Make Vaxrank's epitope/vaccine peptide scoring/filtering/ranking more configurable via YAML

.github/workflows/tests.yml

@@ -60,3 +60,5 @@ jobs:
           ./test.sh
       - name: Publish coverage to Coveralls
         uses: coverallsapp/[email protected]
+        with:
+          parallel: true

deploy.sh

@@ -4,5 +4,8 @@ python3 -m pip install --upgrade build && \
 python3 -m pip install --upgrade twine && \
 rm -rf dist && \
 python3 -m build && \
-python3 -m twine upload dist/*
+git --version && \
+python3 -m twine upload dist/* && \
+git tag "$(python3 vaxrank/version.py)" &&  \
+git push --tags
 

develop.sh

@@ -1,3 +1,3 @@
 set -e
 
-pip install -e .
+uv pip install -e .

requirements.txt

@@ -1,19 +1,18 @@
-six
-numpy>=1.14.0
-pandas
-pyensembl>=1.5.0
-varcode>=0.5.9
-isovar>=1.1.1
-mhctools>=1.5.0
+numpy>=1.14.0,<2.0.0
+pandas>=2.1.4,<3.0.0
+pyensembl>=2.0.0,<3.0.0
+varcode>=1.1.0,<2.0.0
+isovar>=1.3.0,<2.0.0
+mhctools>=1.8.2,<2.0.0
 roman
 jinja2<3.1
 pdfkit  # needs wkhtmltopdf: brew install Caskroom/cask/wkhtmltopdf
 pypandoc  # needs pandoc: brew install pandoc
 shellinford>=0.3.4
-xlsxwriter
-xlrd>=1.0.0,<2.0.0
+openpyxl
 xvfbwrapper
 future>=0.16.0  # needed by pylint
 astropy
 datacache
 pysam>=0.15.2
+msgspec>=0.18.6,<1.0.0

setup.py

@@ -11,7 +11,9 @@
 # limitations under the License.
 
 
-from __future__ import (absolute_import,)
+from __future__ import (
+    absolute_import,
+)
 
 import os
 import logging
@@ -20,68 +22,52 @@
 from setuptools import setup
 
 readme_dir = os.path.dirname(__file__)
-readme_path = os.path.join(readme_dir, 'README.md')
+readme_path = os.path.join(readme_dir, "README.md")
 
 try:
-    with open(readme_path, 'r') as f:
+    with open(readme_path, "r") as f:
         readme_markdown = f.read()
 except:
     logging.warn("Failed to load %s" % readme_path)
     readme_markdown = ""
 
-with open('vaxrank/__init__.py', 'r') as f:
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        f.read(),
-        re.MULTILINE).group(1)
+with open("vaxrank/version.py", "r") as f:
+    match = re.search(r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]', f.read(), re.MULTILINE)
+    if not match:
+        raise RuntimeError("Cannot find version information")
+    else:
+        version = match.group(1)
 
 if not version:
     raise RuntimeError("Cannot find version information")
 
-if __name__ == '__main__':
+
+with open("requirements.txt") as f:
+    requirements = [req.strip() for req in f.read().splitlines() if req.strip()]
+
+
+if __name__ == "__main__":
     setup(
-        name='vaxrank',
+        name="vaxrank",
         version=version,
         description="Mutant peptide ranking for personalized cancer vaccines",
         author="Alex Rubinsteyn, Julia Kodysh",
         author_email="[email protected], [email protected]",
         url="https://github.com/openvax/vaxrank",
         license="http://www.apache.org/licenses/LICENSE-2.0.html",
         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',
+            "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",
         ],
-        install_requires=[
-            'numpy>=1.14.0,<2.0.0',
-            'pandas>=2.1.4,<3.0.0',
-            'pyensembl>=2.0.0,<3.0.0',
-            'varcode>=1.1.0,<2.0.0',
-            'isovar>=1.3.0,<2.0.0',
-            'mhctools>=1.8.2,<2.0.0',
-            'roman',
-            'jinja2<3.1',
-            'pdfkit',
-            'pypandoc',
-            'shellinford>=0.3.4',
-            'xlrd>=1.0.0,<2.0.0',
-            'xlsxwriter',
-            'xvfbwrapper',
-            'future>=0.16.0',  # needed by pylint
-            'astropy',
-        ],
-
+        install_requires=requirements,
         long_description=readme_markdown,
-        long_description_content_type='text/markdown',
-        packages=['vaxrank'],
-        package_data={'vaxrank': ['templates/*', 'data/*', 'logging.conf']},
-        entry_points={
-            'console_scripts': [
-                'vaxrank = vaxrank.cli:main'
-            ]
-        }
+        long_description_content_type="text/markdown",
+        packages=["vaxrank"],
+        package_data={"vaxrank": ["templates/*", "data/*", "logging.conf"]},
+        entry_points={"console_scripts": ["vaxrank = vaxrank.cli.entry_point:main"]},
     )

tests/test_epitope_prediction.py

@@ -13,7 +13,8 @@
 from mhctools import RandomBindingPredictor
 from pyensembl import genome_for_reference_name
 from varcode import Variant
-from vaxrank.epitope_prediction import predict_epitopes, EpitopePrediction
+from vaxrank.epitope_logic import predict_epitopes
+from vaxrank.epitope_prediction import EpitopePrediction
 from vaxrank.mutant_protein_fragment import MutantProteinFragment
 from vaxrank.vaccine_peptide import VaccinePeptide
 

tests/test_shell_script.py

@@ -17,7 +17,7 @@
 from tempfile import NamedTemporaryFile
 
 import pandas as pd
-from xlrd import open_workbook
+
 
 from vaxrank.cli import main as run_shell_script
 
@@ -112,12 +112,14 @@ def test_isovar_csv():
 
 def test_xlsx_report():
     with NamedTemporaryFile(mode="r") as f:
+
         xlsx_args = cli_args_for_b16_seqdata + ["--output-xlsx-report", f.name]
-        run_shell_script(xlsx_args)
-        book = open_workbook(f.name)
-        assert book.nsheets > 1
-
 
+        print("vaxrank %s" % (" ".join(xlsx_args))) 
+        run_shell_script(xlsx_args)
+        df = pd.read_excel(f.name, engine='openpyxl')
+        assert len(df) == 2
+
 
 
 def test_html_report():

vaxrank/__init__.py

@@ -1 +1,30 @@
-__version__ = "1.5.0"
+# 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 .core_logic import run_vaxrank
+from .epitope_prediction import EpitopePrediction
+from .epitope_logic import predict_epitopes
+from .vaccine_peptide import VaccinePeptide
+from .version import __version__
+from .cli.epitope_config_args import EpitopeConfig
+from .cli.vaccine_config_args import VaccineConfig
+
+__all__ = [
+    "__version__",
+    "EpitopePrediction",
+    "VaccinePeptide",
+    "run_vaxrank",
+    "predict_epitopes",
+    "EpitopeConfig",
+    "VaccineConfig",
+]