forrustts 0.1.3

Tools for forward simulation with tree sequence recording
Documentation

Forward simulation with tree sequence recording in rust

This package is currently "experimental"!

forrustts (pronounced "forests") is a port of many ideas from the fwdpp library from C++ to rust.

It is licensed under the GNU General Public License, version 3 or later ("GPL3+").

Getting started

Install the GNU Scientific Library. For example:

apt install libgsl-dev

You may use conda or brew as you see fit.

Install rust

Then:

cargo build
cargo test

Example programs are in the subdirectory forrustts_examples:

cd forrustts_examples
cargo build --release

The binaries will then be found in target/release/.

These programs use clap for command-line options. Pass --help to any of them for usage information.

Development information

CI

CI testing is done using GitHub actions for both Linux and macOS. These actions include using clippy, which is a very strict code linter. The actions also check code format using rustfmt.

Code coverage

Use tarpaulin. The documentation for that crate is excellent. The short version is:

cargo tarpaulin -o html

This command will run the tests and generate a nice html report.

Change log

2021-03-29, Version 0.1.3

Commits

  • [99821a933c] Bump version to 0.1.3 (molpopgen)
  • [a34d582e02] add change log info for 0.1.2 (molpopgen)
  • [cfcfb7e657] Merge pull request #72 from molpopgen/tskit_tools (Kevin R. Thornton)
  • [d69bf0889e] update name in examples (molpopgen)
  • [7e65155553] rename crate::tskit to crate::tskit_tools (molpopgen)
  • [dffc91a41c] Merge pull request #71 from molpopgen/fix_doc_issues (Kevin R. Thornton)
  • [a6b929818c] Fix various links in docs. (molpopgen)
  • [9e56d40662] Merge pull request #69 from molpopgen/streamline_simplification_code_organization (Kevin R. Thornton)
  • [e441f9202a] Move all simplification code into one source file (molpopgen)
  • [4123c16adf] Merge pull request #70 from molpopgen/update_cancel_action (Kevin R. Thornton)
  • [f694d05abd] Add cancel to macos. Update token. (molpopgen)
  • [22150f32fe] Merge pull request #68 from ForwardSimulation/dependabot/add-v2-config-file (Kevin R. Thornton)
  • [3c9ed4f211] Create Dependabot config file (dependabot-preview[bot])
  • [01a529220c] Merge pull request #67 from ForwardSimulation/dependabot/cargo/GSL-4.0.0 (dependabot-preview[bot])
  • [c8567deedf] Update GSL requirement from 2.0.1 to 4.0.0 (dependabot-preview[bot])

2021-03-26, Version 0.1.2

Commits

  • [21a77982a8] bump version to 0.1.2 (molpopogen)
  • [4653a8b5d1] Merge pull request #64 from molpopgen/update_tskit_dependency (Kevin R. Thornton)
  • [6bc5030d9e] Fix string format lint in assert. (molpopogen)
  • [f36c6c91df] update to tskit 0.1.1 (molpopogen)
  • [b1424be2f8] Merge pull request #62 from molpopgen/doc_fixes (Kevin R. Thornton)
  • [5771eb18d6] Document other differences from tskit. (molpopgen)