pyoomph · cdiddens · Aug 7, 2026 · Aug 4, 2026 · Aug 7, 2026
diff --git a/CLAUDE.md b/CLAUDE.md
@@ -15,7 +15,22 @@ bash gen_page.sh
 
 `gen_page.sh` writes into `_generated/` and is the only build step. There are no tests, no linter, and no local dev server — open `_generated/index.html` in a browser to check output (relative paths to `css/` and `media/` resolve correctly from there).
 
-Deployment is automatic: `.github/workflows/deploy.yml` runs the same commands on every push/PR to `main` and publishes `_generated/` to GitHub Pages via `JamesIves/github-pages-deploy-action`.
+Deployment is automatic once a change reaches `main` — see [Publishing](#publishing) below.
+
+## Publishing
+
+The live site is served from **`pyoomph/pyoomph.github.io`**, which is the `upstream` remote. `origin` is the fork `cdiddens/pyoomph.github.io`. Check with `git remote -v` before pushing anywhere — a push to `upstream/main` publishes immediately, with no review step.
+
+The established flow (how PRs #19–#21 landed):
+
+1. Commit the change — on a feature branch, or on the fork's `main`; both have been used.
+2. `git push -u origin <branch>`
+3. `gh pr create --repo pyoomph/pyoomph.github.io --base main --head cdiddens:<branch>`
+4. Merge the PR. **Merging is what publishes the site**, so it is the user's call, not something to do unprompted.
+
+The merge pushes to `upstream/main`, which triggers `.github/workflows/deploy.yml`: it installs the dependencies, runs `gen_page.sh` and force-pushes `_generated/` to the `gh-pages` branch via `JamesIves/github-pages-deploy-action`. That run takes ~20 s and is followed by GitHub's own "pages build and deployment" run. Check both with `gh run list --repo pyoomph/pyoomph.github.io`.
+
+**A PR from a fork always shows a failing check — this is expected and not a defect in the change.** `deploy.yml` triggers on `pull_request` to `main` as well as on push, but for fork PRs GitHub scopes `GITHUB_TOKEN` to read-only regardless of the `permissions: contents: write` declaration. The build succeeds and only the final push to `gh-pages` fails with a 403, so nothing is published. The check goes green on merge, because a push to `main` runs with a writable token. Gating the deploy step with `if: github.event_name != 'pull_request'` would suppress the red X.
 
 ## How pages are assembled
 
@@ -46,6 +61,29 @@ Renders `pubs.bib` into the numbered publication list on the About page.
 - Journal names are shortened via the `abbrevs` dict (lowercase key → abbreviation); add an entry there rather than editing the `.bib`. A `journal` starting with `arXiv` renders as *submitted*.
 - PDF link: `eprint` (labelled "arXiv preprint" if the URL contains arxiv.org, else "Open Access"), otherwise a local `pdf/<citekey>.pdf` if present.
 
+## Finding new publications for `pubs.bib`
+
+The About page lists publications that **use** pyoomph, which is a smaller set than the publications that *cite* it. New entries are found by looking at what cites the main paper (Diddens & Rocha, J. Comput. Phys. **518**, 113306, 2024, `10.1016/j.jcp.2024.113306`) and then screening each candidate.
+
+1. **Collect citing works.** Three DOI-based indexes, all open and without authentication — query all three, they disagree:
+
+   ```bash
+   # OpenAlex (W4401074401 is the JCP paper)
+   curl -sS "https://api.openalex.org/works?filter=cites:W4401074401&per-page=200"
+   # Semantic Scholar
+   curl -sS "https://api.semanticscholar.org/graph/v1/paper/DOI:10.1016/j.jcp.2024.113306/citations?fields=title,year,externalIds,venue,authors&limit=100"
+   # OpenCitations (-L is required, the endpoint redirects)
+   curl -sSL "https://opencitations.net/index/coci/api/v1/citations/10.1016/j.jcp.2024.113306"
+   ```
+
+   Merge and dedupe on DOI. The same work routinely appears twice — as preprint (arXiv, SSRN) and as published version — and OpenAlex sometimes holds two records for one DOI. Because all three indexes are DOI-based, theses and non-DOI preprints are invisible to them; Google Scholar reports a somewhat higher count for that reason.
+
+2. **Subtract** what is already in `pubs.bib` and what is already listed in **`pubs_excluded.md`** — both match on DOI, `grep -i` is enough.
+
+3. **Screen the remainder**: the paper must actually *use* pyoomph, not merely cite it. Papers citing the JCP paper for bifurcation tracking, Marangoni modelling or multiphysics coupling in general are common and usually do not use the framework.
+
+4. **Add** what passes to the top of `pubs.bib` (order is literal, see `gen_pubs.py` above), and **append what fails** to `pubs_excluded.md` with the date, so it is not screened again.
+
 ## Files under `_generated/` that are committed
 
