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Add orcids #23

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10edc10
Add orcids
Grufoony Nov 17, 2025
c127ac9
Update citations
Grufoony Nov 17, 2025
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Prova
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non penso serva
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ma va?
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Butto via tutto
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Ultima prova di oggi
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2 changes: 2 additions & 0 deletions .github/workflows/on-pull-request.yaml
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Expand Up @@ -16,6 +16,8 @@ permissions:
jobs:
update-citations:
uses: ./.github/workflows/update-citations.yaml
secrets:
GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }}

build-preview:
needs: update-citations
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1 change: 1 addition & 0 deletions .github/workflows/on-push.yaml
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Expand Up @@ -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
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Copilot AI Nov 17, 2025

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Using secrets: inherit passes all repository secrets to the reusable workflow, but the update-citations.yaml workflow declares GOOGLE_SCHOLAR_API_KEY as a required secret. This is inconsistent - either make the secret optional in update-citations.yaml or explicitly pass it here like in on-pull-request.yaml to make the dependency clear.

Suggested change
secrets: inherit
secrets:
GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }}

Copilot uses AI. Check for mistakes.

build-site:
needs: update-citations
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1 change: 1 addition & 0 deletions .github/workflows/on-schedule.yaml
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Expand Up @@ -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
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Copilot AI Nov 17, 2025

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Using secrets: inherit passes all repository secrets to the reusable workflow, but the update-citations.yaml workflow declares GOOGLE_SCHOLAR_API_KEY as a required secret. This is inconsistent - either make the secret optional in update-citations.yaml or explicitly pass it here like in on-pull-request.yaml to make the dependency clear.

Suggested change
secrets: inherit
secrets:
GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }}

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with:
open-pr: true
15 changes: 15 additions & 0 deletions .github/workflows/update-citations.yaml
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Expand Up @@ -7,6 +7,9 @@ on:
inputs:
open-pr:
type: boolean
secrets:
GOOGLE_SCHOLAR_API_KEY:
required: true
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The update-citations workflow now requires a GOOGLE_SCHOLAR_API_KEY secret (lines 10-12), but the workflows that call it (on-pull-request.yaml, on-push.yaml, and on-schedule.yaml) don't pass this secret. This will cause those workflows to fail.

To fix this, the calling workflows need to pass the secret using the secrets parameter. For example:

update-citations:
  uses: ./.github/workflows/update-citations.yaml
  secrets:
    GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }}

Alternatively, if you want the secret to be optional when called from workflow_dispatch, you could set required: false on line 12.

Suggested change
required: true
required: false

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outputs:
changed:
value: ${{ jobs.update-citations.outputs.changed }}
Expand All @@ -28,6 +31,18 @@ jobs:
timeout-minutes: 15

steps:
- name: Check GOOGLE_SCHOLAR_API_KEY presence
run: |
echo "========================================";
echo "Checking GOOGLE_SCHOLAR_API_KEY...";
if [ -z "${GOOGLE_SCHOLAR_API_KEY}" ]; then
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The environment variable GOOGLE_SCHOLAR_API_KEY is referenced but never set in the workflow. The secret needs to be explicitly assigned to an environment variable using env: before it can be accessed in the shell script. Add env: GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }} to the step.

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echo "❌ GOOGLE_SCHOLAR_API_KEY is EMPTY or not set";
else
echo "✅ GOOGLE_SCHOLAR_API_KEY appears to be set (length > 0)";
echo "First 4 chars: ${GOOGLE_SCHOLAR_API_KEY:0:4}********";
fi
echo "========================================";

- name: Debug dump
if: runner.debug == '1'
uses: crazy-max/ghaction-dump-context@v2
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0 ...he/83/3e/ae5b97aaab5884ffb7ac78cc980c.val → ...he/83/49/b8bf0543405d52748756507193d4.val
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File renamed without changes.
Binary file modified _cite/.cache/cache.db
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2 changes: 1 addition & 1 deletion _cite/cite.py
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Expand Up @@ -29,7 +29,7 @@
sources = []

# in-order list of plugins to run
plugins = ["google-scholar", "pubmed", "orcid", "arxiv", "sources"]
plugins = ["google-scholar", "pubmed", "orcid", "sources"]

# loop through plugins
for plugin in plugins:
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59 changes: 0 additions & 59 deletions _cite/plugins/arxiv.py
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46 changes: 44 additions & 2 deletions _data/citations.yaml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
10 changes: 10 additions & 0 deletions _data/google-scholar.yaml
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@@ -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
6 changes: 4 additions & 2 deletions _data/orcid.yaml
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@@ -1,2 +1,4 @@
- orcid: 0000-0002-9633-0017
- orcid: 0000-0003-0316-3449
- orcid: 0000-0002-9633-0017 # Armando Bazzani
- orcid: 0000-0003-0316-3449 # Mirko Degli Esposti
- orcid: 0000-0002-0005-0441 # Giulio Colombini
- orcid: 0009-0004-7797-9138 # Gregorio Berselli
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