JOSS submission (#70)

* Generate JOSS paper workflow
* Copy over JOSS paper template materials
* Add gitignore files
* Fix LaTeX template
* First draft
* Use hash for checkout action in JOSS workflow
* Add test for JOSS paper template
* Update text on testing
* Simplify JOSS render workflow

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Marion <56403724+MarionBWeinzierl@users.noreply.github.com>
Co-authored-by: Don Setiawan <landungs@uw.edu>

Author: 4 people

.github/answers/render_joss_paper.yml

@@ -0,0 +1,18 @@
+# Answers to be passed to the JOSS paper workflow during testing
+_commit: 3ca4cf1
+_src_path: .
+build_docs_timeout: 15
+build_sys_file_paths:
+- '**/Makefile'
+carbon_aware: false
+deploy_docs: false
+docs_file_paths:
+- '**/*.md'
+joss_render_timeout: 5
+joss_upload_timeout: 5
+requirements_file_paths:
+- requirements-dev.txt
+source_file_paths:
+- '**/*.jinja'
+static_analysis_timeout: 5
+test_suite_timeout: 15

.github/patches/test_suite.patch

@@ -21,6 +21,13 @@
 -          fi
 -          rm tmp.patch
 -
+-      - name: Test JOSS paper template
+-        run: |
+-          copier copy --answers-file .github/answers/render_joss_paper.yml --force --quiet . .
+-          if ! git diff .github/workflows/render_joss_paper.yml; then
+-            exit 1
+-          fi
+-
 -      - name: Test test suite template
 -        run: |
 -          copier copy --answers-file .github/answers/test_suite.yml --force --quiet . .

.github/workflows/render_joss_paper.yml

@@ -0,0 +1,57 @@
+# Workflow to render a submission to the Journal of Open Source Software (JOSS)
+name: Render JOSS paper
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pushes to the "main" branch, i.e., PR merges
+  push:
+    branches: [ "main" ]
+    paths:
+      - '.github/workflows/render_joss_paper.yml'
+      - 'paper/*'
+
+  # Triggers the workflow on pushes to open pull requests to main with documentation changes
+  pull_request:
+    paths:
+      - '.github/workflows/render_joss_paper.yml'
+      - 'paper/*'
+
+# Cancel jobs running if new commits are pushed
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# No write permission by default
+permissions: {}
+
+jobs:
+  # Builds a draft of the JOSS paper
+  build-draft:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    # The timeout minutes for the job to complete
+    timeout-minutes: 5
+    # We trust the deploy action with write permissions
+    permissions:
+      id-token: write
+
+    steps:
+      # Checkout your repository under $GITHUB_WORKSPACE so your job can access it
+      - name: Checkout
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        with:
+          persist-credentials: false
+
+      # Build the paper using the openjournals action
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@85a18372e48f551d8af9ddb7a747de685fbbb01c
+        with:
+          journal: joss
+          paper-path: paper/paper.md
+
+      # Upload the paper build
+      - name: Upload draft PDF
+        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
+        with:
+          name: paper
+          path: paper/paper.pdf

.github/workflows/test_suite.yml

@@ -68,6 +68,13 @@ jobs:
           fi
           rm tmp.patch
 
+      - name: Test JOSS paper template
+        run: |
+          copier copy --answers-file .github/answers/render_joss_paper.yml --force --quiet . .
+          if ! git diff .github/workflows/render_joss_paper.yml; then
+            exit 1
+          fi
+
       - name: Test test suite template
         run: |
           copier copy --answers-file .github/answers/test_suite.yml --force --quiet . .

.gitignore

@@ -0,0 +1 @@
+*.copier-answers.yml

paper/.gitignore

@@ -0,0 +1,2 @@
+paper.pdf
+compile.sh