs=LIB_DIRS,
-            libraries=["tiledbsoma"] + (["tiledb"] if os.name == "nt" else []),
+            libraries=["tiledbsoma"],
             extra_link_args=CXX_FLAGS,
-            extra_compile_args=["-std=c++17" if os.name != "nt" else "/std:c++17"]
-            + CXX_FLAGS,
+            extra_compile_args=["-std=c++17"] + CXX_FLAGS,
             language="c++",
         )
     ],

apis/python/src/tiledbsoma/_dataframe.py

@@ -691,11 +691,8 @@ def _canonicalize_schema(
         raise ValueError("DataFrame requires one or more index columns")
 
     if SOMA_JOINID in schema.names:
-        joinid_type = schema.field(SOMA_JOINID).type
-        if joinid_type != pa.int64():
-            raise ValueError(
-                f"{SOMA_JOINID} field must be of type Arrow int64 but is {joinid_type}"
-            )
+        if schema.field(SOMA_JOINID).type != pa.int64():
+            raise ValueError(f"{SOMA_JOINID} field must be of type Arrow int64")
     else:
         # add SOMA_JOINID
         schema = schema.append(pa.field(SOMA_JOINID, pa.int64()))

apis/python/src/tiledbsoma/_general_utilities.py

@@ -6,7 +6,7 @@
 """General utility functions.
 """
 
-import platform
+import os
 import sys
 
 import tiledb
@@ -64,5 +64,5 @@ def show_package_versions() -> None:
     )
     print("libtiledbsoma version()      ", libtiledbsoma_version())
     print("python version               ", ".".join(str(v) for v in sys.version_info))
-    u = platform.uname()
-    print("OS version                   ", u.system, u.release)
+    u = os.uname()
+    print("OS version                   ", u.sysname, u.release)

apis/python/src/tiledbsoma/_read_iters.py

@@ -478,14 +478,10 @@ def _coords_strider(
     elif isinstance(coords, int):
         coords = np.array([coords], dtype=np.int64)
     elif isinstance(coords, Sequence):
-        coords = np.array(coords, dtype=np.int64)
+        coords = np.array(coords).astype(np.int64)
     elif isinstance(coords, (pa.Array, pa.ChunkedArray)):
-        coords = coords.to_numpy().astype(np.int64, copy=False)
-    elif isinstance(coords, np.ndarray):
-        coords = coords.astype(np.int64)
-    elif isinstance(coords, slice):
-        pass
-    else:
+        coords = coords.to_numpy()
+    elif not isinstance(coords, (np.ndarray, slice)):
         raise TypeError("Unsupported slice coordinate type")
 
     if isinstance(coords, slice):

apis/python/src/tiledbsoma/_tiledb_array.py

@@ -21,9 +21,7 @@
 
 def _load_libs() -> None:
     """Loads the required TileDB-SOMA native library."""
-    if os.name == "nt":
-        lib_name = "tiledbsoma.dll"
-    elif sys.platform == "darwin":
+    if sys.platform == "darwin":
         lib_name = "libtiledbsoma.dylib"
     else:
         lib_name = "libtiledbsoma.so"

apis/python/src/tiledbsoma/io/ingest.py

@@ -1163,7 +1163,7 @@ def _write_dataframe(
         else:
             df.rename(columns={"index": id_column_name}, inplace=True)
 
-    df[SOMA_JOINID] = np.asarray(axis_mapping.data, dtype=np.int64)
+    df[SOMA_JOINID] = np.asarray(axis_mapping.data)
 
     df.set_index(SOMA_JOINID, inplace=True)
 

apis/python/tests/test_factory.py

@@ -1,4 +1,3 @@
-from time import sleep
 from typing import Type
 
 import numpy as np
@@ -73,8 +72,6 @@ def tiledb_object_uri(tmp_path, object_type, metadata_typename, encoding_version
 )
 def test_open(tiledb_object_uri, expected_soma_type: Type):
     """Happy path tests"""
-    # TODO: Fix Windows test failures without the following.
-    sleep(0.01)
     soma_obj = soma.open(tiledb_object_uri)
     assert isinstance(soma_obj, expected_soma_type)
     typed_soma_obj = soma.open(tiledb_object_uri, soma_type=expected_soma_type)
@@ -135,8 +132,6 @@ def test_open_wrong_type(tiledb_object_uri, wrong_type):
 )
 def test_factory_unsupported_version(tiledb_object_uri):
     """All of these should raise, as they are encoding formats from the future"""
-    # TODO: Fix Windows test failures without the following.
-    sleep(0.01)
     with pytest.raises(ValueError):
         soma.open(tiledb_object_uri)
 

apis/python/tests/test_metadata.py

@@ -56,7 +56,6 @@ def test_metadata(soma_object):
     # Verify the metadata is empty to start. "Empty" defined as no keys
     # other than soma_ keys.
     uri = soma_object.uri
-    timestamp = soma_object.tiledb_timestamp_ms
     with soma_object:
         assert non_soma_metadata(soma_object) == {}
         non_soma_keys = [k for k in soma_object.metadata if not k.startswith("soma_")]
@@ -71,7 +70,7 @@ def test_metadata(soma_object):
     with pytest.raises(soma.SOMAError):
         soma_object.metadata["x"] = "y"
 
