diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000..41b0232
Binary files /dev/null and b/.DS_Store differ
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 0000000..7147277
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,34 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install ruff
+      - run: ruff check pepdata/
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: |
+          pip install pytest pytest-cov
+          pip install -r requirements.txt
+          pip install .
+      - run: pytest tests/
diff --git a/.hypothesis/unicode_data/13.0.0/charmap.json.gz b/.hypothesis/unicode_data/13.0.0/charmap.json.gz
new file mode 100644
index 0000000..d975496
Binary files /dev/null and b/.hypothesis/unicode_data/13.0.0/charmap.json.gz differ
diff --git a/lint.sh b/lint.sh
index 386fa76..7d7bc32 100755
--- a/lint.sh
+++ b/lint.sh
@@ -1,9 +1,6 @@
 #!/bin/bash
 set -o errexit
 
-find pepdata test -name '*.py' \
-  | xargs pylint \
-  --errors-only \
-  --disable=print-statement
+ruff check pepdata/ tests/
 
-echo 'Passes pylint check'
+echo 'Passes ruff check'
diff --git a/pepdata/.DS_Store b/pepdata/.DS_Store
new file mode 100644
index 0000000..0a224be
Binary files /dev/null and b/pepdata/.DS_Store differ
diff --git a/pepdata/amino_acid.py b/pepdata/amino_acid.py
index 53aea1e..3c2aa4c 100644
--- a/pepdata/amino_acid.py
+++ b/pepdata/amino_acid.py
@@ -11,8 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 class AminoAcid(object):
     def __init__(
             self, full_name, short_name, letter, contains=None):
diff --git a/pepdata/amino_acid_alphabet.py b/pepdata/amino_acid_alphabet.py
index 1789b0d..07150db 100644
--- a/pepdata/amino_acid_alphabet.py
+++ b/pepdata/amino_acid_alphabet.py
@@ -15,8 +15,6 @@
 Quantify amino acids by their physical/chemical properties
 """
 
-from __future__ import print_function, division, absolute_import
-
 import numpy as np
 
 from .amino_acid import AminoAcid
diff --git a/pepdata/amino_acid_properties.py b/pepdata/amino_acid_properties.py
index 394cc08..47306d9 100644
--- a/pepdata/amino_acid_properties.py
+++ b/pepdata/amino_acid_properties.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from .amino_acid_alphabet import letter_to_index
 
 """
diff --git a/pepdata/blosum.py b/pepdata/blosum.py
index a58e18b..8b5b036 100644
--- a/pepdata/blosum.py
+++ b/pepdata/blosum.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from os.path import join
 
 from .static_data import MATRIX_DIR
diff --git a/pepdata/chou_fasman.py b/pepdata/chou_fasman.py
index 59cbbe4..54172ce 100644
--- a/pepdata/chou_fasman.py
+++ b/pepdata/chou_fasman.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from .amino_acid_alphabet import amino_acid_name_indices
 
 # Chou-Fasman of structural properties from
diff --git a/pepdata/common.py b/pepdata/common.py
index bd0dd40..5d64beb 100644
--- a/pepdata/common.py
+++ b/pepdata/common.py
@@ -13,8 +13,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 import numpy as np
 
 def transform_peptide(peptide, property_dict):
diff --git a/pepdata/iedb/alleles.py b/pepdata/iedb/alleles.py
index 09617d2..210a90b 100644
--- a/pepdata/iedb/alleles.py
+++ b/pepdata/iedb/alleles.py
@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 from collections import namedtuple
 import os
 import xml
@@ -63,7 +62,7 @@ class and source organism.
             continue
         name = name_element.text
 
