Refine research visibility, identity, and open report links

assets/data/publications.json

@@ -174,28 +174,30 @@
       "journal": "Instituto del Mar del Perú (IMARPE)",
       "type": "Technical Protocol",
       "doi": "",
-      "url": "",
+      "url": "https://www.gob.pe/institucion/imarpe/informes-publicaciones/7947433-elaboracion-de-las-tablas-de-decision-para-la-determinacion-del-limite-maximo-total-de-captura-permisible-por-temporada-de-pesca-en-la-pesqueria-del-stock-norte-centro-de-la-anchoveta-peruana",
       "institutional_author": "Instituto del Mar del Perú (IMARPE)",
       "identifier": "Ed. 06 · Rev. 00",
       "role": "Contributor",
       "summary": "Risk-based methodology linking abundance-at-length, biological parameters, environmental and exploitation scenarios, and spawning-biomass projections to seasonal harvest advice.",
       "source": "Career master",
       "output_category": "Reports & technical outputs",
-      "curated": true
+      "curated": true,
+      "open_access": true
     },
     {
       "title": "North-central Peruvian anchovy stock status and 2026 first-season exploitation outlook",
       "year": "2026",
       "journal": "Instituto del Mar del Perú (IMARPE)",
       "type": "Stock Assessment & Management Advice",
       "doi": "",
-      "url": "",
+      "url": "https://www.gob.pe/institucion/imarpe/informes-publicaciones/7960391-informe-correspondiente-al-oficio-n-0507-2026-imarpe-pe",
       "institutional_author": "Instituto del Mar del Perú (IMARPE)",
       "role": "Contributor",
       "summary": "Integrated stock-status assessment combining environmental conditions, fishery indicators, acoustic biomass, size structure, biological condition, and exploitation scenarios for management advice.",
       "source": "Career master",
       "output_category": "Reports & technical outputs",
-      "curated": true
+      "curated": true,
+      "open_access": true
     },
     {
       "title": "North-central Peruvian anchovy status and 2025 second-season exploitation outlook",

contact/index.qmd

@@ -7,7 +7,7 @@ toc: false
 ## Contact
 
 **Elmer Quispe-Salazar**  
-Marine Quantitative Ecologist · Fisheries Scientist  
+Quantitative Fisheries Scientist  
 [Instituto del Mar del Perú (IMARPE)](https://www.gob.pe/imarpe)  
 Callao, Peru
 

includes/profile-sidebar.html

@@ -5,7 +5,7 @@
       <img src="/images/profile.png" alt="Portrait of Elmer Quispe-Salazar">
     </div>
     <p class="qs-sidebar-name">Elmer Quispe-Salazar</p>
-    <p class="qs-sidebar-role">Marine Quantitative Ecologist<br>Fisheries Scientist</p>
+    <p class="qs-sidebar-role">Quantitative Fisheries Scientist</p>
     <div class="qs-sidebar-context qs-sidebar-affiliation"><i class="bi bi-building" aria-hidden="true"></i><span>Instituto del Mar del Perú (IMARPE)</span></div>
     <div class="qs-sidebar-context"><i class="bi bi-geo-alt-fill" aria-hidden="true"></i><span>Peru · Humboldt Current</span></div>
     <div class="qs-sidebar-context"><i class="bi bi-water" aria-hidden="true"></i><span>Pelagic fisheries · Statistical ecology</span></div>
@@ -16,11 +16,5 @@
       <a href="https://github.com/qselmer"><i class="bi bi-github" aria-hidden="true"></i><span>GitHub</span></a>
       <a href="https://www.linkedin.com/in/elmer-quispe-salazar-104b6b1a4/"><i class="bi bi-linkedin" aria-hidden="true"></i><span>LinkedIn</span></a>
     </nav>
-    <p class="qs-sidebar-section-label">Research metrics</p>
-    <div class="qs-sidebar-metrics-list" aria-label="Research metrics">
-      <div class="qs-sidebar-metric-row"><span>ORCID works</span><strong>5</strong></div>
-<div class="qs-sidebar-metric-row"><span>OpenAlex works</span><strong>3</strong></div>
-    </div>
-    <p class="qs-sidebar-metrics-note">Public ORCID and OpenAlex records.</p>
   </div>
 </aside>

projects/index.qmd

@@ -4,12 +4,12 @@ description: "Research themes, projects at different stages of maturity, and rel
 css: research.css
 ---
 
