Joss paper (#128)

* ADD-WIP: adding a tempalte for the paper and bib * WIP: moved to paper dir * ADD: template and general paper structure * ADD: template and general paper structure x2 * ADD: planning * WIP-ADD: new github action for joss paper * ADD-WIP: correct naming for jobs joss action * WIP: testing joss action * WIP: testing joss action x2 * WIP: testing joss action x3 * MERGE-WIP: testing joss action x4 * WIP: testing joss action x5 * WIP: testing joss action x6 * WIP: testing joss action x7 * FIX: compatibility with main ci
ibois-epfl · Nov 19, 2024 · 650adfa · 650adfa
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diff --git a/.github/workflows/joss-pdf-build.yml b/.github/workflows/joss-pdf-build.yml
@@ -0,0 +1,99 @@
+name: joss-pdf-build
+
+# #TODO: to activate when ready to release
+# on:
+#   push:
+#     paths:
+#     - paper/**
+#     - .github/workflows/joss-pdf-build.yml
+
+on:
+  push:
+    branches: ["main", "joss_paper"]
+  pull_request:
+    branches: ["main", "joss_paper"]
+
+jobs:
+  paper-build:
+    runs-on: ubuntu-latest
+    name: JOSS-paper-build
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper-artifact
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
+
+  paper-commit:
+    runs-on: ubuntu-latest
+    name: add-pdf-to-repo
+    needs: JOSS-paper-build
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Download
+        uses: actions/download-artifact@v2
+        with:
+          name: paper-artifact
+          path: paper
+
+      - name: Install GitHub CLI
+        run: |
+          choco install gh
+      - name: Authenticate GitHub CLI
+        run: |
+          echo ${{ secrets.GITHUB_TOKEN }} | gh auth login --with-token
+
+      - name: Delete branch remotely version-ac-branch (if exists)
+        run: |
+          git fetch --prune
+          if git branch -r | grep -q 'origin/version-ac-branch'; then
+            git push origin --delete version-ac-branch
+          else
+            echo "Branch version-ac-branch does not exist."
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        shell: bash
+
+      - name: Create new branch and commit version change
+        run: |
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+          git checkout -b version-ac-branch
+          git commit -am "ACTION_BOT: AC JOSS paper draft PDF"
+          git push --set-upstream origin version-ac-branch
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Close existing pull requests for version-ac-branch
+        run: |
+          gh pr list --state open --head version-ac-branch --json number --jq '.[].number' | ForEach-Object { gh pr close $_ }
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        shell: pwsh
+
+      - name: Create pull request
+        run: |
+          gh pr create --title "ACTION_BOT: AC JOSS paper draft PDF" --body "AC JOSS paper draft PDF" --base main --head version-ac-branch --label ACTION_BOT
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Merge pull request
+        run: |
+          $pr = gh pr list --head version-ac-branch --json number --jq '.[0].number'
+          gh pr merge $pr --squash --delete-branch --admin
+        env:
+          GITHUB_TOKEN: ${{ secrets.ADMIN_PAT_TOKEN }}
+        shell: pwsh
diff --git a/paper/01_fig_placeholder.png b/paper/01_fig_placeholder.png
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -0,0 +1,59 @@
+@article{Pearson:2017,
+  	url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P},
+  	Archiveprefix = {arXiv},
+  	Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.},
+  	Eprint = {1703.04627},
+  	Journal = {ArXiv e-prints},
+  	Keywords = {Astrophysics - Astrophysics of Galaxies},
+  	Month = mar,
+  	Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}},
+  	Year = 2017
+}
+
+@book{Binney:2008,
+  	url = {http://adsabs.harvard.edu/abs/2008gady.book.....B},
+  	Author = {{Binney}, J. and {Tremaine}, S.},
+  	Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.},
+  	Publisher = {Princeton University Press},
+  	Title = {{Galactic Dynamics: Second Edition}},
+  	Year = 2008
+}
+
+@article{gaia,
+    author = {{Gaia Collaboration}},
+    title = "{The Gaia mission}",
+    journal = {Astronomy and Astrophysics},
+    archivePrefix = "arXiv",
+    eprint = {1609.04153},
+    primaryClass = "astro-ph.IM",
+    keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes},
+    year = 2016,
+    month = nov,
+    volume = 595,
+    doi = {10.1051/0004-6361/201629272},
+    url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
+}
+
+@article{astropy,
+    author = {{Astropy Collaboration}},
