Merge branch 'develop' into 161-cabin

.github/workflows/ci.yml

@@ -0,0 +1,34 @@
+name: Build and Deploy
+
+on: 
+  push:
+    branches: 
+      - '**' # Push events on all branches
+    paths-ignore:
+      - '.github/workflows/init.yml'
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10 including semver
+
+jobs:
+
+  build_docs:
+    runs-on: ubuntu-22.04
+    name: Build, Install, Package documentation
+    if: "!contains(github.event.head_commit.message, 'docs skip')"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install credentials
+      run: echo https://$GITHUB_OAUTH:@github.com > $HOME/.git-credentials
+      env:
+        GITHUB_OAUTH: ${{ secrets.CR_PAT_WORKFLOW }}
+    - name: Build
+      run: |
+        npm install
+        npm run antora
+    - name: Deploy
+      uses: JamesIves/github-pages-deploy-action@v4
+      if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop'
+      with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: public # The folder the action should deploy.

.github/workflows/trigger.yml

@@ -2,7 +2,7 @@ name: Trigger Toolbox Update
 
 on: 
   push:
-    branches: master
+    branches: [master,develop]
 
 jobs:
   build:
@@ -21,4 +21,4 @@ jobs:
         ORG: feelpp
         REPO: book.feelpp.org
       run: |
-        curl -d "{\"event_type\": \"${EVENT}\"}" -H "Content-Type: application/json" -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.everest-preview+json" "https://api.github.com/repos/${ORG}/${REPO}/dispatches"
+        curl -d "{\"event_type\": \"${EVENT}\"}" -H "Content-Type: application/json" -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.everest-preview+json" "https://api.github.com/repos/${ORG}/${REPO}/dispatches"

.gitignore

@@ -4,7 +4,11 @@ Thumbs.db
 *.kate-swp
 build/
 *~
-*.DS_Store
+**/.DS_Store
 *bak
 **/feelppdb
-**/node_modules
+**/node_modules
+public/
+node_modules/
+cache/
+jupyter/

.vscode/settings.json

@@ -22,7 +22,6 @@
     "spellright.documentTypes": [
     ],
     "asciidoc.asciidoctor_command": "asciidoctor",
-    "asciidoc.asciidoctorpdf_command": "asciidoctor-pdf",
     "asciidoc.forceUnixStyleSeparator": true,
     "asciidoc.preview.breaks": false,
     "asciidoc.preview.doubleClickToSwitchToEditor": true,
@@ -31,14 +30,12 @@
     "asciidoc.preview.lineHeight": 1.6,
     "asciidoc.preview.linkify": true,
     "asciidoc.preview.markEditorSelection": true,
-    "asciidoc.preview.openAsciiDocLinks": "inPreview",
-    "asciidoc.preview.scrollEditorWithPreview": true,
+    "asciidoc.preview.scrollEditorWithPreview": false,
     "asciidoc.preview.scrollPreviewWithEditor": true,
     "asciidoc.preview.useEditorStyle": true,
     "asciidoc.previewFrontMatter": "hide",
     "asciidoc.preview.attributes": {},
     "asciidoc.preview.style": "",
     "asciidoc.trace": "off",
-    "asciidoc.use_asciidoctor_js": true,
-    "asciidoc.use_asciidoctorpdf": false
+    "asciidoc.use_asciidoctor_js": true
 }

Gemfile

@@ -1 +1,2 @@
+source "https://rubygems.org"
 gem 'liquid'

README.adoc

@@ -5,6 +5,11 @@ ifdef::env-github,env-browser[]
 endif::[]
 :stem: latexmath
 
+
+image::https://api.netlify.com/api/v1/badges/4026f83d-53a1-4ad6-86e7-b6bda4298cc6/deploy-status[link:https://app.netlify.com/sites/dashing-twilight-9661e1/deploys[Netlify Status]]
+
+
+
 List of Toolboxes
 
 * <<examples/modules/csm/pages/README#,Computational Solid Mechanics>>

contribute/antora.yml

@@ -1,6 +1,13 @@
 name: contribute
-title: Toolbox Contribution Guide
-version: master
+title: Toolboxes Contribution Guide
+version: ~
+asciidoc:
+  attributes:
+    project_name: Toolboxes Contribution Guide
+    plotly: plotly
+    vtkjs: VTK.js
+    feelpp: Feel++
+    girder: Girder    
 nav:
 - modules/ROOT/nav.adoc
 - modules/girder/nav.adoc

