verus 0.1.1__tar.gz

verus-0.1.1/.github/workflows/static.yml

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+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy Documentation to Pages
+
+on:
+    # Runs on pushes targeting the default branch
+    push:
+        branches: ["main"]
+
+    # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+    contents: read
+    pages: write
+    id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+    group: "pages"
+    cancel-in-progress: false
+
+jobs:
+    # Single deploy job since we're just deploying
+    deploy:
+        environment:
+            name: github-pages
+            url: ${{ steps.deployment.outputs.page_url }}
+        runs-on: ubuntu-latest
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v4
+
+            - name: Set up Python
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.10"
+
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  # Install all documentation dependencies
+                  pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints nbsphinx
+                  # If you have a requirements file, also install it
+                  if [ -f requirements.txt ]; then
+                    pip install -r requirements.txt
+                  fi
+                  # Display installed packages for debugging
+                  pip freeze
+
+            - name: Build documentation
+              run: |
+                  mkdir -p docs/source
+
+                  # Check and modify existing conf.py if needed
+                  if [ -f docs/source/conf.py ]; then
+                    # Backup the original file
+                    cp docs/source/conf.py docs/source/conf.py.bak
+                    
+                    # Check for problematic extensions and create a simplified version if found
+                    if grep -q "sphinx_autodoc_typehints" docs/source/conf.py; then
+                      echo "Fixing conf.py by removing problematic extensions"
+                      # Create a simplified conf.py
+                      echo 'project = "VERUS"' > docs/source/conf.py
+                      echo 'copyright = "2025, LES2 Team"' >> docs/source/conf.py
+                      echo 'author = "oão Carlos N. Bittencourt"' >> docs/source/conf.py
+                      echo 'extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]' >> docs/source/conf.py
+                      echo 'html_theme = "sphinx_rtd_theme"' >> docs/source/conf.py
+                    fi
+                  else
+                    # Create minimal conf.py if it doesn't exist
+                    echo 'project = "VERUS"' > docs/source/conf.py
+                    echo 'copyright = "2025, LES2 Team"' >> docs/source/conf.py
+                    echo 'author = "João Carlos N. Bittencourt"' >> docs/source/conf.py
+                    echo 'extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]' >> docs/source/conf.py
+                    echo 'html_theme = "sphinx_rtd_theme"' >> docs/source/conf.py
+                  fi
+
+                  # Create minimal index.rst if it doesn't exist
+                  if [ ! -f docs/source/index.rst ]; then
+                    echo 'VERUS Documentation' > docs/source/index.rst
+                    echo '===================' >> docs/source/index.rst
+                    echo '' >> docs/source/index.rst
+                    echo 'Welcome to VERUS documentation.' >> docs/source/index.rst
+                    echo '' >> docs/source/index.rst
+                    echo 'Contents' >> docs/source/index.rst
+                    echo '========' >> docs/source/index.rst
+                    echo '' >> docs/source/index.rst
+                    echo '.. toctree::' >> docs/source/index.rst
+                    echo '   :maxdepth: 2' >> docs/source/index.rst
+                    echo '' >> docs/source/index.rst
+                  fi
+
+                  # Display the content of conf.py for debugging
+                  echo "Content of conf.py:"
+                  cat docs/source/conf.py
+
+                  # Build the documentation
+                  cd docs
+                  mkdir -p _build/html
+                  sphinx-build -b html source _build/html
+
+                  # Create .nojekyll file to prevent GitHub from using Jekyll
+                  touch _build/html/.nojekyll
+
+            - name: Setup Pages
+              uses: actions/configure-pages@v4
+
+            - name: Upload artifact
+              uses: actions/upload-pages-artifact@v3
+              with:
+                  # Upload the sphinx build directory
+                  path: "docs/_build/html"
+
+            - name: Deploy to GitHub Pages
+              id: deployment
+              uses: actions/deploy-pages@v4

verus-0.1.1/.gitignore

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+# OS
+.DS_store
+*cache
+
+# Result files
+*.html
+*.geojson
+*.csv
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyPI configuration file
+.pypirc

verus-0.1.1/.readthedocs.yml

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+version: 2
+
+sphinx:
+    configuration: docs/source/conf.py
+
+formats:
+    - pdf
+    - epub
+
+python:
+    version: "3.8"
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - docs

verus-0.1.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to the VERUS project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+## [0.1.1] - 2025-06-10
+
+### Added
+
+- Support for loading custom region boundaries from GeoJSON files in HexagonGridGenerator
+
+### Improved
+
+- Updated documentation with examples of GeoJSON file usage
+- Enhanced hexagon grid generator with file validation and error handling
+
+## [0.1.0] - 2025-03-13
+
+### Added
+
+-   Initial release of VERUS framework
+-   Core functionality for Points of Temporal Influence (PoTIs)
+-   Vulnerability zone calculation with hexagonal grid support
+-   Time window-based analysis
+-   Data extraction from OpenStreetMap
+-   Basic visualization tools
+-   Gaussian and inverse weighted distance methods for vulnerability calculation
+-   Clustering pipeline using OPTICS and KMeans algorithms
+
+### Known Issues
+
+-   Limited support for time windows
+-   Main function can expose more parameters for experimentation
+-   PoI filtering to select really influential points is not yet implemented
+
+### Future Improvements
+
+-   Implement a CLI for easier usage of the framework

verus-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 João Carlos N. Bittencourt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

verus-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: verus
+Version: 0.1.1
+Summary: A scientific tool to extract and analyze urban spatiotemporal vulnerability.
+Author-email: "João Carlos N. Bittencourt" <joaocarlos@ufrb.edu.br>
+Maintainer: LES2 FEUP faculty memebers
+License: MIT License
+Project-URL: Homepage, https://github.com/les2feup/verus
+Project-URL: Bug Tracker, https://github.com/les2feup/verus/issues
+Project-URL: Documentation, https://les2feup.github.io/verus/
+Project-URL: Code Repository, https://github.com/les2feup/verus
+Keywords: GIS,Vulnerability,Assessment,OpenStreetMap,Clustering
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Scientific/Engineering :: GIS
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: geopandas>=0.10.0
+Requires-Dist: shapely>=1.8.0
+Requires-Dist: pyproj>=3.0.0
+Requires-Dist: osmnx>=1.1.0
+Requires-Dist: rtree>=1.0.0
+Requires-Dist: folium>=0.12.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: plotly>=5.3.0
+Requires-Dist: scikit-learn>=1.0.0
+Requires-Dist: colorama>=0.4.4
+Requires-Dist: tqdm>=4.62.0
+Requires-Dist: requests>=2.26.0
+Requires-Dist: haversine>=2.3.0
+Requires-Dist: branca>=0.4.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.2.5; extra == "dev"
+Requires-Dist: black>=22.1.0; extra == "dev"
+Requires-Dist: isort>=5.10.1; extra == "dev"
+Requires-Dist: flake8>=4.0.1; extra == "dev"
+Requires-Dist: mypy>=0.910; extra == "dev"
+Requires-Dist: coverage>=6.2; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.3.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.0.0; extra == "docs"
+Requires-Dist: nbsphinx>=0.8.8; extra == "docs"
+Provides-Extra: viz
+Requires-Dist: seaborn>=0.11.2; extra == "viz"
+Requires-Dist: plotly>=5.3.0; extra == "viz"
+Dynamic: license-file
+
+![LES2 Logo](./src/figures/les2banner.png)
+
+# VERUS
+
+_Vulnerability Evaluation for Resilient Urban Systems_
+
+![Python](https://img.shields.io/badge/Python-3.8%2B-blue?style=for-the-badge&logo=python)
+![Jupyter Notebook](https://img.shields.io/badge/Jupyter-Notebook-orange?style=for-the-badge&logo=jupyter)
+![OSMnx](https://img.shields.io/badge/OSMnx-1.1.1-blue?style=for-the-badge&logo=openstreetmap)
+![Folium](https://img.shields.io/badge/Folium-0.12.1-green?style=for-the-badge&logo=folium)
+[![Documentation](https://img.shields.io/badge/docs-latest-brightgreen?style=for-the-badge)](https://les2feup.github.io/verus/)
+
+## Description
+
+VERUS (Vulnerability Evaluation for Resilient Urban Systems) is a Python library for extracting points of interest from OpenStreetMap, clustering them based on spatial proximity and time-based vulnerability indices, and analyzing urban vulnerability patterns.
+
+## Documentation
+
+Comprehensive documentation is available at [https://les2feup.github.io/verus/](https://les2feup.github.io/verus/)
+
+## Publications
+
+-   Bittencourt, J. C. N., Costa, D. G., Portugal, P., & Vasques, F. (2024). A data-driven clustering approach for assessing spatiotemporal vulnerability to urban emergencies. Sustainable Cities and Society, 108, 105477. <https://doi.org/10.1016/j.scs.2024.105477>
+
+## Installation
+
+```bash
+pip install verus
+```
+
+## Reproducing Results
+
+To reproduce the results from the latest article, run the following Jupyter Notebooks:
+
+-   [Porto, Portugal](./notebooks/experiments/01-Porto.ipynb)
+-   [Lisbon, Portugal](./notebooks/experiments/02-Lisbon.ipynb)
+-   [Paris, France](./notebooks/experiments/03-Paris.ipynb)
+
+## Basic Usage
+
+```python
+from verus import VERUS
+from verus.data import DataExtractor, TimeWindowGenerator
+from verus.grid import HexagonGridGenerator
+
+# Extract default urban data from OpenStreetMap
+extractor = DataExtractor(region="Porto, Portugal")
+poi_data = extractor.run()
+
+# Define default time-based vulnerability scenarios
+twg = TimeWindowGenerator(reference_date="2023-11-06")
+time_windows = twg.generate_from_schedule()
+
+# Generate analysis grid
+grid = HexagonGridGenerator(region="Porto, Portugal", edge_length=250)
+hex_grid = grid.run()
+
+# Run vulnerability assessment
+assessor = VERUS(place_name="Porto")
+
+# Load extracted data
+assessor.load(
+    potis_df=poi_data,
+    time_windows_dict=time_windows,
+    zones_gdf=hex_grid,
+)
+
+# Perform assessment and get results
+evaluation_time = tw_gen.to_unix_epoch("2023-11-06 17:30:00")
+results = assessor.run(evaluation_time=evaluation_time)
+
+# Visualize results
+map_obj = assessor.visualize()
+
+# Save results to file
+assessor.save("./results/porto/")
+```
+
+## Features
+
+-   Extract points of interest from OpenStreetMap for any city
+-   Create hexagonal grid systems for spatial analysis
+-   Implement OPTICS density-based clustering for identifying urban patterns
+-   Apply K-means clustering with Haversine distance for geographic data
+-   Generate time-dependent vulnerability assessments
+-   Create interactive maps for visualization with folium
+-   Export results in various formats (GeoJSON, CSV, HTML)
+
+## Contributions
+
+Contributions are welcome! To contribute:
+
+1. Fork the repository
+2. Create a feature branch: `git checkout -b feature/amazing-feature`
+3. Commit changes: `git commit -m 'Add amazing feature'`
+4. Push to branch: `git push origin feature/amazing-feature`
+5. Open a pull request
+
+Please make sure to update tests and documentation as appropriate.
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Acknowledgments
+
+-   Research developed at the Laboratory of Emergent Smart Systems (LES2) at the Faculty of Engineering of University of Porto
+-   This work was supported by the Associate Laboratory Advanced Production and Intelligent Systems – ARISE LA/P/0112/2020 (DOI 10.54499/LA/P/0112/2020), by the Base Funding (UIDB/00147/2020) and Programmatic Funding (UIDP/00147/2020) of the R\&D Unit Center for Systems and Technologies -- SYSTEC, and by the Fundação para a Ciência e a Tecnologia (FCT) through the PhD scholarship (2024.02446.BD).