-::: {.qs-footnote-note}
-**Project-stage note.** This catalogue includes active analyses, manuscripts in development, reusable research infrastructure, and planned studies. The stage shown on each card describes its current maturity; inclusion here does not imply that all projects are being pursued simultaneously.
-:::
-
 {{< include _generated.md >}}
 
 ::: {.qs-footnote-note}
 **Research catalogue.** Each project card represents a canonical research repository or a stable public project record linked to its source repository. Formal publication, talk, software, teaching, and post metadata remain authoritative in their respective catalogues. [Explore the public Research Graph](/research-graph/) to see these records connected through common themes, projects, repositories, and provenance.
 :::
+
+::: {.qs-footnote-note}
+**Project-stage note.** This catalogue includes active analyses, manuscripts in development, reusable research infrastructure, and planned studies. The stage shown on each card describes its current maturity; inclusion here does not imply that all projects are being pursued simultaneously.
+:::

projects/research.css

@@ -83,3 +83,38 @@
     white-space: normal;
   }
 }
+
+/* Repository visibility is explicit without exposing private GitHub links. */
+.qs-project-topline {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+  gap: .55rem;
+}
+
+.qs-project-visibility {
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  width: 1.45rem;
+  height: 1.45rem;
+  border-radius: 50%;
+  font-size: .82rem;
+  line-height: 1;
+}
+
+.qs-project-visibility-private {
+  color: #9a6200;
+  background: rgba(196, 132, 0, .11);
+}
+
+.qs-project-visibility-public {
+  color: #39724d;
+  background: rgba(57, 114, 77, .10);
+}
+
+.qs-project-repository-state {
+  color: #6b7280;
+  font-size: .84rem;
+  white-space: nowrap;
+}

publications/_generated.md

@@ -3,33 +3,38 @@
 <nav class="qs-publication-nav" aria-label="Publication sections">
 <a href="#papers"><strong>Papers</strong></a>
 <a href="#theses"><strong>Theses</strong></a>
+<a href="#reports"><strong>Reports</strong></a>
 </nav>
 
 <p class="qs-publication-profile"><em>My ORCID iD is</em> <a href="https://orcid.org/0000-0001-9229-6379"><strong>0000-0001-9229-6379</strong></a>.</p>
 <p class="qs-publication-profile"><em>My Google Scholar profile is</em> <a href="https://scholar.google.com/citations?user=wz83egoAAAAJ"><strong>here</strong></a>.</p>
 
