goatd 0.1.2__tar.gz

goatd-0.1.2/AGENTS.md

@@ -0,0 +1,30 @@
+# Agent Instructions — goatd
+
+`CLAUDE.md` is the instruction file for this repository. `AGENTS.md` is a
+relative symlink to it so agents read the same rules. Edit this file, not the
+symlink.
+
+goatd is a public Rust library and CLI: a graph goes in and a tree
+decomposition comes out. Library code, solver code, tests, documentation, and
+vendored dependencies live here. Every tracked file and commit is public.
+
+[`CONTRIBUTING.md`](docs/CONTRIBUTING.md) binds in full. In particular:
+
+- Run the complete gate set before reporting a change finished, including
+  `--all-targets` so the CLI and examples are covered.
+- For a bug fix, add a regression test and confirm that it fails on the
+  unfixed parent.
+- Keep the library single-threaded. Consumers own parallelism across graph
+  instances.
+- Keep budgets and seeds explicit. Library code does not read the process
+  environment.
+- Reject an inert CLI flag with an error naming both the flag and the order
+  that accepts it.
+- Put public-surface tests in top-level `tests/`; put tests of private or
+  crate-visible items in a `tests/` directory inside their module.
+- Extend shared implementations, fixtures, and tables instead of creating a
+  second path that must be kept in sync.
+- Update [docs/algorithms.md](docs/algorithms.md) when an algorithm or its
+  selection policy changes.
+- The first build compiles the vendored C++ code. Compiler setup is in
+  [docs/building.md](docs/building.md).

goatd-0.1.2/CLAUDE.md

@@ -0,0 +1,30 @@
+# Agent Instructions — goatd
+
+`CLAUDE.md` is the instruction file for this repository. `AGENTS.md` is a
+relative symlink to it so agents read the same rules. Edit this file, not the
+symlink.
+
+goatd is a public Rust library and CLI: a graph goes in and a tree
+decomposition comes out. Library code, solver code, tests, documentation, and
+vendored dependencies live here. Every tracked file and commit is public.
+
+[`CONTRIBUTING.md`](docs/CONTRIBUTING.md) binds in full. In particular:
+
+- Run the complete gate set before reporting a change finished, including
+  `--all-targets` so the CLI and examples are covered.
+- For a bug fix, add a regression test and confirm that it fails on the
+  unfixed parent.
+- Keep the library single-threaded. Consumers own parallelism across graph
+  instances.
+- Keep budgets and seeds explicit. Library code does not read the process
+  environment.
+- Reject an inert CLI flag with an error naming both the flag and the order
+  that accepts it.
+- Put public-surface tests in top-level `tests/`; put tests of private or
+  crate-visible items in a `tests/` directory inside their module.
+- Extend shared implementations, fixtures, and tables instead of creating a
+  second path that must be kept in sync.
+- Update [docs/algorithms.md](docs/algorithms.md) when an algorithm or its
+  selection policy changes.
+- The first build compiles the vendored C++ code. Compiler setup is in
+  [docs/building.md](docs/building.md).

goatd-0.1.2/Cargo.lock

@@ -0,0 +1,107 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
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+ "shlex",
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+ "libc",
+ "r-efi",
+ "rand_core",
+]
+
+[[package]]
+name = "goatd"
+version = "0.1.2"
+dependencies = [
+ "cc",
+ "rand",
+ "rustc-hash",
+]
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+[[package]]
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+dependencies = [
+ "chacha20",
+ "getrandom",
+ "rand_core",
+]
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+[[package]]
+name = "rand_core"
+version = "0.10.1"
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goatd-0.1.2/Cargo.toml

@@ -0,0 +1,48 @@
+[package]
+name = "goatd"
+version = "0.1.2"
+edition = "2024"
+# The floor let-chains (`if let … && let …`) set for edition 2024.
+rust-version = "1.88"
+license = "Apache-2.0"
+repository = "https://github.com/Tractables/goatd"
+documentation = "https://docs.rs/goatd"
+description = "Greatest Of All Tree Decompositions: tree decompositions of graphs — elimination orders, FlowCutter, multilevel bisection — with PACE .gr/.td I/O and a command-line solver."
+keywords = ["treewidth", "tree-decomposition", "graph", "pace", "elimination-order"]
+categories = ["algorithms", "science", "mathematics", "command-line-utilities"]
+readme = "README.md"
+# Allowlist: `cargo package` ships exactly these. `vendor/treedecomp` is the
+# C++ FlowCutter builder `build.rs` compiles; it sits under the package root
+# because `include` cannot reach outside it.
+include = [
+    "src/**/*.rs",
+    "tests/**/*.rs",
+    "examples/**/*.rs",
+    "build.rs",
+    "Cargo.toml",
+    "README.md",
+    "CLAUDE.md",
+    "AGENTS.md",
+    "docs/**/*.md",
+    "docs/logo.png",
+    "LICENSE",
+    "vendor/**",
+]
+# `build.rs` compiles the vendored FlowCutter into `libtreedecomp.a`. Declaring
+# `links` reserves that native library name, so two copies of this crate can
+# never be linked into one program.
+links = "treedecomp"
+
+[lib]
+name = "goatd"
+
+[[bin]]
+name = "goatd"
+path = "src/bin/goatd.rs"
+
+[dependencies]
+rand = "0.10"
+rustc-hash = "2"
+
+[build-dependencies]
+cc = "1"

