From 10edc109cc16a967ded3465949006199a1abe197 Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:00:57 +0100 Subject: [PATCH 01/22] Add orcids --- _cite/cite.py | 2 +- _cite/plugins/arxiv.py | 59 ------------------------------------------ _data/orcid.yaml | 2 ++ 3 files changed, 3 insertions(+), 60 deletions(-) delete mode 100644 _cite/plugins/arxiv.py 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/orcid.yaml b/_data/orcid.yaml index b5616c24..67e7e7ed 100644 --- a/_data/orcid.yaml +++ b/_data/orcid.yaml @@ -1,2 +1,4 @@ - orcid: 0000-0002-9633-0017 - orcid: 0000-0003-0316-3449 +- orcid: 0009-0004-7797-9138 +- orcid: 0000-0002-0005-0441 From c127ac9d26aa3365de71acd496a687321c7a631d Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:03:07 +0000 Subject: [PATCH 02/22] Update citations --- .../b8bf0543405d52748756507193d4.val} | Bin _cite/.cache/cache.db | Bin 94208 -> 98304 bytes _data/citations.yaml | 46 +++++++++++++++++- 3 files changed, 44 insertions(+), 2 deletions(-) rename _cite/.cache/83/{3e/ae5b97aaab5884ffb7ac78cc980c.val => 49/b8bf0543405d52748756507193d4.val} (100%) 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 80cafddf29ccae698398794f1f9be3ffa6cf8a8b..3ba60c082da89cd853da8652dfa84707a0d415e5 100644 GIT binary patch delta 15385 zcmd5@d3;pW**<6X%o?(h1PsHzPBJr@NoGKnunYncVqIu!1%_l`29iuN3mCRx07W2z z@dhqxTR?Ebf`L(jqBd@I7ptY8QtMV16a*2pv{n1P@42~mE+JIDF28>B$9?BH_qp#q z_bksj=brbjd|$nCrRKI?>U=^-ev5T1&EGfY1&dw@Far-Jt|+q~HzPBX8}XScbubdH567cDH&M=C zlCRiAxTPh%3KPl_MJK7+UmXN$Xi30IayPEv+Ddw6Em!uX)$!We*|nj%P)t8~dI zC7Bkwg!_C<8Dzch*u2D2i?XjGoi%M!fzqw$E^FE~J(UjOOkJpc_Ph{e8*iswjp-L= 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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 From 0abc7b35e3aa55fe4a88f59f1e60acdcdad96c9e Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:16:15 +0100 Subject: [PATCH 03/22] Prova --- .github/workflows/update-citations.yaml | 2 ++ _data/orcid.yaml | 8 ++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml index dce46efd..c8c1ab7b 100644 --- a/.github/workflows/update-citations.yaml +++ b/.github/workflows/update-citations.yaml @@ -58,6 +58,8 @@ jobs: - name: Build updated citations if: github.event.action != 'closed' + env: + GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }} run: python _cite/cite.py timeout-minutes: 15 diff --git a/_data/orcid.yaml b/_data/orcid.yaml index 67e7e7ed..11174bdb 100644 --- a/_data/orcid.yaml +++ b/_data/orcid.yaml @@ -1,4 +1,4 @@ -- orcid: 0000-0002-9633-0017 -- orcid: 0000-0003-0316-3449 -- orcid: 0009-0004-7797-9138 -- orcid: 0000-0002-0005-0441 +- orcid: 0000-0002-9633-0017 # Armando Bazzani +- orcid: 0000-0003-0316-3449 # Mirko Degli Esposti +- orcid: 0000-0002-0005-0441 # Giulio Colombini +- orcid: 0009-0004-7797-9138 # Gregorio Berselli From c52d1456831eaf5ae7a33ebffa5ad12ec76456fb Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:22:01 +0100 Subject: [PATCH 04/22] Proviaml --- _data/google-scholar.