 ## Peer-reviewed articles {#papers}
 
-- **Quispe-Salazar, E.**, Sánchez, J., & Perea, Á. (2025). Classification models based on the gonadosomatic index to determine gonadal maturity stages: a case study in the Peruvian anchovy Engraulis ringens. *Scientia Marina, 89*(4), e117. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-blue" href="https://doi.org/10.3989/scimar.05636.117"><span class="qs-badge-label">DOI</span><span class="qs-badge-value">10.3989/scimar.05636.117</span></a><a class="qs-badge qs-badge-green" href="https://doi.org/10.3989/scimar.05636.117"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a><a class="qs-badge qs-badge-amber" href="/projects/#life-history"><span class="qs-badge-label">Research</span><span class="qs-badge-value">Reproduction &amp; growth</span></a></span> <details class="qs-publication-bibtex"><summary aria-label="Show BibTeX citation"><span class="qs-badge qs-badge-neutral"><span class="qs-badge-label">BibTeX</span><span class="qs-badge-value">view</span></span></summary><pre><code>@article{quispesalazar2025classification,
-  author = {Elmer Quispe-Salazar and Javier Sánchez and Ángel Perea},
-  title = {Classification models based on the gonadosomatic index to determine gonadal maturity stages: a case study in the Peruvian anchovy Engraulis ringens},
-  year = {2025},
-  journal = {Scientia Marina},
-  volume = {89},
-  number = {4},
-  pages = {e117},
-  doi = {10.3989/scimar.05636.117},
-  url = {https://doi.org/10.3989/scimar.05636.117}
-}</code></pre></details>
+- **Quispe-Salazar, E.**, Sánchez, J., & Perea, Á. (2025). Classification models based on the gonadosomatic index to determine gonadal maturity stages: a case study in the Peruvian anchovy Engraulis ringens. *Scientia Marina, 89*(4), e117. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-blue" href="https://doi.org/10.3989/scimar.05636.117"><span class="qs-badge-label">DOI</span><span class="qs-badge-value">10.3989/scimar.05636.117</span></a><a class="qs-badge qs-badge-green" href="https://doi.org/10.3989/scimar.05636.117"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>
 
