torchfits 0.1.1__tar.gz

torchfits-0.1.1/.gitattributes

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+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

torchfits-0.1.1/.github/workflows/README.md

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+# GitHub Workflows
+
+This directory contains the GitHub Actions CI/CD workflows for torchfits.
+
+## Active Workflows
+
+### `ci.yml` - Comprehensive CI Pipeline
+**Triggers:** Push to main/develop branches, Pull Requests, Releases  
+**Purpose:** Complete build, test, quality assurance, and deployment pipeline
+
+**Jobs:**
+1. **Code Quality** - Code formatting and linting (Python 3.12)
+   - black (formatting)
+   - ruff (linting)
+   
+2. **Build & Test** - Multi-version builds and tests
+   - **OS:** Ubuntu
+   - **Python:** 3.11, 3.12
+   - **System deps:** cfitsio, wcslib
+   - **Tests:** Full pytest suite
+   
+3. **Memory Safety** - Memory leak detection (placeholder for valgrind)
+
+4. **Performance Benchmarks** - Performance regression testing (placeholder)
+
+5. **Documentation** - Documentation build verification (placeholder)
+
+6. **Publish** - Automated PyPI publishing on GitHub releases
+
+**Key Features:**
+- C++ extension compilation with cfitsio/wcslib
+- Cross-Python version testing
+- Code quality enforcement
+- Automated PyPI releases
+
+## CI Configuration
+
+- **Python Versions:** 3.11, 3.12
+- **Code Quality Tools:** black, ruff
+- **Build Dependencies:** cfitsio, wcslib (installed via apt)
+- **PyPI Publishing:** Requires `PYPI_API_TOKEN` repository secret
+
+## Setup for PyPI Publishing
+
+Add the following secret to your GitHub repository settings:
+- `PYPI_API_TOKEN`: Your PyPI API token
+
+The workflow automatically publishes to PyPI when you create a GitHub release.

torchfits-0.1.1/.github/workflows/ci.yml

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+name: Comprehensive CI
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+  release:
+    types: [published]
+
+env:
+  FORCE_COLOR: 1
+
+jobs:
+  code-quality:
+    name: Code Quality
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    
+    - name: Install code quality tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install black ruff
+    
+    - name: Check formatting with black
+      run: black --check --diff src/ tests/ examples/ benchmarks/
+    
+    - name: Lint with ruff
+      run: ruff check --output-format=github .
+
+  build-test:
+    name: Build & Test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install system dependencies (Ubuntu)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcfitsio-dev wcslib-dev build-essential
+    
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+        pip install torch --index-url https://download.pytorch.org/whl/cpu
+        pip install numpy astropy fitsio pytest nanobind scikit-build-core
+        pip install pytorch-frame psutil
+    
+    - name: Build package
+      run: |
+        pip install -e .
+    
+    - name: Run full test suite
+      run: |
+        pytest tests/ -v --tb=short
+
+  memory-safety:
+    name: Memory Leak Detection
+    runs-on: ubuntu-latest
+    needs: build-test
+    
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y valgrind libcfitsio-dev wcslib-dev build-essential
+    
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+        pip install torch --index-url https://download.pytorch.org/whl/cpu
+        pip install numpy astropy fitsio pytest pybind11
+        pip install -e .
+    
+    - name: Run memory leak tests
+      run: |
+        echo "Memory leak testing would run here with valgrind"
+        echo "Skipping for initial release"
+
+  performance-benchmark:
+    name: Performance Benchmarks
+    runs-on: ubuntu-latest
+    needs: build-test
+    
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcfitsio-dev wcslib-dev build-essential
+    
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+        pip install torch --index-url https://download.pytorch.org/whl/cpu
+        pip install numpy astropy fitsio pytest pybind11
+        pip install -e .
+    
+    - name: Run performance benchmarks
+      run: |
+        echo "Performance benchmarks would run here"
+        echo "Skipping for now - benchmark files need to be verified"
+    
+    - name: Generate performance report
+      run: |
+        python -c "
+        import torchfits
+        print('=== Performance Summary ===')
+        print('torchfits successfully built and tested')
+        print('See test output above for detailed benchmarks')
+        "
+
+  documentation:
+    name: Documentation Build
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install sphinx sphinx-rtd-theme
+    
+    - name: Build documentation
+      run: |
+        # Add when docs/ directory exists
+        echo "Documentation build would go here"
+        echo "README.md exists: $(ls -la README.md)"
+
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs: [code-quality, build-test, memory-safety]
+    if: github.event_name == 'release' && github.event.action == 'published'
+    
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+    
+    - name: Build package
+      run: |
+        python -m build
+    
+    - name: Publish to PyPI
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        twine upload dist/*

