Merge pull request #496 from IvoLeist/add-dash-ngl

Added dash-ngl component.

Author: HammadTheOne

.Rbuildignore

@@ -7,6 +7,11 @@ lib/
 .builderrc
 .eslintrc
 .npmignore
+.editorconfig
+.eslintignore
+.prettierrc
+.circleci
+.github
 
 # demo folder has special meaning in R
 # this should hopefully make it still
@@ -15,14 +20,15 @@ demo/.*\.js
 demo/.*\.html
 demo/.*\.css
 
-# ignore python files/folders
+# ignore Python files/folders
+setup.py
+usage.py
 setup.py
-index.py
-config.py
 requirements.txt
 MANIFEST.in
 CHANGELOG.md
-tests/
-.pylintrc
+test/
+# CRAN has weird LICENSE requirements
+LICENSE.txt
 ^.*\.Rproj$
 ^\.Rproj\.user$

.circleci/config.yml

@@ -34,7 +34,7 @@ jobs:
                     . venv/bin/activate
                     git clone --depth 1 https://github.com/plotly/dash.git dash-main
                     cd dash-main && pip install -e .[dev,testing]
-                    cd dash-renderer && npm run build && pip install -e . && cd ../..
+                    cd dash-renderer && npm ci && npm run build && pip install -e . && cd ../..
                     npm run build
 
             - run:
@@ -84,7 +84,7 @@ jobs:
                     . venv/bin/activate
                     git clone --depth 1 https://github.com/plotly/dash.git dash-main
                     cd dash-main && pip install -e .[dev,testing]
-                    cd dash-renderer && npm run build && pip install -e . && cd ../..
+                    cd dash-renderer && npm ci && npm run build && pip install -e . && cd ../..
 
             - run:
                 name: Run pylint

.gitignore

@@ -31,6 +31,7 @@ venv
 *.pyc
 
 # builds
+dash-main/
 dash_bio.egg-info
 dist
 *__pycache__*
@@ -41,3 +42,7 @@ __pycache__/
 venv/
 
 .env
+
+# editors
+.vscode/
+.idea/

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.5.0] - 2020-10-05
+### Added
+* [#496](https://github.com/plotly/dash-bio/pull/496) Added Dash-NGL-Moleculeviewer component.
+
 ## [0.4.8] - 2020-03-16
 ### Changed
 * [#489](https://github.com/plotly/dash-bio/pull/489) Renamed async modules with hyphen `-` instead of tilde `~`