 `css/`, `media/` (minus `media/tutorial/`), `docs.html` and `pdf.html` (meta-refresh redirects to readthedocs), `google3a5a7a86d2ed869e.html` (Search Console verification) and `sitemap.xml` are hand-maintained and tracked in git. The build only *adds* the three page files plus `media/tutorial/` on top of them — never clean the directory.

diff --git a/_generated/css/style.css b/_generated/css/style.css
@@ -36,6 +36,22 @@ a {text-decoration:underline; color:#000000;}
 #menu a {color:#FFF; text-decoration:none; padding:4px;}
 
 #menu a:hover {color: #DDD}
+
+/* small icon in front of every menu entry */
+#menu .menu-icon {
+  width: 0.95em;
+  height: 0.95em;
+  vertical-align: -0.11em;
+  margin-right: 0.35em;
+  fill: currentColor;   /* the three internal entries follow their label */
+}
+/* white variants: the "light logo" Read the Docs publishes for dark backgrounds,
+   and one of the colours GitHub permits for the Invertocat */
+#menu .menu-icon-rtd { fill: #FAFAFA; }
+#menu .menu-icon-github { fill: #FFF; }
+
+/* keep the mark on the same line as its label when the menu wraps */
+#menu a { white-space: nowrap; }
 #menu li.selected a {color: #FFF}
 
 

diff --git a/header.html b/header.html
@@ -31,11 +31,11 @@
 <div id="content">
 <div id="menu">
 <ul>
-<li><a href="index.html">Features</a></li>
-<li><a href="about.html">About</a></li>
-<li><a href="installation.html">Installation</a></li>
-<li><a href="https://pyoomph.readthedocs.io/en/latest/">Documentation</a></li>
-<li><a href="https://github.com/pyoomph/pyoomph">Source&nbsp;Code</a></li>
+<li><a href="index.html"><svg class="menu-icon" viewBox="0 0 24 24" aria-hidden="true" focusable="false"><path d="M12 2l2.47 6.6 7.04.31-5.52 4.39 1.89 6.79L12 16.2l-5.88 3.89 1.89-6.79L2.49 8.91l7.04-.31z"/></svg>Features</a></li>
+<li><a href="about.html"><svg class="menu-icon" viewBox="0 0 24 24" aria-hidden="true" focusable="false"><path fill-rule="evenodd" d="M12 1.5A10.5 10.5 0 1 0 12 22.5 10.5 10.5 0 1 0 12 1.5zm0 1.9a8.6 8.6 0 1 1 0 17.2 8.6 8.6 0 1 1 0-17.2zm0 2.2a1.5 1.5 0 1 0 0 3 1.5 1.5 0 1 0 0-3zm-1.3 4.6h2.6v7.4h-2.6z"/></svg>About</a></li>
+<li><a href="installation.html"><svg class="menu-icon" viewBox="0 0 24 24" aria-hidden="true" focusable="false"><path d="M10.6 2.5h2.8v8.3h3.4L12 16.6l-4.8-5.8h3.4zM3.2 14.6v4.6a2.2 2.2 0 0 0 2.2 2.2h13.2a2.2 2.2 0 0 0 2.2-2.2v-4.6h-2.6v4.2H5.8v-4.2z"/></svg>Installation</a></li>
+<li><a href="https://pyoomph.readthedocs.io/en/latest/"><svg class="menu-icon menu-icon-rtd" viewBox="0 0 24 24" aria-hidden="true" focusable="false"><path d="M7.732 0a59.316 59.316 0 0 0-4.977.218V24a62.933 62.933 0 0 1 3.619-.687c.17-.028.34-.053.509-.078.215-.033.43-.066.644-.096l.205-.03zm1.18.003V22.96a61.042 61.042 0 0 1 12.333-.213V1.485A60.859 60.859 0 0 0 8.912.003zm1.707 1.81a.59.59 0 0 1 .015 0c3.06.088 6.125.404 9.167.95a.59.59 0 0 1 .476.686.59.59 0 0 1-.569.484.59.59 0 0 1-.116-.009 60.622 60.622 0 0 0-8.992-.931.59.59 0 0 1-.573-.607.59.59 0 0 1 .592-.572zm-4.212.028a.59.59 0 0 1 .578.565.59.59 0 0 1-.564.614 59.74 59.74 0 0 0-2.355.144.59.59 0 0 1-.04.002.59.59 0 0 1-.595-.542.59.59 0 0 1 .54-.635c.8-.065 1.6-.114 2.401-.148a.59.59 0 0 1 .035 0zm4.202 2.834a.59.59 0 0 1 .015 0 61.6 61.6 0 0 1 9.167.8.59.59 0 0 1 .488.677.59.59 0 0 1-.602.494.59.59 0 0 1-.076-.006 60.376 60.376 0 0 0-8.99-.786.59.59 0 0 1-.584-.596.59.59 0 0 1 .582-.583zm-4.211.097a.59.59 0 0 1 .587.555.59.59 0 0 1-.554.622c-.786.046-1.572.107-2.356.184a.59.59 0 0 1-.04.003.59.59 0 0 1-.603-.533.59.59 0 0 1 .53-.644c.8-.078 1.599-.14 2.4-.187a.59.59 0 0 1 .036 0zM10.6 7.535a.59.59 0 0 1 .015 0c3.06-.013 6.125.204 9.167.65a.59.59 0 0 1 .498.67.59.59 0 0 1-.593.504.59.59 0 0 1-.076-.006 60.142 60.142 0 0 0-8.992-.638.59.59 0 0 1-.592-.588.59.59 0 0 1 .573-.592zm1.153 2.846a61.093 61.093 0 0 1 8.02.515.59.59 0 0 1 .509.66.59.59 0 0 1-.586.514.59.59 0 0 1-.076-.005 59.982 59.982 0 0 0-8.99-.492.59.59 0 0 1-.603-.577.59.59 0 0 1 .578-.603c.382-.008.765-.012 1.148-.012zm1.139 2.832a60.92 60.92 0 0 1 6.871.394.59.59 0 0 1 .52.652.59.59 0 0 1-.577.523.59.59 0 0 1-.076-.004 59.936 59.936 0 0 0-8.991-.344.59.59 0 0 1-.61-.568.59.59 0 0 1 .567-.611c.765-.028 1.53-.042 2.296-.042z"/></svg>Documentation</a></li>
+<li><a href="https://github.com/pyoomph/pyoomph"><svg class="menu-icon menu-icon-github" viewBox="0 0 24 24" aria-hidden="true" focusable="false"><path d="M12 .297c-6.63 0-12 5.373-12 12 0 5.303 3.438 9.8 8.205 11.385.6.113.82-.258.82-.577 0-.285-.01-1.04-.015-2.04-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729 1.205.084 1.838 1.236 1.838 1.236 1.07 1.835 2.809 1.305 3.495.998.108-.776.417-1.305.76-1.605-2.665-.3-5.466-1.332-5.466-5.93 0-1.31.465-2.38 1.235-3.22-.135-.303-.54-1.523.105-3.176 0 0 1.005-.322 3.3 1.23.96-.267 1.98-.399 3-.405 1.02.006 2.04.138 3 .405 2.28-1.552 3.285-1.23 3.285-1.23.645 1.653.24 2.873.12 3.176.765.84 1.23 1.91 1.23 3.22 0 4.61-2.805 5.625-5.475 5.92.42.36.81 1.096.81 2.22 0 1.606-.015 2.896-.015 3.286 0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12"/></svg>Source&nbsp;Code</a></li>
 </ul>
 </div>
 
