gicentre · kachkaev · Mar 26, 2018 · Mar 26, 2018 · Mar 26, 2018 · Mar 26, 2018
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+out/**/* linguist-generated
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
 .DS_Store
 node_modules
 npm-debug.log
+yarn-error.log
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,175 @@
+## 0.34.0
+
+- Sync fork with the upstream `mume` library
+- Upgrade vega to 5.21.0, vega-lite to 5.1.1, vega-embed to 6.19.1 and vega-loader to 4.4.1
+- Upgrade some auxiliary dependencies and make a few small refactors
+
+## 0.33.1
+
+- Fix apache arrow loader
+
+## 0.33.0
+
+- Upgrade `vega-lite` from v4 to v5
+- Change how `vega`, `vega-embed`, `vega-lite`, `vega-loader`, `loader-arrow` and `apache-arrow` are embedded.
+  The versions are no longer pinned.
+  To upgrade to the latest version in the curren semver major band, all you need is to reinstall the extension.
+
+## 0.32.0
+
+- Upgrade vega to 5.19.1
+- Upgrade `immer` to 8.0.1 to mitigate [CVE-2020-28477](https://nvd.nist.gov/vuln/detail/CVE-2020-28477)
+
+## 0.31.0
+
+- Upgrade vega to 5.18.0, vega-embed to 6.15.0, apache-arrow to 2.0.0 and vega-loader-arrow to 0.0.9
+
+## 0.30.0
+
+- Upgrade vega to 5.17.0, vega-lite to 4.17.0 and vega-embed to 6.12.2
+
+## 0.29.0
+
+- Upgrade vega to 5.15.0 and vega-lite to 4.15.0
+- Fix caching issue (<https://github.com/gicentre/litvis/issues/47>)
+- Bump dependencies
+
+## 0.28.0
+
+- Sync this fork with the upstream project
+- Upgrade vega to 5.14.0 and vega-embed to 6.11.1, fix CDN vega versions
+
+## 0.27.0
+
+- Upgrade vega-lite to 4.14.1 and vega-embed to 6.10.0
+
+## 0.26.0
+
+- Upgrade vega to 5.13.0, vega-lite to 4.13.1 and vega-embed to 6.9.0
+
+## 0.25.0
+
+- Upgrade vega to 5.10.1, vega-lite to 4.10.2 and vega-embed to 6.5.2
+
+## 0.24.0
+
+- Upgrade vega-lite to 4.8.1 and vega-embed to 6.5.1
+
+## 0.23.0
+
+- Upgrade vega to 5.10.0, vega-lite to 4.5.1, vega-embed to 6.3.2 and apache-arrow to 0.16.0
+
+## 0.22.0
+
+- Upgrade vega-lite to 4.3.1
+
+## 0.21.0
+
+- Upgrade vega to 5.9.1, vega-lite to 4.1.1 and vega-embed to 6.2.2
+
+## 0.20.1
+
+- Upgrade vega to 5.9.0, vega-lite to 4.0.0 and vega-embed to 6.2.1
+
+## 0.20.0
+
+- Upgrade vega-lite to 4.0.0-beta.11, fix outdated vega versions in CDN links (affects interactive mode only)
+
+## 0.19.0
+
+- Fix compatibility with Atom 1.41
+- Update apache-arrow to 0.15.0, vega to 5.7.3, vega-lite to 4.0.0-beta.10 and vega-embed to 6.0.0
+
+## 0.18.0
+
+- Upgrade vega to 5.7.0, vega-lite to 4.0.0-beta.8, vega-embed to 5.1.3 and vega-loader-arrow to 0.14.1
+
+## 0.17.0
+
+- Sync with upstream package to resolve various issues in the latest versions of editors (<https://github.com/gicentre/markdown-preview-enhanced-with-litvis/pull/1>)
+
+## 0.16.0
+
+- Upgrade vega to 5.4.0 and vega-embed to 4.2.0
+- Support apache-arrow files in vega specs (<https://github.com/gicentre/litvis/issues/31>)
+- Fix incorrect parsing of keys in elm string representation (<https://github.com/gicentre/litvis/issues/29#issuecomment-496008915>)
+
+## 0.15.3
+
+- Upgrade vega to 5.3.5 and vega-lite to 3.2.1
+- \[elm-string-representation] Allow any strings in keys except `" = "`
+
+## 0.15.2
+
+- Upgrade vega to 5.3.2, vega-lite to 3.0.2 and vega-embed to 4.0.0
+- Use JSDelivr as lib CDN instead of CloudFlare
+
+## 0.15.1
+
