sigma2 0.0.1__tar.gz

sigma2-0.0.1/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Build
+        run: |
+          pip install build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

sigma2-0.0.1/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+.venv/

sigma2-0.0.1/LICENSE

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+License TBD.
+
+Copyright (c) 2026 Jan P Hummel. All rights reserved.

sigma2-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: sigma2
+Version: 0.0.1
+Summary: Mutational signature analysis — package name reservation.
+Project-URL: Homepage, https://github.com/sigscape/sigma2
+Author: Jan Philipp Hummel
+License-File: LICENSE
+Classifier: Development Status :: 1 - Planning
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+
+# sigma2
+
+*Placeholder — package name reservation only.*

sigma2-0.0.1/README.md

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+# sigma2
+
+*Placeholder — package name reservation only.*

sigma2-0.0.1/environment.yml

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+name: sigma2
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip
+  - pip:
+      - build
+      - twine
+      - hatchling

sigma2-0.0.1/export.py

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+#!/usr/bin/env python3
+"""Export a Python/Rust(maturin)/R library repository into a single text file for LLM context."""
+import os
+import argparse
+from pathlib import Path
+
+INCLUDE_EXTENSIONS = {
+    # Python
+    ".py", ".pyi", ".pyx", ".pxd",
+    # Rust
+    ".rs", ".toml",
+    # R
+    ".R", ".r", ".Rmd", ".Rd", ".Rproj",
+    # Config / build
+    ".cfg", ".ini", ".inf", ".yaml", ".yml", ".json",
+    ".sh", ".bash", ".zsh",
+    ".sql", ".graphql",
+    # Docs / text
+    ".md", ".mdx", ".rst", ".txt",
+    # C/C++ (common in extensions)
+    ".c", ".h", ".cpp", ".hpp",
+    # Data schemas / fixtures
+    #".csv", ".tsv",
+    # Nix / Docker
+    ".nix", ".dockerfile",
+}
+
+INCLUDE_ROOT_FILES = {
+    # Python
+    "pyproject.toml", "setup.py", "setup.cfg",
+    "MANIFEST.in", "requirements.txt", "requirements-dev.txt",
+    "tox.ini", "noxfile.py", ".flake8",
+    "ruff.toml", ".ruff.toml", "mypy.ini", ".mypy.ini",
+    "pytest.ini", "conftest.py",
+    # Rust / maturin
+    "Cargo.toml", "Cargo.lock", "build.rs", "rust-toolchain.toml",
+    # R
+    "DESCRIPTION", "NAMESPACE", ".Rbuildignore", ".Rinstignore",
+    # General
+    "Makefile", "justfile", "Dockerfile", "docker-compose.yml",
+    ".env.example", ".gitignore", ".editorconfig",
+    "LICENSE", "LICENSE.md", "LICENSE.txt",
+    "README.md", "README.rst", "CHANGELOG.md", "CONTRIBUTING.md",
+}
+
+SKIP_DIRS = {
+    # Python
+    "__pycache__", ".mypy_cache", ".pytest_cache", ".ruff_cache",
+    ".tox", ".nox", ".eggs", "*.egg-info",
+    ".venv", "venv", "env", ".env",
+    "dist", "build", "sdist", "wheelhouse",
+    # Rust
+    "target",
+    # R
+    "renv", "packrat", "revdep",
+    # General
+    "node_modules", ".git", ".hg", ".svn",
+    ".cache", "coverage", "htmlcov",
+    ".ipynb_checkpoints", ".DS_Store",
+    "site", "_build", "docs/_build",
+}
+
+SKIP_FILES = {
+    "Cargo.lock", "package-lock.json", "yarn.lock",
+    "pnpm-lock.yaml", "bun.lockb",
+    ".DS_Store", "Thumbs.db",
+}
+
+MAX_FILE_SIZE = 900_000  # bytes
+
+
+def _matches_skip_dir(name: str) -> bool:
+    """Check against SKIP_DIRS, supporting glob-style wildcard entries like '*.egg-info'."""
+    if name in SKIP_DIRS:
+        return True
+    for pattern in SKIP_DIRS:
+        if pattern.startswith("*") and name.endswith(pattern[1:]):
+            return True
+    return False
+
+
+def should_include(path: Path, root: Path) -> bool:
+    if path.name in SKIP_FILES:
+        return False
+    try:
+        if path.stat().st_size > MAX_FILE_SIZE:
+            return False
+    except OSError:
+        return False
+    # Always include recognised root-level config files
+    if path.parent == root and path.name in INCLUDE_ROOT_FILES:
+        return True