torchfits-0.1.1/.github/workflows/memory_tests.yml.backup

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+name: Memory Leak Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  basic-tests:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest torch numpy astropy pybind11
+        
+    - name: Test installation
+      run: |
+        pip install -e .
+        
+    - name: Run basic functionality tests
+      run: |
+        python -c "
+        import torchfits
+        import torch
+        print('TorchFits imported successfully')
+        
+        # Test basic file reading
+        data = torchfits.read('examples/basic_example.fits')
+        print(f'Read data shape: {data.shape}')
+        
+        # Test table reading  
+        table_data = torchfits.read('examples/table_example.fits', hdu=1)
+        print(f'Table has {len(table_data)} columns')
+        
+        print('Basic tests passed!')
+        "
+
+  memory-tests:
+    runs-on: ubuntu-latest
+    needs: basic-tests
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y valgrind build-essential
+    
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest torch numpy astropy pybind11
+        pip install -e .
+    
+    
+    - name: Run memory tests
+      run: |
+        # Create memory test script
+        cat > memory_test.py << 'EOF'
+        import torchfits
+        import torch
+        import os
+        
+        # Test basic file reading with existing example file
+        print("Testing basic FITS reading...")
+        data = torchfits.read("examples/basic_example.fits")
+        print(f"Read data shape: {data.shape}")
+        
+        # Test table reading
+        print("Testing table reading...")
+        table_data = torchfits.read("examples/table_example.fits", hdu=1)
+        print(f"Table columns: {list(table_data.keys())}")
+        
+        # Test header reading
+        print("Testing header reading...")
+        header = torchfits.get_header("examples/basic_example.fits")
+        print(f"Header keys: {len(header)} entries")
+        
+        # Test WCS if header has WCS info
+        try:
+            coords = torch.tensor([[10.0, 10.0]], dtype=torch.float64)
+            if any(key.startswith('CTYPE') for key in header.keys()):
+                world_coords = torchfits.pixel_to_world(coords, header)
+                pixel_coords = torchfits.world_to_pixel(world_coords, header)
+                print("WCS transformations successful")
+            else:
+                print("No WCS info in header, skipping WCS tests")
+        except Exception as e:
+            print(f"WCS test failed (expected for basic example): {e}")
+        
+        # Test cache clearing
+        try:
+            torchfits._clear_cache()
+            print("Cache cleared successfully")
+        except Exception as e:
+            print(f"Cache clearing failed: {e}")
+            
+        print("All tests completed successfully!")
+        EOF
+        
+        # Run with valgrind to check for memory leaks
+        valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --error-exitcode=1 python memory_test.py

torchfits-0.1.1/.gitignore

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+# Ignore environment/lock artifacts
+pixi.lock
+# .gitignore for torchfits
+
+# General Python ignores
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+*.egg-info/
+*.egg
+build/
+dist/
+
+# C++ build artifacts
+*.o
+*.os
+*.obj
+*.dll
+*.lib
+*.a
+*.exe
+
+# Compiled dynamic libraries
+*.so
+*.so.*
+*.dylib
+*.pyd
+
+# Jupyter Notebooks
+.ipynb_checkpoints/
+
+# IDE and Editor files
+.vscode/
+*~
+\#*\#
+.\#*
+.dir-locals.el
+*.swp
+*.swo
+*.swn
+*.swx
+*.un~
+[._]*.s[a-v][a-z]
+[._]*.sw[a-z]
+Session.vim
+tags
+
+# OS files
+.DS_Store
+Thumbs.db
+Desktop.ini
+
+# External dependencies (built locally)
+fitsio/
+
+# Distribution / packaging
+.Python
+develop-eggs/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+.installed.cfg
+MANIFEST
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Testing and coverage
+.coverage
+.pytest_cache/
+htmlcov/
+.tox/
+
+# Test data and debugging files
+test_data/
+debug_*
+check_*
+test_*.py  # Exclude ad-hoc test files (but not tests/ directory)
+!/tests/test_*.py  # But keep official test files
+
+
+# pixi environments
+.pixi/
+
+# Temporary and cache files
+.cache/
+*.tmp
+*.temp
+
+# Build artifacts and compiled extensions
+*.cpython-*.so
+*.cpython-*.pyd
+
+# Log files
+*.log
+
+# Backup files
+*~
+*.bak
+*.orig
+
+# CMake build files
+CMakeCache.txt
+CMakeFiles/
+cmake_install.cmake
+Makefile
+
+# Additional Python artifacts
+*.pyi
+.mypy_cache/
+
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
+# Benchmark outputs
+benchmark_results/
+torchfits_exhaustive_*/
+*.csv
+*.png
+*.pdf
+*.json
+*.fits
+
+# Example-generated files
+examples/data_*/
+examples/mnist_data/
+examples/sdss_data/
+examples/test_examples.py

torchfits-0.1.1/.gitmodules

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+[submodule "extern/cfitsio"]
+	path = extern/cfitsio
+	url = https://github.com/HEASARC/cfitsio.git

torchfits-0.1.1/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+        language_version: python3
+        args: [--line-length=88]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: [--profile=black]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: [--max-line-length=88, --extend-ignore=E203,W503]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        additional_dependencies: [torch, numpy]
+        args: [--ignore-missing-imports]