Develop

.github/workflows/semantic-release.yaml

@@ -11,13 +11,17 @@ jobs:
   release:
     if: ${{ github.event.label.name == 'semantic versioning' }}
     runs-on: ubuntu-latest
+    concurrency: release
+    permissions:
+      id-token: write
+      contents: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Python Semantic Release
-      uses: relekang/python-semantic-release@v7.33.2
+      uses: relekang/python-semantic-release@master
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         repository_username: __token__
-        repository_password: ${{ secrets.PYPI_TOKEN }}
+        repository_password: ${{ secrets.PYPI_TOKEN }}

docs/conf.py

@@ -15,12 +15,12 @@
 
 sys.path.insert(0, os.path.abspath("."))
 sys.path.insert(0, os.path.abspath(".."))
-from scar.main.__version__ import __version__, _copyright, _author
+from scar import __version__
 
 # -- Project information -----------------------------------------------------
 project = "scAR"
-copyright = _copyright
-author = _author
+copyright = "Novartis Institute for BioMedical Research, 2022"
+author = "Caibin Sheng"
 release = __version__
 
 

pyproject.toml

@@ -1,3 +1,47 @@
 [build-system]
 requires = ["setuptools>=68.1.2"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "scar"
+version = "0.5.5"
+requires-python = ">= 3.10"
+dependencies = [
+    "torch >= 1.10.0",
+    "torchvision >= 0.9.0",
+    "tqdm >= 4.62.3",
+    "seaborn >= 0.11.2",
+    "scikit-learn >= 1.0.1",
+    "pyro-ppl >= 1.8.0",
+    "scanpy >= 1.9.2"
+]
+authors = [
+    {name = "Caibin Sheng", email = "caibin.sheng.res@gmail.com"}
+]
+description = "scAR (single-cell Ambient Remover) is a package for denoising the ambient signals in droplet-based single cell omics"
+readme = "README.md"
+license = {text = "MIT License"}
+keywords = ["single cell omics", "variational autoencoder", "machine learning", "generative model", "cite-seq", "scCRISPRseq", "scRNAseq"]
+
+[project.urls]
+Homepage = "https://github.com/Novartis/scAR"
+Documentation = "https://scar-tutorials.readthedocs.io/en/main/"
+Repository = "https://github.com/Novartis/scar.git"
+Issues = "https://github.com/Novartis/scAR/issues"
+Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
+
+[tool.semantic_release]
+version_toml = ["pyproject.toml:project.version"]
+major_on_zero = false
+branch = "develop"
+upload_to_release = false
+hvcs = "github"
+upload_to_repository = false
+upload_to_pypi = false
+patch_without_tag = false
+
+[tool.semantic_release.changelog]
+changelog_file="docs/Release_notes.md"
+
+[project.gui-scripts]
+scar = "scar.main.__main__:main"

scar/__init__.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
+from importlib.metadata import version
+__version__ = version("scar")
 
-from .main.__version__ import __version__
 from .main._scar import model
 from .main._setup import setup_anndata
 from .main import _data_generater as data_generator

scar/main/__main__.py

@@ -8,7 +8,7 @@
 import scanpy as sc
 from scipy.sparse import csr_matrix
 from ._scar import model
-from .__version__ import __version__
+from ..__init__ import __version__
 from ._utils import get_logger