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 _data/google-scholar.yaml diff --git a/_data/google-scholar.yaml b/_data/google-scholar.yaml new file mode 100644 index 00000000..3473f307 --- /dev/null +++ b/_data/google-scholar.yaml @@ -0,0 +1,10 @@ +# Google Scholar author IDs +# To find a researcher's Google Scholar ID: +# 1. Go to https://scholar.google.com +# 2. Search for the researcher +# 3. Click on their profile +# 4. The URL will look like: https://scholar.google.com/citations?user=XXXXXXXXX +# 5. Use XXXXXXXXX as the gsid below + +- gsid: flhs-gwAAAAJ # Mirko Degli Esposti +- gsid: Z6lHULUAAAAJ # Gregorio Berselli From 6606c64309dcfc85550bb6c74f973ed40c383822 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:22:29 +0000 Subject: [PATCH 05/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 3ba60c082da89cd853da8652dfa84707a0d415e5..2b542c227889466df20a2360f72e39c81a50514c 100644 GIT binary patch delta 395 zcmZvX%T59@6o%X~&>0oS1mO)THmATMSR& zWB3X_g%BW^=vjW}&pF>8MTsa%j8Pq+iCursS=u%qjlF|RY%v*~fE%_VN0 z=-5&b#iU|XR&)WjK$por9x&SH9v%#Z5>)VbMdwY!tyOcdnUp7-DG$rDfcAzW5TPvV ztRZd{WXy$ITi0pmT8j`Rv^R~ibFUsN>XaF~r8S*|4xl0Dm@}WL)TTz0FSn2fH|BeP z7u*@AUAnx@L&sXFq3bGaS^ue_*D`F*H$DsSA)9K?{vkc%e_hc_5pFNJ?~}ni{ak@N tOL{EA^e`YC`=aZiC-d1ZZ9V?FMnWab!M8=Lg)Ke_sFq delta 395 zcmZvX%T59@6o%odiHe>o+cEz$1JFOPY1dS z?SxcBF{v1p`RNX0%Z~eLXj@w~)GffO^`9Dg&B4lQKj-1) shCYaJuN@GMeNp#NWIk)z^YO21Bvb--2n|CYjh3F Date: Mon, 17 Nov 2025 12:23:10 +0100 Subject: [PATCH 06/22] non penso serva --- .github/workflows/update-citations.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml index c8c1ab7b..dce46efd 100644 --- a/.github/workflows/update-citations.yaml +++ b/.github/workflows/update-citations.yaml @@ -58,8 +58,6 @@ jobs: - name: Build updated citations if: github.event.action != 'closed' - env: - GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }} run: python _cite/cite.py timeout-minutes: 15 From bae82b0588aa5a254db0929f24c6b3f43d26ff4b Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:24:49 +0000 Subject: [PATCH 07/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 2b542c227889466df20a2360f72e39c81a50514c..6853919ee9176a4c074da0ad0725ca051ed4b7b3 100644 GIT binary patch delta 374 zcmZvXO-jQ+6o8!!cB&%PYMZ1LG%ImoLXo-=Z15t(Fo|~TBvUgJ@n>Q10zt=rUAvBW z0*~PpJcTW_RM74BKHmFYmX)%sR1_{))^G0KP8F_}6*<5x4#Jc9d=WZjsfc1yF)FQm z1-3!JWDoZl?eP%z6QKkZeA>#J+VvWC1GZ-55oapI@-(L1M8qPMW^QZZ*}&50UbA6B z&-igDq1}PW&cd~+T3*+MXI5*_0W{?ta~3f*yPhw-e|ifQaIL>~x515eI`s=(fsQc= zLsvFz8~=r&7ZbKdlZeH5pADji=g{+z|1CvNHMlwEQAGM9`_Y11V|pmkxg;hWM%;fBx)cAs;{F40S{2W$^e*VdN`cjg7%!ZuBg*llesqw{?dC3_?