YeAST [](https://travis-ci.org/yvan-sraka/YeAST) ========================================================================================================================= *Yet Another Shell Trick* What's that? ------------ YeAST is an extension of the bourne shell [shebangsyntax](https://en.wikipedia.org/wiki/Shebang_\(Unix\)). YeAST aims to solve issues of interoperability, parallel programming, quick prototyping and progressive refactoring by invite users to use in their scripts and software features of UNIX systems and build things more [KISS](https://en.wikipedia.org/wiki/KISS_principle). You can read more about it through: - [a blog post](https://yvan-sraka.github.io/1970/01/05/yeast.html) on my web page - [a lightning talkpresentation](https://raw.githubusercontent.com/yvan-sraka/yvan-sraka.github.io/master/YeAST.pdf) of the core idea, implementation, and real-world applications Quick Running ------------- These instructions will get you the last stable binaries of yeast on your local machine for standard usage purposes. ### Binaries installation #### ..on macOS using `brew`: You can install YeAST on macOS using our [Homebrew](https://brew.sh/) custom Tap: ``` {.shell} brew install yvan-sraka/YeAST/yeast ``` #### ..on others UNIX-like using the install script: Run the following line in your terminal, then follow the onscreen instructions: ``` {.shell} curl https://raw.githubusercontent.com/yvan-sraka/YeAST/master/install.sh -sSf | sh ``` > If you wonder what this previous command do, don't hesitate to inspect > the script: it runs all instructions of the **Getting Started** > section. ### Bootstraping To make scripts easily work out of the box, you can add this little hack at the beggining of your files: ``` {.shell} #! /bin/sh #! @ignore if ! [ -x "$(command -v yeast)" ]; then curl "https://raw.githubusercontent.com/yvan-sraka/YeAST/master/install.sh" -sSf | sh fi yeast "$0" exit ``` ### Editors integration You now have YeAST installed on your machine! Cool next thing to do could be to get a syntax support extension for your favorite code editor: - [VisualStudioCode](https://marketplace.visualstudio.com/items?itemName=yvan-sraka.yeast) Getting Started --------------- These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. ### Prerequisites Get a stable [Rust](https://www.rust-lang.org/) toolchain: ``` {.shell} curl https://sh.rustup.rs -sSf | sh ``` ### Building and running ``` {.shell} git clone git@github.com:yvan-sraka/YeAST.git cd YeAST cargo run basic_example.yst ``` Ecosystem --------- - [Kombucha](https://github.com/yvan-sraka/Kombucha): a simple aliases manager for YeAST - [Palombe](https://github.com/yvan-sraka/Palombe): which lets you send and receive messages synchronously through different processes - [Cleopatra](https://github.com/yvan-sraka/Cleopatra): make YeAST be called in place of your standard interpreter in the current environment Real-World Examples ------------------- The [basic_example](https://github.com/yvan-sraka/YeAST/blob/master/basic_example.yst) available in this repository is fun to get a general idea behind YeAST! But to understand the purpose of this tool, we will go through examples inspired from *REAL WORLD*, mainly by my scientific domain: "Bioinformatics and Modeling". ### YeAST works like `cat` outside interpreters ``` {.yeast} #! /usr/bin/env yeast This text will be printed on standard output! Besides we experiment with a Python code we expect to say "Hello World": #! python3 print("Hello, World!") #! Enjoy this nice way of writing code in notebook style. ``` ### It provides multithreading by default ``` {.yeast} #! /usr/bin/env yeast Here we try to fold 3 different sequences, so we do it in parallel by allocating 3 threads, there is no additional syntax needed: #! python3 folding.py ;LCBO - Prolactin precursor - Bovine ; a sample sequence in FASTA format MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC* !# Shebang in YeAST could be any shell command that's accepting as last argument a given file, here we use the syntax to call our external script `folding.py`. #! python3 folding.py >MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA DIDGDGQVNYEEFVQMMTAK* !# Bonus: the output of this multithreading computation will be displayed the right order as soon that the information is available! #! python3 folding.py >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY !# ``` Roadmap ------- - [x] Create a Makefile to handle `make`, `make test` & `make install` intructions. - [x] Validate builds using Travis CI. - [x] Read input file line by line using a Buffer. - [x] Use [clap.rs](https://github.com/kbknapp/clap-rs) to enhance command line interactions. - [x] Allow sub-scripts to read command-line arguments, using `$0`, `$1`, etc ... - [x] ... and `$*` for all input args. - [x] Handle scripts errors correctly and display a `BACKTRACE` in `=1|full` mode - [x] Let the use of `#! /usr/bin/env yeast` not failed in stack overflow due to an infinite loop of self-calls. - [x] Fix rules for inlining shell commands in scripts. - [x] Let the user write multiline commands as he did in an interactive shell. - [x] Add bunch of input / output tests scripts. - [x] Provide true multithreading by getting ride of the waiting lock of shell command output! - [ ] Write a beautiful and comprehensive `man` page. - [x] Create an install script for handling one-instruction installation. - [ ] Create packages for most UNIX distributions. - [ ] Host a beautiful landing page on the `gh-page` branch of this repository. - [ ] Add Windows support (use `cmd` instead of `sh` and [Windowsnamedpipes](https://msdn.microsoft.com/en-us/library/windows/desktop/aa365590\(v=vs.85\).aspx) instead of `mkfifo`). - [x] Create a small lib in each language to uniform the use of named pipes in sharing serialized data between processes. - [x] Provide a collection of alias by adding a special environment to the `PATH` of command launch by YeAST. - [x] Add a simple script in the path to update aliases by running a `git pull`. - [x] Provide plugins for syntactic coloration in VSCode. - [x] Let user define a top level interpreter by set `YEAST_CONTEXT` env variable Contributing ------------ Please read [CONTRIBUTING.md](https://github.com/yvan-sraka/YeAST/blob/master/CONTRIBUTING.md) for details on our code of conduct, and the process for submitting a pull requests to us. Authors ------- - [Yvan Sraka](https://github.com/yvan-sraka) - for the original idea - [Mattia Primavera](https://github.com/MattiaPrimavera/) - who provide constant positive feedback and was the very first beta-tester See also the list of [contributors](https://github.com/yvan-sraka/YeAST/graphs/contributors) who participated in this project. License ------- This project is licensed under the 3rd version of the GPL License - see the [LICENSE](https://github.com/yvan-sraka/YeAST/blob/master/LICENSE) file for details.