+- Downgrade vega from 5.3.0 to 5.1.0 to avoid `Error: Cycle detected in dataflow graph`
+
+## 0.15.0
+
+- New command: _Markdown Preview Enhanced with Litvis: Clear Cache_ (useful when need to upgrade Elm dependencies or when cache is corrupt)
+- Fix a number of regressions in Elm output parsing and URL fetching
+- Improve error handling in a couple of edge cases
+- Upgrade vega to 5.3.0
+
+## 0.14.0
+
+- Upgrade vega to 5.0.0, vega-lite to 3.0.0-rc14 and vega-embed to 4.0.0-rc1 ([gicentre/mume-with-litvis#11bc9651](https://github.com/gicentre/mume-with-litvis/commit/11bc96514feedadd7e125398f3fee3fc5ff3a630))
+
+## 0.13.0
+
+- Add ability to highlight lines of code ([gicentre/litvis#9](https://github.com/gicentre/litvis/issues/9), [shd101wyy/mume#100](https://github.com/shd101wyy/mume/pull/100), [mume-with-litvis#5074ca39](https://github.com/gicentre/mume-with-litvis/commit/5074ca39a24ff86ef8ddc63c35f33b212e2da984))
+
+## 0.12.0
+
+- Upgrade vega to 4.4.0, vega-lite to 3.0.0-rc10 and vega-embed to 3.26.1 ([gicentre/mume-with-litvis#429dcf63](https://github.com/gicentre/mume-with-litvis/commit/429dcf6370191cfc8b421923a6283d4f7bdc7625))
+
+- Fix a few minor bugs ([gicentre/litvis#11](https://github.com/gicentre/litvis/issue/11),
+  [gicentre/litvis#12](https://github.com/gicentre/litvis/issue/12),
+  [gicentre/litvis#13](https://github.com/gicentre/litvis/issue/13),
+  [gicentre/litvis#14](https://github.com/gicentre/litvis/issue/14),
+  [gicentre/litvis#15](https://github.com/gicentre/litvis/issue/15),
+  [gicentre/litvis#16](https://github.com/gicentre/litvis/issue/16),
+  [gicentre/litvis#17](https://github.com/gicentre/litvis/issue/17))
+
+## 0.11.0
+
+- Implement markdown output from litvis blocks ([gicentre/litvis#10](https://github.com/gicentre/litvis/pull/10))
+
+## 0.10.0
+
+- **Switch to Elm 0.19**. Elm 0.18 users please use version 0.9.0 of this atom package (`apm install [email protected]`)
+- Upgrade vega to 4.3.0, vega-lite to 3.0.0-rc6 and vega-embed to 3.20.0
+
+## 0.9.0
+
+- Upgrade vega to 4.2.0, Vega-Lite to 3.0.0-rc3 and vega-embed to 3.18.2
+
+## 0.7.0
+
+- Improve parsing of narrative schemas, support label aliases and fix rules
+
+## 0.6.1
+
+- Suggest installing dependencies of `linter-ui-default` too to reduce the number of clicks by user
+
+## 0.6.0
+
+- Use `atom-package-deps` to prompt about installing `linter-ui-default`
+- Merge from upstream to use better config defaults
+
+## 0.5.2-0.5.6
+
+- Fix path detection for elm binaries
+
+## 0.5.1
+
+- Use a local copy of `elm` to avoid its setup via npm
+- use an OS-specific temp directory (`echo $TMPDIR`) instead of hard-coded `/tmp/literate-elm`
+
+## 0.5.0
+
+- Upgrade `vega` to `3.3.1`, `vega-lite` to `2.4.0` and `vega-embed` to `3.7.2` ([shd101wyy/mume#65](https://github.com/shd101wyy/mume/pull/65)).
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,3 +1,43 @@
+# litvis
+
+_contributions by https://github.com/orgs/gicentre/people_
+
+BSD 3-Clause License
+
+```
+Copyright (c) 2017-present, giCentre, City University London
+All rights reserved.
+```
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+- Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# original markdown-preview-enhanced
+
+_https://github.com/shd101wyy/markdown-preview-enhanced_
+
 University of Illinois/NCSA
 Open Source License
 