-        synonyms = set([])
+        synonyms = set()
         for synonym_element in allele.iterfind("Synonyms"):
             for synonym in synonym_element.text.split(","):
                 synonyms.add(synonym.strip())
diff --git a/pepdata/iedb/memoize.py b/pepdata/iedb/memoize.py
index 93ef44a..84e61b5 100644
--- a/pepdata/iedb/memoize.py
+++ b/pepdata/iedb/memoize.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from functools import wraps
 
 def _prepare_memoization_key(args, kwargs):
diff --git a/pepdata/iedb/mhc.py b/pepdata/iedb/mhc.py
index b3843b7..9cbaaf9 100644
--- a/pepdata/iedb/mhc.py
+++ b/pepdata/iedb/mhc.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -10,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import logging
 import os
 
diff --git a/pepdata/iedb/tcell.py b/pepdata/iedb/tcell.py
index b946e87..dbe2b6d 100644
--- a/pepdata/iedb/tcell.py
+++ b/pepdata/iedb/tcell.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -11,7 +13,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
 import logging
 import os
 
@@ -24,15 +25,9 @@
 from .common import  bad_amino_acids, cache
 from .columns import (
     get_assay_method,
-    get_assay_num_tested,
-    get_assay_response_measured,
-    get_assay_units,
     get_host_name,
     get_mhc_allele,
-    get_mhc_assay,
     get_mhc_class,
-    get_epitope_source_organism,
-    get_epitope_type,
     get_epitope_name,
     
 )
@@ -119,10 +114,10 @@ def load_dataframe(
             encoding="latin-1")
     
     mhc = get_mhc_allele(df)
-    mhc_class = get_mhc_class(df)
+    mhc_class_series = get_mhc_class(df)
     epitopes = get_epitope_name(df)
     organism = get_host_name(df)
-    assay_method = get_assay_method(df)
+    assay_method_series = get_assay_method(df)
 
 
     # Sometimes the IEDB seems to put in an extra comma in the
@@ -177,23 +172,19 @@ def load_dataframe(
     #  "HLA-Class I,allele undetermined"
     #  or
     #  "Class I,allele undetermined"
-]
-
-    if hla:
-        mask &= df[mhc_allele_column_key].str.contains(hla, na=False)
 
-    if exclude_hla:
-        mask &= ~(df[mhc_allele_column_key].str.contains(exclude_hla, na=False))
+    if mhc_pattern:
+        mask &= mhc.str.contains(mhc_pattern, na=False)
 
-    if assay_group:
-        mask &= df[assay_group_column_key].str.contains(assay_group)
+    if exclude_mhc:
+        mask &= ~(mhc.str.contains(exclude_mhc, na=False))
 
-    if assay_method:
-        mask &= df[assay_method_column_key].str.contains(assay_method)
+    if assay_method is not None and assay_method_series is not None:
+        mask &= assay_method_series.str.contains(assay_method, na=False)
 
     if peptide_length:
         assert peptide_length > 0
-        mask &= df[epitope_column_key].str.len() == peptide_length
+        mask &= epitopes.str.len() == peptide_length
 
     df = df[mask]
 
diff --git a/pepdata/peptide_vectorizer.py b/pepdata/peptide_vectorizer.py
index 05cc9de..86fa6a7 100644
--- a/pepdata/peptide_vectorizer.py
+++ b/pepdata/peptide_vectorizer.py
@@ -13,8 +13,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 import numpy as np
 from sklearn.feature_extraction.text import CountVectorizer
 from sklearn.preprocessing import normalize
@@ -28,7 +26,7 @@ def make_count_vectorizer(reduced_alphabet, max_ngram):
     return CountVectorizer(
         analyzer='char',
         ngram_range=(1, max_ngram),
-        dtype=np.float,
+        dtype=np.float64,
         preprocessor=preprocessor)
 
 class PeptideVectorizer(object):
diff --git a/pepdata/pmbec.py b/pepdata/pmbec.py
index 529d6c1..d97b8b6 100644
--- a/pepdata/pmbec.py
+++ b/pepdata/pmbec.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 from os.path import join
 
