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reCTBN
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62-feature-rectbnpy
AlessandroBregoli 2 years ago
parent 014bad4c7d
commit 3dae67a80c
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  1. 86
      poetry.lock
  2. 16
      pyproject.toml
  3. 69
      reCTBNpy/.github/workflows/CI.yml
  4. 72
      reCTBNpy/.gitignore
  5. 15
      reCTBNpy/Cargo.toml
  6. 14
      reCTBNpy/pyproject.toml
  7. 18
      reCTBNpy/src/lib.rs
  8. 35
      reCTBNpy/src/pyctbn.rs
  9. 49
      reCTBNpy/src/pyparams.rs

86
poetry.lock generated
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16
pyproject.toml
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[tool.poetry]
name = "rectbnpy"
version = "0.1.0"
description = ""
authors = ["AlessandroBregoli <alessandroxciv@gmail.com>"]
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.10"
maturin = "^0.13.3"
numpy = "^1.23.3"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

69
reCTBNpy/.github/workflows/CI.yml
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name: CI
on:
push:
branches:
- main
- master
pull_request:
jobs:
linux:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: messense/maturin-action@v1
with:
manylinux: auto
command: build
args: --release --sdist -o dist --find-interpreter
- name: Upload wheels
uses: actions/upload-artifact@v2
with:
name: wheels
path: dist
windows:
runs-on: windows-latest
steps:
- uses: actions/checkout@v3
- uses: messense/maturin-action@v1
with:
command: build
args: --release -o dist --find-interpreter
- name: Upload wheels
uses: actions/upload-artifact@v2
with:
name: wheels
path: dist
macos:
runs-on: macos-latest
steps:
- uses: actions/checkout@v3
- uses: messense/maturin-action@v1
with:
command: build
args: --release -o dist --universal2 --find-interpreter
- name: Upload wheels
uses: actions/upload-artifact@v2
with:
name: wheels
path: dist
release:
name: Release
runs-on: ubuntu-latest
if: "startsWith(github.ref, 'refs/tags/')"
needs: [ macos, windows, linux ]
steps:
- uses: actions/download-artifact@v2
with:
name: wheels
- name: Publish to PyPI
uses: messense/maturin-action@v1
env:
MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
with:
command: upload
args: --skip-existing *

72
reCTBNpy/.gitignore vendored
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/target
# Byte-compiled / optimized / DLL files
__pycache__/
.pytest_cache/
*.py[cod]
# C extensions
*.so
# Distribution / packaging
.Python
.venv/
env/
bin/
build/
develop-eggs/
dist/
eggs/
lib/
lib64/
parts/
sdist/
var/
include/
man/
venv/
*.egg-info/
.installed.cfg
*.egg
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
pip-selfcheck.json
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml
# Translations
*.mo
# Mr Developer
.mr.developer.cfg
.project
.pydevproject
# Rope
.ropeproject
# Django stuff:
*.log
*.pot
.DS_Store
# Sphinx documentation
docs/_build/
# PyCharm
.idea/
# VSCode
.vscode/
# Pyenv
.python-version

15
reCTBNpy/Cargo.toml
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[package]
name = "reCTBNpy"
version = "0.1.0"
edition = "2021"
[lib]
crate-type = ["cdylib"]
[workspace]
[dependencies]
pyo3 = { version = "0.17.1", features = ["extension-module"] }
numpy = "*"
reCTBN = { path="../reCTBN" }

14
reCTBNpy/pyproject.toml
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[build-system]
requires = ["maturin>=0.13,<0.14"]
build-backend = "maturin"
[project]
name = "reCTBNpy"
requires-python = ">=3.7"
classifiers = [
"Programming Language :: Rust",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
]

18
reCTBNpy/src/lib.rs
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use pyo3::prelude::*;
pub mod pyctbn;
pub mod pyparams;
/// A Python module implemented in Rust.
#[pymodule]
fn reCTBNpy(py: Python, m: &PyModule) -> PyResult<()> {
let network_module = PyModule::new(py, "network")?;
network_module.add_class::<pyctbn::PyCtbnNetwork>()?;
m.add_submodule(network_module)?;
let params_module = PyModule::new(py, "params")?;
params_module.add_class::<pyparams::PyDiscreteStateContinousTime>()?;
m.add_submodule(params_module)?;
Ok(())
}

35
reCTBNpy/src/pyctbn.rs
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use std::collections::BTreeSet;
use pyo3::prelude::*;
use reCTBN::{ctbn, network::Network};
#[pyclass]
pub struct PyCtbnNetwork {
ctbn_network: ctbn::CtbnNetwork,
}
#[pymethods]
impl PyCtbnNetwork {
#[new]
pub fn new() -> Self {
PyCtbnNetwork {
ctbn_network: ctbn::CtbnNetwork::new(),
}
}
pub fn get_number_of_nodes(&self) -> usize {
self.ctbn_network.get_number_of_nodes()
}
pub fn add_edge(&mut self, parent: usize, child: usize) {
self.ctbn_network.add_edge(parent, child);
}
pub fn get_parent_set(&self, node: usize) -> BTreeSet<usize> {
self.ctbn_network.get_parent_set(node)
}
pub fn get_children_set(&self, node: usize) -> BTreeSet<usize> {
self.ctbn_network.get_children_set(node)
}
}

49
reCTBNpy/src/pyparams.rs
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use numpy::{self, ToPyArray};
use pyo3::{exceptions::PyValueError, prelude::*};
use reCTBN::params::{self, ParamsTrait};
use std::collections::BTreeSet;
pub struct PyParamsError(params::ParamsError);
impl From<PyParamsError> for PyErr {
fn from(error: PyParamsError) -> Self {
PyValueError::new_err(error.0.to_string())
}
}
impl From<params::ParamsError> for PyParamsError {
fn from(other: params::ParamsError) -> Self {
Self(other)
}
}
#[pyclass]
pub struct PyDiscreteStateContinousTime {
param: params::DiscreteStatesContinousTimeParams,
}
#[pymethods]
impl PyDiscreteStateContinousTime {
#[new]
pub fn new(label: String, domain: BTreeSet<String>) -> Self {
PyDiscreteStateContinousTime {
param: params::DiscreteStatesContinousTimeParams::new(label, domain),
}
}
pub fn get_cim<'py>(&self, py: Python<'py>) -> Option<&'py numpy::PyArray3<f64>> {
match self.param.get_cim() {
Some(x) => Some(x.to_pyarray(py)),
None => None,
}
}
pub fn set_cim<'py>(&mut self, py: Python<'py>, cim: numpy::PyReadonlyArray3<f64>) -> Result<(), PyParamsError> {
self.param.set_cim(cim.as_array().to_owned())?;
Ok(())
}
pub fn get_label(&self) -> String {
self.param.get_label().to_string()
}
}
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