diff --git a/README.md b/README.md
@@ -1,83 +1,91 @@
-<h1 align="center"> Markdown Preview Enhanced </h1>
-<p align="center">
-<a href="https://github.com/shd101wyy/markdown-preview-enhanced/releases"><img src="https://img.shields.io/github/tag/shd101wyy/markdown-preview-enhanced.svg"></a>
-<a href="https://github.com/shd101wyy/markdown-preview-enhanced"><img src="https://img.shields.io/apm/dm/markdown-preview-enhanced.svg"></a>
-<a href="https://github.com/shd101wyy/markdown-preview-enhanced"><img src="https://img.shields.io/github/stars/shd101wyy/markdown-preview-enhanced.svg?style=social&label=Star"></a>
-</p>
-<br>
+# Atom `markdown-preview-enhanced` with [litvis](http://litvis.org/)
 
-![intro](https://user-images.githubusercontent.com/1908863/28227953-eb6eefa4-68a1-11e7-8769-96ea83facf3b.png)
+This project is a fork of [`markdown-preview-enhanced`](https://github.com/shd101wyy/markdown-preview-enhanced), which is a popular [Atom package](https://atom.io/packages/markdown-preview-enhanced) for previewing markdown files.
+Most of the code in this fork is inherited from the upstream repository and is thus courtesy of [@shd101wyy](https://github.com/shd101wyy) and other [contributors](https://github.com/shd101wyy/markdown-preview-enhanced/graphs/contributors) to `markdown-preview-enhanced`.
 
-<p align="center">
-<a href="https://shd101wyy.github.io/markdown-preview-enhanced/#/"> English &nbsp;&nbsp; </a>
-<a href="https://shd101wyy.github.io/markdown-preview-enhanced/#/zh-cn/"> 简体中文 &nbsp;&nbsp; </a>
-<a href="https://shd101wyy.github.io/markdown-preview-enhanced/#/zh-tw/"> 正體中文 &nbsp;&nbsp; </a>
-<a href="https://shd101wyy.github.io/markdown-preview-enhanced/#/ja-jp/"> 日本語 &nbsp;&nbsp; </a> <br>
-</p>
+The fork produces an Atom package called [`markdown-preview-enhanced-with-litvis`](https://atom.io/packages/markdown-preview-enhanced-with-litvis), which enables _Literate Visualisation_ ([litvis](http://litvis.org/)) in rendered markdown previews.
 
-<p align="center">
-<a href="https://atom.io/packages/markdown-preview-enhanced">atom</a>
-&
-<a href="https://marketplace.visualstudio.com/items?itemName=shd101wyy.markdown-preview-enhanced">vscode</a>
-</p>
+Litvis functionality has been designed and developed at [giCentre](https://www.gicentre.net/) by [Jo Wood](https://github.com/jwoLondon), [Alexander Kachkaev](https://github.com/kachkaev) and [Jason Dykes](https://github.com/jsndyks).
+This research was in part supported by the EU under the EC Grant Agreement No. FP7-IP-608142 to Project [VALCRI](http://valcri.org/).
 
-If you are interested, please also try out our new prototype web app: [0xGG/crossnote](https://github.com/0xGG/crossnote)
+## Prerequisites
 
-## Supporting this project
+Please ensure that you have `elm` installed on your machine before proceeding to the setup.
+The following command will ensure that this tool is in place and is up-to-date.
 
-Markdown Preview Enhanced is an open source project released under the [University of Illinois/NCSA Open Source License](LICENSE.md). Its ongoing development is made possible thanks to the support by these awesome [backers](https://shd101wyy.github.io/markdown-preview-enhanced/#/backers). You can help make this project better by [supporting us on GitHub Sponsors](https://github.com/sponsors/shd101wyy), [PayPal](https://shd101wyy.github.io/markdown-preview-enhanced/#/paypal), or [微信支付 Wechat Pay](https://shd101wyy.github.io/markdown-preview-enhanced/#/wechat). Thank you!
+```bash
+npm install --global elm
+```
 
-## Sponsors
+If you don’t have npm, please download it as a part of Node.js from https://nodejs.org/.
 
