From aa58f8bc11a962e90af1f93185056a35f51493dd Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Thu, 29 Jan 2026 22:40:11 +0000
Subject: [PATCH 1/4] Add pyproject.toml

---
 pyproject.toml | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..6ddc4c0
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,58 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyvdrm"
+version = "0.3.1"
+description = "Tools for interpreting drug resistance mutations in viral amino acid sequences"
+readme = "README.md"
+authors = [
+    { name = "British Columbia Centre for Excellence in HIV/AIDS", email = "vmysak@bccfe.ca" },
+]
+requires-python = ">=3.8,<3.15"
+dependencies = [
+    "pyparsing",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Software Development :: Libraries",
+]
+
+[project.optional-dependencies]
+test = [
+    # Dependencies required for running the test suite
+    "pytest>=6.0",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/cfe-lab/pyvdrm"
+"Source" = "https://github.com/cfe-lab/pyvdrm"
+"Bug Tracker" = "https://github.com/cfe-lab/pyvdrm/issues"
+
+[tool.hatch.build.targets.sdist]
+include = ["pyvdrm"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["pyvdrm"]
+
+[tool.pytest.ini_options]
+testpaths = ["pyvdrm/tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]

From ae4df9c3ad1f5d7143378491a49add5da64ca695 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Thu, 29 Jan 2026 22:40:30 +0000
Subject: [PATCH 2/4] Refactor dependency installation and test command in CI
 workflow

---
 .github/workflows/main.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index be4f9a9..009d478 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -17,8 +17,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
-          pip install pytest
+          pip install -e .[test]
 
       - name: Run tests
-        run: pytest -v pyvdrm/tests/
+        run: pytest -v

From 161b7ccf814a8eaf4ed30310ad33c215a4f6313f Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Thu, 29 Jan 2026 22:41:06 +0000
Subject: [PATCH 3/4] Delete old setup files

---
 setup.cfg |  2 --
 setup.py  | 17 -----------------
 2 files changed, 19 deletions(-)
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 9af7e6f..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[aliases]
-test=pytest
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 95bd854..0000000
--- a/setup.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from setuptools import setup
-
-setup(
-    name='pyvdrm',
-    version='0.3.1',
-    description='',
-
-    url='',
-    author='',
-    author_email='',
-
-    packages=(['pyvdrm']),
-    python_requires='>=3',
-    install_requires=['pyparsing'],
-
-    setup_requires=['pytest-runner'],
-    tests_require=['pytest'])

From aaf4d5ad3fb210625941f91836bb3c14fe2b658b Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Thu, 29 Jan 2026 22:42:14 +0000
Subject: [PATCH 4/4] Remove outdated travis CI links

---
 README.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/README.md b/README.md
index 827a40b..4b62ac7 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,4 @@
 # pyvdrm
-[![Build
-Status](https://travis-ci.org/cfe-lab/pyvdrm.svg?branch=master)](https://travis-ci.org/cfe-lab/pyvdrm)
 
 Tools for interpreting drug resistance mutations in viral amino acid sequences