Merge branch 'main' into desposti-patch-1

Author: Grufoony

.github/workflows/on-pull-request.yaml

@@ -16,6 +16,7 @@ permissions:
 jobs:
   update-citations:
     uses: ./.github/workflows/update-citations.yaml
+    secrets: inherit
 
   build-preview:
     needs: update-citations

.github/workflows/on-push.yaml

@@ -18,6 +18,7 @@ jobs:
     # skip first run because nothing enabled or setup yet
     if: github.run_number != 1
     uses: ./.github/workflows/update-citations.yaml
+    secrets: inherit
 
   build-site:
     needs: update-citations

.github/workflows/on-schedule.yaml

@@ -18,5 +18,6 @@ jobs:
     # only run on user instance of template, not template itself
     if: github.repository != 'greenelab/lab-website-template'
     uses: ./.github/workflows/update-citations.yaml
+    secrets: inherit
     with:
       open-pr: true

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 Reference: common-changelog.org
 
+## 1.3.8 - 2025-11-17
+
+### Changed
+
+- Inherit secrets in GitHub Actions workflows where appropriate
+- Add commented out ORCID plugin code to discard source if no ID
+
 ## 1.3.7 - 2025-07-31
 
 ### Changed

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.3.7
-date-released: 2025-07-31
+version: 1.3.8
+date-released: 2025-11-17
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"
@@ -11,4 +11,7 @@ authors:
   - family-names: "Greene"
     given-names: "Casey"
     orcid: "https://orcid.org/0000-0001-8713-9213"
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.17228741
 cff-version: 1.2.0

README.md

@@ -1,10 +1,9 @@
+![on-push](../../actions/workflows/on-push.yaml/badge.svg)
+![on-pull-request](../../actions/workflows/on-pull-request.yaml/badge.svg)
+![on-schedule](../../actions/workflows/on-schedule.yaml/badge.svg)
 
-  ![on-push](../../actions/workflows/on-push.yaml/badge.svg)
-  ![on-pull-request](../../actions/workflows/on-pull-request.yaml/badge.svg)
-  ![on-schedule](../../actions/workflows/on-schedule.yaml/badge.svg)
+# physycom's Website
 
-  # physycom's Website
+Visit **[physycom.github.io/website](https://physycom.github.io/website)** 🚀
 
-  Visit **[physycom.github.io/website](https://physycom.github.io/website)** 🚀
-
-  _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+_Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_

_cite/.cache/96/5b/38074930471bda8ad43962205b18.val

@@ -84,6 +84,10 @@ def sort_id(_id):
         id_type = get_safe(_id, "external-id-type", "")
         id_value = get_safe(_id, "external-id-value", "")
 
+        # if no available ids, skip source completely
+        # if not id_type or not id_value:
+        #     continue
+
         # create source
         source = {}
 

_cite/plugins/orcid.py

@@ -10,7 +10,7 @@
   publisher: Chaos, Solitons & Fractals
   date: '2025-12-01'
   link: https://doi.org/g9749f
-  orcid: 0000-0002-9633-0017
+  orcid: 0000-0002-0005-0441
   plugin: orcid.py
   file: orcid.yaml
 - id: doi:10.1103/PhysRevAccelBeams.28.014001
@@ -81,7 +81,7 @@
   publisher: 'Journal of Statistical Mechanics: Theory and Experiment'
   date: '2022-02-01'
   link: https://doi.org/g89wjq
-  orcid: 0000-0002-9633-0017
+  orcid: 0000-0002-0005-0441
   plugin: sources.py
   file: sources.yaml
   type: paper
@@ -1265,3 +1265,45 @@
   orcid: 0000-0003-0316-3449
   plugin: orcid.py
   file: orcid.yaml
+- id: doi:10.1101/2025.03.27.25324700
+  title: Human mobility and sewage data correlate with COVID-19 epidemic evolution
+    in the metropolitan area of Bologna
+  authors:
+  - Francesco Durazzi
+  - Enrico Lunedei
+  - Giulio Colombini
+  - Giulia Gatti
+  - Vittorio Sambri
+  - Alessandra de Cesare
+  - Cecilia Crippa
+  - "Fr\xE9d\xE9rique Pasquali"
+  - Gastone Castellani
+  - Daniel Remondini
+  - Armando Bazzani
+  publisher: Cold Spring Harbor Laboratory
+  date: '2025-03-28'
+  link: https://doi.org/hbbn9g
+  orcid: 0000-0002-0005-0441
+  plugin: orcid.py
+  file: orcid.yaml
+- id: doi:10.1186/s12879-025-11520-2
+  title: Human mobility and sewage data correlate with COVID-19 epidemic evolution
+    in a 3-year surveillance of the metropolitan area of Bologna
+  authors:
+  - Francesco Durazzi
+  - Enrico Lunedei
+  - Giulio Colombini
+  - Giulia Gatti
+  - Vittorio Sambri
+  - Alessandra De Cesare
+  - Cecilia Crippa
+  - "Fr\xE9d\xE9rique Pasquali"
+  - Gastone Castellani
+  - Daniel Remondini
+  - Armando Bazzani
+  publisher: BMC Infectious Diseases
+  date: '2025-10-31'
+  link: https://doi.org/hbbn9h
+  orcid: 0000-0002-0005-0441
+  plugin: orcid.py
+  file: orcid.yaml

_data/citations.yaml

@@ -0,0 +1,10 @@
+# Google Scholar author IDs
+# To find a researcher's Google Scholar ID:
+# 1. Go to https://scholar.google.com
+# 2. Search for the researcher
+# 3. Click on their profile
+# 4. The URL will look like: https://scholar.google.com/citations?user=XXXXXXXXX
+# 5. Use XXXXXXXXX as the gsid below
+
+- gsid: flhs-gwAAAAJ # Mirko Degli Esposti
+- gsid: Z6lHULUAAAAJ # Gregorio Berselli