Merge pull request computorg#76 from computorg/master

Various fixes

Author: jchiquet

.gitignore

@@ -2,6 +2,8 @@
 /.quarto/
 *.html
 !_site/**/*.html
+# redirect pages for renamed article repositories (declared in _quarto.yml resources)
+!/published-*/index.html
 /**/.DS_Store
 */.DS_Store
 /_freeze/

_quarto.yml

@@ -5,6 +5,9 @@ project:
     - "*.qmd"
     - "site/**/*.qmd"
     - "blog/**/*.qmd"
+  resources:
+    # redirect pages for renamed article repositories (old URL -> new URL)
+    - published-202306-sanou-multiscale_glasso/index.html
   post-render:
     - scripts/fix-sitemap.lua
 website:
@@ -17,7 +20,7 @@ website:
     locale: en_US
   twitter-card:
     card-style: summary_large_image
-  favicon: assets/favicon.ico
+  favicon: assets/img/logo_notext.png
   navbar:
     background: primary
     logo-alt: Computo’s Logo

blog/2023-07-04-what-reproducibility/index.qmd

@@ -39,7 +39,7 @@ When applicable, the switch from external to editorial reproducibility is done w
 ## Examples of data transfer solutions
 
 ### Intermediate results storage
-- in python environment: the [`joblib.Memory`](https://joblib.readthedocs.io/en/latest/memory.html) class which provides a caching mechanism for python functions, and can be used to save the results of a function call to disk, and load it back later.
+- in python environment: the [`joblib.Memory`](https://joblib.readthedocs.io/en/stable/generated/joblib.Memory.html) class which provides a caching mechanism for python functions, and can be used to save the results of a function call to disk, and load it back later.
 - in R environment: the `.RData` file format, which can be loaded back in R with the `load()` function.
 
 ### Transfer of the results to the notebook environment

blog/2026-07-26-google-scholar/index.qmd

@@ -1,6 +1,7 @@
 ---
 title: Google Scholar Indexing
 date: '2026-07-26'
+date-modified: '2026-09-16'
 description: How Computo ensures Google Scholar indexing and understanding URL selection
 categories:
   - indexing
@@ -29,51 +30,58 @@ Computo articles also include the following recommended tags for richer indexing
 
 - `citation_journal_title` -- "Computo"
 - `citation_issn` -- "2824-7795"
-- `citation_pdf_url` -- link to the article PDF
-- `citation_abstract_html_url` -- link to the article landing page
+- `citation_pdf_url` -- link to the article PDF (`main.pdf`)
+- `citation_fulltext_html_url` -- link to the article landing page
 - `citation_doi` -- the article DOI
 
 ### The `google-scholar` flag
 
-All Computo article repositories include `google-scholar: true` in their `_quarto.yml` configuration. When this flag is set, the [Computo Quarto extension](https://github.com/computorg/computo-quarto-extension) automatically generates the complete set of Highwire Press meta tags from the article's frontmatter and `citation:` block. This happens at render time -- no manual intervention is needed.
+All Computo article repositories include `google-scholar: true` in their `_quarto.yml` configuration. When this flag is set, [Quarto](https://quarto.org/docs/authoring/create-citeable-articles.html#google-scholar) itself generates the complete set of Highwire Press meta tags at render time, from the document metadata (`title`, `author`, `date`) and from the `citation:` block. No manual intervention is needed.
 
-Here is what the configuration looks like in a published article's `_quarto.yml`:
+Here is what the configuration looks like in a published article's `_quarto.yml` (for a repository named `published-YYYYMM-name`):
 
 ```yaml
+title: "Article Title"
+author:
+  - name: "Author Name"
+    orcid: 0000-0000-0000-0000
+    affiliations:
+      - name: "Institution"
+date: 2024-01-01
 google-scholar: true
 citation:
-  title: "Article Title"
-  author:
-    - id: author1
-      name: "Author Name"
-      affiliation: "Institution"
-  date: 2024-01-01
-  doi: "10.57750/xxxxx"
-  journal: "Computo"
+  type: article-journal
+  container-title: "Computo"
   publisher: "French Statistical Society"
-  ISSN: "2824-7795"
-  url: "https://computo-journal.org/article-slug/"
-  pdf: "article-slug.pdf"
-  abstract: "..."
+  issn: "2824-7795"
+  doi: "10.57750/xxxxx"
+  url: "https://computo-journal.org/published-YYYYMM-name/"
+  pdf-url: "https://computo-journal.org/published-YYYYMM-name/main.pdf"
 ```
 
+::: {.callout-warning}
+### Keep all metadata in `_quarto.yml`
+Do not repeat metadata in the front matter of `main.qmd`. A `citation:` block there **replaces** the one in `_quarto.yml` entirely (dropping `url` and `pdf-url`), and an `author:` list that differs from the one in `_quarto.yml` leads to duplicated authors in the generated citation.
+:::
+
 From this, Quarto generates HTML meta tags like:
 
 ```html
 <meta name="citation_title" content="Article Title">
 <meta name="citation_author" content="Author Name">
-<meta name="citation_publication_date" content="2024/01/01">
+<meta name="citation_publication_date" content="2024-01-01">
 <meta name="citation_journal_title" content="Computo">
 <meta name="citation_issn" content="2824-7795">
-<meta name="citation_pdf_url" content="https://computo-journal.org/article-slug/article-slug.pdf">
+<meta name="citation_fulltext_html_url" content="https://computo-journal.org/published-YYYYMM-name/">
+<meta name="citation_pdf_url" content="https://computo-journal.org/published-YYYYMM-name/main.pdf">
 <meta name="citation_doi" content="10.57750/xxxxx">
 ```
 