 from .static_data import MATRIX_DIR
diff --git a/pepdata/reduced_alphabet.py b/pepdata/reduced_alphabet.py
index c257333..f7121ae 100644
--- a/pepdata/reduced_alphabet.py
+++ b/pepdata/reduced_alphabet.py
@@ -18,8 +18,6 @@
 Peterson, Kondev, et al.
 http://www.rpgroup.caltech.edu/publications/Peterson2008.pdf
 """
-from __future__ import print_function, division, absolute_import
-
 def dict_from_list(groups):
     aa_to_group = {}
     for i, group in enumerate(groups):
diff --git a/pepdata/residue_contact_energies.py b/pepdata/residue_contact_energies.py
index 3bb133e..d5961c2 100644
--- a/pepdata/residue_contact_energies.py
+++ b/pepdata/residue_contact_energies.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from os.path import join
 
 from .amino_acid_alphabet import canonical_amino_acid_letters, dict_to_amino_acid_matrix
diff --git a/pepdata/static_data.py b/pepdata/static_data.py
index 7c69805..ee803cf 100644
--- a/pepdata/static_data.py
+++ b/pepdata/static_data.py
@@ -11,7 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
 from os.path import dirname, realpath, join
 
 PACKAGE_DIR = dirname(realpath(__file__))
diff --git a/pepdata/version.py b/pepdata/version.py
index f8aa15b..8b75a2c 100644
--- a/pepdata/version.py
+++ b/pepdata/version.py
@@ -1,4 +1,4 @@
-__version__ = "1.2.0"
+__version__ = "1.2.2"
 
 
 def print_version():
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..a50892f
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pepdata"
+requires-python = ">=3.9"
+authors = [{name="Alex Rubinsteyn", email="alex.rubinsteyn@mssm.edu"}]
+description = "Immunological peptide datasets and amino acid properties"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+readme = "README.md"
+dynamic = ["version", "dependencies"]
+
+[tool.setuptools.dynamic]
+version = {attr = "pepdata.version.__version__"}
+dependencies = {file = ["requirements.txt"]}
+
+[tool.setuptools.packages.find]
+exclude = ["test", "test.*"]
+
+[project.urls]
+"Homepage" = "https://github.com/openvax/pepdata"
+"Bug Tracker" = "https://github.com/openvax/pepdata/issues"
+
+[tool.ruff.lint]
+select = ["E", "F"]
+ignore = ["F821", "E501", "F841", "E731", "E741", "E722", "E721"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]
+"test*/*" = ["F401"]
diff --git a/requirements.txt b/requirements.txt
index 321e6fa..251113e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-numpy>=1.7
+numpy>=2.0.0,<3.0.0
 scipy>=0.9
 pandas>=0.17
 scikit-learn>=0.14.1
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 1a011ae..0000000
--- a/setup.py
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright (c) 2014-2018. Mount Sinai School of Medicine
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-from __future__ import print_function, division, absolute_import
-import os
-import re
-
-from setuptools import setup, find_packages
-
-readme_dir = os.path.dirname(__file__)
-readme_path = os.path.join(readme_dir, 'README.md')
-
-try:
-    with open(readme_path, 'r') as f:
-        readme_markdown = f.read()
-except:
-    print("Failed to load README file")
-    readme_markdown = ""
-
-try:
-    import pypandoc
-    readme_restructured = pypandoc.convert(readme_markdown, to='rst', format='md')
-except:
-    readme_restructured = readme_markdown
-    print("Conversion of long_description from markdown to reStructuredText failed, skipping...")
-
-with open('pepdata/__init__.py', 'r') as f:
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        f.read(),
-        re.MULTILINE).group(1)
-
-if __name__ == '__main__':
-    setup(
-        name='pepdata',
-        version=version,
-        description="Immunological peptide datasets and amino acid properties",
-        author="Alex Rubinsteyn",
-        author_email="alex.rubinsteyn@mssm.edu",
-        url="https://github.com/openvax/pepdata",
-        license="http://www.apache.org/licenses/LICENSE-2.0.html",
-        classifiers=[
-            'Development Status :: 3 - Alpha',
-            'Environment :: Console',
-            'Operating System :: OS Independent',
-            'Intended Audience :: Science/Research',
-            'License :: OSI Approved :: Apache Software License',
-            'Programming Language :: Python',
-            'Topic :: Scientific/Engineering :: Bio-Informatics',
-        ],
-        install_requires=[
-            'numpy>=1.7',
-            'scipy>=0.9',
-            'pandas>=0.17',
-            'scikit-learn>=0.14.1',
-            'progressbar33',
-            'biopython>=1.65',
-            'datacache>=0.4.4',
-            'lxml',
-        ],
-        long_description=readme_restructured,
-        packages=find_packages(exclude="test"),
-        include_package_data=True
-    )
diff --git a/tests/test_amino_acids.py b/tests/test_amino_acids.py
index d335068..9b29073 100644
--- a/tests/test_amino_acids.py
+++ b/tests/test_amino_acids.py
@@ -1,4 +1,3 @@
-from nose.tools import eq_
 from pepdata.amino_acid_alphabet import (
     canonical_amino_acids,
     canonical_amino_acid_letters,
@@ -13,7 +12,7 @@ def test_canonical_amino_acids_letters():
     assert len(canonical_amino_acid_letters) == 20
     assert "X" not in canonical_amino_acid_letters
     expected_letters = [aa.letter for aa in canonical_amino_acids]
-    eq_(expected_letters, canonical_amino_acid_letters)
+    assert expected_letters == canonical_amino_acid_letters
 
