version 1.5.4

.github/workflows/ci.yml

@@ -1,11 +1,10 @@
-name: ci 
+name: ci
 on:
   push:
-    branches:
-      - master
-      - ci
+    tags:
+      - v*
 jobs:
-  deploy:
+  deploy-doc:
     runs-on: ubuntu-latest
     steps:
       #----------------------------------------------
@@ -17,16 +16,12 @@ jobs:
         id: setup-python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
+          python-version: 3.9
       #----------------------------------------------
-      #  -----  install & configure poetry  -----
+      #         install & configure poetry
       #----------------------------------------------
       - name: Install Poetry
         uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          installer-parallel: true
       #----------------------------------------------
       #       load cached venv if cache exists
       #----------------------------------------------
@@ -45,5 +40,17 @@ jobs:
       #----------------------------------------------
       #              run test suite
       #----------------------------------------------
-      - run: poetry run pytest
-      - run: poetry run mkdocs gh-deploy --force
+      - name: Tests
+        run: poetry run pytest
+      - name: Deploy doc
+        run: poetry run mkdocs gh-deploy --force
+  publish:
+    needs: [deploy-doc]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build and publish to pypi
+        uses: JRubics/[email protected]
+        with:
+          python_version: "3.9"
+          pypi_token: ${{ secrets.PYPI_TOKEN }}

CHANGELOG.md

@@ -0,0 +1,6 @@
+## [1.5.4] - 2024-01-08
+
+### Added
+- `CHANGELOG.md` file
+- Fix NA presence in `refine_fit` when not all pops are predicted [#27](https://github.com/MICS-Lab/scyan/issues/27)
+- Deploy on PyPI when pushing a new version (i.e., a tag that starts with `v`)

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="https://github.com/MICS-Lab/scyan/raw/master/docs/assets/logo.png" alt="scyan_logo" width="500"/>
+  <img src="https://github.com/MICS-Lab/scyan/raw/master/docs/assets/logo.png" alt="scyan_logo" width="400"/>
 </p>
 
 [![PyPI](https://img.shields.io/pypi/v/scyan.svg)](https://pypi.org/project/scyan)

docs/index.md

@@ -1,7 +1,7 @@
 # Scyan documentation
 
 <p align="center">
-  <img src="./assets/logo.png" alt="scyan_logo" width="500px"/>
+  <img src="./assets/logo.png" alt="scyan_logo" width="400px"/>
 </p>
 
 Scyan stands for **S**ingle-cell **Cy**tometry **A**nnotation **N**etwork. Based on biological knowledge prior, it provides a fast cell population annotation without requiring any training label. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding, cell sampling, and population discovery.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "scyan"
-version = "1.5.3"
+version = "1.5.4"
 description = "Single-cell Cytometry Annotation Network"
 documentation = "https://mics-lab.github.io/scyan/"
 homepage = "https://mics-lab.github.io/scyan/"