Release

.github/workflows/python-app.yml

@@ -36,13 +36,15 @@ jobs:
         run: tox -e type
 
       - name: Confirm Documentation Builds
+        if: always()
         run: tox -e docs
 
   tests:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [ "3.11", "3.12" ]
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ "3.11", "3.12", "3.13" ]
 
     steps:
       - name: Checkout DesignerDNA Project
@@ -58,7 +60,16 @@ jobs:
           python -m pip install -U pip
           pip install wheel setuptools
           pip install tox
-          echo "TOX_VERSION=py$(echo ${{ matrix.python-version }} | tr -d .)-tests" >> $GITHUB_ENV
+
+      - name: Setup tox python version
+        if: matrix.os != 'windows-latest'
+        run: |
+            echo "TOX_VERSION=py$(echo ${{ matrix.python-version }} | tr -d .)-tests" >> $GITHUB_ENV
+
+      - name: Setup tox python version
+        if: matrix.os == 'windows-latest'
+        run: |
+          "TOX_VERSION=py$(echo ${{ matrix.python-version }} | tr -d .)-tests" >> $env:GITHUB_ENV
 
       - name: Unit Testing
         run: |
@@ -67,7 +78,7 @@ jobs:
       - name: Save Coverage Data Temporarily
         uses: actions/upload-artifact@v4
         with:
-          name: coverage-data-${{ matrix.python-version }}
+          name: coverage-data-${{ matrix.os }}-${{ matrix.python-version }}
           path: .coverage.*
           retention-days: 1
           if-no-files-found: ignore

.github/workflows/python-publish.yml

@@ -5,33 +5,84 @@ name: Upload Python Package
 
 on:
   release:
-    types: [published]
+    types: [ published ]
 
 permissions:
   contents: read
 
 jobs:
-  deploy:
+  sdist:
     runs-on: ubuntu-latest
-    if: github.event_name == 'release'
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout Project
+      uses: actions/checkout@v5
+
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
+        python-version-file: .python-version-default
 
     - name: Install dependencies
       run: |
         python -m pip install -U pip --disable-pip-version-check
         python -m pip install setuptools wheel build
 
-    - name: Build package
-      run: python -m build
+    - name: Build Package
+      run: python -m build --sdist
 
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+    - name: Upload distributions
+      uses: actions/upload-artifact@v4
       with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        name: ci-sdist
+        path: dist/*.tar.gz
+
+  wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [
+          ubuntu-latest, ubuntu-24.04-arm,
+          windows-latest, windows-11-arm,
+          macos-15-intel, macos-14
+        ]
+
+    steps:
+      - name: Checkout Project
+        uses: actions/checkout@v5
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux' && runner.arch == 'X64'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: all
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.2.0
+        env:
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_ARCHS_LINUX: ${{ runner.arch == 'X64' && 'auto ppc64le s390x' || 'auto' }}
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: ci-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: [ sdist, wheels ]
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: ci-*
+          path: dist/
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v.1.13.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

src/designer_dna/_oligos.pyi

@@ -118,6 +118,19 @@ def reverse_complement(sequence: str, dna: bool = ...) -> str:
 
     """
 
+def m_palindrome(sequence: array[int], dna: bool = ...) -> tuple[int, int]:
+    """Find the longest palindromic substring within a nucleotide sequence.
+
+    Args:
+        sequence (uchar[]): Nucleotide sequence writeable memory view.
+        dna (bool): Sequence is DNA, else RNA.
+
+    Returns:
+        (int, int) start and end indices denoting the longest found
+        palindromic subsequence within sequence.
+
+    """
+
 def palindrome(sequence: str, dna: bool = ...) -> str:
     """Find the longest palindromic substring within a nucleotide sequence.
 

src/designer_dna/_oligos.pyx

@@ -185,9 +185,8 @@ cpdef void m_complement(unsigned char[:] sequence, bint dna = True):
     """
     cdef:
         Py_ssize_t length = sequence.shape[0]
-        unsigned char* c_string = &sequence[0]
 
-    c_complement(c_string, length, dna)
+    c_complement(&sequence[0], length, dna)
 
 
 cpdef str complement(str sequence, bint dna = True):
@@ -253,11 +252,11 @@ cdef void c_reverse_complement(
 
     Args:
         sequence (uchar*): Nucleotide sequence pointer.
-        length (Py_ssize_t): Length of seq.
+        length (Py_ssize_t): Length of sequence.
         dna (bint): Sequence is DNA, else RNA.
 
     Returns:
-        (void) Complement seq in place.
+        (void) Complement sequence in place.
 
     """
     if dna:
@@ -354,6 +353,18 @@ cdef inline (Py_ssize_t, Py_ssize_t) c_palindrome(
     Py_ssize_t size,
     bint dna
 ) noexcept:
+    """Find the longest palindromic substring within a nucleotide sequence.
+
+    Args:
+        seq (uchar*): Nucleotide sequence pointer.
+        size (Py_ssize_t): Length of seq.
+        dna (bint): Sequence is DNA, else RNA.
+
+    Returns:
+        (tuple[Py_ssize_t, Py_ssize_t]) longest palindromic subsequence within sequence,
+        described by start (inclusive) and end (exclusive) index.
+
+    """
     cdef:
         unsigned char* com = <unsigned char*> malloc((size + 1) * sizeof(unsigned char))
         Py_ssize_t i, left, right, current, length = 0, start = 0, end = 0
@@ -383,6 +394,30 @@ cdef inline (Py_ssize_t, Py_ssize_t) c_palindrome(
     return start, end
 
 
+cpdef (int, int) m_palindrome(
+    unsigned char[:] sequence,
+    bint dna = True
+):
+    """Find the longest palindromic substring within a nucleotide sequence.
+
+    Args:
+        sequence (uchar[]): Nucleotide sequence writeable memory view.
+        dna (bool): Sequence is DNA, else RNA.
+
+    Returns:
+        (int, int) start and end indices denoting the longest found
+        palindromic subsequence within sequence.
+
+    """
+    cdef:
+        int start, end
+        Py_ssize_t length = sequence.shape[0]
+
+    start, end = c_palindrome(&sequence[0], length, dna)
+
+    return start, end
+
+
 cpdef str palindrome(str sequence, bint dna = True):
     """Find the longest palindromic substring within a nucleotide sequence.
 
@@ -479,19 +514,10 @@ cpdef int stretch(str sequence):
 
     """
     cdef:
+        int longest
         StringView view = str_to_view(sequence)
-        Py_ssize_t j
-        int longest = 0, current = 0
-        unsigned char prev = view.ptr[0]
 
-    for j in range(1, view.size):
-        if view.ptr[j] == prev:
-            current += 1
-            if current > longest:
-                longest = current
-        else:
-            current = 0
-            prev = view.ptr[j]
+    longest = c_stretch(view.ptr, view.size)
     free(view.ptr)
 
     return longest
@@ -530,7 +556,11 @@ cdef inline void _assign(
         count += 1
 
 
-cdef int c_nrepeats(unsigned char* sequence, int length, int n) noexcept:
+cdef inline int c_nrepeats(
+    unsigned char* sequence,
+    int length,
+    int n
+) noexcept:
     """Calculate the maximum observed repeats of composite pattern size n characters.
 
     Args: