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Wildlife","monthly_downloads":208,"total_dependent_repos":0,"total_dependent_packages":2,"readme":"# Circuitscape\n\n[![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://docs.circuitscape.org/Circuitscape.jl/latest/)\n[![Build Status](https://github.com/Circuitscape/Circuitscape.jl/workflows/CI/badge.svg)](https://github.com/Circuitscape/Circuitscape.jl/actions?query=workflow%3ACI)\n[![codecov.io](https://codecov.io/github/Circuitscape/Circuitscape.jl/coverage.svg?branch=master)](https://codecov.io/github/Circuitscape/Circuitscape.jl?branch=master)\n\nCircuitscape is an open-source program that uses circuit theory to model connectivity\nin heterogeneous landscapes. Its most common applications include modeling movement and gene flow\nof plants and animals, as well as identifying areas important for connectivity conservation.\n\nCircuitscape is written in [Julia](https://julialang.org) for high performance and scalability.\nMore detail about the implementation can be found in the\n[JuliaCon paper](https://proceedings.juliacon.org/papers/10.21105/jcon.00058).\n\n\u003e [!NOTE]\n\u003e Circuitscape.jl requires [Julia v1.11](https://julialang.org/downloads/) or later.\n\n## Installation\n\n1. [Install Julia](https://julialang.org/downloads/).\n\n2. At the Julia prompt, install Circuitscape:\n\n```julia\njulia\u003e using Pkg\njulia\u003e Pkg.add(\"Circuitscape\")\n```\n\nTo install the latest development version:\n\n```julia\njulia\u003e Pkg.add(PackageSpec(name=\"Circuitscape\", rev=\"master\"))\n```\n\nRun the test suite with:\n\n```julia\njulia\u003e Pkg.test(\"Circuitscape\")\n```\n\n## Usage\n\nCircuitscape jobs are configured via INI files. See the\n[documentation](https://docs.circuitscape.org/Circuitscape.jl/latest/) for a full guide\non data types, calculation modes, and all available options.\n\n```julia\njulia\u003e using Circuitscape\njulia\u003e compute(\"path/to/config/file.ini\")\n```\n\nYou can also build INI files interactively using the built-in terminal UI:\n\n```julia\njulia\u003e using Circuitscape\njulia\u003e Circuitscape.INIBuilder.start()\n```\n\nOr construct a configuration programmatically:\n\n```julia\njulia\u003e using Circuitscape\njulia\u003e cfg = Circuitscape.init_config()\njulia\u003e cfg[\"habitat_file\"] = \"resistance_map.asc\"\njulia\u003e cfg[\"point_file\"] = \"focal_nodes.asc\"\njulia\u003e cfg[\"scenario\"] = \"pairwise\"\njulia\u003e cfg[\"output_file\"] = \"output/results.out\"\njulia\u003e compute(cfg)\n```\n\nExample INI files can be found in the\n[test folder](https://github.com/Circuitscape/Circuitscape.jl/tree/master/test/input).\n\n## Features\n\n### Solver Modes\n\nCircuitscape supports four solver modes:\n\n- **CG+AMG** (default) — an iterative solver using algebraic multigrid preconditioning. Scales well to large problems.\n- **CHOLMOD** — a direct solver using [Cholesky decomposition](https://en.wikipedia.org/wiki/Cholesky_decomposition) via the [SuiteSparse](https://people.engr.tamu.edu/davis/suitesparse.html) library. Can be significantly faster for smaller problems, but memory use grows quickly with problem size due to [fill-in](https://algowiki-project.org/en/Cholesky_method#Reordering_to_reduce_the_number_of_fill-in_elements).\n- **Apple Accelerate** — a direct solver using Apple's [Accelerate](https://developer.apple.com/documentation/accelerate/sparse_solvers) framework sparse Cholesky, available as a package extension on macOS (requires macOS 13.4+). Requires `using AppleAccelerate` before `using Circuitscape`.\n- **Pardiso** — a direct solver via [Pardiso.jl](https://github.com/JuliaSparse/Pardiso.jl), available as a package extension. Requires `using Pardiso` before `using Circuitscape`.\n\nTo select a solver, add to your INI file:\n```\nsolver = cholmod   # or accelerate, pardiso\n```\n\n### Parallel Computing\n\nCircuitscape supports multi-threaded computation on Linux, macOS, and Windows.\nStart Julia with `julia -t N` to use N threads, or set `parallelize = True` in\nyour INI file.\n\n### Single Precision\n\nCircuitscape can run in single precision for reduced memory use at the cost of solution\naccuracy. Add to your INI file:\n```\nprecision = single\n```\n\n## Performance\n\nCircuitscape.jl is up to **4x faster** than the legacy Python version (Circuitscape v4.0.5)\non 16 parallel processes, with the CHOLMOD solver providing the best performance on\nsuitable problem sizes.\n\n\u003cimg src=\"https://raw.githubusercontent.com/Circuitscape/Circuitscape.jl/master/docs/src/benchmark/benchmark.png\" width=650 height=450\u003e\n\nBenchmarks were run on a Linux (Ubuntu) server with an Intel Xeon Silver 4114 CPU\n(2.20 GHz, 20 cores, 384 GB RAM) using problems from the\n[benchmark suite](https://github.com/Circuitscape/BigTests).\n\n## Related Projects\n\n- [Omniscape.jl](https://github.com/Circuitscape/Omniscape.jl) — Omnidirectional connectivity analysis built on Circuitscape\n- [AlgebraicMultigrid.jl](https://github.com/JuliaLinearAlgebra/AlgebraicMultigrid.jl) — The default iterative solver used by Circuitscape\n\n## Contributing\n\nIf you encounter any issues or would like to ask a question, please file\na report [here](https://github.com/Circuitscape/Circuitscape.jl/issues).\nContributions in the form of\n[pull requests](https://github.com/Circuitscape/Circuitscape.jl/pulls) are welcome!\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["geo","ecology","gdal","geospatial-data","arrays","connectivity","julia-package","circuitscape","circuit-theory","unconstrained-optimization"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/4262","html_url":"https://ost.ecosyste.ms/projects/4262"}