diff --git a/pubs_excluded.md b/pubs_excluded.md
@@ -0,0 +1,18 @@
+# Screened out of `pubs.bib`
+
+Publications that **cite** the main pyoomph paper (Diddens & Rocha, J. Comput. Phys. **518**,
+113306, 2024, `10.1016/j.jcp.2024.113306`) but do **not use** pyoomph, and therefore do not
+belong on the About page.
+
+They are recorded here so that they do not have to be screened again every time the citing
+literature is checked. See the *Finding new publications for `pubs.bib`* section of `CLAUDE.md`
+for the full workflow; append a row here whenever a candidate fails the screening.
+
+This file is documentation only — no build step reads it.
+
+| DOI | Reference | Screened |
+|---|---|---|
+| `10.1016/j.apm.2026.117152` | Napieralski, Huete, Coenen, Kurdyumov, Douglas & Sánchez-Sanz, *Modal, non-modal and sensitivity analysis of planar deflagrations with low molecular diffusivity and branching kinetics*, Appl. Math. Model. (2026) | 2026-08-04 |
+| `10.1016/j.jcp.2025.114348` | Saini, Sanjay, Saade, Lohse & Popinet, *Implementation of integral surface tension formulations in a volume of fluid framework and their applications to Marangoni flows*, J. Comput. Phys. (2025) — also indexed as SSRN preprint `10.2139/ssrn.5132266` | 2026-08-04 |
+| `10.1016/j.ijnonlinmec.2025.105066` | Li, Liu, Liu, Wu, Li, Ding & Feng, *Analysis and control of coexisting attractor transitions in a class of rigid vibro-impact systems*, Int. J. Non-Linear Mech. (2025) | 2026-08-04 |
+| `10.1016/j.compstruc.2024.107615` | Nahed & de Lamare, *Dynamic characterization of cross-physics coupling strengths, a methodology to coupling and reordering partitioned solvers for multiphysics applications*, Comput. Struct. (2024) | 2026-08-04 |