https://github.com/yamaton/h2o-curated-data

Semi-hand curated command-line option data for many CLI programs, geared toward bioinformatics tools. Shell completion scripts are also available.
https://github.com/yamaton/h2o-curated-data

bash bioinformatics cli dataset fish shell vscode-extension zsh

Last synced: about 23 hours ago
JSON representation

Semi-hand curated command-line option data for many CLI programs, geared toward bioinformatics tools. Shell completion scripts are also available.

• Host: GitHub
• URL: https://github.com/yamaton/h2o-curated-data
• Owner: yamaton
• Created: 2021-06-15T15:48:50.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-04-17T14:57:14.000Z (7 months ago)
• Last Synced: 2024-04-17T16:02:47.357Z (7 months ago)
• Topics: bash, bioinformatics, cli, dataset, fish, shell, vscode-extension, zsh
• Language: Shell
• Homepage:
• Size: 37.9 MB
• Stars: 10
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# CLI curated data for shell completion

This repository contains command-line specs for [Shell Completion](https://marketplace.visualstudio.com/items?itemName=tetradresearch.vscode-h2o) for VS Code. This repository also contains tab completion scripts for bash/zsh/fish shells.

Shell completion scripts for bioinformatics tools are located in the separate repositories:

  * [yamaton/fish-completions-bio](https://github.com/yamaton/fish-completions-bio)

  * [yamaton/zsh-completions-bio](https://github.com/yamaton/zsh-completions-bio)

## Loading the data in VS Code

* In VS Code,  type `Ctrl`+`Shift`+`P` (or `⌘`+`⇧`+`P` on macOS) and run following commands:

  * `Shell Completion: Load Common CLI Data` to load commands in [general.txt](https://github.com/yamaton/h2o-curated-data/blob/main/general.txt)

  * `Shell Completion: Load Bioinformatics CLI Data` to load commands in [bio.txt](https://github.com/yamaton/h2o-curated-data/blob/main/bio.txt)

## Shell completion for bash/zsh/fish

They would be useful especially for bioinformaticians.

### bash

Copy files ([general](https://github.com/yamaton/h2o-curated-data/tree/main/general/bash)) to `~/.bash_completion.d/`, and add the following to `~/.bashrc`.

```bash

for bcfile in ~/.bash_completion.d/* ; do

    . "$bcfile"

done

```

### zsh

Save files ([bio](https://github.com/yamaton/zsh-completions-bio/tree/main/completions), [general](https://github.com/yamaton/h2o-curated-data/tree/main/general/zsh)) to `~/.zfunc`, then add the following line to `~/.zshrc`.

```zsh

fpath=( ~/.zfunc "${fpath[@]}" )

```

### fish

Save files ([bio](https://github.com/yamaton/fish-completions-bio/tree/main/completions), [general](https://github.com/yamaton/h2o-curated-data/tree/main/general/fish)) to `~/.config/fish/completions/`.

## How I prepare the data

I use `h2o` (closed source code) to extract CLI specs, and then apply [yq](https://github.com/mikefarah/yq) to convert from JSON to YAML.

Here is how I extracted the CLI info from [medaka](https://github.com/nanoporetech/medaka), for example.

```shell

# Just see how it works

$ h2o --command medaka

# ...OK. H2o seems to fail parsing some.

# So save the help document as text file for manual editing...

$ medaka --help > medaka.txt

# Edit medaka.txt s.t. command options, subcommands, and descriptions are placed nicely.

# ...

# ...

# After finishing the edit, extract the data as YAML file.

$ h2o --file medaka.txt --format json | yq eval -P > bio/yaml/medaka.yaml

# Add TLDR to the YAML, then convert it to JSON and bash/zsh/fish scripts

# group=bio sets the environment variable and run make

# The makefile calls multiple scripts including

#    - Add TLDR to YAML

#    - Convert YAML to JSON

#    - Create bash/zsh/fish scripts

#    - Take the entire JSON as an array, create a gzipped JSON file

$ group=bio make

```

## Data structure

Here is a sample file.

```yaml

name: tar

description: an archiving utility

options:

  - names:

      - -x

      - --extract

      - --get

    argument: ""

    description: extract files from an archive

  - names:

      - -v

      - --verbose

    argument: ""

    description: verbosely list files processed

version: tar (GNU tar) 1.34

```

As you can see,  an entry has following key-values:

* name (string)

* description (string)

* options (list)

  * names (list of strings)

  * argument (string)

  * description (string)

* [optional] positionalArguments

  * name (string)

  * description (string)

* **[optional]** subcommands:

  * (Here comes a list of the entire structure. Nested.)

* [optional] inheritedOptions (same type as options)

* [optional] usage (string)

* [optional] version (string)

* [optional] tldr (string)