Support sparse matrices in vectorize_counts_and_tree

.github/workflows/ci.yml

@@ -36,7 +36,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
@@ -59,7 +59,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0  # to prevent a "Git clone too shallow" warning by Sphinx
       - uses: conda-incubator/setup-miniconda@v3
@@ -85,7 +85,7 @@ jobs:
           python doc/editmap.py
       - name: Save documentation
         if: github.event_name == 'push'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: docpack
           path: doc/build/html/
@@ -106,7 +106,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest, ubuntu-24.04-arm, macos-15-intel]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
@@ -136,7 +136,7 @@ jobs:
           cd ci && coverage lcov --rcfile ../.coveragerc
       - name: Upload coverage reports to Codecov
         if: runner.os == 'Linux' && runner.arch == 'X64'
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: scikit-bio/scikit-bio
@@ -156,7 +156,7 @@ jobs:
         python_version: ${{ fromJSON(needs.conf.outputs.supported_pythons) }}
         use_conda: [true, false]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       # set up conda environment
       - name: Setup conda environment
         if: ${{ matrix.use_conda }}
@@ -168,7 +168,7 @@ jobs:
       # set up CPython environment (pip)
       - name: Setup CPython environment
         if: ${{ !matrix.use_conda }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
       # conda installation
@@ -205,13 +205,13 @@ jobs:
     steps:
       # load documentation built by job "doc"
       - name: Load documentation
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: docpack
           path: docpack
       # checkout website repo
       - name: Check out website
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: scikit-bio/scikit-bio.github.io
           path: website

.github/workflows/release.yml

@@ -25,12 +25,12 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Setup Python environment
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.latest_python }}
 
@@ -51,7 +51,7 @@ jobs:
           python doc/editmap.py
 
       - name: Check out website
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: scikit-bio/scikit-bio.github.io
           path: website

.github/workflows/website.yml

@@ -21,7 +21,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up conda
         uses: conda-incubator/setup-miniconda@v3
@@ -47,7 +47,7 @@ jobs:
 
       - name: Save website package
         if: github.event_name == 'push'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: webpack
           path: web/_build/html/
@@ -62,16 +62,16 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Load website package
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: webpack
           path: webpack
 
       - name: Check out website repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: scikit-bio/scikit-bio.github.io
           path: website

.github/workflows/wheels.yml

@@ -37,21 +37,21 @@ jobs:
         #     cibw_archs: 'arm64'
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
       - name: Build wheels
         # This may need to be updated for new Python versions, double check before release.
-        uses: pypa/cibuildwheel@v3.2.1
+        uses: pypa/cibuildwheel@v3.4.0
         env:
         # Run full tests on release, manual trigger, and schedule (twice a month). Otherwise (i.e. on PRs) do simple import/print test.
           CIBW_TEST_COMMAND: >
             ${{ ((github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'workflow_dispatch' || github.event_name == 'schedule') &&
                 'python -m skbio.test' ||
                 'python -c "import skbio; print(skbio.__version__)"' }}
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         with:
           name: wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
@@ -60,12 +60,12 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.latest_python }}
 
@@ -77,7 +77,7 @@ jobs:
       - name: Build sdist
         run: python -m build --sdist
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         with:
           name: sdist
           path: dist/*.tar.gz
@@ -88,13 +88,13 @@ jobs:
     # Only upload to PyPI on tagged commits
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           pattern: wheels-*
           path: dist
           merge-multiple: true
 
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           name: sdist
           path: dist

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## Version 0.7.3-dev
 
+### Features
+
+* Support sparse matrix representations within the tree-based diversity calculation framework ([#2414](https://github.com/scikit-bio/scikit-bio/pull/2414)).
+* Added support to `TreeNode.from_taxonomy` for parsing taxonomic lineage strings into trees with an optional `extract_rank` parameter. ([#2406](https://github.com/scikit-bio/scikit-bio/pull/2406))
+
 
 ## Version 0.7.2