verus-0.1.1/README.md

@@ -0,0 +1,108 @@
+![LES2 Logo](./src/figures/les2banner.png)
+
+# VERUS
+
+_Vulnerability Evaluation for Resilient Urban Systems_
+
+![Python](https://img.shields.io/badge/Python-3.8%2B-blue?style=for-the-badge&logo=python)
+![Jupyter Notebook](https://img.shields.io/badge/Jupyter-Notebook-orange?style=for-the-badge&logo=jupyter)
+![OSMnx](https://img.shields.io/badge/OSMnx-1.1.1-blue?style=for-the-badge&logo=openstreetmap)
+![Folium](https://img.shields.io/badge/Folium-0.12.1-green?style=for-the-badge&logo=folium)
+[![Documentation](https://img.shields.io/badge/docs-latest-brightgreen?style=for-the-badge)](https://les2feup.github.io/verus/)
+
+## Description
+
+VERUS (Vulnerability Evaluation for Resilient Urban Systems) is a Python library for extracting points of interest from OpenStreetMap, clustering them based on spatial proximity and time-based vulnerability indices, and analyzing urban vulnerability patterns.
+
+## Documentation
+
+Comprehensive documentation is available at [https://les2feup.github.io/verus/](https://les2feup.github.io/verus/)
+
+## Publications
+
+-   Bittencourt, J. C. N., Costa, D. G., Portugal, P., & Vasques, F. (2024). A data-driven clustering approach for assessing spatiotemporal vulnerability to urban emergencies. Sustainable Cities and Society, 108, 105477. <https://doi.org/10.1016/j.scs.2024.105477>
+
+## Installation
+
+```bash
+pip install verus
+```
+
+## Reproducing Results
+
+To reproduce the results from the latest article, run the following Jupyter Notebooks:
+
+-   [Porto, Portugal](./notebooks/experiments/01-Porto.ipynb)
+-   [Lisbon, Portugal](./notebooks/experiments/02-Lisbon.ipynb)
+-   [Paris, France](./notebooks/experiments/03-Paris.ipynb)
+
+## Basic Usage
+
+```python
+from verus import VERUS
+from verus.data import DataExtractor, TimeWindowGenerator
+from verus.grid import HexagonGridGenerator
+
+# Extract default urban data from OpenStreetMap
+extractor = DataExtractor(region="Porto, Portugal")
+poi_data = extractor.run()
+
+# Define default time-based vulnerability scenarios
+twg = TimeWindowGenerator(reference_date="2023-11-06")
+time_windows = twg.generate_from_schedule()
+
+# Generate analysis grid
+grid = HexagonGridGenerator(region="Porto, Portugal", edge_length=250)
+hex_grid = grid.run()
+
+# Run vulnerability assessment
+assessor = VERUS(place_name="Porto")
+
+# Load extracted data
+assessor.load(
+    potis_df=poi_data,
+    time_windows_dict=time_windows,
+    zones_gdf=hex_grid,
+)
+
+# Perform assessment and get results
+evaluation_time = tw_gen.to_unix_epoch("2023-11-06 17:30:00")
+results = assessor.run(evaluation_time=evaluation_time)
+
+# Visualize results
+map_obj = assessor.visualize()
+
+# Save results to file
+assessor.save("./results/porto/")
+```
+
+## Features
+
+-   Extract points of interest from OpenStreetMap for any city
+-   Create hexagonal grid systems for spatial analysis
+-   Implement OPTICS density-based clustering for identifying urban patterns
+-   Apply K-means clustering with Haversine distance for geographic data
+-   Generate time-dependent vulnerability assessments
+-   Create interactive maps for visualization with folium
+-   Export results in various formats (GeoJSON, CSV, HTML)
+
+## Contributions
+
+Contributions are welcome! To contribute:
+
+1. Fork the repository
+2. Create a feature branch: `git checkout -b feature/amazing-feature`
+3. Commit changes: `git commit -m 'Add amazing feature'`
+4. Push to branch: `git push origin feature/amazing-feature`
+5. Open a pull request
+
+Please make sure to update tests and documentation as appropriate.
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Acknowledgments
+
+-   Research developed at the Laboratory of Emergent Smart Systems (LES2) at the Faculty of Engineering of University of Porto
+-   This work was supported by the Associate Laboratory Advanced Production and Intelligent Systems – ARISE LA/P/0112/2020 (DOI 10.54499/LA/P/0112/2020), by the Base Funding (UIDB/00147/2020) and Programmatic Funding (UIDP/00147/2020) of the R\&D Unit Center for Systems and Technologies -- SYSTEC, and by the Fundação para a Ciência e a Tecnologia (FCT) through the PhD scholarship (2024.02446.BD).