 def test_extended_amino_acids():
     assert len(extended_amino_acids) > 20
@@ -23,4 +22,4 @@ def test_extended_amino_acids_letters():
     assert "X" in extended_amino_acid_letters
     assert "J" in extended_amino_acid_letters
     expected_letters = [aa.letter for aa in extended_amino_acids]
-    eq_(expected_letters, extended_amino_acid_letters)
+    assert expected_letters == extended_amino_acid_letters
diff --git a/tests/test_iedb_alleles.py b/tests/test_iedb_alleles.py
index 9cc40bd..b1e7f8f 100644
--- a/tests/test_iedb_alleles.py
+++ b/tests/test_iedb_alleles.py
@@ -11,33 +11,30 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
-from nose.tools import eq_
 
 from pepdata import iedb
 
 def test_iedb_human_class1_allele():
     allele_dict = iedb.alleles.load_alleles_dict()
     allele = allele_dict["HLA-C*07:02"]
-    eq_(allele.mhc_class, "I")
-    eq_(allele.locus, "C")
+    assert allele.mhc_class == "I"
+    assert allele.locus == "C"
 
 def test_iedb_human_class2_allele():
     allele_dict = iedb.alleles.load_alleles_dict()
     allele = allele_dict["HLA-DRA*01:01/DRB1*04:04"]
-    eq_(allele.mhc_class, "II")
-    eq_(allele.locus, "DR")
+    assert allele.mhc_class == "II"
+    assert allele.locus == "DR"
 
 
 def test_iedb_mouse_class1_allele():
     allele_dict = iedb.alleles.load_alleles_dict()
     allele = allele_dict["H-2-Ds"]
-    eq_(allele.mhc_class, "I")
-    eq_(allele.locus, "D")
+    assert allele.mhc_class == "I"
+    assert allele.locus == "D"
 
 def test_iedb_mouse_class2_allele():
     allele_dict = iedb.alleles.load_alleles_dict()
     allele = allele_dict["H-2-IAq"]
-    eq_(allele.mhc_class, "II")
-    eq_(allele.locus, "IA")
+    assert allele.mhc_class == "II"
+    assert allele.locus == "IA"
diff --git a/tests/test_iedb_mhc.py b/tests/test_iedb_mhc.py
index 4f467af..f9ce353 100644
--- a/tests/test_iedb_mhc.py
+++ b/tests/test_iedb_mhc.py
@@ -12,8 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from pepdata import iedb
 
 def test_mhc_hla_a2():
diff --git a/tests/test_ngram.py b/tests/test_ngram.py
index c8ad3e5..da90c2d 100644
--- a/tests/test_ngram.py
+++ b/tests/test_ngram.py
@@ -12,8 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-from six.moves import cPickle
+import pickle
 
 from pepdata import PeptideVectorizer