From 6dff171e276fbe6e9ce15536a41103e4e3aa546b Mon Sep 17 00:00:00 2001 From: chudicek Date: Fri, 12 Jan 2024 09:25:47 +0100 Subject: [PATCH] docs: updated readme --- README.md | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 839f852..4c7229b 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,29 @@ -[![Crates.io](https://img.shields.io/crates/v/biodivine-lib-logical-models?style=flat-square)](https://crates.io/crates/biodivine-lib-logical-models) -[![Api Docs](https://img.shields.io/badge/docs-api-yellowgreen?style=flat-square)](https://docs.rs/biodivine-lib-logical-models/) +[![Crates.io](https://img.shields.io/crates/v/biodivine-lib-logical-models?style=flat-square)](https://crates.io/crates/biodivine-lib-logical-models) +[![Api Docs](https://img.shields.io/badge/docs-api-yellowgreen?style=flat-square)](https://docs.rs/biodivine-lib-logical-models/) [![Continuous integration](https://img.shields.io/github/actions/workflow/status/sybila/biodivine-lib-logical-models/build.yml?branch=master&style=flat-square)](https://github.com/sybila/biodivine-lib-logical-models/actions?query=workflow%3Abuild) -[![Coverage](https://img.shields.io/codecov/c/github/sybila/biodivine-lib-logical-models?style=flat-square)](https://codecov.io/gh/sybila/biodivine-lib-logical-models) -[![GitHub issues](https://img.shields.io/github/issues/sybila/biodivine-lib-logical-models?style=flat-square)](https://github.com/sybila/biodivine-lib-logical-models/issues) -[![Dev Docs](https://img.shields.io/badge/docs-dev-orange?style=flat-square)](https://biodivine.fi.muni.cz/docs/biodivine-lib-logical-models/latest/) -[![GitHub last commit](https://img.shields.io/github/last-commit/sybila/biodivine-lib-logical-models?style=flat-square)](https://github.com/sybila/biodivine-lib-logical-models/commits/master) +[![Coverage](https://img.shields.io/codecov/c/github/sybila/biodivine-lib-logical-models?style=flat-square)](https://codecov.io/gh/sybila/biodivine-lib-logical-models) +[![GitHub issues](https://img.shields.io/github/issues/sybila/biodivine-lib-logical-models?style=flat-square)](https://github.com/sybila/biodivine-lib-logical-models/issues) +[![Dev Docs](https://img.shields.io/badge/docs-dev-orange?style=flat-square)](https://biodivine.fi.muni.cz/docs/biodivine-lib-logical-models/latest/) +[![GitHub last commit](https://img.shields.io/github/last-commit/sybila/biodivine-lib-logical-models?style=flat-square)](https://github.com/sybila/biodivine-lib-logical-models/commits/master) [![Crates.io](https://img.shields.io/crates/l/biodivine-lib-logical-models?style=flat-square)](https://github.com/sybila/biodivine-lib-logical-models/blob/master/LICENSE) - # Biodivine logical models library -**This is a work in progress. At the moment, there is practically no functionality implemented yet.** +**This project is still WIP. The version available in `main` is deprecated, as major rewrite has taken place - see branch `rewrite`.** + +- Though no new features were introduced, the API has changed. The readability of `rewrite` should be significantly better. Performance is also slightly improved. + +--- A Rust library for working with logical models (Boolean/multi-valued networks) in systems biology. ### Goals -- [ ] Can load/store file formats common in systems biology (sbml, bnet, aeon, bma). -- [ ] Can perform basic static analysis on such models (unused variables,  invalid regulations, input inlining or general reduction). +- [X] Can load/store file formats common in systems biology (sbml, bnet, aeon, bma). +- [X] Can perform basic static analysis on such models (unused variables,  invalid regulations, input inlining or general reduction). - [ ] Can represent unknown/uncertain behaviour within the logical model. -- [ ] Can represent and manipulate the state-transition graph of a logical model symbolically (maybe using multiple different encodings?). -- [ ] Provides some basic utility algorithms for (a) exploring the structural properties of the model (feedback vertex sets, cycles, etc.) (b) exploring the model dynamics (reachability, fixed-points, trap spaces, etc.). - +- [X] Can represent and manipulate the state-transition graph of a logical model symbolically (maybe using multiple different encodings?). +- [X] Provides some basic utility algorithms for (a) exploring the structural properties of the model (feedback vertex sets, cycles, etc.) (b) exploring the model dynamics (reachability, fixed-points, trap spaces, etc.). ### Running reachability integration test @@ -36,7 +38,7 @@ python3 reachability_integration_test.py 1m fwd ``` The process dumps all results into an appropriate `./data/results-*` directory. -The script will not overwrite existing results, +The script will not overwrite existing results, so you have to delete the directory manually before running the test again. You should see an output similar to the following: @@ -51,4 +53,4 @@ You should see an output similar to the following: ``` If you see a `[FAIL]` somewhere, it means an inconsistency has been detected. -You can then check the results to examine the specific case. \ No newline at end of file +You can then check the results to examine the specific case.