goatd-0.1.2/LICENSE

@@ -0,0 +1,201 @@
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goatd-0.1.2/PKG-INFO

@@ -0,0 +1,77 @@
+Metadata-Version: 2.4
+Name: goatd
+Version: 0.1.2
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Rust
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+License-File: notices/LICENSE
+License-File: notices/THIRD-PARTY.md
+Summary: Greatest Of All Tree Decompositions: tree decompositions of graphs — elimination orders, FlowCutter, multilevel bisection — with PACE .gr/.td text in and out.
+License-Expression: Apache-2.0
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Documentation, https://docs.rs/goatd
+Project-URL: Repository, https://github.com/Tractables/goatd
+
+# goatd for Python
+
+Python bindings for [goatd](https://github.com/Tractables/goatd), built with
+[PyO3](https://pyo3.rs) and [maturin](https://www.maturin.rs).
+
+```sh
+pip install goatd
+```
+
+Wheels cover CPython 3.10 and later on Linux x86-64, macOS arm64 and Windows
+x64. Anywhere else, pip builds from the source distribution, which needs a
+Rust toolchain and a C++20 compiler.
+
+```python
+import goatd
+
+graph = goatd.Graph(4, [(0, 1), (1, 2), (2, 3), (3, 0), (0, 2)])
+td = goatd.decompose(graph, order="portfolio", budget_ms=100)
+
+td.treewidth        # 2
+td.bags             # [[0, 1, 2], [0, 2, 3]]
+td.edges            # [(0, 1)] — pairs of positions in td.bags
+td.validate(graph)  # raises goatd.Error if td does not decompose graph
+print(td.to_td())   # PACE .td text
+```
+
+`decompose` takes the solver's knobs under the solver's names: `order` is one
+of `minfill`, `mindegree`, `nested-dissection`, `flowcutter` and `portfolio`;
+`seed` breaks ties; `ties="sample"` and `weights` control weighted sampling for
+the two greedy orders; `steps` gives flowcutter a repeatable step budget in
+place of a clock; `refine=True` re-cuts the result along FlowCutter separators.
+An argument the chosen order cannot act on raises `ValueError` naming both.
+Budgets are milliseconds, so the name is `budget_ms` rather than the command
+line's `--budget`.
+
+`goatd.Graph.from_gr` and `TreeDecomposition.from_td` read the PACE formats;
+`to_gr` and `to_td` write them.
+
+goatd is single-threaded. The interpreter lock is released for the whole of a
+solve, so a caller can decompose several graphs at once from Python threads.
+
+## Building
+
+The extension builds against the published `goatd` crate rather than the
+checkout around it, so it needs a Rust toolchain, a C++20 compiler for the
+vendored FlowCutter, and maturin.
+
+PEP 639 resolves `license-files` against the directory holding
+`pyproject.toml` and forbids `..`, so the two notice files are copied in from
+the repository root first rather than kept here in a second copy:
+
+```sh
+mkdir -p bindings/python/notices
+cp LICENSE docs/THIRD-PARTY.md bindings/python/notices/
+pip install maturin
+maturin build --release --manifest-path bindings/python/Cargo.toml
+```
+
+`maturin develop` installs the extension into the active virtualenv for
+`pytest bindings/python/tests`.
+

