spires 0.2.2__tar.gz

spires-0.2.2/.envrc

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+# Auto-activate spipy14 conda environment
+# Requires direnv (https://direnv.net/)
+# Run 'direnv allow' after creating this file
+
+layout anaconda spipy14

spires-0.2.2/.gitattributes

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+spires/_version.py export-subst
+# LFS tracking for smaller test data files
+tests/data/lut_sentinel2b_b2to12_3um_dust.mat filter=lfs diff=lfs merge=lfs -text
+tests/data/sentinel_r_subset.nc filter=lfs diff=lfs merge=lfs -text
+tests/data/sentinel_r0_subset.nc filter=lfs diff=lfs merge=lfs -text
+tests/data/r0.tiff filter=lfs diff=lfs merge=lfs -text
+examples/r0.tiff filter=lfs diff=lfs merge=lfs -text
+# Legacy patterns (for backward compatibility)
+*.hdf filter=lfs diff=lfs merge=lfs -text

spires-0.2.2/.github/workflows/build.yml

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+name: Build and Test
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Full history for setuptools-scm
+        lfs: false  # Don't auto-pull LFS, we'll cache it
+
+    - name: Cache Git LFS files
+      uses: actions/cache@v4
+      id: lfs-cache
+      with:
+        path: .git/lfs
+        key: lfs-${{ hashFiles('.gitattributes') }}
+
+    - name: Download test data from Zenodo
+      run: |
+        # Download lookup tables from Zenodo (avoids LFS quota issues)
+        mkdir -p tests/data
+        echo "Downloading Sentinel-2 LUT from Zenodo..."
+
+        # Sentinel-2 LUT (70 MB) - required for test_swig.py and test_comparison.py
+        curl -L -o tests/data/lut_sentinel2b_b2to12_3um_dust.mat \
+          https://zenodo.org/records/18701286/files/lut_sentinel2b_b2to12_3um_dust.mat
+
+        echo "✓ Sentinel-2 LUT downloaded"
+        echo "Note: Original LUT_MODIS.mat not available on Zenodo (different structure)"
+        echo "      test_legacy.py will be skipped"
+
+    - name: Download large test data (optional)
+      run: |
+        # Optionally download full test imagery from Zenodo
+        # Uncomment to enable full-resolution image tests (adds ~15 minutes to CI time)
+        # curl -L -o tests/data/sentinel_r.nc https://zenodo.org/records/18704072/files/sentinel_r.nc
+        # curl -L -o tests/data/sentinel_r0.nc https://zenodo.org/records/18704072/files/sentinel_r0.nc
+        echo "Using LUTs only - full imagery available at:"
+        echo "  https://doi.org/10.5281/zenodo.18704072"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        channels: conda-forge
+        channel-priority: strict
+
+    - name: Install build dependencies from conda-forge
+      shell: bash -l {0}
+      run: |
+        conda install -c conda-forge swig gcc gxx nlopt
+
+    - name: Install Python dependencies
+      shell: bash -l {0}
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools-scm wheel
+        pip install '.[test]'
+
+    - name: Build SWIG extensions
+      shell: bash -l {0}
+      run: |
+        python setup.py build_ext --inplace
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        # Skip test_legacy.py - requires original LUT_MODIS.mat not on Zenodo
+        # The Zenodo dataset has lut_modis_b1to7_3um_dust.mat with different structure
+        pytest -v --ignore=tests/test_legacy.py
+
+    - name: Test import and version
+      shell: bash -l {0}
+      run: |
+        python -c "import spires; print(f'SpiPy version: {spires.__version__}')"

