Require Python 3.11 and test through 3.14

.github/workflows/tests.yml

@@ -0,0 +1,32 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  quality:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install BLAST and Python dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y ncbi-blast+
+          python -m pip install --upgrade pip
+          python -m pip install -e . pytest build twine
+          python -m pip check
+      - name: Run tests
+        run: MPLBACKEND=Agg python -m pytest test -q
+      - name: Check release artifacts
+        run: |
+          python -m build
+          python -m twine check --strict dist/*

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/openvax/phipkit.svg?branch=main)](https://travis-ci.com/openvax/phipkit)
+[![Tests](https://github.com/openvax/phipkit/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/phipkit/actions/workflows/tests.yml)
 
 # phipkit
 PhIP-seq data analysis toolkit
@@ -16,6 +16,8 @@ control comparisons or other analyses appropriate to the study.
 
 ## Installation
 
+PhIPKit requires Python 3.11 or newer.
+
 All dependencies except BLAST (required by `phipkit-blast` command) can be
 installed by pip:
 

phipkit/__init__.py

@@ -2,7 +2,7 @@
 phipkit - analysis package for Phage Immunoprecipitation Sequencing (phip-seq)
 """
 
-__version__ = "0.0.2"
+__version__ = "0.0.3"
 from . import antigen_analysis
 from . import call_antigens
 from . import call_hits

phipkit/antigen_analysis.py

@@ -195,7 +195,7 @@ def plot_antigen(
         title = antigen.split("OS")[0].strip()
         title += "\nHits in %d of %d clones" % (
             self.clone_by_sample_hits_matrix.reindex(
-                all_coverage_by_clone.index).fillna(0)[all_samples].any(1).sum(),
+                all_coverage_by_clone.index).fillna(0)[all_samples].any(axis=1).sum(),
             len(all_coverage_by_clone))
 
         pyplot.suptitle(title)

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 requires = [
-    "setuptools>=42",
+    "setuptools>=77",
     "wheel"
 ]
 build-backend = "setuptools.build_meta"

setup.cfg

@@ -11,13 +11,17 @@ project_urls =
     Bug Tracker = https://github.com/openvax/phipkit/issues
 classifiers =
     Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
+    Programming Language :: Python :: 3.14
     Topic :: Scientific/Engineering :: Bio-Informatics
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
 
 [options]
 packages = find:
-python_requires = >=3.3
+python_requires = >=3.11
 install_requires =
     pandas
     dna_features_viewer

test/test_integration.py

@@ -1,9 +1,11 @@
 import random
+import shutil
 import tempfile
 import os
 
 import numpy
 import pandas
+import pytest
 
 from phipkit.blast import run_blast
 from phipkit.score import compute_scores
@@ -74,6 +76,10 @@
 TEST_PROTEINS["S_redundant"] = TEST_PROTEINS["S"]
 
 
+@pytest.mark.skipif(
+    not all(shutil.which(name) for name in ("makeblastdb", "blastp")),
+    reason="NCBI BLAST executables are not installed",
+)
 def test_integrated(save_dir=None):
     """
     Run the integration test.