underworldcode · lmoresi · Nov 27, 2024 · Nov 4, 2024 · Nov 4, 2024 · Nov 4, 2024
diff --git a/.binder/apt.txt b/.binder/apt.txt
diff --git a/.binder/environment.yml b/.binder/environment.yml
diff --git a/.binder/postBuild b/.binder/postBuild
diff --git a/.binder/start b/.binder/start
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -2,8 +2,8 @@ name: Draft PDF (JOSS)
 on:
   push:
     paths:
-      - joss-paper/paper.md
-      - joss-paper/paper.bib
+      - docs/joss-paper/paper.md
+      - docs/joss-paper/paper.bib
       # - assets/img1.png
       # - assets/img2.png
       - .github/workflows/draft-pdf.yml
@@ -20,12 +20,12 @@ jobs:
         with:
           journal: joss
           # This should be the path to the paper within your repo.
-          paper-path: joss-paper/paper.md
+          paper-path: docs/joss-paper/paper.md
       - name: Upload
         uses: actions/upload-artifact@v3
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md. In the case we have (symlink), the paper is in the subdir
-          path: joss-paper/paper.pdf
+          path: docs/joss-paper/paper.pdf
diff --git a/README.md b/README.md
@@ -8,6 +8,9 @@ Welcome to `Underworld3`, a mathematically self-describing, finite-element code
 
 All `Underworld3` source code is released under the LGPL-3 open source licence. This covers all files in `underworld3` constituting the Underworld3 Python module. Notebooks, stand-alone documentation and Python scripts which show how the code is used and run are licensed under the Creative Commons Attribution 4.0 International License.
 
+HTML: <a href="https://joss.theoj.org/papers/4f7a1ed76bde560968c246fa8eff778d"><img src="https://joss.theoj.org/papers/4f7a1ed76bde560968c246fa8eff778d/status.svg"></a>
+Markdown: [![status](https://joss.theoj.org/papers/4f7a1ed76bde560968c246fa8eff778d/status.svg)](https://joss.theoj.org/papers/4f7a1ed76bde560968c246fa8eff778d)
+
 ## Documentation
 
 Start with the online [Quick Start Guide](https://underworldcode.github.io/underworld3/development/_quickstart/index.html) for a brief overview of the code.
@@ -18,9 +21,9 @@ The `underworld3` module (API) documentation can be found online:
 
 ## Binder demonstration version
 
- Main Branch: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/underworldcode/underworld3/main)
+ - [Main Branch on Binder](https://mybinder.org/v2/gh/underworld-community/uw3-demo-launcher/HEAD?labpath=underworld3%2Fdocs%2Fuser%2FNotebooks%2FNotebook_Index.ipynb)
+ - [Development Branch on Binder](https://mybinder.org/v2/gh/underworld-community/uw3-demo-launcher-dev/HEAD?labpath=underworld3%2Fdocs%2Fuser%2FNotebooks%2FNotebook_Index.ipynb)
 
-Development Branch: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/underworldcode/underworld3/development)
 
 ## Installation Guide
 

diff --git a/joss-paper/JOSS_Checklist.md → docs/joss-paper/JOSS_Checklist.md b/joss-paper/JOSS_Checklist.md → docs/joss-paper/JOSS_Checklist.md
diff --git a/joss-paper/paper.bib → docs/joss-paper/paper.bib b/joss-paper/paper.bib → docs/joss-paper/paper.bib
@@ -18,6 +18,7 @@ @article{behnel2011cython
   volume = {13},
   number = {2},
   pages = {31--39},
+  doi = {10.1109/MCSE.2010.118},
   publisher = {IEEE}
 }
 

diff --git a/docs/joss-paper/paper.crossref b/docs/joss-paper/paper.crossref
@@ -0,0 +1,225 @@
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+          <doi>10.21105/joss</doi>
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+          <ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
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diff --git a/joss-paper/paper.html → docs/joss-paper/paper.html b/joss-paper/paper.html → docs/joss-paper/paper.html
diff --git a/joss-paper/paper.md → docs/joss-paper/paper.md b/joss-paper/paper.md → docs/joss-paper/paper.md
diff --git a/docs/joss-paper/paper.pdf b/docs/joss-paper/paper.pdf
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diff --git a/...per_files/libs/bootstrap/bootstrap.min.js → ...per_files/libs/bootstrap/bootstrap.min.js b/...per_files/libs/bootstrap/bootstrap.min.js → ...per_files/libs/bootstrap/bootstrap.min.js
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diff --git a/...r_files/libs/quarto-html/tippy.umd.min.js → ...r_files/libs/quarto-html/tippy.umd.min.js b/...r_files/libs/quarto-html/tippy.umd.min.js → ...r_files/libs/quarto-html/tippy.umd.min.js
diff --git a/docs/user/Notebooks/1-Meshes.ipynb b/docs/user/Notebooks/1-Meshes.ipynb
@@ -468,7 +468,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,

diff --git a/docs/user/Notebooks/2-Variables.ipynb b/docs/user/Notebooks/2-Variables.ipynb
@@ -367,7 +367,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.10"
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