-<p><a title="Try CodeStream" href="https://sponsorlink.codestream.com/?utm_source=vscmarket&amp;utm_campaign=shd101wyy-markdown&amp;utm_medium=banner"><img src="https://alt-images.codestream.com/codestream_logo_shd101wyy-markdown.png"></a></br>
-Manage pull requests and conduct code reviews in your IDE with full source-tree context. Comment on any line, not just the diffs. Use jump-to-definition, your favorite keybindings, and code intelligence with more of your workflow.<br> <a title="Try CodeStream" href="https://sponsorlink.codestream.com/?utm_source=vscmarket&amp;utm_campaign=shd101wyy-markdown&amp;utm_medium=banner">Learn More</a></p>
+## Setup for Atom users
 
-<br>
+### Via Atom’s GUI
 
-<a href="https://github.com/sponsors/shd101wyy">
-  <img src="https://github.blog/wp-content/uploads/2019/05/mona-heart-featured.png?" width="200"></a><br>
+1.  Go to _Preferences_ → _Packages_ and disable `markdown-preview` (Atom’s standard preview tool)
 
-These [GitHub Sponsors](https://github.com/sponsors/shd101wyy#sponsors) and [Backers](https://shd101wyy.github.io/markdown-preview-enhanced/#/backers) help push this project forward 🎉.
+1.  If you are using `markdown-preview-enhanced`, temporary disable it too while you are trying out this fork.
 
-## Introduction
+1.  Switch to _Install_ section in _Preferences_ and search for `markdown-preview-enhanced-with-litvis`.
+    Click _Install_ and reload Atom.
 
-Markdown Preview Enhanced is an extension that provides you with many useful functionalities such as automatic scroll sync, [math typesetting](https://shd101wyy.github.io/markdown-preview-enhanced/#/math), [mermaid](https://shd101wyy.github.io/markdown-preview-enhanced/#/diagrams?id=mermaid), [PlantUML](https://shd101wyy.github.io/markdown-preview-enhanced/#/diagrams?id=plantuml), [pandoc](https://shd101wyy.github.io/markdown-preview-enhanced/#/pandoc), PDF export, [code chunk](https://shd101wyy.github.io/markdown-preview-enhanced/#/code-chunk), [presentation writer](https://rawgit.com/shd101wyy/markdown-preview-enhanced/master/docs/presentation-intro.html), etc. A lot of its ideas are inspired by [Markdown Preview Plus](https://github.com/atom-community/markdown-preview-plus) and [RStudio Markdown](http://rmarkdown.rstudio.com/).
+### Via command line
 
-Feel free to ask questions, post issues, submit pull request, and request new features.
+This section contains shortcut commands for the instructions above.
 
-For more information about this project and how to use this extension, please check out our documentation ⬇︎
+```
+apm disable markdown-preview
+apm disable markdown-preview-enhanced
+apm install markdown-preview-enhanced-with-litvis
+```
 
-## Documentation
+## Getting started with litvis narratives
 
-To check out the documentation, visit
+Literate visualization uses [Elm](http://elm-lang.org) and [Vega-Lite](https://vega.github.io/vega-lite) in the form of a declarative visualization language [elm-vega](http://package.elm-lang.org/packages/gicentre/elm-vega/latest).
+While you don't have to use elm-vega in a litvis document, it does enable quick declarative generation of interactive data graphics and therefore considerably enhances the capability of a litvis document.
 
-- [English](https://shd101wyy.github.io/markdown-preview-enhanced/#/)
-- [简体中文](https://shd101wyy.github.io/markdown-preview-enhanced/#/zh-cn/)
-- [正體中文](https://shd101wyy.github.io/markdown-preview-enhanced/#/zh-tw/)
-- [日本語](https://shd101wyy.github.io/markdown-preview-enhanced/#/ja-jp/)
+Creating your own litvis narrative is as easy as writing a markdown file.
+You can start with exploring the examples available at
+https://github.com/gicentre/litvis/tree/master/examples.
 
-Contact me if you are willing to help translate the documentation :)
+## Formatting litvis narratives
 
-## Keybindings
+It is possible to automatically format litvis-enabled markdown files (including Elm code blocks) using [Prettier](https://prettier.io/), which is a popular code formatting tool.
 
-> The <kbd>cmd</kbd> key for _Windows_ is <kbd>ctrl</kbd>.
+Prettier is available in Atom via [`prettier-atom`](https://github.com/prettier/prettier-atom) package, but it does not format literate Elm code blocks in markdown files out of the box.
 