`FZ)J z#p3q|>io#L2A4m|U8Z6Q7fr zn_0r8-p{`IroI3_W836cc4mwnlNIg7>f8C56`2qYV{esYHf6%*F!l-J%!Uw|+|0cA zv`nC*LDsSNgTygi%HAi+tP2y*%}p$TsP2_uHin62<(G07Z&X)b#g$ejq!uy-~&EOTIV000ovd?^3` From dd4d86e482ecf6cc8dd3789a2908b36058d426a1 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:32:38 +0000 Subject: [PATCH 08/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 6853919ee9176a4c074da0ad0725ca051ed4b7b3..263384ce6cd17d702b8c7557c343e15aa17814f9 100644 GIT binary patch delta 374 zcmZo@U~6b#+ps~8QDO2%Jtu29W_ga1#Ps;gyp+@m-hNqTMULW<#FEV7lFZ~{iGB@c zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^e)Y+E`cjf=%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;{lN0qN8C51%>q|>1GwU-!)g&h-X8=`ZR;4O1i1sT@-k>ioq{ytum|U8Z6Q7fr zn_0r8-Y>uTroI3_Y3?4r5;-&TI&g$<54* zPs;>48e|>&a*#NtOWBu+GV8*`b8{05AgY&2FdM@}v+_&1i}Dh4;&by;QrVYGK4>qd ixfsc`#L|-d__D<0($ZY^MId(~Jj1@Q$zhoTqXPiavVLg* delta 374 zcmZvXO-jQ+6o8!!cB&%PYMZ1LG%ImoLXo-=Z15t(Fo|~TBvUgJ@n>Q10zt=rUAvBW z0*~PpJcTW_RM74BKHmFYmX)%sR1_{))^G0KP8F_}6*<5x4#Jc9d=WZjsfc1yF)FQm z1-3!JWDoZl?eP%z6QKkZeA>#J+VvWC1GZ-55oapI@-(L1M8qPMW^QZZ*}&50UbA6B z&-igDq1}PW&cd~+T3*+MXI5*_0W{?ta~3f*yPhw-e|ifQaIL>~x515eI`s=(fsQc= zLsvFz8~=r&7ZbKdlZeH5pADji=g{+z|1CvNHMlwEQAGM9`_Y11V|pmkxg;hWM Date: Mon, 17 Nov 2025 12:33:42 +0100 Subject: [PATCH 09/22] ma va? --- .github/workflows/on-pull-request.yaml | 1 + .github/workflows/on-push.yaml | 1 + .github/workflows/on-schedule.yaml | 1 + 3 files changed, 3 insertions(+) diff --git a/.github/workflows/on-pull-request.yaml b/.github/workflows/on-pull-request.yaml index 5cdf21a2..67b4367a 100644 --- a/.github/workflows/on-pull-request.yaml +++ b/.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 diff --git a/.github/workflows/on-push.yaml b/.github/workflows/on-push.yaml index 06dd0013..703957d7 100644 --- a/.github/workflows/on-push.yaml +++ b/.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 diff --git a/.github/workflows/on-schedule.yaml b/.github/workflows/on-schedule.yaml index e1f8898b..5e2fc505 100644 --- a/.github/workflows/on-schedule.yaml +++ b/.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 From fdc564c1d5eef0aa3a08ec0932c98bf84539d173 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:34:12 +0000 Subject: [PATCH 10/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 263384ce6cd17d702b8c7557c343e15aa17814f9..b39debd5b7b0ff6b1b14cfc7f29796aa88833e6b 100644 GIT binary patch delta 374 zcmZvXTTTKo6hJMF6g388!ej75=gXinbwvCzk%=2=nlehIGez1VK0chdf%)hjOneXG z23&?)a1}z3V4}b0p4@wG9B1P=o2CxfF$3rLa0{;IG(9CeZ21?S06w*st9c@WU<#2%DkeM-+{wA2f!Ac1W8 hC^a9=V)gacHX3P3`jkacfL_L(vuDurt#{`E?;EqJe~AD9 delta 374 zcmZo@U~6b#+ps~8QDO2%Jtu29W_ga1#Ps;gyp+@m-hNqTMULW<#FEV7lFZ~{iGB@c zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^e)Y+E`cjf=%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;{lN0qN8C51%>q|>1GwU-!)g&h-X8=`ZR;4O1i1sT@-k>ioq{ytum|U8Z6Q7fr zn_0r8-Y>uTroI3_Y3?4r5;-&TI&g$<54* zPs;>48e|>&a*#NtOWBu+GV8*`b8{05AgY&2FdM@}v+_&1i}Dh4;&by;QrVYGK4>qd ixfsc`#L|-d__D<0($ZY^MId(~Jj1@Q$zhoTqXPiavVLg* From 214fe3ef2aefae5cd49c21632921e0ecf2e386a3 Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:39:04 +0100 Subject: [PATCH 11/22] Dai --- .github/workflows/update-citations.yaml | 3 +++ 1 file changed, 3 insertions(+) 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: ${{ jobs.update-citations.outputs.changed }} From d21c3367e3e95fecfe24fcc2cc26df019c5f66ef Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:39:29 +0000 Subject: [PATCH 12/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index b39debd5b7b0ff6b1b14cfc7f29796aa88833e6b..6aad00ae6c2125cf34be4c3c5816a3e643408366 100644 GIT binary patch delta 374 zcmZo@U~6b#+ps~8(PHvOJtu23W_ga1#Ps;gyp+@m-hNYNMULW<#FEV7lFZ~{iGBxW zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^e*4LK`cjg1%!ZuBg*llesqw{?dC3_?`FZ)J z#p3<8lN0qN8Eqz4>q|>nGwU-!)g&h-X8=`ZR;4O1i1u4e-k>ioWXY_^m|U8Z6Q7fr zn_0r8-fzD7roI3_Y3?4r4zc&TI&g$<54* zPs;>48e|>&evmk(OWF5{GV8*`b8{05AgcFDFdM@}v+_&1i}Dh4;&by;QrY)RK4>qd ixf{u}#L|-d__D<0($ZY^T_ATNJj1@T$zhoTqXPhxpn$0W delta 374 zcmZvXTTTKo6hJMF6g388!ej75=gXinbwvCzk%=2=nlehIGez1VK0chdf%)hjOneXG z23&?)a1}z3V4}b0p4@wG9B1P=o2CxfF$3rLa0{;IG(9CeZ21?S06w*st9c@WU<#2%DkeM-+{wA2f!Ac1W8 hC^a9=V)gacHX3P3`jkacfL_L(vuDurt#{`E?;EqJe~AD9 From 6b21e095d03cb5547def8c87b9364bd5b46a1f8f Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:48:38 +0100 Subject: [PATCH 13/22] Debug --- .github/workflows/update-citations.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml index d5e79600..37f8ec10 100644 --- a/.github/workflows/update-citations.yaml +++ b/.github/workflows/update-citations.yaml @@ -35,6 +35,16 @@ jobs: if: runner.debug == '1' uses: crazy-max/ghaction-dump-context@v2 + - name: Check GOOGLE_SCHOLAR_API_KEY presence + if: github.event.action != 'closed' + run: | + if [ -z "${GOOGLE_SCHOLAR_API_KEY}" ]; then + 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: ${GOOGLE_SCHOLAR_API_KEY:0:4}******** (truncated)"; + fi + - name: Checkout branch contents if: github.event.action != 'closed' uses: actions/checkout@v4 From a6769874b844c0993f2017c3c64a3223815b53b2 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:49:08 +0000 Subject: [PATCH 14/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 6aad00ae6c2125cf34be4c3c5816a3e643408366..d5861fa622cf4a0d814ad96b6a9e476ec184b923 100644 GIT binary patch delta 374 zcmZo@U~6b#+ps~8(Pi>RJtu1?W_ga1#Ps;gyp+@m-hM}BMULW<#FEV7lFZ~{iGCku zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^e(%Y8`cjf!