 ## Theses {#theses}
 
-- **Quispe-Salazar, E.** (2025). Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022. *Cybertesis Revistas UNMSM Fondo editorial*. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-blue" href="https://doi.org/10.5281/zenodo.17452484"><span class="qs-badge-label">DOI</span><span class="qs-badge-value">10.5281/zenodo.17452484</span></a><a class="qs-badge qs-badge-green" href="https://zenodo.org/doi/10.5281/zenodo.17452484"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a><a class="qs-badge qs-badge-amber" href="/projects/#life-history"><span class="qs-badge-label">Research</span><span class="qs-badge-value">Reproduction &amp; growth</span></a></span> <details class="qs-publication-bibtex"><summary aria-label="Show BibTeX citation"><span class="qs-badge qs-badge-neutral"><span class="qs-badge-label">BibTeX</span><span class="qs-badge-value">view</span></span></summary><pre><code>@misc{quispesalazar2025interannual,
-  author = {Elmer Quispe-Salazar},
-  title = {Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022},
-  year = {2025},
-  howpublished = {Cybertesis Revistas UNMSM Fondo editorial},
-  doi = {10.5281/zenodo.17452484},
-  url = {https://zenodo.org/doi/10.5281/zenodo.17452484},
-  note = {Dissertation Thesis}
-}</code></pre></details>
+- **Quispe-Salazar, E.** (2025). Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022. *Cybertesis Revistas UNMSM Fondo editorial*. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-blue" href="https://doi.org/10.5281/zenodo.17452484"><span class="qs-badge-label">DOI</span><span class="qs-badge-value">10.5281/zenodo.17452484</span></a><a class="qs-badge qs-badge-green" href="https://zenodo.org/doi/10.5281/zenodo.17452484"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>
+
+## Reports and institutional technical outputs {#reports}
+
+### 2026
+
+- IMARPE Pelagic Resources Team (2026). Decision-table protocol for seasonal catch advice in the north-central Peruvian anchovy fishery. Risk-based methodology linking abundance-at-length, biological parameters, environmental and exploitation scenarios, and spawning-biomass projections to seasonal harvest advice. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-green" href="https://www.gob.pe/institucion/imarpe/informes-publicaciones/7947433-elaboracion-de-las-tablas-de-decision-para-la-determinacion-del-limite-maximo-total-de-captura-permisible-por-temporada-de-pesca-en-la-pesqueria-del-stock-norte-centro-de-la-anchoveta-peruana"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>
+- IMARPE Pelagic Resources Team (2026). North-central Peruvian anchovy stock status and 2026 first-season exploitation outlook. Integrated stock-status assessment combining environmental conditions, fishery indicators, acoustic biomass, size structure, biological condition, and exploitation scenarios for management advice. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-green" href="https://www.gob.pe/institucion/imarpe/informes-publicaciones/7960391-informe-correspondiente-al-oficio-n-0507-2026-imarpe-pe"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>
+
+### 2025
+
+- IMARPE Pelagic Resources Team (2025). Jack mackerel fishery status in 2025 and exploitation outlook for 2026. Assessment synthesis covering the 2025 jack-mackerel fishery, stock status, spawning biomass, fishing mortality, recruitment, exploitation scenarios, and catch-limit advice; individual contribution is not attributed in the report itself.
+- IMARPE Pelagic Resources Team (2025). North-central Peruvian anchovy status and 2025 second-season exploitation outlook. Seasonal assessment integrating fishery performance, environmental conditions, acoustic biomass, demographic structure, reproductive condition, and exploitation perspectives.
+- IMARPE Pelagic Resources Team (2025). Southern Peruvian anchovy status and 2026 first-season exploitation outlook. Regional assessment of southern anchoveta availability, fishery indicators, biomass projections, exploitation scenarios, and management advice.
+
+### 2024
+
+- SPRFMO Connectivity Task Team (2024). Critical appraisal of research approaches to inform evidence of connectivity of Trachurus murphyi – a systematic review of 11 topics. *SPRFMO 12th Meeting of the Scientific Committee*. Systematic evidence synthesis across 11 research domains relevant to population connectivity and management of Chilean jack mackerel. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-green" href="https://www.sprfmo.int/assets/Meetings/02-SC/12th-SC-2024/Working-Papers/SC12-WP03-CJM_connectivity_TG_Desk_Study-FINAL-v2.pdf"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>
+- Geronimo, M., Lujan, C., Torrejón, J., & **Quispe-Salazar, E.** (2024). The Joint Jack Mackerel (JJM) model: a user guide to IMARPE's proposal. *SPRFMO 12th Meeting of the Scientific Committee*. Documents the population-dynamics equations, AD Model Builder implementation, inputs, outputs, model execution, and practical use of the JJM stock-assessment model. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-green" href="https://www.sprfmo.int/assets/Meetings/02-SC/12th-SC-2024/Jack-Mackerel/SC12-JM08-PER-Joint-Jack-Mackerel-Model-User-Guide.pdf"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>
+
+### 2023
+
+- Gutiérrez, M., Tarazona, A., Grados, D., Valdez, C., **Quispe-Salazar, E.**, Pereyra, N., Peraltilla, S., Meneses, G., & Vásquez, L. (2023). Habitat conditions of jack mackerel (Trachurus murphyi) and chub mackerel (Scomber japonicus) in the Peruvian sea between 2021 and 2023. *SPRFMO 11th Meeting of the Scientific Committee*. Links oceanographic and habitat conditions with the distribution of jack mackerel and chub mackerel in Peruvian waters. <span class="qs-badge-row qs-publication-badges"><a class="qs-badge qs-badge-green" href="https://www.sprfmo.int/assets/Meetings/02-SC/11th-SC-2023/Habitat-Monitoring/SC11-HM02-PER-Habitat-conditions-of-jack-mackerel-and-chub-mackerel-in-the-Peruvian-sea-between-2021-and-2023-.pdf"><span class="qs-badge-label">Open</span><span class="qs-badge-value">access</span></a></span>

scripts/build_home.py

@@ -109,7 +109,7 @@ def render_sidebar(data: dict, identity: dict) -> str:
       <img src="/images/profile.png" alt="Portrait of {name}">
     </div>
     <p class="qs-sidebar-name">{name}</p>
-    <p class="qs-sidebar-role">Marine Quantitative Ecologist<br>Fisheries Scientist</p>
+    <p class="qs-sidebar-role">{html.escape(str(identity["headline"]))}</p>
     <div class="qs-sidebar-context qs-sidebar-affiliation"><i class="bi bi-building" aria-hidden="true"></i><span>Instituto del Mar del Perú (IMARPE)</span></div>
     <div class="qs-sidebar-context"><i class="bi bi-geo-alt-fill" aria-hidden="true"></i><span>Peru · Humboldt Current</span></div>
     <div class="qs-sidebar-context"><i class="bi bi-water" aria-hidden="true"></i><span>Pelagic fisheries · Statistical ecology</span></div>

scripts/build_projects.py

@@ -82,24 +82,39 @@ def render_badges(items: list[dict], owner: str, expected_labels: tuple[str, ...
 