 ### Additional discoverability features
 
 Beyond meta tags, Computo articles benefit from several features that help Google Scholar's crawlers:
 
-- **Sitemap**: Quarto auto-generates a `sitemap.xml` (thanks to `site-url` being configured in the main site's `_quarto.yml`), which helps search engines discover all article URLs.
+- **Sitemap**: Quarto auto-generates a `sitemap.xml` for the journal website (thanks to `site-url` being configured in the main site's `_quarto.yml`), and a post-render script adds the URL of every published article, which helps search engines discover them.
 - **Open access**: All articles are freely accessible without login walls or paywalls, meeting Google Scholar's requirement for crawlable full text.
 - **Stable URLs**: Each article has a permanent URL on `computo-journal.org` and a DOI, ensuring persistent access.
 - **Abstract visibility**: The full author-written abstract is clearly visible on each article's landing page.
@@ -115,6 +123,17 @@ For the full official documentation, see Google Scholar's [Inclusion Guidelines
 
 ## Indexing status report
 
+::: {.callout-important}
+### Update: September 2026
+A September 2026 audit found that, contrary to what this post initially stated, the `citation_pdf_url` tag was **missing from all Computo articles** until September 15, 2026, as well as from two landing pages that were redirect-only. All articles have since been fixed:
+
+- every article now declares `pdf-url` in its `citation:` block, and the tag is present on all article pages;
+- article metadata was moved from `main.qmd` to `_quarto.yml`, which also removed duplicated authors from the generated citation of three articles;
+- re-indexing of all article pages has been requested through Google Search Console.
+
+The report below reflects the July 2026 situation, before these fixes.
+:::
+
 ::: {.callout-note}
 ### Report date: July 2026
 The following status was verified by searching Google Scholar for each published article.
@@ -139,7 +158,7 @@ The following status was verified by searching Google Scholar for each published
 
 ### Not yet indexed in Google Scholar
 
-The following 18 published articles were **not found** in Google Scholar as of July 2026:
+The following 16 published articles were **not found** in Google Scholar as of July 2026:
 
 | # | Article | Authors | Year |
 |---|---------|---------|------|

news.yml

@@ -12,7 +12,7 @@
 
     Computo has been presented at the [2nd Toronto Workshop on reproducibility](https://canssiontario.utoronto.ca/toronto_workshop_on_reproducibility_2022/) !
 
-    🤩 [slides are online here](http://computo.sfds.asso.fr/comm/)
+    🤩 [slides are online here](https://computo-journal.org/comm/)
 
 - date: 2022-06-14 07:59:00-0400
   description: >2+
@@ -34,20 +34,20 @@
 
     [François-David](https://fradav.github.io/) and
 
-    [Ghislain](https://gdurif.perso.math.cnrs.fr/) [in the team](board) 👨‍💻 !
+    [Ghislain](https://gdurif.perso.math.cnrs.fr/) [in the team](site/board.html) 👨‍💻 !
 
     Thanks for their support.
 
 - date: 2023-02-08 07:59:00-0400
   description: >2
 
-    We have [updated our templates for submitting to Computo](https://computo.sfds.asso.fr/submit/): all based on Quarto, but now with more specific and hoefully friendly set-ups for R, Python or Julia users.
+    We have [updated our templates for submitting to Computo](https://computo-journal.org/site/guidelines-authors.html): all based on Quarto, but now with more specific and hoefully friendly set-ups for R, Python or Julia users.
 - date: 2023-06-21 07:59:00-0400
   description: >2+
 
     Delighted to welcome
 
-    [Marie-Pierre](httpshttps://marieetienne.github.io/) [in the team](board) 👨‍💻 !
+    [Marie-Pierre](https://marieetienne.github.io/) [in the team](site/board.html) 👨‍💻 !
 
 - date: 2023-06-21 07:59:00-0400
   description: >2+
@@ -64,7 +64,7 @@
 
     Delighted to welcome
 
-    [Aymeric Stamm](https://astamm.github.io/) [in the team](board) 👨‍💻 !
+    [Aymeric Stamm](https://astamm.github.io/) [in the team](site/board.html) 👨‍💻 !
 
 - date: 2025-09-16 07:59:00-0400
   description: >2+
@@ -83,9 +83,9 @@
 
     Happy to welcome
 
-    [Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) [in the team](board) 👨‍💻 !
+    [Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) [in the team](site/board.html) 👨‍💻 !
 
-- date: 2026-12-16 07:59:00-0400
+- date: 2026-06-16 07:59:00-0400
   description: >2+
 
     The next [2026 French Statistics Days](https://jds2026.sciencesconf.org/) is fast approaching and will take place in Clermont-Ferrand. To mark the occasion, [François-David Collin](https://fradav.perso.math.cnrs.fr/) is running a [workshop](https://computo-journal.org/jds-workshop/) on how to use Computo templates to help you prepare your submission with ease.