Merge branch 'main' into precipitation-planetary

.github/workflows/check-links.yml

@@ -13,3 +13,4 @@ jobs:
         with:
           use-quiet-mode: 'yes'
           use-verbose-mode: 'yes'
+          config-file: .markdown-link-check.json

.github/workflows/publish.yml

@@ -8,6 +8,24 @@ permissions:
   id-token: write
 
 jobs:
+  test-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install .[doc]
+          python -c "import pypandoc; pypandoc.download_pandoc()"
+
+      - name: Test Docs
+        run: mkdocs build
+
   test:
     uses: ./.github/workflows/ci_template.yml
     secrets:
@@ -73,9 +91,29 @@ jobs:
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
 
+  paper:
+    runs-on: ubuntu-latest
+    needs: publish-PyPI
+    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
 
   publish-docs:
-    needs: publish-PyPI
+    needs: paper
     runs-on: ubuntu-latest
 
     steps:
@@ -86,7 +124,9 @@ jobs:
           python-version: "3.11"
 
       - name: Install dependencies
-        run: pip install .[doc]
+        run: |
+          pip install .[doc]
+          python -c "import pypandoc; pypandoc.download_pandoc()"
 
       - name: Deploy Docs
         run: mkdocs gh-deploy --force

.markdown-link-check.json

@@ -0,0 +1,7 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": ".*/paper.pdf"
+    }
+  ]
+}

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
       - id: check-merge-conflict
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.7.2"
+    rev: "v0.7.4"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -20,7 +20,7 @@ repos:
     rev: v0.42.0
     hooks:
       - id: markdownlint
-        args: ["--disable", "MD013", "--"]
+        args: ["--disable", "MD013", "--disable", "MD025", "--"]
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0

README.md

@@ -5,6 +5,8 @@
 [![Test and build](https://github.com/ImperialCollegeLondon/SWMManywhere/actions/workflows/ci.yml/badge.svg)](https://github.com/ImperialCollegeLondon/SWMManywhere/actions/workflows/ci.yml)
 [![DOI](https://zenodo.org/badge/741903266.svg)](https://zenodo.org/doi/10.5281/zenodo.13837741)
 [![codecov](https://codecov.io/gh/ImperialCollegeLondon/SWMManywhere/graph/badge.svg)](https://codecov.io/gh/ImperialCollegeLondon/SWMManywhere)
+[![status](https://joss.theoj.org/papers/b9901c3b612b995bf6977377b65f368a/status.svg)](https://joss.theoj.org/papers/b9901c3b612b995bf6977377b65f368a)
+
 <!-- markdown-link-check-enable -->
 
 SWMManywhere is a tool to synthesise urban drainage network models (UDMs) using

docs/index.md

@@ -6,6 +6,7 @@ derive a synthetic urban drainage network anywhere in the world.
 ## Table of contents
 <!-- markdownlint-disable MD007 -->
 - [Home](index.md)
+- [About](./paper/paper.pdf)
 - [Quickstart](quickstart.md)
 - Guides:
     - [Configuration file](config_guide.md)
@@ -24,4 +25,5 @@ derive a synthetic urban drainage network anywhere in the world.
     - [Post processing](reference-post-processing.md)
     - [Preprocessing](reference-preprocessing.md)
     - [Config](reference-defs.md)
-<!---  - [Coverage report](coverage.md)--->
+- [Coverage report](https://app.codecov.io/gh/ImperialCollegeLondon/SWMManywhere)
+<!---  --->