 
 def render_card(project: dict) -> list[str]:
-    """Render a GitHub-backed project while making its maturity explicit."""
+    """Render a GitHub-backed project while making maturity and repository visibility explicit."""
     slug = clean_class(project.get("slug"), "project slug")
     title = str(project.get("title") or "").strip()
     summary = str(project.get("summary") or "").strip()
     context = str(project.get("context") or "").strip()
     stage = str(project.get("stage") or "").strip()
     repository = str(project.get("source_repository") or "").strip()
+    site_path = str(project.get("site_path") or "").strip()
     if not all((title, summary, context, stage, repository)):
         raise RuntimeError(f"Project {slug} is missing card content, stage, or source_repository")
-    target = f"https://github.com/{repository}"
+
+    repository_url = f"https://github.com/{repository}"
+    is_private = bool(site_path) and not re.match(r"^https?://", site_path, flags=re.I)
+    target = site_path if is_private else repository_url
+    visibility = "Private repository" if is_private else "Public repository"
+    visibility_class = "private" if is_private else "public"
+    visibility_icon = "bi-lock-fill" if is_private else "bi-unlock-fill"
+    repository_action = (
+        '<span class="qs-project-repository-state">Private repository</span>'
+        if is_private
+        else f'<a href="{html.escape(repository_url, quote=True)}">Repository</a>'
+    )
 
     return [
         '<article class="qs-project-tile">',
         '<div class="qs-project-body">',
+        '<div class="qs-project-topline">',
         '<span class="qs-project-type">PROJECT</span>',
+        f'<span class="qs-project-visibility qs-project-visibility-{visibility_class}" title="{html.escape(visibility, quote=True)}" aria-label="{html.escape(visibility, quote=True)}"><i class="bi {visibility_icon}" aria-hidden="true"></i></span>',
+        '</div>',
         f'<h3><a href="{html.escape(target, quote=True)}">{html.escape(title)}</a></h3>',
         f'<p class="qs-project-card-summary">{html.escape(summary)}</p>',
-        f'<div class="qs-project-footer"><span><strong>Stage:</strong> {html.escape(stage)} · {html.escape(context)}</span><a href="{html.escape(target, quote=True)}">Repository</a></div>',
+        f'<div class="qs-project-footer"><span><strong>Stage:</strong> {html.escape(stage)} · {html.escape(context)}</span>{repository_action}</div>',
         "</div>",
         "</article>",
     ]

scripts/postprocess_site.py

@@ -20,6 +20,7 @@
 PUBLICATIONS = ROOT / "assets" / "data" / "publications.json"
 SOFTWARE = ROOT / "assets" / "data" / "software.json"
 BLOG = ROOT / "blog" / "registry.json"
+CONFIG = ROOT / "config" / "site.json"
 PERSON_ID = SITE_URL + "/#person"
 
 
@@ -121,14 +122,16 @@ def apply_social_preview(text: str, route: str) -> str:
 
 
 def person_schema() -> dict:
+    identity = load_json(CONFIG).get("identity") or {}
+    headline = str(identity.get("headline") or "Quantitative Fisheries Scientist")
     return {
         "@context": "https://schema.org",
         "@type": "Person",
         "@id": PERSON_ID,
         "name": "Elmer Quispe-Salazar",
         "url": SITE_URL + "/",
         "image": SITE_URL + "/images/profile.png",
-        "jobTitle": ["Marine Quantitative Ecologist", "Fisheries Scientist"],
+        "jobTitle": headline,
         "worksFor": {
             "@type": "Organization",
             "name": "Instituto del Mar del Perú (IMARPE)",