spires-0.2.2/.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches: [main, master]
+    tags:
+      - 'v*'
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:  # Allow manual triggering
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Full history for setuptools-scm versioning
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y pandoc
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r doc/requirements.txt
+
+    - name: Build documentation
+      run: |
+        cd doc
+        make html
+      env:
+        SPHINXOPTS: "--keep-going"  # Continue on errors, don't fail on warnings
+
+    - name: Upload documentation artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentation-html
+        path: doc/build/html/
+        retention-days: 30
+
+    # Optional: Deploy to GitHub Pages
+    # Uncomment the following steps to enable GitHub Pages deployment
+    # - name: Deploy to GitHub Pages
+    #   if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    #   uses: peaceiris/actions-gh-pages@v3
+    #   with:
+    #     github_token: ${{ secrets.GITHUB_TOKEN }}
+    #     publish_dir: ./doc/build/html
+    #     force_orphan: true

spires-0.2.2/.github/workflows/publish-pypi.yml

@@ -0,0 +1,120 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:  # Allow manual triggering for testing
+
+jobs:
+  build-wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        # Windows build requires nlopt which is challenging to build
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Full history for setuptools-scm
+
+    - name: Build wheels
+      uses: pypa/cibuildwheel@v2.17.0
+      env:
+        # Build for Python 3.9-3.14
+        CIBW_BUILD: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
+        # Skip 32-bit builds and musl
+        CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"
+        # Use manylinux_2_28 (AlmaLinux 8) instead of manylinux2014 (CentOS 7 EOL)
+        CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+        CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
+        # Install dependencies before building - build nlopt from source
+        # Install to /usr (not /usr/local) so auditwheel can find it
+        # Run ldconfig to update library cache for auditwheel
+        CIBW_BEFORE_BUILD_LINUX: >
+          yum install -y wget gcc-c++ cmake swig &&
+          wget https://github.com/stevengj/nlopt/archive/v2.7.1.tar.gz &&
+          tar -xzf v2.7.1.tar.gz &&
+          cd nlopt-2.7.1 &&
+          mkdir build && cd build &&
+          cmake .. -DCMAKE_INSTALL_PREFIX=/usr &&
+          make && make install &&
+          ldconfig &&
+          cd ../.. && rm -rf nlopt-2.7.1 v2.7.1.tar.gz
+        CIBW_BEFORE_BUILD_MACOS: brew install swig nlopt
+        # Bundle nlopt library into wheel for standalone distribution
+        CIBW_REPAIR_WHEEL_COMMAND_LINUX: "auditwheel repair -w {dest_dir} {wheel} --plat manylinux_2_28_x86_64"
+        CIBW_REPAIR_WHEEL_COMMAND_MACOS: "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
+        # Skip wheel test for now - SWIG module import needs investigation
+        # CIBW_TEST_COMMAND: python -c "import spires; print(spires.__version__)"
+        # CIBW_TEST_REQUIRES: pytest
+        # Build verbosely
+        CIBW_BUILD_VERBOSITY: 1
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.os }}
+        path: ./wheelhouse/*.whl
+
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Full history for setuptools-scm
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: '3.11'
+        channels: conda-forge
+        channel-priority: strict
+
+    - name: Install build dependencies
+      shell: bash -l {0}
+      run: |
+        conda install -c conda-forge swig gcc gxx nlopt
+        python -m pip install --upgrade pip
+        pip install build setuptools-scm
+
+    - name: Build sdist
+      shell: bash -l {0}
+      run: python -m build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: sdist
+        path: dist/*.tar.gz
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: [build-wheels, build-sdist]
+    runs-on: ubuntu-latest
+    # Only publish on tag push or manual workflow dispatch
+    if: github.event_name == 'release' || github.event_name == 'workflow_dispatch'
+    permissions:
+      id-token: write  # Required for trusted publishing
+
+    steps:
+    - name: Download all artifacts
+      uses: actions/download-artifact@v4
+      with:
+        path: dist
+        merge-multiple: true
+
+    - name: List distributions
+      run: ls -lh dist/
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        # Production PyPI (Trusted Publishing configured)
+        verbose: true

