Draft for method paper submission to Journal of Open Source Software (JOSS) (#430)

* Add a workflow for compiling JOSS template.

* Add paper template.

* Started to update paper draft

* Updated general information

* draft summary

* Added further structure and some background

* Some re-phrasing

* Started w/ modularisation section

* Draft for "other codes" section

* Added verification and documentation section

* Authors

* Affiliation

* abstract

* main text

* modularisation

* Corrected figure insert

* modularisation top part

* authors

* figure fix

* modularisation

* citations framework

* fix compile failure

* fix compile failure 2

* 3

* 4

* reinstate full text

* intend affiliation

* lists

* refs 1

* similar codes

* refs 2 discussions

* main text

* renamed paper dir

* back

* updated schematic

* added zalmoxis

* read through 1

* fix figure

* first complete draft version

* updated citation

* authors, citations

* street name

* citation order agni

* suggestions by harrison, changes to figure

* figure bug fix

* one more :>

* spelling

* minor phrasings

* orcid

* Some adjustments to the JOSS template following comments.

* Changed path to proteus_schematic

* Corrected file path

* Additional comments to draft 1

* Figure width

* read through

* Penultimate version

* doi and paper title updates

* Code version comment

* minor updates

* Bump cited version

* Update bib

* Fix typos

* Final typo

* Version and .cff file

---------

Co-authored-by: Laurent Soucasse <135331272+lsoucasse@users.noreply.github.com>
Co-authored-by: Tim Lichtenberg <timlichtenberg@Tims-iMac.local>

Author: 3 people

.github/workflows/draft-pdf.yml

@@ -0,0 +1,28 @@
+name: Draft PDF
+on:
+  push:
+    paths:
+      - docs/paper/**
+      - .github/workflows/draft-pdf.yml
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    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: docs/paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        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
+          path: docs/paper/paper.pdf

.vscode/settings.json

@@ -12,5 +12,6 @@
     ],
     "python.analysis.diagnosticMode": "openFilesOnly",
     "julia.environmentPath": "${workspaceFolder}/AGNI",
-    "fortran.fortls.disabled": true
+    "fortran.fortls.disabled": true,
+    "markdown.validate.enabled": true
 }

CITATION.cff

@@ -1,4 +1,4 @@
-cff-version: 1.2.0
+cff-version: 1.3.0
 message: "If you use this software, please cite it as below."
 
 authors:
@@ -14,11 +14,6 @@ authors:
   given-names: "Laurent"
   orcid: "https://orcid.org/0000-0002-5422-8794"
 
-- given-names: "Stef"
-  family-names: "Smeets"
-  affiliation: "Netherlands eScience Center"
-  orcid: "https://orcid.org/0000-0001-5107-3531"
-
 - family-names: "Sastre"
   given-names: "Mariana"
   orcid: "https://orcid.org/0000-0000-0000-0000"
@@ -31,8 +26,43 @@ authors:
   given-names: "Dan"
   orcid: "https://orcid.org/0000-0002-0673-4860"
 
+- given-names: "Flavia C."
+  family-names: "Pascal"
+  orcid: "https://orcid.org/0009-0007-4663-1456"
+
+- given-names: "Robb"
+  family-names: "Calder"
+  orcid: "https://orcid.org/0009-0002-9247-2437
+
+- given-names: "Ben"
+  family-names: "Riegler"
+
+- given-names: "Hanno"
+  family-names: "Spreeuw"
+  orcid: "https://orcid.org/0000-0002-5057-0322"
+
+- given-names: "Mark"
+  family-names: "Hammond"
+  orcid: "https://orcid.org/0000-0002-6893-522X"
+
+- given-names: "Stef"
+  family-names: "Smeets"
+  orcid: "https://orcid.org/0000-0002-5413-9038"
+
+- given-names: "Shang-Min"
+  family-names: "Tsai"
+  orcid: "https://orcid.org/0000-0002-8163-4608"
+
+- given-names: "Oliver"
+  family-names: "Shorttle"
+  orcid: "https://orcid.org/0000-0002-8713-1446"
+
+- given-names: "Raymond T."
+  family-names: "Pierrehumbert"
+  orcid: "https://orcid.org/0000-0002-5887-1197"
+
 title: "PROTEUS"
-version: 25.05.20
+version: 25.07.31
 doi: 10.xx/xx.xx
-date-released: 2025-05-20
+date-released: 2025-07-31
 url: "https://github.com/FormingWorlds/PROTEUS"

docs/assets/schematic.png

@@ -8,14 +8,6 @@
 
 
 ```bibtex
-@ARTICLE{Lichtenberg_2026_JOSS,
-       author = {Tim Lichtenberg, Harrison Nicholls, Laurent Soucasse, Mariana Sastre, Emma Postolec, Dan J. Bower, Flavia C. Pascal, Ben Riegler, Hanno Spreeuw, Robb Calder, Mark Hammond, Stef Smeets, Shang-Min Tsai, Raymond T. Pierrehumbert},
-        title = "The PROTEUS framework for planetary evolution",
-      journal = {JOSS},
-         year = {in prep.},
-        month = jan,
-}
-
 @ARTICLE{Nicholls_2025_MNRAS,
        author = {{Nicholls}, Harrison and {Pierrehumbert}, Raymond T. and {Lichtenberg}, Tim and {Soucasse}, Laurent and {Smeets}, Stef},
         title = "{Convective shutdown in the atmospheres of lava worlds}",