Rust engine backend + keep Python frontend

.github/workflows/release.yml

@@ -0,0 +1,62 @@
+name: Release to PyPI
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-wheels:
+    name: Build wheels - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build wheels
+      uses: PyO3/maturin-action@v1
+      with:
+        args: --release --out dist
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.os }}
+        path: dist
+
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build sdist
+      uses: PyO3/maturin-action@v1
+      with:
+        command: sdist
+        args: --out dist
+
+    - name: Upload sdist
+      uses: actions/upload-artifact@v4
+      with:
+        name: wheels-sdist
+        path: dist
+
+  publish:
+    name: Publish to PyPI
+    needs: [build-wheels, build-sdist]
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Download artifacts
+      uses: actions/download-artifact@v4
+      with:
+        pattern: wheels-*
+        merge-multiple: true
+        path: dist
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yml

@@ -24,8 +24,6 @@ jobs:
             test-file: pepmatch/tests/test_best_match.py
           - name: Discontinuous Epitope
             test-file: pepmatch/tests/test_discontinuous_search.py
-          - name: Parallel
-            test-file: pepmatch/tests/test_parallel_match.py
           - name: Output
             test-file: pepmatch/tests/test_output.py
 

.gitignore

@@ -16,6 +16,7 @@ notebooks/
 old_code/
 pepmatch.egg-info/
 pepmatch/__pycache__
+pepmatch/rs-engine/target/
 proteomes/*.pdb
 proteomes/*.phr
 proteomes/*.pin
@@ -31,4 +32,4 @@ test.csv
 wheelhouse/
 
 # keep test data
-!pepmatch/tests/data/
+!pepmatch/tests/data/

pepmatch/__init__.py

@@ -1,8 +1,6 @@
 from .preprocessor import Preprocessor
 from .matcher import Matcher
-from .parallel_match import ParallelMatcher
-from .benchmarker import Benchmarker
 
 from .version import __version__
 
-__all__ = ['Preprocessor', 'Matcher', 'ParallelMatcher', 'Benchmarker', '__version__']
+__all__ = ['Preprocessor', 'Matcher', '__version__']