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Merge pull request #1716 from virtualcell/add-zenodo-going-forward
Add Zenodo going-forward archiving (CITATION.cff, .zenodo.json, workflows)
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‎.github/workflows/zenodo-archive.yml‎

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name: Archive release to Zenodo
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# On each published GitHub Release, archive it as a new version of the VCell
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# Zenodo concept (10.5281/zenodo.7796386) via the zenodo-maint reusable workflow.
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# Replaces the old native Zenodo<->GitHub integration (now disabled). Concept and
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# deposit metadata come from CITATION.cff (doi:) and .zenodo.json at the repo root.
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#
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# Requires an org/repo secret ZENODO_TOKEN belonging to the account that OWNS the
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# concept record (creating new versions requires ownership).
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on:
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release:
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types: [published]
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jobs:
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archive:
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uses: virtualcell/zenodo-maint/.github/workflows/archive.reusable.yml@v1
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with:
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tag: ${{ github.event.release.tag_name }}
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secrets:
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ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }}

‎.github/workflows/zenodo-drift.yml‎

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name: Zenodo drift check
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# Weekly no-secret safety net: opens a tracking issue if the latest GitHub release
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# is not the latest version on the Zenodo concept — i.e. if release archiving has
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# silently stopped. Uses public APIs only. Concept comes from CITATION.cff (doi:).
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#
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# NOTE: this compares the latest release to the concept's newest-by-creation
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# version. While curated "Virtual Cell X.Y" major records sit on top (until the
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# next release is archived), this may report drift; it self-resolves once the next
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# release is archived and becomes the newest version.
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on:
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schedule:
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- cron: '0 12 * * 1'
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workflow_dispatch: {}
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jobs:
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drift:
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uses: virtualcell/zenodo-maint/.github/workflows/drift.reusable.yml@v1

‎.zenodo.json‎

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{
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"upload_type": "software",
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"title": "Virtual Cell (VCell)",
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"description": "The Virtual Cell (VCell) is a comprehensive platform for modeling and simulation in cell biology, developed since 1997 at the Center for Cell Analysis and Modeling (CCAM) at UConn Health.",
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"license": "cc-by-4.0",
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"creators": [
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{
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"name": "Schaff, James C.",
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"affiliation": "University of Connecticut School of Medicine",
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"orcid": "0000-0003-3286-7736"
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},
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{
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"name": "Vasilescu, Dan",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Morgan, Frank",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Gao, Fei",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Weatherby, Gerard",
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"affiliation": "University of Connecticut School of Medicine",
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"orcid": "0000-0002-0462-4633"
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},
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{
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"name": "Ye, Li",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Drescher, Logan",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Valencia, Ezequiel",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Lakshminarayana, Anuradha",
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"affiliation": "University of Connecticut School of Medicine"
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},
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{
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"name": "Blinov, Michael L.",
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"affiliation": "University of Connecticut School of Medicine",
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"orcid": "0000-0002-9363-9705"
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},
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{
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"name": "Cowan, Ann",
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"affiliation": "University of Connecticut School of Medicine",
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"orcid": "0000-0002-3215-9951"
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},
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{
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"name": "Moraru, Ion I.",
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"affiliation": "University of Connecticut School of Medicine",
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"orcid": "0000-0002-3746-9676"
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}
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],
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"related_identifiers": []
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}

‎CITATION.cff‎

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cff-version: 1.2.0
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message: "If you use this software, please cite it using these metadata."
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title: "Virtual Cell (VCell)"
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type: software
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url: "https://vcell.org"
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repository-code: "https://github.com/virtualcell/vcell"
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license: MIT
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doi: 10.5281/zenodo.7796386 # concept DOI (all versions)
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authors:
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- family-names: "Schaff"
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given-names: "James C."
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affiliation: "University of Connecticut School of Medicine"
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orcid: "https://orcid.org/0000-0003-3286-7736"
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- family-names: "Vasilescu"
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given-names: "Dan"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Morgan"
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given-names: "Frank"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Gao"
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given-names: "Fei"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Weatherby"
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given-names: "Gerard"
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affiliation: "University of Connecticut School of Medicine"
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orcid: "https://orcid.org/0000-0002-0462-4633"
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- family-names: "Ye"
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given-names: "Li"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Drescher"
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given-names: "Logan"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Valencia"
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given-names: "Ezequiel"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Lakshminarayana"
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given-names: "Anuradha"
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affiliation: "University of Connecticut School of Medicine"
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- family-names: "Blinov"
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given-names: "Michael L."
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affiliation: "University of Connecticut School of Medicine"
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orcid: "https://orcid.org/0000-0002-9363-9705"
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- family-names: "Cowan"
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given-names: "Ann"
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affiliation: "University of Connecticut School of Medicine"
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orcid: "https://orcid.org/0000-0002-3215-9951"
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- family-names: "Moraru"
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given-names: "Ion I."
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affiliation: "University of Connecticut School of Medicine"
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orcid: "https://orcid.org/0000-0002-3746-9676"

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