From 442f6b77f47a8c32f8034b308bf7e4c08f118bb7 Mon Sep 17 00:00:00 2001 From: "Mayra L. Ruiz Tejada Segura" Date: Tue, 24 Feb 2026 12:34:14 +0100 Subject: [PATCH 1/3] Update README.md add zenodo badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index dff93fb..ac64d27 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # NicheSphere -[![DOI](https://zenodo.org)](https://doi.org) +[![DOI](https://zenodo.org/badge/685916590.svg)](https://doi.org/10.5281/zenodo.18756710) NicheSphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting nearest neighbors of each type for each cell in single cell spatial data like MERFISH or CODEX. From bfbd342a3d705fa68860dcb7cf2783a969bdfe51 Mon Sep 17 00:00:00 2001 From: "Mayra L. Ruiz Tejada Segura" Date: Tue, 24 Feb 2026 12:35:52 +0100 Subject: [PATCH 2/3] Update CITATION.cff add doi --- CITATION.cff | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 016a2af..e89f405 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,6 +7,6 @@ authors: given-names: "James" title: "NicheSphere" version: 1.0.0 -doi: 10.5281/zenodo.XXXXX # Update this AFTER you get your DOI from Zenodo -date-released: 2026-02-24 # Use today's date -url: "https://github.com/CostaLab/NicheSphere" \ No newline at end of file +doi: 10.5281/zenodo.1875671 +date-released: 2026-02-24 +url: "https://github.com/CostaLab/NicheSphere" From 155b03babfee29f566714c32ee38f5b4b04fec33 Mon Sep 17 00:00:00 2001 From: "Mayra L. Ruiz Tejada Segura" Date: Tue, 24 Feb 2026 14:07:29 +0100 Subject: [PATCH 3/3] Create publish.yml automatic pypi publishing of releases --- .github/workflows/publish.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/publish.yml diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..faaa277 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,25 @@ +name: Publish to PyPI + +on: + release: + types: [published] + +jobs: + pypi-publish: + name: Build and publish to PyPI + runs-on: ubuntu-latest + permissions: + id-token: write # Mandatory for Trusted Publishing + contents: read + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.10" + - name: Install Poetry + run: pip install poetry + - name: Build package + run: poetry build + - name: Publish package + uses: pypa/gh-action-pypi-publish@release/v1