%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;*lN0qN89gRf>q|?yGwU-!)g&h-X8=`ZR;4O1i1xcp-k>ioY3?4r4zf&TI&g$<54* zPs;>48e|>&X^=RkOW99}GV8*`b8{05AgWJFFdM@}v+_&1i}Dh4;&by;QrS;TK4>qd ic^t{K#L|-d__D<0($ZY^V<2}TJi~sp$zhoTqXPhSmx0Lu delta 374 zcmZo@U~6b#+ps~8(PHvOJtu23W_ga1#Ps;gyp+@m-hNYNMULW<#FEV7lFZ~{iGBxW zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^e*4LK`cjg1%!ZuBg*llesqw{?dC3_?`FZ)J z#p3<8lN0qN8Eqz4>q|>nGwU-!)g&h-X8=`ZR;4O1i1u4e-k>ioWXY_^m|U8Z6Q7fr zn_0r8-fzD7roI3_Y3?4r4zc&TI&g$<54* zPs;>48e|>&evmk(OWF5{GV8*`b8{05AgcFDFdM@}v+_&1i}Dh4;&by;QrY)RK4>qd ixf{u}#L|-d__D<0($ZY^T_ATNJj1@T$zhoTqXPhxpn$0W From 1a954b556a328b75633f7911fe3a510e44a9fa4e Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:55:36 +0100 Subject: [PATCH 15/22] Debug --- .github/workflows/update-citations.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml index 37f8ec10..1a5c0ac3 100644 --- a/.github/workflows/update-citations.yaml +++ b/.github/workflows/update-citations.yaml @@ -31,19 +31,21 @@ jobs: timeout-minutes: 15 steps: - - name: Debug dump - if: runner.debug == '1' - uses: crazy-max/ghaction-dump-context@v2 - - name: Check GOOGLE_SCHOLAR_API_KEY presence - if: github.event.action != 'closed' run: | + echo "========================================"; + echo "Checking GOOGLE_SCHOLAR_API_KEY..."; if [ -z "${GOOGLE_SCHOLAR_API_KEY}" ]; then - echo "GOOGLE_SCHOLAR_API_KEY is EMPTY or not set"; + 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}******** (truncated)"; + echo "✅ GOOGLE_SCHOLAR_API_KEY appears to be set (length > 0)"; + echo "First 4 chars: ${GOOGLE_SCHOLAR_API_KEY:0:4}********"; fi + echo "========================================"; + + - name: Debug dump + if: runner.debug == '1' + uses: crazy-max/ghaction-dump-context@v2 - name: Checkout branch contents if: github.event.action != 'closed' From 871f4b0cab91f832c0521ba4f8434d7135c1dec3 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:56:17 +0000 Subject: [PATCH 16/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index d5861fa622cf4a0d814ad96b6a9e476ec184b923..85e33bf4aa5c512cc0d81500f748cbfbfed05e7e 100644 GIT binary patch delta 374 zcmZo@U~6b#+ps~8F<|mWJtu2FW_ga1#Ps;gyp+@m-hN+ZMULW<#FEV7lFZ~{iT(&? zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^{_x3q`cjf%%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;;lN0qN8AB#l>q|=oGwU-!)g&h-X8=`ZR;4O1i1r6f-k>io6v(W|m|U8Z6Q7fr zn_0r8-tWKproI3_Y3?4r9L|&TI&g$<54* zPs;>48e|>&b&xowOWCi9GV8*`b8{05AgZrQFdM@}v+_&1i}Dh4;&by;QrWLeK4>qd ic^S#H#L|-d__D<0($ZY^OCWb5Ji~sm$zhoTqXPg|j)Lg` delta 374 zcmZo@U~6b#+ps~8(Pi>RJtu1?W_ga1#Ps;gyp+@m-hM}BMULW<#FEV7lFZ~{iGCku zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^e(%Y8`cjf!