diff --git a/Readme.md b/Readme.md index 4df155c..041f55f 100644 --- a/Readme.md +++ b/Readme.md @@ -5,22 +5,22 @@ This is a [language server] for [language server]: https://langserver.org/ -[![Tests](https://github.com/rabix/benten/workflows/Tests/badge.svg)](https://github.com/rabix/benten/actions?query=workflow%3ATests) -[![codecov](https://codecov.io/gh/rabix/benten/branch/master/graph/badge.svg)](https://codecov.io/gh/rabix/benten) +[![Tests](https://github.com/denbi/denbi-benten/workflows/Tests/badge.svg)](https://github.com/denbi/denbi-benten/actions?query=workflow%3ATests) +[![codecov](https://codecov.io/gh/denbi/denbi-benten/branch/main/graph/badge.svg)](https://codecov.io/gh/denbi/denbi-benten) [![Codacy - Badge](https://api.codacy.com/project/badge/Grade/20839ce29ebe4004b3578d4d02031a1c)](https://www.codacy.com/app/kaushik-work/benten?utm_source=github.com&utm_medium=referral&utm_content=rabix/benten&utm_campaign=Badge_Grade) + Badge](https://api.codacy.com/project/badge/Grade/20839ce29ebe4004b3578d4d02031a1c)](https://www.codacy.com/app/denbi/denbi-benten?utm_source=github.com&utm_medium=referral&utm_content=denbi/denbi-benten&utm_campaign=Badge_Grade) [![PyPI - version](https://badge.fury.io/py/benten.svg)](https://badge.fury.io/py/benten) + version](https://badge.fury.io/py/denbi-benten.svg)](https://badge.fury.io/py/denbi-benten) [![Conda - Version](https://img.shields.io/conda/vn/conda-forge/benten.svg)](https://anaconda.org/conda-forge/benten) + Version](https://img.shields.io/conda/vn/conda-forge/denbi-benten.svg)](https://anaconda.org/conda-forge/denbi-benten) [![Visual Studio Marketplace - Version](https://img.shields.io/visual-studio-marketplace/v/sbg-rabix.benten-cwl?label=VS%20Code%20Ext)](https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl) + Version](https://img.shields.io/visual-studio-marketplace/v/denbi.denbi-benten-cwl?label=VS%20Code%20Ext)](https://marketplace.visualstudio.com/items?itemName=denbi.denbi-benten-cwl) [![Open - VSX](https://img.shields.io/open-vsx/v/sbg-rabix/benten-cwl)](https://open-vsx.org/extension/sbg-rabix/benten-cwl) + VSX](https://img.shields.io/open-vsx/v/denbi/denbi-benten-cwl)](https://open-vsx.org/extension/denbi/denbi-benten-cwl) ## Features -[(Click for feature screenshot gallery)](https://github.com/rabix/benten/blob/master/docs/features.md) +[(Click for feature screenshot gallery)](https://github.com/denbi/denbi-benten/blob/main/docs/features.md) - Syntax highlighting (CWL and JS) - Evaluate expression on hover @@ -32,7 +32,7 @@ This is a [language server] for - Port validations - Display language documentation on hover -![Benten + VS Code](https://raw.githubusercontent.com/rabix/benten/master/media/2019.12.03/full-window.png) +![Benten + VS Code](https://raw.githubusercontent.com/denbi/denbi-benten/main/media/2019.12.03/full-window.png) _Benten_ is written using Python3 and developed against VS Code. The language @@ -43,8 +43,8 @@ extension. The VS Code extension is written in Typescript. # Install VS Code extension Search for -"[Benten](https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl)" -in the marketplace. The name of the client extension is Rabix/benten. Follow the +"[Benten](https://marketplace.visualstudio.com/items?itemName=denbi.denbi-benten-cwl)" +in the marketplace. The name of the client extension is deNBI/denbi-benten. Follow the usual method to install the extension. If you have not installed the Benten server separately (see below) then the @@ -61,7 +61,7 @@ If you will be installing from source you will need ## Using pipx -A neat way to install `benten` in a virtual env (isolating it from your +A neat way to install `denbi-benten` in a virtual env (isolating it from your system python) and still be able to call it as a regular executable is to use `pipx` @@ -72,18 +72,18 @@ pipx ensurepath # ensures CLI application directory is on your $PATH Now you can install Benten with ``` -pipx install benten +pipx install denbi-benten ``` If you already have Benten installed you can upgrade it ``` -pipx upgrade benten +pipx upgrade denbi-benten ``` If your base python install is earlier than 3.7 you can tell `pipx` to use 3.7 for Benten ``` -pipx install benten --python python3.7 +pipx install denbi-benten --python python3.7 ``` @@ -114,25 +114,25 @@ have to shutdown the server (e.g. by exiting VS Code) before updating. ### Installing versions directly from github -To install from the master branch +To install from the main branch ``` -pipx install git+https://github.com/rabix/benten.git +pipx install git+https://github.com/denbi/denbi-benten.git ``` To install from develop branch (or some other branch): ``` -pipx install git+https://github.com/rabix/benten.git@develop +pipx install git+https://github.com/denbi/denbi-benten.git@develop ``` Or, if you have cloned the repository and want to play with the server code itself: ``` -pipx install -e benten # benten is the name of the directory with the cloned code +pipx install -e denbi-benten # denbi-benten is the name of the directory with the cloned code ``` # Using with VI/Vim -See [this page](https://github.com/rabix/benten/blob/master/docs/vim.md) please. +See [this page](https://github.com/denbi/denbi-benten/blob/main/docs/vim.md) please. # Expression evaluations on hover @@ -192,7 +192,7 @@ See the [development documentation](docs/developer.md) auto-downloading feature on the VS Code extension. [Peter van Heusden](https://github.com/pvanheus/) for the -Benten Conda [distribution](https://github.com/conda-forge/benten-feedstock). +Benten Conda [distribution](https://github.com/conda-forge/denbi-benten-feedstock). The low level client-server communication [code][jsonrpc-code] is taken from [Sourcegraph's (now defunct) Python Language Server][sourcegraph-python] as is the VS Code client code (which diff --git a/docs/developer.md b/docs/developer.md index fcc1ce1..1d12259 100644 --- a/docs/developer.md +++ b/docs/developer.md @@ -63,7 +63,7 @@ vsce package Upload the `.vsix` file to [Marketplace] [Marketplace]: -https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl +https://marketplace.visualstudio.com/items?itemName=denbi.denbi-benten-cwl ### Code organization @@ -144,4 +144,4 @@ $ virtualenv --python python3 build-fpm/usr/share/$python/dist/benten $ build-fpm/usr/share/python-3.7/dist/benten/bin/pip install . $ fpm -s dir -t deb -v $version -n benten -C build-fpm --depends python3 usr/share/$python/dist/benten/bin/benten-ls=/usr/bin/ . -``` \ No newline at end of file +``` diff --git a/docs/features.md b/docs/features.md index 8404286..bf93f3a 100644 --- a/docs/features.md +++ b/docs/features.md @@ -1,61 +1,61 @@ # Feature screenshots
- +
Syntax highlighting (CWL and JS)
- +
Evaluate expression on hover
- +
File path autocomplete for linked files in `run` field
- +
Port completion for workflow
- +
Navigate to linked sub-workflows and includes
- +
Outline view (Symbols) + Step symbols
- +
Type validations
- +
Port validations
- +
Language documentation on hover
- +
CWL Formatting
