From eb6b247acfa44d4c0e0c2efad992b5dd731e22e9 Mon Sep 17 00:00:00 2001 From: egrace479 Date: Fri, 14 Nov 2025 13:51:02 -0500 Subject: [PATCH 1/5] Update version and set release date --- CITATION.cff | 11 ++++++----- README.md | 4 ++-- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 1ba1790..17e6a84 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -24,10 +24,10 @@ authors: orcid: 'https://orcid.org/0000-0003-0846-2413' repository-code: 'https://github.com/Imageomics/TreeOfLife-toolbox' identifiers: - - description: "The GitHub release URL of tag v0.2.0-beta." + - description: "The GitHub release URL of tag v0.4.0-beta." type: url - value: "https://github.com/Imageomics/TreeOfLife-toolbox/releases/tag/v0.2.0-beta" - - description: "The GitHub URL of the commit tagged with v0.2.0-beta." + value: "https://github.com/Imageomics/TreeOfLife-toolbox/releases/tag/v0.4.0-beta" + - description: "The GitHub URL of the commit tagged with v0.4.0-beta." type: url value: "https://github.com/Imageomics/TreeOfLife-toolbox/tree/" # update post release abstract: >- @@ -42,5 +42,6 @@ keywords: - "dataset generation" - "MPI application" license: MIT -version: 0.2.0-beta -date-released: '2025' # update on release +version: 0.4.0-beta +date-released: '2025-11-14' +# doi: Add Version-agnostic DOI post-release diff --git a/README.md b/README.md index 3ba3d86..cbfcc61 100644 --- a/README.md +++ b/README.md @@ -120,10 +120,10 @@ If using the [TreeOfLife-200M dataset](https://huggingface.co/datasets/imageomic @software{Kopanev_TreeOfLife-toolbox_2025, author = {Kopanev, Andrei and Zhang, Net and Gu, Jianyang and Stevens, Samuel and Thompson, Matthew J and Campolongo, Elizabeth G}, license = {MIT}, - month = may, + month = nov, title = {{TreeOfLife-toolbox}}, url = {https://github.com/Imageomics/TreeOfLife-toolbox}, - version = {0.2.0-beta}, + version = {0.4.0-beta}, year = {2025} } ``` From f8191dd5edf8fdc23c7b8ace7e8f8a922e71fdc1 Mon Sep 17 00:00:00 2001 From: egrace479 Date: Fri, 14 Nov 2025 13:51:29 -0500 Subject: [PATCH 2/5] Add Zenodo metadata and test for file --- .github/workflows/validate-zenodo.yaml | 23 +++++++++++ .zenodo.json | 54 ++++++++++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 .github/workflows/validate-zenodo.yaml create mode 100644 .zenodo.json diff --git a/.github/workflows/validate-zenodo.yaml b/.github/workflows/validate-zenodo.yaml new file mode 100644 index 0000000..cb4ee12 --- /dev/null +++ b/.github/workflows/validate-zenodo.yaml @@ -0,0 +1,23 @@ +name: Check zenodo metadata + +on: + push: + paths: + - '.zenodo.json' + - '.github/workflows/validate-zenodo.yaml' + +jobs: + check-zenodo-metadata: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 + with: + node-version: '22' + - name: Install dependencies + run: npm install zenodraft@0.14.1 + - name: Check .zenodo.json file + run: | + npx zenodraft metadata validate .zenodo.json diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..b87a602 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,54 @@ +{ + "creators": [ + { + "name": "Kopanev, Andrei", + "affiliation": "The Ohio State University" + }, + { + "name": "Zhang, Net", + "affiliation": "The Ohio State University" + }, + { + "name": "Gu, Jianyang", + "affiliation": "The Ohio State University" + }, + { + "name": "Stevens, Samuel", + "affiliation": "The Ohio State University" + }, + { + "name": "Thompson, Matthew J.", + "affiliation": "The Ohio State University" + }, + { + "name": "Campolongo, Elizabeth G.", + "affiliation": "The Ohio State University" + } + ], + "description": "A tool for processing datasets that were downloaded using the distributed-downloader package, specifically used for constructing the TreeOfLife-200M