Dev

.github/workflows/ci.yml

@@ -80,7 +80,9 @@ jobs:
       run: |
         echo "Starting Docker deployment to GHCR for sigprofilersuite..."
 
-        VERSION_TAG=$(grep "VERSION = " setup.py | cut -d'"' -f2)
+        python -m pip install --upgrade setuptools_scm
+        VERSION_TAG=$(python -m setuptools_scm)
+        VERSION_TAG=${VERSION_TAG//+/-}
 
         # Get the repository name and convert it to lowercase
         REPO_NAME=$(basename ${{ github.repository }} | tr '[:upper:]' '[:lower:]')

.github/workflows/release.yml

@@ -0,0 +1,92 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.12"
+
+    - name: Install build tooling
+      run: |
+        python -m pip install --upgrade pip build twine
+
+    - name: Build distributions
+      run: |
+        python -m build
+
+    - name: Check distributions
+      run: |
+        python -m twine check dist/*
+
+    - name: Verify package version
+      run: |
+        python -m pip install dist/*.whl
+        python -c "import SigProfilerExtractor; print(SigProfilerExtractor.__version__)"
+
+    - name: Upload distributions
+      uses: actions/upload-artifact@v7
+      with:
+        name: python-package-distributions
+        path: dist/
+        if-no-files-found: error
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/SigProfilerExtractor
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish package distributions to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/SigProfilerExtractor
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -27,7 +27,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
-SigProfilerExtractor/version.py 
+SigProfilerExtractor/_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -139,4 +139,4 @@ test_vcf_output/
 test_matrix_*_output/
 SigProfilerExtractor/data/VCFInput/logs/
 SigProfilerExtractor/data/VCFInput/input/
-SigProfilerExtractor/data/VCFInput/output/
+SigProfilerExtractor/data/VCFInput/output/

SigProfilerExtractor/version.py

@@ -0,0 +1,27 @@
+try:
+    from ._version import version as _scm_version
+except Exception:
+    _scm_version = None
+
+try:
+    from importlib.metadata import PackageNotFoundError, version as _dist_version
+except Exception:  # pragma: no cover
+    PackageNotFoundError = Exception  # type: ignore
+
+    def _dist_version(_name: str) -> str:  # type: ignore
+        raise PackageNotFoundError()
+
+
+def _resolve_version() -> str:
+    if _scm_version is not None:
+        return _scm_version
+
+    try:
+        return _dist_version("SigProfilerExtractor")
+    except PackageNotFoundError:
+        return "0+unknown"
+
+
+short_version = _resolve_version()
+version = short_version
+Update = "Managed by setuptools_scm from git tags"

pyproject.toml

@@ -1,3 +1,9 @@
 [build-system]
-requires = ["setuptools>=61", "wheel", "build"]
+requires = ["setuptools>=69", "setuptools_scm[toml]>=8", "wheel"]
 build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+tag_regex = "^v(?P<version>.+)$"
+version_scheme = "guess-next-dev"
+local_scheme = "node-and-date"
+fallback_version = "0+unknown"

setup.py

@@ -1,40 +1,11 @@
-from setuptools import setup
-import shutil
-import os
-import sys
-import subprocess
+from pathlib import Path
 
-# remove the dist folder first if exists
-if os.path.exists("dist"):
-    shutil.rmtree("dist")
+from setuptools import find_namespace_packages, setup
 
-VERSION = "1.2.7"
 
+LONG_DESCRIPTION = Path("README.md").read_text(encoding="utf-8")
 
-with open("README.md") as f:
-    long_description = f.read()
-
-
-def write_version_py(filename="SigProfilerExtractor/version.py"):
-    # Copied from numpy setup.py
-    cnt = """
-# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
-short_version = '%(version)s'
-version = '%(version)s'
-Update = 'v1.2.7: Removed nimfa dependency and implemented NNDSVD directly for NumPy 2.0 compatibility'
-
-    """
-    fh = open(filename, "w")
-    fh.write(
-        cnt
-        % {
-            "version": VERSION,
-        }
-    )
-    fh.close()
-
-
-requirements = [
+INSTALL_REQUIRES = [
     "scipy>=1.6.3",
     "torch>=1.8.1",
     "numpy>=2.0.0",
@@ -47,61 +18,25 @@ def write_version_py(filename="SigProfilerExtractor/version.py"):
     "psutil>=5.6.1",
 ]
 
-operating_system = sys.platform
-print(operating_system)
-if operating_system in ["win32", "cygwin", "windows"]:
-    requirements.remove("matplotlib>=3.3.0")
-    requirements.remove("torch==1.5.1")
-    print("Trying to install pytorch!")
-    code = 1
-    try:
-        code = subprocess.call(
-            [
-                "pip",
-                "install",
-                "torch===1.5.1+cpu",
-                "-f",
-                "https://download.pytorch.org/whl/torch_stable.html",
-            ]
-        )
-        if code != 0:
-            raise Exception("Torch  instalation failed !")
-    except:
-        try:
-            code = subprocess.call(
-                [
-                    "pip3",
-                    "install",
-                    "torch===1.5.1+cpu",
-                    "-f",
-                    "https://download.pytorch.org/whl/torch_stable.html",
-                ]
-            )
-            if code != 0:
-                raise Exception("Torch instalation failed !")
-        except:
-            print(
-                "Failed to install pytorch, please install pytorch manually be following the simple instructions over at: https://pytorch.org/get-started/locally/"
-            )
-    if code == 0:
-        print(
-            "Successfully installed pytorch version! (If you need the GPU version, please install it manually, checkout the mindsdb docs and the pytroch docs if you need help)"
-        )
+VERSION_TEMPLATE = "version = '{version}'\n"
 
 
-write_version_py()
 setup(
     name="SigProfilerExtractor",
-    version=VERSION,
+    use_scm_version={
+        "write_to": "SigProfilerExtractor/_version.py",
+        "write_to_template": VERSION_TEMPLATE,
+        "fallback_version": "0+unknown",
+    },
     description="Extracts mutational signatures from mutational catalogues",
-    long_description=long_description,
-    long_description_content_type="text/markdown",  # This is important!
+    long_description=LONG_DESCRIPTION,
+    long_description_content_type="text/markdown",
     url="https://github.com/SigProfilerSuite/SigProfilerExtractor.git",
     author="S Mishu Ashiqul Islam",
     author_email="m0islam@ucsd.edu",
     license="UCSD",
-    packages=["SigProfilerExtractor"],
-    install_requires=requirements,
+    packages=find_namespace_packages(include=["SigProfilerExtractor*"]),
+    install_requires=INSTALL_REQUIRES,
     include_package_data=True,
     python_requires=">=3.9",
     entry_points={