@@ -1,174 +1,49 @@
-/.quarto/
+# R and co
+.Rhistory
+.Rprofile
+.Rapp.history
+.RData
+.Ruserdata
+*.Rproj
+.Rproj.user
+.Rproj.user/
+/*.Rcheck/
+renv/
+
+# Python and co
+_environment
+/.micromamba/
 /.joblib
-/_extensions/
-*.html
-*.ipynb
-*.tex
-*_files/
-.jupyter_cache/
-/.luarc.json
-/.micromamba
-_site/
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
+/.pytest_cache/
+scripts/__pycache__/
 
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
+# Quarto tmp files
+/.quarto/
+/*_files
+/*_cache
+/_freeze
+_site/
+/cache/
 
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
+# Quarto extension files
+_extensions/
+logo_text_white.pdf
+logo_notext_white.png
 
-# Translations
-*.mo
-*.pot
+# Quarto output files
+main.pdf
+main.html
+main.ipynb
+main.tex
 
-# Django stuff:
+# Latex compilation files
+*.aux
 *.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
+*.toc
 
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
+# Various system files
+DS_Store
+/.luarc.json
 
-# Cython debug symbols
-cython_debug/
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-/*.pdf
+**/*.quarto_ipynb
@@ -1,4 +1,4 @@
-# Visualizing Data using t-SNE (mock contributon)
+# Visualizing Data using t-SNE (mock contribution)
 Laurens van der Maaten, Geoffrey Hinton
 2008-08-11
 
@@ -10,18 +10,14 @@ illustrate the Computo spirit.*
 
 [![build and
 publish](https://github.com/computorg/published-paper-tsne-R/actions/workflows/build.yml/badge.svg)](https://github.com/computorg/published-paper-tsne-R/actions/workflows/build.yml)
-[![DOI:10.57750/xxxxxx](https://img.shields.io/badge/DOI-10.57750/xxxxxx-034E79.svg)](https://doi.org/10.57750/xxxxxx)
+[![DOI:10.57750/xxx-xxx](https://img.shields.io/badge/DOI-10.57750%2Fxxx--xxx-034E79.svg)](https://doi.org/10.57750/xxx-xxx)
 [![Creative Commons
 License](https://i.creativecommons.org/l/by/4.0/80x15.png)](http://creativecommons.org/licenses/by/4.0/)
 
-<!-- [![reviews](https://img.shields.io/badge/review-report-blue)](https://github.com/computorg/published-paper-tsne-R/issues?q=is%3Aopen+is%3Aissue+label%3Areview) -->
-
 ### Authors
 
-- [Laurens van der Maaten](https://lvdmaaten.github.io/) (TiCC, Tilburg
-  University)
-- [Geoffrey Hinton](https://www.cs.toronto.edu/~hinton/) (Department of
-  Computer Science, University of Toronto)
+- [Laurens van der Maaten](https://lvdmaaten.github.io/) (TiCC, Tilburg University)
+- [Geoffrey Hinton](https://www.cs.toronto.edu/~hinton/) (Department of Computer Science, University of Toronto)
 
 ### Abstract
 
@@ -45,14 +41,13 @@ including Sammon mapping, Isomap, and Locally Linear Embedding. The
 visualization produced by t-SNE are significantly better than those
 produced by other techniques on almost all of the data sets.
 
-<div id="refs" class="references csl-bib-body hanging-indent"
-entry-spacing="0">
+<div id="refs" class="references csl-bib-body hanging-indent">
 
 <div id="ref-hinton:stochastic" class="csl-entry">
 
 Hinton, Geoffrey E, and Sam Roweis. 2003. “Stochastic Neighbor
 Embedding.” In *Advances in Neural Information Processing Systems*,
-edited by S. Becker, S. Thrun, and K. Obermayer. Vol. 15. MIT Press.
+edited by S. Becker, S. Thrun, and K. Obermayer, vol. 15. MIT Press.
 <https://proceedings.neurips.cc/paper/2002/file/6150ccc6069bea6b5716254057a194ef-Paper.pdf>.
 
 </div>
 
@@ -5,15 +5,12 @@ format: gfm-commonmark
 _{{< meta description >}}_
 
 [![build and publish](https://github.com/{{< meta github-user >}}/{{< meta repo >}}/actions/workflows/build.yml/badge.svg)](https://github.com/{{< meta github-user >}}/{{< meta repo >}}/actions/workflows/build.yml)
-[![DOI:{{< meta citation.doi >}}](https://img.shields.io/badge/DOI-{{< meta citation.doi >}}-034E79.svg)](https://doi.org/{{< meta citation.doi >}})
+[![DOI:{{< meta citation.doi >}}](https://img.shields.io/badge/DOI-{{< shields-encode citation.doi >}}-034E79.svg)](https://doi.org/{{< meta citation.doi >}})
 [![Creative Commons License](https://i.creativecommons.org/l/by/4.0/80x15.png)](http://creativecommons.org/licenses/by/4.0/)
 
-<!-- [![reviews](https://img.shields.io/badge/review-report-blue)](https://github.com/{{< meta github-user >}}/{{< meta repo >}}/issues?q=is%3Aopen+is%3Aissue+label%3Areview) -->
-
 ### Authors
 
-- [{{< meta by-author.1.name.literal >}}]({{< meta by-author.1.url >}}) ({{< meta by-affiliation.1.name >}})
-- [{{< meta by-author.2.name.literal >}}]({{< meta by-author.2.url >}}) ({{< meta by-affiliation.2.name >}})
+{{< author-list >}}
 
 ### Abstract
 
 
@@ -1,7 +1,7 @@
 project:
   type: default
   render:
-    - published-paper-tsne.qmd
+    - main.qmd
     - README.qmd
 
 title: "Visualizing Data using t-SNE (mock contribution)"
@@ -10,6 +10,7 @@ date: 2008-08-11
 date-modified: last-modified
 description: |
   This page is a reworking of the original t-SNE article using the Computo template. It aims to help authors submitting to the journal by using some advanced formatting features. We warmly thank the authors of t-SNE and the editor of JMLR for allowing us to use their work to illustrate the Computo spirit.
+license: "CC BY"
 author: 
   - name: Laurens van der Maaten
     url: https://lvdmaaten.github.io/
@@ -28,14 +29,14 @@ keywords: [visualization, dimensionality reduction, manifold learning, embedding
 bibliography: references.bib
 github-user: computorg
 repo: "published-paper-tsne-R"
-draft: false
-published: true
+status: published
 citation:
   type: article-journal
   container-title: "Computo"
-  doi: "10.57750/xxxxxx"
+  doi: "10.57750/xxx-xxx"
   publisher: "French Statistical Society"
   issn: "2824-7795"
+  url: "https://computo-journal.org/published-paper-tsne/"
 
 format: 
   computo-html: default