spires-0.2.2/.gitignore

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+__pycache__/
+*.ipynb_checkpoints*
+*.egg-info*
+/build
+/spires/spires_wrap.cpp
+/spires/_core.cpython*
+/spires/core.py
+/doc/build/
+/venv/
+/spires/.vscode/
+/dist/
+*.DS_Store
+*.aux.xml
+.idea/
+
+# Secrets and credentials (prevent accidental commits)
+*.env
+.env.*
+!.envrc
+*.pem
+*.key
+**/credentials*
+**/secrets*
+
+# Internal/OPSEC documents (not for public release)
+/OPSEC/
+
+# Large test data files (download from Zenodo or use subsets)
+tests/data/LUT_MODIS.mat
+tests/data/sentinel_r.nc
+tests/data/sentinel_r0.nc

spires-0.2.2/.gitlab-ci.yml

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+# GitLab CI configuration for SpiPy
+# Tests across Python 3.9-3.14 to match GitHub workflows
+
+image: continuumio/miniconda3
+
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+  GIT_LFS_SKIP_SMUDGE: "1"  # Skip LFS downloads to avoid quota issues
+
+cache:
+  paths:
+    - .cache/pip
+
+# Test matrix across Python versions 3.9-3.14
+.test_template: &test_template
+  script:
+    - python --version
+    - conda create -y -n buildenv python=$PYTHON_VERSION
+    - source activate buildenv
+    - conda install -c conda-forge nlopt swig gxx gcc make
+    - pip install --editable ".[test]"
+    - python -c "import spires; print('Version:', spires.__version__)"
+    # Download test data from Zenodo (avoids LFS quota issues)
+    - mkdir -p tests/data
+    - echo "Downloading Sentinel-2 LUT from Zenodo..."
+    - wget -O tests/data/lut_sentinel2b_b2to12_3um_dust.mat https://zenodo.org/records/18701286/files/lut_sentinel2b_b2to12_3um_dust.mat
+    - echo "✓ Sentinel-2 LUT downloaded ($(du -h tests/data/lut_sentinel2b_b2to12_3um_dust.mat | cut -f1))"
+    # Run tests, skipping test_legacy.py which needs LUT_MODIS.mat (not on Zenodo)
+    - pytest --doctest-modules --ignore=tests/test_legacy.py
+
+test:python3.9:
+  <<: *test_template
+  variables:
+    PYTHON_VERSION: "3.9"
+
+test:python3.10:
+  <<: *test_template
+  variables:
+    PYTHON_VERSION: "3.10"
+
+test:python3.11:
+  <<: *test_template
+  variables:
+    PYTHON_VERSION: "3.11"
+
+test:python3.12:
+  <<: *test_template
+  variables:
+    PYTHON_VERSION: "3.12"
+
+test:python3.13:
+  <<: *test_template
+  variables:
+    PYTHON_VERSION: "3.13"
+
+test:python3.14:
+  <<: *test_template
+  variables:
+    PYTHON_VERSION: "3.14"
+
+build:
+  before_script:
+    - conda create -y -n buildenv python=3.11
+    - source activate buildenv
+    - conda install -c conda-forge nlopt swig gxx gcc make
+    - pip install .
+  script:
+    - python setup.py build_ext --inplace --verbose
+  artifacts:
+    paths:
+      - build/*
+
+docs:
+  before_script:
+    - conda create -y -n buildenv python=3.11
+    - source activate buildenv
+    - conda install -c conda-forge nlopt swig gxx gcc make
+    - pip install .
+  script:
+    - pip install --editable ".[docs]"
+    - cd doc
+    - make html
+    - mv build/html/ ../public/
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+  allow_failure: true  # Don't block pipeline if docs fail
+
+deploy:
+  stage: deploy
+  script: echo "PyPI deployment handled by GitHub Actions"
+  environment: production
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+  when: manual

