propagate package & branch rename

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

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/ .
 
-```
+```

docs/features.md

@@ -1,61 +1,61 @@
 # Feature screenshots
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/syntax-highlighting.png"></img>    
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/syntax-highlighting.png"></img>    
     <figcaption>Syntax highlighting (CWL and JS)</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/expression-evaluation-on-hover.png"></img>    
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/expression-evaluation-on-hover.png"></img>    
     <figcaption>Evaluate expression on hover</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/file-picker.png"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/file-picker.png"></img>
     <figcaption>File path autocomplete for linked files in `run` field</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/port-connection-picker.png"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/port-connection-picker.png"></img>
     <figcaption>Port completion for workflow</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/jump-to-definition.gif"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/jump-to-definition.gif"></img>
     <figcaption>Navigate to linked sub-workflows and includes</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/outline-view.png"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/outline-view.png"></img>
     <figcaption>Outline view (Symbols) + Step symbols</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/type-warnings.png"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/type-warnings.png"></img>
     <figcaption>Type validations</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2019.10.22/workflow-connection-validations.png"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2019.10.22/workflow-connection-validations.png"></img>
     <figcaption>Port validations</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2020.03.09/documentation-on-hover.png"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2020.03.09/documentation-on-hover.png"></img>
     <figcaption>Language documentation on hover</figcaption>
 </figure>  
 <hr/>
 
 <figure>
-    <img src="https://github.com/rabix/benten/blob/master/media/2020.09.15/format-document.gif"></img>
+    <img src="https://github.com/denbi/benten/blob/main/media/2020.09.15/format-document.gif"></img>
     <figcaption>CWL Formatting</figcaption>
 </figure>  
 <hr/>

docs/vim.md

@@ -1,7 +1,7 @@
 # Running Benten with vim 
 
 <img height="400px"
-src="https://github.com/rabix/benten/blob/master/media/2019.10.22/vi-type-hover.png"></img>
+src="https://github.com/denbi/denbi-benten/blob/main/media/2019.10.22/vi-type-hover.png"></img>
 
 
 ## Ensure you have a recent version of VIM

setup.py

@@ -33,11 +33,9 @@
     },
 
     author='Seven Bridges Genomics Inc.',
-    maintainer='Seven Bridges Genomics Inc.',
-    maintainer_email='[email protected]',
-    author_email='[email protected]',
-    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,

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]

vscode-client/Readme.md

@@ -1,6 +1,6 @@
 # VS Code plugin for Rabix/Benten CWL language server
 
-<img height="400px" src="https://raw.githubusercontent.com/rabix/benten/master/media/2019.12.03/full-window.png"></img>
+<img height="400px" src="https://raw.githubusercontent.com/denbi/denbi-benten/main/media/2019.12.03/full-window.png"></img>
 
 - 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).
 
 <div align="right">
 <sub>(c) 2019-2021 Seven Bridges Genomics. Rabix is a registered trademark of Seven Bridges Genomics</sub>

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": "[email protected]"
+    "url": "https://github.com/denbi/denbi-benten/issues"
   },
   "categories": [
     "Programming Languages"