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.
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)