spires-0.2.2/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# Build documentation in the doc/ directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+  fail_on_warning: false
+
+# Build all formats (HTML, PDF, ePub)
+formats:
+  - pdf
+  - epub
+
+# Python version and build environment
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  apt_packages:
+    - pandoc
+  jobs:
+    post_checkout:
+      # Fetch full git history for setuptools_scm version detection
+      - git fetch --unshallow || true
+
+# Python dependencies
+# Note: We skip installing the package itself to avoid building C++ extensions
+# Sphinx will use autodoc_mock_imports for the C++ modules
+python:
+  install:
+    - requirements: doc/requirements.txt

spires-0.2.2/.zenodo.json

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+{
+  "title": "SpiPy: Python implementation of SPIRES snow property inversion",
+  "description": "SpiPy is a Python implementation of SPIRES (SPectral Inversion of REflectance from Snow), a spectral unmixing algorithm for analyzing snow reflectance data from satellite imagery. It retrieves snow properties (grain size, dust concentration, fractional snow-covered area) using lookup tables generated from Mie-scattering theory. This implementation features a hybrid Python/C++ architecture achieving 3000x speedup over pure Python implementations.",
+  "creators": [
+    {
+      "name": "Bair, Ned",
+      "affiliation": "University of California, Santa Barbara",
+      "orcid": "0000-0002-7654-3210"
+    },
+    {
+      "name": "Griessbaum, Niklas",
+      "affiliation": "Leidos, Inc.",
+      "orcid": "0000-0000-0000-0000"
+    }
+  ],
+  "license": "MIT",
+  "keywords": [
+    "remote sensing",
+    "snow properties",
+    "spectral unmixing",
+    "satellite imagery",
+    "MODIS",
+    "Sentinel-2",
+    "Landsat",
+    "Python",
+    "C++"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "10.1109/TGRS.2020.3040328",
+      "relation": "isSupplementTo",
+      "scheme": "doi"
+    }
+  ],
+  "grants": [
+    {
+      "id": "W913E523C0002"
+    }
+  ]
+}

spires-0.2.2/CITATION.cff

@@ -0,0 +1,49 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite both the software and the algorithm paper below."
+title: "SpiPy: Python implementation of SPIRES snow property inversion"
+authors:
+  - family-names: Bair
+    given-names: Ned
+    email: edwardbair@ucsb.edu
+    affiliation: "University of California, Santa Barbara"
+    orcid: "https://orcid.org/0000-0002-7654-3210"  # Update with actual ORCID if available
+  - family-names: Griessbaum
+    given-names: Niklas
+    affiliation: "Leidos, Inc."
+    orcid: "https://orcid.org/0000-0000-0000-0000"  # Update with actual ORCID if available
+version: 0.2.0
+date-released: 2024-11-06
+repository-code: "https://github.com/edwardbair/SpiPy"
+url: "https://github.com/edwardbair/SpiPy"
+license: MIT  # Update if different
+keywords:
+  - remote sensing
+  - snow properties
+  - spectral unmixing
+  - satellite imagery
+  - MODIS
+  - Sentinel-2
+  - Landsat
+abstract: >
+  SpiPy is a Python implementation of SPIRES (SPectral Inversion of REflectance from Snow),
+  a spectral unmixing algorithm for analyzing snow reflectance data from satellite imagery.
+  It retrieves snow properties (grain size, dust concentration, fractional snow-covered area)
+  using lookup tables generated from Mie-scattering theory. This implementation features a
+  hybrid Python/C++ architecture achieving 3000x speedup over pure Python implementations.
+preferred-citation:
+  type: article
+  title: "Snow Property Inversion From Remote Sensing (SPIReS): A Generalized Multispectral Unmixing Approach With Examples From MODIS and Landsat 8 OLI"
+  authors:
+    - family-names: Bair
+      given-names: E. H.
+    - family-names: Stillinger
+      given-names: T.
+    - family-names: Dozier
+      given-names: J.
+  journal: "IEEE Transactions on Geoscience and Remote Sensing"
+  volume: 59
+  issue: 9
+  start: 7270
+  end: 7284
+  year: 2021
+  doi: 10.1109/TGRS.2020.3040328