From 957749bbfa05126e7911a6e6239b6b2904270dde Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Tue, 4 Aug 2026 16:15:18 -0400 Subject: [PATCH 1/5] Add OpenCite provenance metadata files --- .zenodo.json | 29 +++++++++++++++++++++++++++++ CITATION.cff | 24 ++++++++++++++++++++++++ LICENSE | 21 +++++++++++++++++++++ 3 files changed, 74 insertions(+) create mode 100644 .zenodo.json create mode 100644 CITATION.cff create mode 100644 LICENSE diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..879b8e3 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,29 @@ +{ + "title": "OpenCite", + "upload_type": "software", + "description": "OpenCite generates CITATION.cff and .zenodo.json metadata from a single form to keep release metadata aligned across outputs.", + "version": "v0.1.0", + "publication_date": "2026-07-12", + "license": "MIT", + "keywords": [ + "imageomics", + "citation", + "metadata", + "zenodo" + ], + "creators": [ + { + "name": "OpenCite, Contributors", + "affiliation": "Imageomics Institute" + } + ], + "grants": [ + { + "id": "021nxhr62::2118240" + }, + { + "id": "021nxhr62::2330423" + } + ], + "references": [] +} diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..fa0fc3c --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,24 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite both the software and our paper." +title: "OpenCite" +abstract: "OpenCite generates CITATION.cff and .zenodo.json metadata from a single form to keep release metadata aligned across outputs." +type: software +version: "v0.1.0" +date-released: "2026-07-12" +repository-code: "https://github.com/Imageomics/OpenCite" +license: "MIT" +keywords: + - "imageomics" + - "citation" + - "metadata" + - "zenodo" +authors: + - family-names: "OpenCite" + given-names: "Contributors" +identifiers: + - type: url + description: "The GitHub release URL of tag v0.1.0." + value: "https://github.com/Imageomics/OpenCite/releases/tag/v0.1.0" + - type: url + description: "The GitHub source tree URL aligned to release tag v0.1.0." + value: "https://github.com/Imageomics/OpenCite/tree/v0.1.0" diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..c738916 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2026 Imageomics Institute + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. From 2126be7b7629dc76d457c4564c1bb72e05ad58ea Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Tue, 4 Aug 2026 16:49:03 -0400 Subject: [PATCH 2/5] Add CI workflow to provenance metadata PR --- .github/workflows/ci.yml | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 .github/workflows/ci.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..6f1c7cc --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,33 @@ +name: CI + +on: + pull_request: + push: + branches: + - main + +jobs: + build-and-test: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Setup Node.js + uses: actions/setup-node@v4 + with: + node-version: 22 + cache: npm + + - name: Install dependencies + run: npm ci + + - name: Run tests + run: npm run test + + - name: Build + run: npm run build + + - name: Validate metadata files + run: npm run validate:metadata From 2bfecc75264738df3208dc5ecb70b073c44d9be6 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Fri, 4 Sep 2026 12:39:02 -0400 Subject: [PATCH 3/5] Update CI configuration and metadata files for improved accuracy and dependencies --- .github/workflows/ci.yml | 6 +++--- .zenodo.json | 17 ++++++++++++++--- CITATION.cff | 13 ++++++++++--- package-lock.json | 4 ++-- 4 files changed, 29 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6f1c7cc..1ade234 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -12,12 +12,12 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v7 - name: Setup Node.js - uses: actions/setup-node@v4 + uses: actions/setup-node@v7 with: - node-version: 22 + node-version: 24 cache: npm - name: Install dependencies diff --git a/.zenodo.json b/.zenodo.json index 879b8e3..cfc584e 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -9,11 +9,20 @@ "imageomics", "citation", "metadata", - "zenodo" + "zenodo", + "FAIR", + "provenance", + "attribution", + "cff-format" ], "creators": [ { - "name": "OpenCite, Contributors", + "name": "Lo, Isabella", + "affiliation": "Imageomics Institute" + }, + { + "name": "Campolongo, Elizabeth", + "orcid": "0000-0003-0846-2413", "affiliation": "Imageomics Institute" } ], @@ -25,5 +34,7 @@ "id": "021nxhr62::2330423" } ], - "references": [] + "references": [ + "Imageomics Institute. (n.d.). Collaborative Distributed Science Guide. https://imageomics.github.io/Collaborative-distributed-science-guide/" + ] } diff --git a/CITATION.cff b/CITATION.cff index fa0fc3c..5a91cab 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ cff-version: 1.2.0 -message: "If you use this software, please cite both the software and our paper." +message: "If you find this software helpful in your research, please cite both the software and our paper." title: "OpenCite" abstract: "OpenCite generates CITATION.cff and .zenodo.json metadata from a single form to keep