dataset.", + "keywords": [ + "biology", + "CV", + "imageomics", + "species", + "images", + "parallel", + "distributed", + "processing", + "url", + "imageomics", + "dataset generation", + "MPI application" + ], + "license": { + "id": "MIT" + }, + "publication_date": "2025-11-14", + "title": "TreeOfLife-toolbox", + "version": "0.4.0-beta", + "grants": [ + { + "id": "021nxhr62::2118240" + } + ] +} From 35353e1c65e98afdc04c64aee4e3b786a77e23fb Mon Sep 17 00:00:00 2001 From: egrace479 Date: Fri, 14 Nov 2025 13:53:32 -0500 Subject: [PATCH 3/5] Add more keywords --- .zenodo.json | 8 +++++++- CITATION.cff | 7 +++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index b87a602..32c6f90 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -38,7 +38,13 @@ "url", "imageomics", "dataset generation", - "MPI application" + "MPI application", + "face-detection", + "image filtering", + "animal-detection", + "specimen records", + "citizen science", + "embedding-generation" ], "license": { "id": "MIT" diff --git a/CITATION.cff b/CITATION.cff index 17e6a84..249a5f8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -41,6 +41,13 @@ keywords: - imageomics - "dataset generation" - "MPI application" + - "face-detection" + - "image filtering" + - "animal-detection" + - "specimen records" + - "citizen science" + - imageomics + - embedding-generation license: MIT version: 0.4.0-beta date-released: '2025-11-14' From 9c18d702706ed7734f590bf2f0d517af54f617a8 Mon Sep 17 00:00:00 2001 From: egrace479 Date: Fri, 14 Nov 2025 13:56:30 -0500 Subject: [PATCH 4/5] remove duplicate keyword --- .zenodo.json | 1 - CITATION.cff | 1 - 2 files changed, 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 32c6f90..01482ce 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -36,7 +36,6 @@ "distributed", "processing", "url", - "imageomics", "dataset generation", "MPI application", "face-detection", diff --git a/CITATION.cff b/CITATION.cff index 249a5f8..8b5fa3c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -46,7 +46,6 @@ keywords: - "animal-detection" - "specimen records" - "citizen science" - - imageomics - embedding-generation license: MIT version: 0.4.0-beta From 0017abcaef84816c7775b5f5b221cc37da9ccd94 Mon Sep 17 00:00:00 2001 From: egrace479 Date: Fri, 14 Nov 2025 14:19:30 -0500 Subject: [PATCH 5/5] Standardize use of dashes and quotes --- .zenodo.json | 10 +++++----- CITATION.cff | 22 +++++++++++----------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 01482ce..840edde 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -36,13 +36,13 @@ "distributed", "processing", "url", - "dataset generation", - "MPI application", + "dataset-generation", + "MPI-application", "face-detection", - "image filtering", + "image-filtering", "animal-detection", - "specimen records", - "citizen science", + "specimen-records", + "citizen-science", "embedding-generation" ], "license": { diff --git a/CITATION.cff b/CITATION.cff index 8b5fa3c..ad1fa52 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -34,19 +34,19 @@ abstract: >- A tool for processing datasets that were downloaded using the distributed-downloader package, specifically used for constructing the TreeOfLife-200M dataset. keywords: - - parallel - - distributed - - processing - - url - - imageomics - - "dataset generation" - - "MPI application" + - "parallel" + - "distributed" + - "processing" + - "url" + - "imageomics" + - "dataset-generation" + - "MPI-application" - "face-detection" - - "image filtering" + - "image-filtering" - "animal-detection" - - "specimen records" - - "citizen science" - - embedding-generation + - "specimen-records" + - "citizen-science" + - "embedding-generation" license: MIT version: 0.4.0-beta date-released: '2025-11-14'