diff --git a/.github/workflows/on-pull-request.yaml b/.github/workflows/on-pull-request.yaml index 5cdf21a2..4afdae4d 100644 --- a/.github/workflows/on-pull-request.yaml +++ b/.github/workflows/on-pull-request.yaml @@ -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 diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml index dce46efd..d5e79600 100644 --- a/.github/workflows/update-citations.yaml +++ b/.github/workflows/update-citations.yaml @@ -7,6 +7,9 @@ on: inputs: open-pr: type: boolean + secrets: + GOOGLE_SCHOLAR_API_KEY: + required: true outputs: changed: value: ${{ jobs.update-citations.outputs.changed }} diff --git a/_cite/.cache/83/3e/ae5b97aaab5884ffb7ac78cc980c.val b/_cite/.cache/83/49/b8bf0543405d52748756507193d4.val similarity index 100% rename from _cite/.cache/83/3e/ae5b97aaab5884ffb7ac78cc980c.val rename to _cite/.cache/83/49/b8bf0543405d52748756507193d4.val diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 80cafddf..04447ce0 100644 Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ diff --git a/_cite/cite.py b/_cite/cite.py index b7734cfb..4f11f957 100644 --- a/_cite/cite.py +++ b/_cite/cite.py @@ -29,7 +29,7 @@ sources = [] # in-order list of plugins to run -plugins = ["google-scholar", "pubmed", "orcid", "arxiv", "sources"] +plugins = ["google-scholar", "pubmed", "orcid", "sources"] # loop through plugins for plugin in plugins: diff --git a/_cite/plugins/arxiv.py b/_cite/plugins/arxiv.py deleted file mode 100644 index 7f5ac3b5..00000000 --- a/_cite/plugins/arxiv.py +++ /dev/null @@ -1,59 +0,0 @@ -import json -from urllib.request import Request, urlopen -from urllib.parse import quote -from util import * - - -def main(entry): - """ - receives single list entry from arxiv data file - returns list of sources to cite - """ - - # arxiv api endpoint - endpoint = "http://export.arxiv.org/api/query?search_query=au:$AUTHOR&start=0&max_results=1000" - - # get author from entry - author = get_safe(entry, "author", "") - if not author: - raise Exception('No "author" key') - - # query api - @log_cache - @cache.memoize(name=__file__, expire=1 * (60 * 60 * 24)) - def query(author): - url = endpoint.replace("$AUTHOR", quote(author)) - request = Request(url=url) - response = urlopen(request).read().decode('utf-8') - return response - - response = query(author) - - # list of sources to return - sources = [] - - # parse XML response - import xml.etree.ElementTree as ET - root = ET.fromstring(response) - - # namespace for arxiv - ns = {'atom': 'http://www.w3.org/2005/Atom', - 'arxiv': 'http://arxiv.org/schemas/atom'} - - # go through response and format sources - for work in root.findall('atom:entry', ns): - # extract arxiv id from the id field - id_element = work.find('atom:id', ns) - if id_element is not None and id_element.text: - arxiv_id = id_element.text.split('/abs/')[-1] - - # create source with arxiv identifier for Manubot - source = {"id": f"arxiv:{arxiv_id}"} - - # copy fields from entry to source - source.update(entry) - - # add source to list - sources.append(source) - - return sources diff --git a/_data/citations.yaml b/_data/citations.yaml index dfa97bef..e9894733 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -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 diff --git a/_data/google-scholar.yaml b/_data/google-scholar.yaml new file mode 100644 index 00000000..3473f307 --- /dev/null +++ b/_data/google-scholar.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 diff --git a/_data/orcid.yaml b/_data/orcid.yaml index b5616c24..11174bdb 100644 --- a/_data/orcid.yaml +++ b/_data/orcid.yaml @@ -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