CONTRIBUTING.md

@@ -154,12 +154,14 @@ To run integration tests locally on, say, Google Chrome:
 python -m venv venv
 . venv/bin/activate
 pip install -r tests/requirements.txt
-pip install dash[testing]
-pytest tests/integration
+pip install dash[testing] #if you use zsh run: pip install dash\[testing\]
+pip install dash-bio #if pytest fails try: pip3 install dash-bio
+pytest tests/integration #for testing all apps
+pytest tests/integration/test_yourNewApp #for testing only one app 
 ```
 Do not worry if you get errors running this last command. You will have to
-download a Chrome driver, install it, and add its path. Follow what the error
-messages point to (this will be platform-specific).
+download a Chrome driver (Linux:chromium), install it, and add its path.
+Follow what the error messages point to (this will be platform-specific).
 
 To write more integration tests, please read this
 [tutorial](https://dash.plotly.com/testing).

DESCRIPTION

@@ -1,16 +1,14 @@
 Package: dashBio
 Title: Open-source Bioinformatics Components for Dash
-Version: 0.4.5
+Version: 0.5.0
 Description: A suite of components that makes it simpler to analyze and visualize bioinformatics data and interact with them in a Dash application.
 Depends: R (>= 3.0.2), manhattanly
-Imports: dash 
+Imports: dash
 Suggests: 
+Authors@R: person("The", "Team", role = c("aut", "cre"), email = "[email protected]")
 License: MIT + file LICENSE
 URL: https://github.com/plotly/dash-bio
 BugReports: https://github.com/plotly/dash-bio/issues
 Encoding: UTF-8
 LazyData: true
 KeepSource: true
-Author: The Plotly Team [aut]
-Maintainer: Ryan Patrick Kyle <[email protected]>
-RoxygenNote: 6.1.1

NAMESPACE

@@ -1,4 +1,4 @@
-#AUTO GENERATED FILE - DO NOT EDIT
+# AUTO GENERATED FILE - DO NOT EDIT
 
 export(dashbioAlignmentChart)
 export(dashbioCircos)
@@ -7,9 +7,12 @@ export(dashbioIdeogram)
 export(dashbioMolecule2dViewer)
 export(dashbioMolecule3dViewer)
 export(dashbioNeedlePlot)
+export(dashbioNglMoleculeViewer)
 export(dashbioOncoPrint)
 export(dashbioSequenceViewer)
 export(dashbioSpeck)
-export(dashbioManhattan)
 export(dashbioVolcano)
+export(dashbioManhattan)
 import(manhattanly)
+
+import(dash)

R/dashbioNglMoleculeViewer.R

@@ -0,0 +1,18 @@
+# AUTO GENERATED FILE - DO NOT EDIT
+
+dashbioNglMoleculeViewer <- function(id=NULL, width=NULL, height=NULL, stageParameters=NULL, imageParameters=NULL, downloadImage=NULL, pdbString=NULL, data=NULL, molStyles=NULL) {
+    
+    props <- list(id=id, width=width, height=height, stageParameters=stageParameters, imageParameters=imageParameters, downloadImage=downloadImage, pdbString=pdbString, data=data, molStyles=molStyles)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
+    component <- list(
+        props = props,
+        type = 'NglMoleculeViewer',
+        namespace = 'dash_bio',
+        propNames = c('id', 'width', 'height', 'stageParameters', 'imageParameters', 'downloadImage', 'pdbString', 'data', 'molStyles'),
+        package = 'dashBio'
+        )
+
+    structure(component, class = c('dash_component', 'list'))
+}

R/internal.R

@@ -1,114 +1,126 @@
 .dashBio_js_metadata <- function() {
 deps_metadata <- list(`dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~alignment.js',
+script = 'async-alignment.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~circos.js',
+script = 'async-circos.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~ideogram.js',
+script = 'async-ideogram.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~moleculeviewer2.js',
+script = 'async-moleculeviewer2.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~moleculeviewer3.js',
+script = 'async-moleculeviewer3.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~needle.js',
+script = 'async-needle.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~onco.js',
+script = 'async-nglmoleculeviewer.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~sequence.js',
+script = 'async-onco.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~speck.js',
+script = 'async-sequence.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, async = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~alignment.js.map',
+script = 'async-speck.js',
+stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
+all_files = FALSE, async = TRUE), class = "html_dependency"),
+`dash_bio` = structure(list(name = "dash_bio",
+version = "0.5.0", src = list(href = NULL,
+file = "deps"), meta = NULL,
+script = 'async-alignment.js.map',
+stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
+all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
+`dash_bio` = structure(list(name = "dash_bio",
+version = "0.5.0", src = list(href = NULL,
+file = "deps"), meta = NULL,
+script = 'async-circos.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~circos.js.map',
+script = 'async-ideogram.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~ideogram.js.map',
+script = 'async-moleculeviewer2.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~moleculeviewer2.js.map',
+script = 'async-moleculeviewer3.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~moleculeviewer3.js.map',
+script = 'async-needle.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~needle.js.map',
+script = 'async-nglmoleculeviewer.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~onco.js.map',
+script = 'async-onco.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~sequence.js.map',
+script = 'async-sequence.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = 'async~speck.js.map',
+script = 'async-speck.js.map',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE, dynamic = TRUE), class = "html_dependency"),
 `dash_bio` = structure(list(name = "dash_bio",
-version = "0.4.5", src = list(href = NULL,
+version = "0.5.0", src = list(href = NULL,
 file = "deps"), meta = NULL,
 script = 'bundle.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",

README.md

@@ -42,6 +42,7 @@ The Dash Bio components each fall into one of three categories:
 - Dash Mol2D
 - Dash Mol3D
 - Dash Speck
+- Dash Ngl (experimental)
 
 ## Dash