goatd-0.1.2/README.md

@@ -0,0 +1,106 @@
+# goatd — Greatest Of All Tree Decompositions
+
+<p align="center">
+  <img src="docs/logo.png" alt="goatd logo" width="280">
+</p>
+
+<p align="center">
+  <a href="https://github.com/Tractables/goatd/actions/workflows/ci.yml"><img
+     src="https://github.com/Tractables/goatd/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <a href="LICENSE"><img
+     src="https://img.shields.io/badge/license-Apache--2.0-blue.svg" alt="License: Apache-2.0"></a>
+  <a href="https://crates.io/crates/goatd"><img
+     src="https://img.shields.io/crates/v/goatd.svg" alt="crates.io"></a>
+  <a href="https://docs.rs/goatd"><img
+     src="https://docs.rs/goatd/badge.svg" alt="docs.rs"></a>
+</p>
+
+Tree decompositions of graphs, as a Rust library and command-line solver. The
+portfolio runs several constructions and keeps the narrowest result:
+
+- **portfolio search** — safe reductions, several seeds and construction
+  methods, then optional separator refinement;
+- **greedy elimination** — min-fill and min-degree, with deterministic or
+  weighted-sampling tie breaking;
+- **nested dissection** — recursive multilevel bisection, with each separator
+  eliminated after its two sides;
+- **flow-based separation** — balanced cuts for constructing and refining
+  decompositions. goatd includes a Rust FlowCutter separator search and the
+  vendored PACE 2017 FlowCutter decomposer.
+
+See [Algorithms](docs/algorithms.md) for the details and the differences from
+the upstream methods.
+
+## Solver
+
+```sh
+cargo install goatd
+goatd graph.gr > graph.td
+```
+
+`goatd` reads and writes the PACE `.gr` and `.td` formats. Choose `--order
+minfill`, `mindegree`, `nested-dissection`, `flowcutter`, or `portfolio`; run
+`goatd --help` for budgets, seeds, weighted ties, and refinement.
+
+## Library
+
+```toml
+[dependencies]
+goatd = "0.1"
+```
+
+The [`basic` example](examples/basic.rs) constructs a graph, computes a
+decomposition, validates it, and writes it in PACE format:
+
+```sh
+cargo run --example basic
+```
+
+The public API also exposes graph and hypergraph bisection, the Rust separator
+search, the C++ FlowCutter decomposer, and decomposition projection and
+refinement. Rustdoc documents each entry point.
+
+## Bindings
+
+The same constructions are available from
+[Python](bindings/python/README.md) and from
+[C and C++](bindings/c/README.md).
+
+## Evaluation
+
+The [solver comparison](https://tractables.github.io/goatd/) evaluates the
+shipped portfolio and seven public baselines on component graphs obtained from
+Model Counting Competition CNFs after two seconds of preprocessing. Each
+configuration receives ten seconds on one CPU, and every decomposition is
+checked by the same validator.
+
+The default view excludes tree components and focuses on harder cases: graphs
+where the smallest validated width found is 30 or greater. It also retains 17
+graphs for which no displayed configuration returned a validated
+decomposition. “Exact best” means a tie with the smallest validated width
+found, not a proven optimum.
+
+<!-- Generated table; 6,640 selected graphs. -->
+
+| Solver | Valid | Exact best | Within +1 | Within +4 |
+| --- | ---: | ---: | ---: | ---: |
+| goatd portfolio | 6,442 (97.0%) | **4,047 (60.9%)** | **5,203 (78.4%)** | **6,166 (92.9%)** |
+| Jdrasil heuristic | 6,361 (95.8%) | 2,745 (41.3%) | 3,993 (60.1%) | 5,718 (86.1%) |
+| FlowCutter PACE 2017 | **6,565 (98.9%)** | 1,239 (18.7%) | 1,774 (26.7%) | 3,921 (59.1%) |
+| Tamaki PACE 2017 | 6,400 (96.4%) | 922 (13.9%) | 1,435 (21.6%) | 2,870 (43.2%) |
+| HTD | 6,401 (96.4%) | 381 (5.7%) | 579 (8.7%) | 1,991 (30.0%) |
+| NetworkX min-degree | 6,266 (94.4%) | 157 (2.4%) | 172 (2.6%) | 332 (5.0%) |
+| NetworkX min-fill | 5,564 (83.8%) | 129 (1.9%) | 311 (4.7%) | 1,712 (25.8%) |
+| Arboretum heuristic | 3,059 (46.1%) | 75 (1.1%) | 162 (2.4%) | 820 (12.3%) |
+
+## Building and contributing
+
+Build setup is in [Building](docs/building.md). Contributions follow
+[CONTRIBUTING.md](docs/CONTRIBUTING.md).
+
+## Licence
+
+Apache-2.0. Vendored code and modifications are recorded in
+[THIRD-PARTY.md](docs/THIRD-PARTY.md);
+[ACKNOWLEDGEMENTS.md](docs/ACKNOWLEDGEMENTS.md)
+credits the work behind the algorithms.

goatd-0.1.2/bindings/python/.gitignore

@@ -0,0 +1,6 @@
+/target
+/dist
+
+# Copied in from the repository root before a build; the tracked originals are
+# LICENSE and docs/THIRD-PARTY.md.
+/notices