+    title = "{Astropy: A community Python package for astronomy}",
+    journal = {Astronomy and Astrophysics},
+    archivePrefix = "arXiv",
+    eprint = {1307.6212},
+    primaryClass = "astro-ph.IM",
+    keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
+    year = 2013,
+    month = oct,
+    volume = 558,
+    doi = {10.1051/0004-6361/201322068},
+    url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
+}
+
+@misc{fidgit,
+  author = {A. M. Smith and K. Thaney and M. Hahnel},
+  title = {Fidgit: An ungodly union of GitHub and Figshare},
+  year = {2020},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/arfon/fidgit}
+}
diff --git a/paper/paper.md b/paper/paper.md
@@ -0,0 +1,123 @@
+---
+title: 'Augmented Reality UNIX C++ Engine for Enhanced Visual Guidance in Woodworking'  # TODO: improve title
+tags:
+  - C++
+  - UNIX
+  - augmented reality
+  - engine
+  - digital fabrication
+authors:
+  - name: Andrea Settimi
+    orcid: 0000-0001-5020-7331
+    corresponding: true
+    affiliation: 1
+  - name: Hong-Bin Yang
+    orcid: 0000-0001-8422-5263
+    affiliation: 1
+  - name: Julien Gamerro
+    orcid: 0000-0001-7802-5345
+    affiliation: 2
+  - name: Yves Weinand
+    orcid: 0000-0002-8088-6504
+    affiliation: 2
+
+affiliations:
+ - name: Institution Name, Country
+   index: 1
+ - name: Independent Researcher, Country
+   index: 2
+date: 18 November 2024
+bibliography: paper.bib
+
+---
+
+<!--
+# Structure of the paper
+
+- (0) Summary (MAX 50 words) - ANDREA
+- (1) Statement of need (MAX 125 words) - ANDREA
+- (2) Functionalities (MAX 100 words) - ANDREA
+- (1.1) Layer-stack flow (MAX 150 words) - ANDREA
+- (1.2) Geometry framework (MAX 200 words) - HONG-BIN
+- (1.3) AR rendering (MAX 150 words) - HONG-BIN
+- (1.4) Computed Feedback System (MAX 150 words) - ANDREA
+- (2) Acknowledgements - ANDREA
+- (3) References - ANDREA
+-->
+
+# Summary
+
+test4
+<!-- this is a sort of abstract. (MAX 50 words) -->
+<!-- ![Test image captation.](01_fig_placeholder.png){ width=20% } -->
+
+
+# Statement of need
+
+<!--
+aka "state-of-the-art". This is a context introduction and brief state-of-the-art. (MAX 125 words)
+-->
+
+# Functionalities
+
+<!--
+brief introduction to the general functioning and the following sections. (MAX 75 words)
+It might include details that are no more mentioned in the following sections like:
+- the hardware used (x64, monocular camera, etc.)
+- ...
+-->
+
+## Layer-stack flow
+
+<!--
+this section should illustrate the layer stack system and the applicaton.h how ti workds. To be included:
+    -a) a scheme (mermaid))
+    -b) a description (MAX 150 words)
+-->
+
+## Geometry framework
+
+<!--
+this section should illustrate the layer stack system and the applicaton.h how it workds. To be included:
+    -a) a scheme (mermaid))
+    -b) a description (MAX 150 words)
+-->
+
+
+## Computed Feedback System
+
+<!--
+this section should illustrate the feedback system and how the layerFeeddback can get all the information from the other layers and use the geometry system at its convinience. To be included:
+    -a) a scheme (mermaid))
+    -b) a description (MAX 150 words)
+-->
+
+## AR rendering
+
+<!--
+this section should include:
+    -a) a scheme of the layer system and general application.h structure
+    -b) a brief description of its functioning (maybe with a smal snippet of code on how to instantiate a  point (MAX 150 words)
+-->
+
+# Acknowledgements
+
+<!-- list of contributors -->
+
+# References
+
+<!--
+Citations to entries in paper.bib should be in
+[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
+format.
+
+If you want to cite a software repository URL (e.g. something on GitHub without a preferred
+citation) then you can do it with the example BibTeX entry below for @fidgit.
+
+For a quick reference, the following citation commands can be used:
+- `@author:2001`  ->  "Author et al. (2001)"
+- `[@author:2001]` -> "(Author et al., 2001)"
+- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"
+-->
+
+
diff --git a/paper/planning.md b/paper/planning.md
@@ -0,0 +1,12 @@
+```mermaid
+gantt
+    dateFormat  YYYY-MM-DD
+    title       JOSS publication
+    excludes    weekends
+
+    Additional tests                    :active, addtest, 2024-11-19, 1w
+    Documentation online                :active, absed, 2024-11-19, 2024-12-09
+    Finished repo+docs                  :milestone, crit, repodocs, 2024-12-09, 0d
+    Paper test+diagrams                 :redactipap, 2024-11-20, 2024-12-13
+    Paper submission                    :milestone, crit, subdate, 2024-12-13, 0d
+```