Merge branch 'main' of github.com:brisvag/blik into feature/segment2surf

.github/workflows/ci.yml

@@ -103,7 +103,7 @@ jobs:
           jupyter-book build .
 
       - name: GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_build/html
@@ -136,6 +136,6 @@ jobs:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
 
-      - uses: softprops/action-gh-release@v1
+      - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true

CITATION.cff

@@ -1,10 +1,31 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
 cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
-title: "blik: a Python tool for visualising and interacting with cryo-ET and subtomogram averaging data."
+title: >-
+  blik: a Python tool for visualising and interacting with
+  cryo-ET and subtomogram averaging data.
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
 authors:
-- family-names: "Gaifas"
-  given-names: "Lorenzo"
-  orcid: "https://orcid.org/0000-0003-4875-9422"
-doi: 10.5281/zenodo.10090438
-repository-code: https://github.com/brisvag/blik
-license: GPLv3
+  - given-names: Lorenzo
+    family-names: Gaifas
+    orcid: 'https://orcid.org/0000-0003-4875-9422'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10090438
+    description: blik source code repository on github
+  - type: doi
+    value: 10.1371/journal.pbio.3002447
+    description: main blik publication on Plos Biology
+repository-code: 'https://github.com/brisvag/blik'
+url: 'https://brisvag.github.io/blik/'
+keywords:
+  - cryo-et
+  - cryo-em
+  - tomography
+  - napari
+  - visualisation
+license: GPL-3.0

README.md

@@ -2,12 +2,14 @@
 
 # blik
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10090438.svg)](https://zenodo.org/doi/10.5281/zenodo.10090438)
 [![License](https://img.shields.io/pypi/l/blik.svg?color=green)](https://github.com/brisvag/blik/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/blik.svg?color=green)](https://pypi.org/project/blik)
 [![Python Version](https://img.shields.io/pypi/pyversions/blik.svg?color=green)](https://python.org)
 [![CI](https://github.com/brisvag/blik/actions/workflows/ci.yml/badge.svg)](https://github.com/brisvag/blik/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/brisvag/blik/branch/main/graph/badge.svg)](https://codecov.io/gh/brisvag/blik)
 
+
 ![blik showcase](https://user-images.githubusercontent.com/23482191/161224963-ad746a06-c2e5-46fe-a13b-f356bc4ad72b.png)
 
 **`blik`** is a tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional [napari viewer](https://napari.org) and the scientific python stack.
@@ -63,4 +65,4 @@ There are also widgets for picking of both surfaces and filaments.
 
 # References
 
-A paper preprint about `blik` is available on the bioRxiv: [https://doi.org/10.1101/2023.12.05.570263](https://doi.org/10.1101/2023.12.05.570263).
+If you use `blik`, please cite the repo on zenodo and the paper on Plos Biology: [https://doi.org/10.1371/journal.pbio.3002447](https://doi.org/10.1371/journal.pbio.3002447).