Feature parallelization

.github/workflows/integration_tests.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10' ]
+        python-version: ['3.11']
 
     steps:
     - name: Checkout code

.github/workflows/unit_tests.yml

@@ -8,7 +8,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.11']
 
     steps:
       - name: Checkout code

.gitignore

@@ -14,4 +14,6 @@ out
 vafator/tests/resources/results
 .cache
 .jupyter
-.local
+.local
+run.sh
+VAFator.egg-info/*

requirements.txt

@@ -1,7 +1,11 @@
-pandas~=1.3.3
-pysam~=0.19.1
-cyvcf2~=0.30.14
-logzero~=1.7.0
-pybedtools~=0.9.0
-numpy>=1.20,<2.0
-scipy>=1.0.0,<2.0.0
+pandas>=3.0.1,<4
+# pysam pinned: above 0.21.0 base qualities show up wrong in the presence of soft clipping/insertions/overlapping read pairs or a combination of these factors 
+pysam==0.21.0
+cyvcf2>=0.32.1,<0.33
+logzero>=1.7.0,<2
+pybedtools>=0.12.0,<0.13
+numpy>=2.4.3,<3
+scipy>=1.17.1,<2
+setuptools
+pytest
+pytest-cov

setup.cfg

@@ -1,2 +1,63 @@
 [metadata]
-description-file = README.md
+name = VAFator
+version = 3.1.0
+description = Annotate variants in a VCF file with technical annotations from one or more BAMs 
+description-file = README.md
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = MIT
+url = https://github.com/TRON-Bioinformatics/vafator
+author = Pablo Riesgo Ferreiro, Jonas Ibn-Salem, Luis Kress, Özlem Muslu
+classifiers =
+    Development Status :: 4 - Beta
+    Intended Audience :: Healthcare Industry
+    Intended Audience :: Science/Research
+    Topic :: Scientific/Engineering :: Bio-Informatics
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
+    Programming Language :: Python :: 3 :: Only
+    License :: OSI Approved :: MIT License
+    Operating System :: Unix
+author_email = priesgoferreiro@gmail.com
+
+[options.entry_points]
+console_scripts = 
+    vafator=vafator.command_line:annotator
+    multiallelics-filter=vafator.command_line:multiallelics_filter
+    vafator2decifer=vafator.command_line:vafator2decifer
+    hatchet2bed=vafator.command_line:hatchet2bed
+
+[options]
+packages = find:
+include_package_data = True
+zip_safe = False
+
+python_requires = >=3.11, <3.12
+
+install_requires =
+    pandas>=3.0.1,<4
+    pysam==0.21.0 # above this version base qualities show up wrong in the presence of soft clipping/insertions/both (latest release 0.23.3)
+    cyvcf2>=0.32.1,<0.33
+    logzero>=1.7.0,<2
+    pybedtools>=0.12.0,<0.13
+    numpy>=2.4.3,<3
+    scipy>=1.17.1,<2
+    setuptools
+
+[options.packages.find]
+exclude =
+    tests
+    tests.*
+    legacy
+    legacy.*
+
+[options.extras_require]
+dev =
+    pytest
+    ruff
+    mypy
+test =
+    pytest
+    pytest-cov
+    setuptools

setup.py

@@ -4,49 +4,8 @@
 
 VERSION = vafator.VERSION
 
-
-# parses requirements from file
-with open("requirements.txt") as f:
-    required = f.read().splitlines()
-
 with open("README.md", "r", encoding="utf-8") as f:
     long_description = f.read()
 
 # Build the Python package
-setup(
-    name='vafator',
-    version=VERSION,
-    packages=find_packages(exclude=["legacy"]),
-    entry_points={
-        'console_scripts': [
-            'vafator=vafator.command_line:annotator',
-            'multiallelics-filter=vafator.command_line:multiallelics_filter',
-            'vafator2decifer=vafator.command_line:vafator2decifer',
-            'hatchet2bed=vafator.command_line:hatchet2bed'
-        ],
-    },
-    author="TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz"
-    "- Computational Medicine group",
-    author_email='pablo.riesgoferreiro@tron-mainz.de',
-    description='Annotate a VCF file with AF, AD and DP from tumor and normal BAMs',
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/tron-bioinformatics/vafator",
-    requires=[],
-    install_requires=required,
-    classifiers=[
-        'Development Status :: 4 - Beta',      # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package
-        'Intended Audience :: Healthcare Industry',
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3 :: Only',
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: Unix"
-      ],
-    python_requires='>=3.7',
-    license='MIT'
-)
+setup()

vafator/__init__.py

@@ -1,4 +1,2 @@
-VERSION='2.2.2'
-
-
-AMBIGUOUS_BASES = ['N', 'M', 'R', 'W', 'S', 'Y', 'K', 'V', 'H', 'D', 'B']
+VERSION = '3.1.0'
+