-    with _factory.open(uri, "r", tiledb_timestamp=timestamp) as read_obj:
+    with _factory.open(uri, "r") as read_obj:
         assert non_soma_metadata(read_obj) == {"foobar": True}
         assert "foobar" in read_obj.metadata
         # Double-check the various getter methods
@@ -83,15 +82,15 @@ def test_metadata(soma_object):
         with pytest.raises(soma.SOMAError):
             read_obj.metadata["x"] = "y"
 
-    with _factory.open(uri, "w", tiledb_timestamp=timestamp + 1) as second_write:
+    with _factory.open(uri, "w") as second_write:
         second_write.metadata.update(stay="frosty", my="friends")
         assert non_soma_metadata(second_write) == {
             "foobar": True,
             "stay": "frosty",
             "my": "friends",
         }
 
-    with _factory.open(uri, "w", tiledb_timestamp=timestamp + 2) as third_write:
+    with _factory.open(uri, "w") as third_write:
         del third_write.metadata["stay"]
         third_write.metadata["my"] = "enemies"
         assert non_soma_metadata(third_write) == {"foobar": True, "my": "enemies"}
@@ -125,49 +124,46 @@ def test_add_delete_metadata(soma_object):
 
 def test_delete_add_metadata(soma_object):
     uri = soma_object.uri
-    timestamp = soma_object.tiledb_timestamp_ms
     with soma_object:
         soma_object.metadata["hdyfn"] = "destruction"
         assert non_soma_metadata(soma_object) == {"hdyfn": "destruction"}
 
-    with _factory.open(uri, "w", tiledb_timestamp=timestamp + 1) as second_write:
+    with _factory.open(uri, "w") as second_write:
         assert non_soma_metadata(second_write) == {"hdyfn": "destruction"}
         del second_write.metadata["hdyfn"]
         assert non_soma_metadata(second_write) == {}
         second_write.metadata["hdyfn"] = "somebody new"
         assert non_soma_metadata(second_write) == {"hdyfn": "somebody new"}
 
-    with _factory.open(uri, "r", tiledb_timestamp=timestamp + 1) as reader:
+    with _factory.open(uri, "r") as reader:
         assert non_soma_metadata(reader) == {"hdyfn": "somebody new"}
 
 
 def test_set_set_metadata(soma_object):
     uri = soma_object.uri
-    timestamp = soma_object.tiledb_timestamp_ms
 
     with soma_object:
         soma_object.metadata["content"] = "content"
 
-    with _factory.open(uri, "w", tiledb_timestamp=timestamp + 1) as second_write:
+    with _factory.open(uri, "w") as second_write:
         second_write.metadata["content"] = "confidence"
         second_write.metadata["content"] = "doubt"
 
-    with _factory.open(uri, "r", tiledb_timestamp=timestamp + 1) as reader:
+    with _factory.open(uri, "r") as reader:
         assert non_soma_metadata(reader) == {"content": "doubt"}
 
 
 def test_set_delete_metadata(soma_object):
     uri = soma_object.uri
-    timestamp = soma_object.tiledb_timestamp_ms
 
     with soma_object:
         soma_object.metadata["possession"] = "obsession"
 
-    with _factory.open(uri, "w", tiledb_timestamp=timestamp + 1) as second_write:
+    with _factory.open(uri, "w") as second_write:
         second_write.metadata["possession"] = "funny thing about opinions"
         del second_write.metadata["possession"]
 
-    with _factory.open(uri, "r", tiledb_timestamp=timestamp + 1) as reader:
+    with _factory.open(uri, "r") as reader:
         assert non_soma_metadata(reader) == {}
 
 

libtiledbsoma/cmake/Modules/FindSpdlog_EP.cmake

@@ -87,7 +87,7 @@ if (NOT SPDLOG_FOUND)
         -DCMAKE_PREFIX_PATH=${EP_INSTALL_PREFIX}
         -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}
         -DCMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES}
-        -DCMAKE_BUILD_TYPE=$<CONFIG>
+        -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
         -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
         -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
         -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}