-| Shortcuts                                   | Functionality              |
-| ------------------------------------------- | -------------------------- |
-| <kbd>ctrl-shift-m</kbd>                     | Toggle preview             |
-| <kbd>ctrl-shift-s</kbd>                     | Sync preview / Sync source |
-| <kbd>shift-enter</kbd>                      | Run Code Chunk             |
-| <kbd>ctrl-shift-enter</kbd>                 | Run all Code Chunks        |
-| <kbd>cmd-=</kbd> or <kbd>cmd-shift-=</kbd>  | Preview zoom in            |
-| <kbd>cmd--</kbd> or <kbd>cmd-shift-\_</kbd> | Preview zoom out           |
-| <kbd>cmd-0</kbd>                            | Preview reset zoom         |
-| <kbd>esc</kbd>                              | Toggle sidebar TOC         |
+Please follow these steps to enable full-featured formatting support for litvis in Atom:
 
-## Changelog
+1.  Globally install Prettier and its [Elm plugin](https://github.com/gicentre/prettier-plugin-elm) via npm:
 
-Newest updates for the current minor version can be found at the [newest notes](https://shd101wyy.github.io/markdown-preview-enhanced/#/newest).
-Detailed changes for each old release can be found at [history notes](https://shd101wyy.github.io/markdown-preview-enhanced/#/history).
+    ```
+    npm install --global prettier prettier-plugin-elm
+    ```
 
-## License
+1.  Install `prettier-atom` package via Atom’s _Preferences_ or from a command line:
 
-[University of Illinois/NCSA Open Source License](LICENSE.md)
+    ```bash
+    apm install prettier-atom
+    ```
+
+1.  Enable _Format on save_ in `prettier-atom` package preferences.
+
+## Getting linting feedback for litvis narratives
+
+When a currently opened litvis narrative contains issues such as errors in Elm code blocks, you are automatically shown a list of problems via Atom's built-in linter.
+
+![kapture 2018-03-26 at 21 00 45](https://user-images.githubusercontent.com/608862/37930310-4ba86c40-313a-11e8-99f5-a6b7ac99f38c.gif)
+
+If you have used Atom linting for any programming language before, all the necessary packages should be already installed.
+Otherwise, please install Atom packages named [`linter`](https://atom.io/packages/linter), [`linter-ui-default`](https://atom.io/packages/linter-ui-default), [`intentions`](https://atom.io/packages/intentions) and [`busy-signal`](https://atom.io/packages/busy-signal).
+
+You will be prompted to do so when you open a litvis document for the first time.
+Alternatively, you can install the packages via Atom’s _Preferences_ or by using the following command:
+
+```bash
+apm install linter linter-ui-default intentions busy-signal
+```
+
+When you are working on branching litvis narratives or those depending on narrative schemas, you may benefit from going to `linter-ui-default` settings and changing _Panel Represents_ parameter to _Entire project_.
+This will make the list of reported issues more informative.
diff --git a/keymaps/markdown-preview-enhanced.cson b/keymaps/markdown-preview-enhanced.cson
@@ -11,9 +11,9 @@
 # I disabled this because for package like `language-markdown`, the `data-grammer` attribute is different.
 # 'atom-workspace atom-text-editor[data-grammar*="gfm"], .platform-win32 atom-workspace atom-text-editor[data-grammar*="gfm"], .platform-linux atom-workspace atom-text-editor[data-grammar="source gfm"], .platform-darwin atom-workspace atom-text-editor[data-grammar="source gfm"]':
 'atom-text-editor':
-  'ctrl-shift-m': 'markdown-preview-enhanced:toggle'
+  'ctrl-shift-m': 'markdown-preview-enhanced-with-litvis:toggle'
 
 '.editor[data-grammar*="gfm"], .editor[data-grammar*="md"], .editor[data-grammar*="markdown"]':
-  'shift-enter': 'markdown-preview-enhanced:run-code-chunk'
-  'ctrl-shift-enter': 'markdown-preview-enhanced:run-all-code-chunks'
-  'ctrl-shift-s': 'markdown-preview-enhanced:sync-preview'
+  'shift-enter': 'markdown-preview-enhanced-with-litvis:run-code-chunk'
+  'ctrl-shift-enter': 'markdown-preview-enhanced-with-litvis:run-all-code-chunks'
+  'ctrl-shift-s': 'markdown-preview-enhanced-with-litvis:sync-preview'
diff --git a/markdown.png b/markdown.png