Release 0.40.3

.github/workflows/ci-linters.yml

@@ -10,10 +10,10 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout TileDB-VCF
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 

.github/workflows/macos.yml

@@ -20,7 +20,7 @@ jobs:
   libtiledbvcf:
     runs-on: macos-15
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Setup to build htslib from source
         run: brew install autoconf automake
       - name: Configure libtiledbvcf
@@ -69,7 +69,7 @@ jobs:
     env:
       DYLD_LIBRARY_PATH: "${{ github.workspace }}/dist/lib"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0 # fetch everything for python setuptools_scm
       - name: Download libtiledbvcf artifact
@@ -78,11 +78,11 @@ jobs:
           name: libtiledbvcf
           path: dist
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Install libtiledb
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: ci
           create-args: tiledb
@@ -101,7 +101,7 @@ jobs:
     runs-on: macos-15
     needs: libtiledbvcf
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Download libtiledbvcf artifact
         uses: actions/download-artifact@v4
         with:
@@ -116,13 +116,13 @@ jobs:
   python-standalone:
     runs-on: macos-15
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0 # fetch everything for python setuptools_scm
       - name: Setup to build htslib from source
         run: brew install autoconf automake
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Build tiledbvcf-py

.github/workflows/nightly.yml

@@ -24,25 +24,25 @@ jobs:
       matrix:
         os: [macos-15, ubuntu-24.04]
         branches:
-          - {libtiledb: release-2.30, tiledb-py: 0.36.0}
+          - {libtiledb: release-2.30, tiledb-py: 0.36.1}
           - {libtiledb: main, tiledb-py: main}
     env:
       MACOSX_DEPLOYMENT_TARGET: 10.15
     steps:
       - name: Clone TileDB
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: TileDB-Inc/TileDB
           ref: ${{ matrix.branches.libtiledb }}
           path: TileDB
       - name: Clone TileDB-Py
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: TileDB-Inc/TileDB-Py
           ref: ${{ matrix.branches.tiledb-py }}
           path: TileDB-Py
       - name: Clone TileDB-VCF
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           path: TileDB-VCF
           fetch-depth: 0 # fetch everything for python setuptools_scm
@@ -80,11 +80,13 @@ jobs:
       - name: Test libtiledbvcf
         run: bash TileDB-VCF/ci/nightly/test-libtiledbvcf.sh
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Build tiledb-py from source
         run: bash TileDB-VCF/ci/nightly/build-tiledb-py.sh
+        env:
+          PYBIND11_MAX_VERSION: ${{ matrix.branches.tiledb-py != 'main' && '<3' || '' }}
       - name: Build (and test) tiledbvcf-py
         run: bash TileDB-VCF/ci/nightly/build-tiledbvcf-py.sh
   issue:
@@ -94,7 +96,7 @@ jobs:
     needs: nightly
     if: ( failure() || cancelled() ) && github.repository_owner == 'TileDB-Inc' && github.event_name == 'schedule'
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Open Issue
         uses: TileDB-Inc/github-actions/open-issue@main
         with:

.github/workflows/quarto-render.yml

@@ -9,7 +9,7 @@ jobs:
   quarto-render-and-deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: "Install Quarto"
       uses: quarto-dev/quarto-actions/setup@v2
@@ -25,7 +25,7 @@ jobs:
         # https://github.com/quarto-dev/quarto-cli/issues/493
 
     - name: "Deploy to gh-pages"
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       # Change to the name of your repo's primary branch name:
       if: github.ref == 'refs/heads/main' && github.repository_owner == 'TileDB-Inc'
       with:

.github/workflows/windows.yml

@@ -26,9 +26,9 @@ jobs:
   build:
     runs-on: windows-2022
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install conda env
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ci/gha-win-env.yml
           cache-environment: true

apis/python/src/tiledbvcf/binding/libtiledbvcf.cc

@@ -131,6 +131,7 @@ PYBIND11_MODULE(libtiledbvcf, m) {
           "ingest_samples",
           &Writer::ingest_samples,
           py::call_guard<py::gil_scoped_release>())
+      .def("set_skip_aggregate_stats", &Writer::set_skip_aggregate_stats)
       .def(
           "delete_samples",
           &Writer::delete_samples,

apis/python/src/tiledbvcf/binding/pyarrow_helpers.h

@@ -44,7 +44,7 @@ using namespace tiledb::vcf;
  * @return py::object Arrow table
  */
 py::object _buffer_to_table(std::shared_ptr<ArrayBuffers> buffers) {
-  auto pa = py::module::import("pyarrow");
+  auto pa = py::module_::import("pyarrow");
   auto pa_table_from_arrays = pa.attr("Table").attr("from_arrays");
   auto pa_array_import = pa.attr("Array").attr("_import_from_c");
   auto pa_schema_import = pa.attr("Schema").attr("_import_from_c");

apis/python/src/tiledbvcf/binding/sample_stats.h

@@ -35,7 +35,7 @@ namespace py = pybind11;
 using namespace py::literals;
 using namespace tiledb::vcf;
 
-void load_sample_stats(py::module& m) {
+void load_sample_stats(py::module_& m) {
   m.def(
       "sample_qc",
       [](const std::string& dataset_uri,

apis/python/src/tiledbvcf/binding/vcf_arrow.cc

@@ -316,7 +316,7 @@ void build_arrow_array_from_buffer(
 }
 
 py::object buffers_to_table(std::vector<std::shared_ptr<BufferInfo>>& buffers) {
-  auto pa = py::module::import("pyarrow");
+  auto pa = py::module_::import("pyarrow");
   auto pa_table_from_arrays = pa.attr("Table").attr("from_arrays");
   auto pa_array_import = pa.attr("Array").attr("_import_from_c");
   auto pa_schema_import = pa.attr("Schema").attr("_import_from_c");

apis/python/src/tiledbvcf/binding/writer.cc

@@ -232,6 +232,11 @@ void Writer::ingest_samples() {
   check_error(writer, tiledb_vcf_writer_store(writer));
 }
 
+void Writer::set_skip_aggregate_stats(bool skip) {
+  auto writer = ptr.get();
+  check_error(writer, tiledb_vcf_writer_set_skip_aggregate_stats(writer, skip));
+}
+
 void Writer::delete_samples(std::vector<std::string> samples_to_delete) {
   std::vector<const char*> samples;
   for (std::string& sample : samples_to_delete) {

apis/python/src/tiledbvcf/binding/writer.h

@@ -162,6 +162,8 @@ class Writer {
 
   void ingest_samples();
 
+  void set_skip_aggregate_stats(bool skip);
+
   void delete_samples(std::vector<std::string> samples);
 
   /** Returns schema version number of the TileDB VCF dataset */

apis/python/src/tiledbvcf/dataset.py

@@ -1111,9 +1111,23 @@ def ingest_samples(
     def delete_samples(
         self,
         sample_uris: List[str] = None,
+        skip_aggregate_stats: bool = False,
     ):
+        """
+        Delete samples from the dataset.
+
+        Parameters
+        ----------
+        sample_uris
+            List of sample names to delete.
+        skip_aggregate_stats
+            If True, skip updating allele_count and variant_stats arrays
+            during deletion.
+        """
         if self.mode != "w":
             raise Exception("Dataset not open in write mode")
+        if skip_aggregate_stats:
+            self.writer.set_skip_aggregate_stats(True)
         self.writer.delete_samples(sample_uris)
 
     def tiledb_stats(self) -> str: