Merge pull request #45 from LadnerLab/psp-pypi-package

Psp pypi package

Author: jeffreyHoelzel

.github/workflows/publish.yml

@@ -0,0 +1,91 @@
+name: Publish
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+
+      - name: Lint
+        run: ruff check .
+
+      - name: Run tests
+        run: pytest -m "unit or integration or e2e" --junitxml=pytest-all.xml
+
+      - name: Upload test report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-test-report
+          path: pytest-all.xml
+
+  build:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build artifacts
+        run: |
+          python -m pip install --upgrade pip build twine
+          python -m build
+          python -m twine check dist/*
+
+      - name: Upload dist
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*
+
+  publish-testpypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    needs: publish-testpypi
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -11,6 +11,27 @@
 PepSeqPred is a residue-level epitope prediction pipeline for protein workflows.  
 It converts upstream assay and sequence data into training-ready artifacts, trains feed-forward neural network models on ESM-2 embeddings, produces binary residue masks for downstream inference, and supports post-training evaluation workflows on held-out datasets.
 
+## Quickstart
+
+PepSeqPred can be installed via:
+```bash
+pip install pepseqpred
+```
+
+This API allows you to use any of the pretrained models in your own code, or load your own model(s) for downstream predictions.
+
+Example usage:
+```python
+from pepseqpred import load_predictor
+
+predictor = load_predictor("path/to/model.pt", device="cuda")
+result = predictor.predict_sequence("ACDEFGHIKLMNP")
+
+print(result.binary_mask, result.n_epitopes)
+```
+
+**Disclaimer:** The API is meant to be a simplified version of the overall codebase where you can build epitope inference into your existing/new workflows. To have more control over exactly how PepSeqPred works, feel free to fork this repository and ensure you adhere to the [GPL-3.0 license](LICENSE).
+
 ## About
 
 PepSeqPred is designed for research workflows where you need to:

pyproject.toml

@@ -4,10 +4,23 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pepseqpred"
-version = "1.0.0rc1"
+version = "0.1.2"
 description = "Residue-level epitope prediction pipeline for peptide/protein workflows."
 readme = "README.md"
 requires-python = ">=3.12"
+license = { file = "LICENSE" }
+authors = [
+  { name = "Jeffrey Hoelzel", email = "jmh2338@nau.edu" },
+  { name = "Jason Ladner", email = "jason.ladner@nau.edu" }
+]
+keywords = ["bioinformatics", "epitope", "protein", "esm2", "pytorch"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
 dependencies = [
   "numpy>=2.3,<3",
   "pandas>=2.3,<3",
@@ -17,6 +30,11 @@ dependencies = [
   "optuna>=3.5,<5"
 ]
 
+[project.urls]
+Homepage = "https://github.com/LadnerLab/PepSeqPred"
+Repository = "https://github.com/LadnerLab/PepSeqPred"
+Issues = "https://github.com/LadnerLab/PepSeqPred/issues"
+
 [project.optional-dependencies]
 dev = [
   "pytest>=8.0",

src/pepseqpred/__init__.py

@@ -0,0 +1,25 @@
+"""Top-level package exports for PepSeqPred."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from pepseqpred.api import (
+    PepSeqPredictor,
+    PredictionResult,
+    load_predictor,
+    predict_fasta,
+    predict_sequence
+)
+
+try:
+    __version__ = version("pepseqpred")
+except PackageNotFoundError:
+    __version__ = "0+unknown"
+
+__all__ = [
+    "__version__",
+    "PepSeqPredictor",
+    "PredictionResult",
+    "load_predictor",
+    "predict_sequence",
+    "predict_fasta"
+]

src/pepseqpred/api/__init__.py

@@ -0,0 +1,17 @@
+"""Public-facing API for PepSeqPred inference."""
+
+from pepseqpred.api.predictor import (
+    PepSeqPredictor,
+    load_predictor,
+    predict_fasta,
+    predict_sequence
+)
+from pepseqpred.api.types import PredictionResult
+
+__all__ = [
+    "PepSeqPredictor",
+    "PredictionResult",
+    "load_predictor",
+    "predict_fasta",
+    "predict_sequence"
+]