contribute/modules/ROOT/examples/tree-example.txt

@@ -1,31 +1,30 @@
 examples
 └── modules
     ├── ROOT
-    │   └── pages
+    │   └── pages
     ├── cfd <1>
-    │   ├── examples <2>
-    │   │   ├── cyclone
-    │   │   │   └── attic
-    │   │   └── flow_past_cylinder <3>
-    │   └── pages <4>
-    │       └── flow_past_cylinder
+    │   ├── examples <2>
+    │   │   ├── cyclone
+    │   │   │   └── attic
+    │   │   └── flow_past_cylinder <3>
+    │   └── pages <4>
+    │       └── flow_past_cylinder
     └── csm <5>
-        ├── assets <6>
-        │   └── images <7>
-        │       ├── ribs <8>
-        │       ├── rotating-winch <8>
-        │       ├── sensor <8>
-        │       ├── sheet-rounding <8>
-        │       ├── suspension <8>
-        │       ├── t-beam <8>
-        │       ├── torsion-bar <8>
-        │       └── vierendeel-truss <8>
+        ├─── images <6>
+        │    ├── ribs <7>
+        │    ├── rotating-winch <7>
+        │    ├── sensor <7>
+        │    ├── sheet-rounding <7>
+        │    ├── suspension <7>
+        │    ├── t-beam <7>
+        │    ├── torsion-bar <7>
+        │    └── vierendeel-truss <7>
         └── pages <4>
-            ├── ribs <9>
-            ├── rotating-winch <9>
-            ├── sensor <9>
-            ├── sheet-rounding <9>
-            ├── suspension <9>
-            ├── t-beam <9>
-            ├── torsion-bar <9>
-            └── vierendeel-truss <9>
+            ├── ribs <8>
+            ├── rotating-winch <8>
+            ├── sensor <8>
+            ├── sheet-rounding <8>
+            ├── suspension <8>
+            ├── t-beam <8>
+            ├── torsion-bar <8>
+            └── vierendeel-truss <8>

contribute/modules/ROOT/pages/index.adoc

@@ -55,15 +55,14 @@ This is how the `examples` tree directory may look like
 --
 include::{examplesdir}/tree-example.txt[]
 --
-<1> example module for the computational fluid dynamic (cfd) toolbox
-<2> `examples` contains the examples input dataset
-<3> example directory `flow_past_cylinder` containing the configuration files (`cfg`, `json`, `geo`, ...)
-<4> `pages` contains the documentation pages where Antora look into to transform `.adoc` files into `.html` files
-<5> example module for the computational solid mechanics (csm) toolbox
-<6> the `assets` directory contains images or data associated to the examples.
-<7> the `assets/images` contains the images of each example
-<8> the images of each example are organized by directory named using the slug name of the example,
-<9> each example documentation is located in a topic directory named using the slug name of the example. The topic directory contains `.adoc` files.
+<.> example module for the computational fluid dynamic (cfd) toolbox
+<.> `examples` contains the examples input dataset
+<.> example directory `flow_past_cylinder` containing the configuration files (`cfg`, `json`, `geo`, ...)
+<.> `pages` contains the documentation pages where Antora look into to transform `.adoc` files into `.html` files
+<.> example module for the computational solid mechanics (csm) toolbox
+<.> the `images` directory contains images associated to the examples.
+<.> the images of each example are organized by directory named using the slug name of the example,
+<.> each example documentation is located in a topic directory named using the slug name of the example. The topic directory contains `.adoc` files.
 
 NOTE: the slug name of a `case` does not contain spaces or dots or any special characters and can for example be used in url.
 
@@ -72,12 +71,12 @@ NOTE: the slug name of a `case` does not contain spaces or dots or any special c
 You need to identify which toolbox the example belongs to.
 here is the list of **slug toolbox name**:
 
-cfd:: xref:toolboxes:cfd:index.adoc[Computational Fluid Dynamics]
-csm:: xref:toolboxes:csm:index.adoc[Computation Solid Mechanics]
-heat:: xref:toolboxes:heat:index.adoc[Heat transfer]
-heatfluid:: xref:toolboxes:heatfluid:index.adoc[Heat and CFD coupling]
-fsi:: xref:toolboxes:fsi:index.adoc[Fluid Structure Interaction (FSI)], CFD and CSM coupling
-thermoelectric:: xref:toolboxes:thermoelectric:index.adoc[Electrostatic and heat coupling]
+cfd:: xref:toolboxes:cfd:manual.adoc[Computational Fluid Dynamics]
+csm:: xref:toolboxes:csm:manual.adoc[Computation Solid Mechanics]
+heat:: xref:toolboxes:heat:manual.adoc[Heat transfer]
+heatfluid:: xref:toolboxes:heatfluid:manual.adoc[Heat and CFD coupling]
+fsi:: xref:toolboxes:fsi:manual.adoc[Fluid Structure Interaction (FSI)], CFD and CSM coupling
+thermoelectric:: xref:toolboxes:thermoelectric:manual.adoc[Electrostatic and heat coupling]
 
 
 The example is then located in the model named after The slug name of the toolbox:
@@ -130,10 +129,10 @@ This step may require
 * [x] generating {plotly} interactive graphics embedded in the browser to show 2D data, convergence plots, ...
 
 The generation of {vtkjs} files is now **preferred** as it permits interaction.
-Have a look at the xref:cases:csm:README.adoc[examples in computational solid mechanics] providing both images and {vtkjs} files.
+Have a look at the xref:toolboxes:csm:README.adoc[examples in computational solid mechanics] providing both images and {vtkjs} files.
 