diff --git a/docs/vim.md b/docs/vim.md index 743773a..83e1ca1 100644 --- a/docs/vim.md +++ b/docs/vim.md @@ -1,7 +1,7 @@ # Running Benten with vim +src="https://github.com/denbi/denbi-benten/blob/main/media/2019.10.22/vi-type-hover.png"> ## Ensure you have a recent version of VIM diff --git a/setup.py b/setup.py index 8f3611d..ac1630e 100644 --- a/setup.py +++ b/setup.py @@ -33,11 +33,9 @@ }, author='Seven Bridges Genomics Inc.', - maintainer='Seven Bridges Genomics Inc.', - maintainer_email='kaushik.ghose@sbgenomics.com', - author_email='kaushik.ghose@sbgenomics.com', - description='CWL language server developed by Seven Bridges', - url='https://github.com/rabix/benten', + maintainer='de.NBI', + description='denbi fork of CWL language server developed by Seven Bridges', + url='https://github.com/denbi/denbi-benten', long_description=long_description, long_description_content_type="text/markdown", include_package_data=True, diff --git a/tests/cwl/misc/wf-remote-steps.cwl b/tests/cwl/misc/wf-remote-steps.cwl index 95b87f7..940ec40 100644 --- a/tests/cwl/misc/wf-remote-steps.cwl +++ b/tests/cwl/misc/wf-remote-steps.cwl @@ -11,13 +11,13 @@ inputs: steps: step1: - run: https://raw.githubusercontent.com/rabix/benten/4223a4/tests/cwl/misc/clt1.cwl + run: https://raw.githubusercontent.com/denbi/denbi-benten/4223a4/tests/cwl/misc/clt1.cwl in: in1: in1 out: [out1] step2: - run: https://raw.githubusercontent.com/rabix/benten/5223a4/tests/cwl/misc/clt1.cwl + run: https://raw.githubusercontent.com/denbi/denbi-benten/5223a4/tests/cwl/misc/clt1.cwl in: in1: in1 out: [out1] diff --git a/vscode-client/Readme.md b/vscode-client/Readme.md index f76f363..1a29a2b 100644 --- a/vscode-client/Readme.md +++ b/vscode-client/Readme.md @@ -1,6 +1,6 @@ # VS Code plugin for Rabix/Benten CWL language server - + - Syntax highlighting (CWL and JS) - Evaluate expression on hover @@ -12,18 +12,18 @@ - Port validations - CWL Documentation on hover -[(Click for feature screenshot gallery)](https://github.com/rabix/benten/blob/master/docs/features.md) +[(Click for feature screenshot gallery)](https://github.com/denbi/denbi-benten/blob/main/docs/features.md) # Server installation -This extension requires the [Benten CWL Language -Server](https://github.com/rabix/benten). If you have not already [installed the -server](https://github.com/rabix/benten/tree/kg/dist-installs#server-installation) +This extension requires the [de.NBI Benten CWL Language +Server](https://github.com/denbi/denbi-benten). If you have not already [installed the +server](https://github.com/denbi/denbi-benten/tree/main/dist-installs#server-installation) the extension will attempt to download the matching server version automatically from `github`. -For more detailed information please see the [project page](https://github.com/rabix/benten). +For more detailed information please see the [project page](https://github.com/denbi/denbi-benten).
(c) 2019-2021 Seven Bridges Genomics. Rabix is a registered trademark of Seven Bridges Genomics diff --git a/vscode-client/package.json b/vscode-client/package.json index 4a5cbfa..1d53920 100644 --- a/vscode-client/package.json +++ b/vscode-client/package.json @@ -1,7 +1,7 @@ { "name": "benten-cwl", - "publisher": "sbg-rabix", - "displayName": "CWL (Rabix/Benten)", + "publisher": "denbi", + "displayName": "CWL (de.NBI/Benten)", "description": "Autocomplete, code validation and more for CWL documents", "version": "2021.1.25", "preview": false, @@ -17,11 +17,10 @@ "license": "Apache-2.0", "repository": { "type": "git", - "url": "https://github.com/rabix/benten.git" + "url": "https://github.com/denbi/denbi-benten.git" }, "bugs": { - "url": "https://github.com/rabix/benten/issues", - "email": "rabix@sbgenomics.com" + "url": "https://github.com/denbi/denbi-benten/issues" }, "categories": [ "Programming Languages"