%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;*lN0qN89gRf>q|?yGwU-!)g&h-X8=`ZR;4O1i1xcp-k>ioY3?4r4zf&TI&g$<54* zPs;>48e|>&X^=RkOW99}GV8*`b8{05AgWJFFdM@}v+_&1i}Dh4;&by;QrS;TK4>qd ic^t{K#L|-d__D<0($ZY^V<2}TJi~sp$zhoTqXPhSmx0Lu From 7e453a93bd6b909f6d65efb95b17ee50eea37b77 Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 12:59:09 +0100 Subject: [PATCH 17/22] Debug --- .github/workflows/on-pull-request.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/on-pull-request.yaml b/.github/workflows/on-pull-request.yaml index 67b4367a..4afdae4d 100644 --- a/.github/workflows/on-pull-request.yaml +++ b/.github/workflows/on-pull-request.yaml @@ -16,7 +16,8 @@ permissions: jobs: update-citations: uses: ./.github/workflows/update-citations.yaml - secrets: inherit + secrets: + GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }} build-preview: needs: update-citations From 145d4804e4da60f095ca1287ed5ce3371a6cb7d0 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:59:30 +0000 Subject: [PATCH 18/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 85e33bf4aa5c512cc0d81500f748cbfbfed05e7e..be57556067df244d6931f29bbe06a60940a5a7ab 100644 GIT binary patch delta 374 zcmZo@U~6b#+ps~8F=p~cJtylZW_ga1#Ps;gyp+@m-u_5tMULW<#FEV7lFZ~{iT)I3 zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^{^ZGe`cjff%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;mlN0qN851T~>q|?;GwU-!)g&h-X8=`ZR;4O1i1x=#-k>io6w9p0m|U8Z6Q7fr zn_0r8-XFdBroI3_Y3?4r6~J&TI&g$<54* zPs;>48e|>&V~{weOW7ZZGV8*`b8{05AgUiqFdM@}v+_&1i}Dh4;&by;QrRC&K4>qd ic^}EN#L|-d__D<0($ZY^dmwirJi~ss$zhoTqXPgpg@g$J delta 374 zcmZo@U~6b#+ps~8F<|mWJtu2FW_ga1#Ps;gyp+@m-hN+ZMULW<#FEV7lFZ~{iT(&? zQ^u6c;_Uc>%;fBx)cAs;{F40S{2W$^{_x3q`cjf%%!ZuBg*llesqw{?dC3_?`FZ)J z#p3;;lN0qN8AB#l>q|=oGwU-!)g&h-X8=`ZR;4O1i1r6f-k>io6v(W|m|U8Z6Q7fr zn_0r8-tWKproI3_Y3?4r9L|&TI&g$<54* zPs;>48e|>&b&xowOWCi9GV8*`b8{05AgZrQFdM@}v+_&1i}Dh4;&by;QrWLeK4>qd ic^S#H#L|-d__D<0($ZY^OCWb5Ji~sm$zhoTqXPg|j)Lg` From 869d9b2615625ccf4dbaf5f87bb76cf24d42faa2 Mon Sep 17 00:00:00 2001 From: Grufoony Date: Mon, 17 Nov 2025 14:01:26 +0100 Subject: [PATCH 19/22] Butto via tutto --- .github/workflows/on-pull-request.yaml | 2 -- .github/workflows/on-push.yaml | 1 - .github/workflows/on-schedule.yaml | 1 - .github/workflows/update-citations.yaml | 12 ------------ 4 files changed, 16 deletions(-) diff --git a/.github/workflows/on-pull-request.yaml b/.github/workflows/on-pull-request.yaml index 4afdae4d..5cdf21a2 100644 --- a/.github/workflows/on-pull-request.yaml +++ b/.github/workflows/on-pull-request.yaml @@ -16,8 +16,6 @@ permissions: jobs: update-citations: uses: ./.github/workflows/update-citations.yaml - secrets: - GOOGLE_SCHOLAR_API_KEY: ${{ secrets.GOOGLE_SCHOLAR_API_KEY }} build-preview: needs: update-citations diff --git a/.github/workflows/on-push.yaml b/.github/workflows/on-push.yaml index 703957d7..06dd0013 100644 --- a/.github/workflows/on-push.yaml +++ b/.github/workflows/on-push.yaml @@ -18,7 +18,6 @@ jobs: # skip first run because nothing enabled or setup yet if: github.run_number != 1 uses: ./.github/workflows/update-citations.yaml - secrets: inherit build-site: needs: update-citations diff --git a/.github/workflows/on-schedule.yaml b/.github/workflows/on-schedule.yaml index 5e2fc505..e1f8898b 100644 --- a/.github/workflows/on-schedule.yaml +++ b/.github/workflows/on-schedule.yaml @@ -18,6 +18,5 @@ jobs: # only run on user instance of template, not template itself if: github.repository != 'greenelab/lab-website-template' uses: ./.github/workflows/update-citations.yaml - secrets: inherit with: open-pr: true diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml index 1a5c0ac3..d5e79600 100644 --- a/.github/workflows/update-citations.yaml +++ b/.github/workflows/update-citations.yaml @@ -31,18 +31,6 @@ jobs: timeout-minutes: 15 steps: - - name: Check GOOGLE_SCHOLAR_API_KEY presence - run: | - echo "========================================"; - echo "Checking GOOGLE_SCHOLAR_API_KEY..."; - if [ -z "${GOOGLE_SCHOLAR_API_KEY}" ]; then - 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: ${GOOGLE_SCHOLAR_API_KEY:0:4}********"; - fi - echo "========================================"; - - name: Debug dump if: runner.debug == '1' uses: crazy-max/ghaction-dump-context@v2 From 4b10290b678f4dd59b087085f38e5234433e7a44 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 13:02:06 +0000 Subject: [PATCH 20/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index be57556067df244d6931f29bbe06a60940a5a7ab..230b25f733d4824af2d426177b92c0e5dbbb3e6e 100644 GIT binary patch delta 374 zcmZvXOHRWu5I}J(>Hl7Y-Lld|Go=|- zPM*Lv=rR@IgwcoxI2lSUspN}JE=|*G)MMCMQpcR>0IRc@hC><4RN1*O#H#~tF1(FK 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build-preview: needs: update-citations From f1cc697ff1173659e5e2e71e4d786a46b9c4b736 Mon Sep 17 00:00:00 2001 From: Grufoony <64806874+Grufoony@users.noreply.github.com> Date: Mon, 17 Nov 2025 13:07:30 +0000 Subject: [PATCH 22/22] Commit cache --- _cite/.cache/cache.db | Bin 98304 -> 98304 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 230b25f733d4824af2d426177b92c0e5dbbb3e6e..04447ce04d6111f59797d7234b8284fff24a918e 100644 GIT binary patch delta 374 zcmZvX%Sr<=6hO@co2p1f=+lMHN?bTYDRm>*;*W%ojy5(knNE`0hv483%p(8bdc-gA zGyDa2zMl(QYN?>xa}W2P8^@VA&ZMaWl(}*a_anHORpc16pyl;flPLCObG}w8K3dMnVZH_+lv;8ON=Zhp@UNyPPQx%RxZfkqCsA#bjWJTLyhIayKfc z(6xRXN@#m*vZ1%NkWYFhb&Km7+JI`#F=swg%iD>(zIE4f;KAG-?13j^Hwx#EIcQt+ zFmzvrb?d({^i_n_>BMINK4RnO$vN~n;eSifM;`9ZxbKs2YQL9YZAMRoUWo$2u`gO4 hdNVhT!p`fjZA2@9dxUE3qnAnN{2BCo(Y$Pe<~R9dhDiVb delta 374 zcmZvXOHRWu5I}J(>Hl7Y-Lld|Go=|- zPM*Lv=rR@IgwcoxI2lSUspN}JE=|*G)MMCMQpcR>0IRc@hC><4RN1*O#H#~tF1(FK 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