 NOTE: The image files for the example `electromagnet` in the `thermoelectric` toolbox are in
-link:https://github.com/feelpp/toolbox/tree/master/examples/modules/thermoelectric/assets/images/electromagnet[examples/modules/thermoelectric/assets/images/electromagnet/]
+link:https://github.com/feelpp/toolbox/tree/master/examples/modules/thermoelectric/images/electromagnet[examples/modules/thermoelectric/images/electromagnet/]
 
 NOTE: Read about xref:vtkjs.adoc[how to create and use {vtkjs} files] and about xref:contribute:girder:README.adoc[contributing data using girder].
 

contribute/modules/ROOT/pages/vtkjs.adoc

@@ -15,7 +15,7 @@ The {vtkjs}  are uploaded then to https://girder.math.unistra.fr[Girder] and are
 See
 
 * [x] xref:girder:README.adoc[how to contribute data using Girder]
-* [x] and the xref:data:ROOT:index.adoc[Data manual] to understand {feelpp} data management.
+* [x] and the xref:data:ROOT:manual.adoc[Data manual] to understand {feelpp} data management.
 
 == Import the javascript library in an Antora page
 
@@ -31,52 +31,66 @@ NOTE: the {vtkjs} file is provided by the `supplemental-ui` directory.
 
 == Use WebGL rendering with VTK-js
 
-* Create a `div` with an `id` where you want to place the WebGL window.
-+
-[source,javascript]
-----
-<div id="vtkVisuSection1" ... </div>
-----
+We rely on an Asciidoctor extension to render VTK-js visualization.
 
-* Then, you can call the function `feelppVtkJs.createSceneImporter( divId, options )`. The first argument `divId` is
-the `id` of the `div` defined previouly. The second argument `options` collect the rendering properties :
-** `fileURL` : [mandatory] the url of a vtkjs file
-** `objects` : description of objects to visualize.
-[source,javascript]
+* Create a `vtkjs` block with a file URL:
+
+[,adoc]
+-----
+[vtkjs,https://mydb.com/myfile.vtkjs]
 ----
-  objects: { "deformation":[ { scene:"displacement" }, { scene:"von_mises" }, { scene:"pid" } ],
-              "geometry":[ { scene:"geo_initial", name:"solid" } ] }
 ----
-** `onlyOneObject` : [default=false] rendering is done for only one object of the scene (only work if `objects` is not given)
+-----
+
+* Define how objects will be visualized:
 
-[source,javascript]
+[,adoc]
+-----
+[vtkjs,https://mydb.com/myfile.vtkjs]
 ----
-<script type="text/javascript">
-feelppVtkJs.createSceneImporter( vtkVisuSection1,
-  { fileURL: "https://mydb.com/myfile.vtkjs",
-    objects: { "deformation":[ { scene:"displacement" }, { scene:"von_mises" }, { scene:"pid" } ],
-               "geometry":[ { scene:"geo_initial", name:"solid" } ] } } );
-</script>
+{
+  "deformation": [
+    {
+      "scene": "displacement"
+    },
+    {
+      "scene": "von_mises"
+    },
+    {
+      "scene": "pid"
+    }
+  ],
+  "geometry": [
+    {
+      "scene": "geo_initial",
+      "name": "solid"
+    }
+  ]
+}
 ----
+-----
 
-WARNING: Each `scene` option corresponds to the entries in Paraview' left panel (default is `Export.case`). We advise you to rename each scene consistently with its content before running the Python script.
-
+IMPORTANT: Each `scene` option corresponds to the entries in Paraview' left panel (default is `Export.case`). We advise you to rename each scene consistently with its content before running the Python script.
 
 == An example with Asciidoc in the {feelpp} book
 
-The example of {vtkjs} visualization below is taken from xref:cases:csm:torsion-bar/README.adoc[the Torsion Bar] example.
+The example of {vtkjs} visualization below is taken from xref:toolboxes:csm:torsion-bar/README.adoc[the Torsion Bar] example.
 
 .3D Model of the torsion of a NeoHookean Beam.
-++++
-
-<div class="stretchy-wrapper-16_9">
-<div id="vtkVisuSection1" style="margin: auto; width: 100%; height: 100%;      padding: 10px;"></div>
-</div>
-<script type="text/javascript">
-feelppVtkJs.createSceneImporter( vtkVisuSection1, {
-                                 fileURL: "https://girder.math.unistra.fr/api/v1/file/5a687a58b0e9570150cb252d/download",
-                                 objects: { "object":[ { scene:"displacement" }, { scene:"von_mises_criterions",name:"von_mises" }, { scene:"pid" } ] }
-                                 } );
-</script>
-
-++++
+[vtkjs,https://girder.math.unistra.fr/api/v1/file/5a687a58b0e9570150cb252d/download]
+----
+{
+  "object": [
+    {
+      "scene": "displacement"
+    },
+    {
+      "scene": "von_mises_criterions",
+      "name": "von_mises"
+    },
+    {
+      "scene": "pid"
+    }
+  ]
+}
+----

examples/antora.yml

@@ -1,5 +1,5 @@
-name: cases
-title: Feel++ Toolbox Cases Guide
+name: cases-old
+title: Toolboxes Case Studies (<= 0.110)
 version: 'latest'
 nav:
 - modules/ROOT/nav.adoc