release metadata aligned across outputs." type: software @@ -12,9 +12,16 @@ keywords: - "citation" - "metadata" - "zenodo" + - "FAIR" + - "provenance" + - "attribution" + - "cff-format" authors: - - family-names: "OpenCite" - given-names: "Contributors" + - family-names: "Lo" + given-names: "Isabella" + - family-names: "Campolongo" + given-names: "Elizabeth" + orcid: "https://orcid.org/0000-0003-0846-2413" identifiers: - type: url description: "The GitHub release URL of tag v0.1.0." diff --git a/package-lock.json b/package-lock.json index ca36fba..95f29b3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,8 +13,8 @@ "react-dom": "^18.3.1" }, "devDependencies": { - "@vitejs/plugin-react": "^6.0.2", - "vite": "^8.0.16", + "@vitejs/plugin-react": "^6.0.3", + "vite": "^8.1.1", "zenodraft": "0.14.1" } }, From 200c0d29df9477109bd273ea979fd80dca2a999d Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Fri, 4 Sep 2026 13:04:23 -0400 Subject: [PATCH 4/5] Update metadata files for version 1.0.0 release, including descriptions, publication dates, and references --- .zenodo.json | 8 ++++---- CITATION.cff | 14 +++++++------- package-lock.json | 4 ++-- package.json | 2 +- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index cfc584e..00e5f5b 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,9 +1,9 @@ { "title": "OpenCite", "upload_type": "software", - "description": "OpenCite generates CITATION.cff and .zenodo.json metadata from a single form to keep release metadata aligned across outputs.", - "version": "v0.1.0", - "publication_date": "2026-07-12", + "description": "OpenCite is a web app to generate provenance files (CITATION.cff and .zenodo.json) for GitHub repositories from a single form to keep release metadata aligned across outputs.", + "version": "1.0.0", + "publication_date": "2026-09-04", "license": "MIT", "keywords": [ "imageomics", @@ -35,6 +35,6 @@ } ], "references": [ - "Imageomics Institute. (n.d.). Collaborative Distributed Science Guide. https://imageomics.github.io/Collaborative-distributed-science-guide/" + "Campolongo, E. G., Thompson, M. J., Zhang, N., Duan, Y., Bradley, J., Zarubiieva, I., Taylor, G., & Lapp, H. (2026). Collaborative Distributed Science Guide (Version 2.0.0) [Computer software]. https://doi.org/10.5281/zenodo.17210328" ] } diff --git a/CITATION.cff b/CITATION.cff index 5a91cab..4898ea7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,10 +1,10 @@ cff-version: 1.2.0 message: "If you find this software helpful in your research, please cite both the software and our paper." title: "OpenCite" -abstract: "OpenCite generates CITATION.cff and .zenodo.json metadata from a single form to keep release metadata aligned across outputs." +abstract: "OpenCite is a web app to generate provenance files (CITATION.cff and .zenodo.json) for GitHub repositories from a single form to keep release metadata aligned across outputs." type: software -version: "v0.1.0" -date-released: "2026-07-12" +version: "1.0.0" +date-released: "2026-09-04" repository-code: "https://github.com/Imageomics/OpenCite" license: "MIT" keywords: @@ -24,8 +24,8 @@ authors: orcid: "https://orcid.org/0000-0003-0846-2413" identifiers: - type: url - description: "The GitHub release URL of tag v0.1.0." - value: "https://github.com/Imageomics/OpenCite/releases/tag/v0.1.0" + description: "The GitHub release URL of tag v1.0.0." + value: "https://github.com/Imageomics/OpenCite/releases/tag/v1.0.0" - type: url - description: "The GitHub source tree URL aligned to release tag v0.1.0." - value: "https://github.com/Imageomics/OpenCite/tree/v0.1.0" + description: "The GitHub source tree URL aligned to release tag v1.0.0." + value: "https://github.com/Imageomics/OpenCite/tree/v1.0.0" diff --git a/package-lock.json b/package-lock.json index 95f29b3..4e7edcb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "opencite", - "version": "0.0.0", + "version": "1.0.0", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "opencite", - "version": "0.0.0", + "version": "1.0.0", "dependencies": { "jszip": "^3.10.1", "react": "^18.3.1", diff --git a/package.json b/package.json index cb0286b..d4289fd 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "opencite", "private": true, - "version": "0.0.0", + "version": "1.0.0", "type": "module", "scripts": { "dev": "vite", From 98f4e5f3e489e72f7203566bf5dd67695ac010de Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Fri, 4 Sep 2026 14:18:11 -0400 Subject: [PATCH 5/5] updating commit hash --- CITATION.cff | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 4898ea7..42f2c02 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -27,5 +27,5 @@ identifiers: description: "The GitHub release URL of tag v1.0.0." value: "https://github.com/Imageomics/OpenCite/releases/tag/v1.0.0" - type: url - description: "The GitHub source tree URL aligned to release tag v1.0.0." - value: "https://github.com/Imageomics/OpenCite/tree/v1.0.0" + description: "The GitHub URL of the commit tagged with v1.0.0." + value: "https://github.com/Imageomics/OpenCite/tree/" # Update on release