+    # Include by extension
+    if path.suffix in INCLUDE_EXTENSIONS:
+        return True
+    # Include extensionless root files that are in the allow-list (e.g. DESCRIPTION, NAMESPACE, Makefile)
+    if path.parent == root and path.suffix == "" and path.name in INCLUDE_ROOT_FILES:
+        return True
+    return False
+
+
+def collect_files(root: Path) -> list[Path]:
+    files: list[Path] = []
+    for dirpath, dirnames, filenames in os.walk(root):
+        dirnames[:] = sorted(d for d in dirnames if not _matches_skip_dir(d))
+        for fname in sorted(filenames):
+            fpath = Path(dirpath) / fname
+            if should_include(fpath, root):
+                files.append(fpath)
+    return files
+
+
+def lang_hint(path: Path) -> str:
+    """Return a Markdown code-fence language hint."""
+    mapping = {
+        ".py": "python", ".pyi": "python", ".pyx": "cython", ".pxd": "cython",
+        ".rs": "rust", ".toml": "toml",
+        ".R": "r", ".r": "r", ".Rmd": "rmd", ".Rd": "rd",
+        ".c": "c", ".h": "c", ".cpp": "cpp", ".hpp": "cpp",
+        ".sh": "bash", ".bash": "bash", ".zsh": "zsh",
+        ".yaml": "yaml", ".yml": "yaml",
+        ".json": "json", ".md": "markdown", ".rst": "rst",
+        ".sql": "sql", ".cfg": "ini", ".ini": "ini", ".inf": "ini",
+        #".csv": "csv", ".tsv": "tsv",
+        ".nix": "nix", ".dockerfile": "dockerfile",
+    }
+    if path.name == "Makefile" or path.name == "justfile":
+        return "makefile"
+    if path.name == "Dockerfile":
+        return "dockerfile"
+    return mapping.get(path.suffix, path.suffix.lstrip("."))
+
+
+def export(root: Path, output: Path, tree_only: bool = False) -> None:
+    files = collect_files(root)
+
+    with open(output, "w", encoding="utf-8") as out:
+        out.write("# Project Structure\n\n```\n")
+        for f in files:
+            out.write(f"{f.relative_to(root)}\n")
+        out.write("```\n\n")
+
+        if tree_only:
+            print(f"Tree written to {output} ({len(files)} files)")
+            return
+
+        out.write("# File Contents\n\n")
+        for f in files:
+            rel = f.relative_to(root)
+            try:
+                content = f.read_text(encoding="utf-8")
+            except (UnicodeDecodeError, PermissionError):
+                continue
+            out.write(f"## {rel}\n\n```{lang_hint(f)}\n{content}\n```\n\n")
+
+        size_kb = output.stat().st_size / 1024
+        print(f"Exported {len(files)} files to {output} ({size_kb:.0f} KB)")
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description="Export a Python/Rust/R library repo into a single text file for LLM context."
+    )
+    parser.add_argument("repo", nargs="?", default=".", help="Path to repo root (default: .)")
+    parser.add_argument("-o", "--output", default="repo_export.txt", help="Output file (default: repo_export.txt)")
+    parser.add_argument("--tree-only", action="store_true", help="Export only the file tree, no contents")
+    args = parser.parse_args()
+
+    root = Path(args.repo).resolve()
+
+    # Heuristic: warn if nothing recognisable is found
+    markers = ("pyproject.toml", "setup.py", "Cargo.toml", "DESCRIPTION")
+    if not any((root / m).exists() for m in markers):
+        print(f"Warning: no pyproject.toml, setup.py, Cargo.toml, or DESCRIPTION found in {root}")
+
+    export(root, Path(args.output), args.tree_only)
+
+
+if __name__ == "__main__":
+    main()

sigma2-0.0.1/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "sigma2"
+version = "0.0.1"
+description = "Mutational signature analysis — package name reservation."
+readme = "README.md"
+requires-python = ">=3.9"
+authors = [
+    { name = "Jan Philipp Hummel" },
+]
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.urls]
+Homepage = "https://github.com/sigscape/sigma2"

sigma2-0.0.1/sigma2/__init__.py

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+"""sigma2 — mutational signature analysis (placeholder)."""
+
+__version__ = "0.0.1"