Testing the new versions

Author: Joao Felipe Rocha

.github/workflows/run_tests.yml

@@ -24,19 +24,19 @@ jobs:
       fail-fast: false
       matrix:
         config:
+        - {name: '3.13', os: ubuntu-latest, python: '3.13', r: 'release'}
+        - {name: '3.12', os: ubuntu-latest, python: '3.12', r: 'release'}
         - {name: '3.11', os: ubuntu-latest, python: '3.11', r: 'release'}
         - {name: '3.10', os: ubuntu-latest, python: '3.10', r: 'release'}
         - {name: '3.9', os: ubuntu-latest, python: '3.9', r: 'release'}
-        - {name: '3.8', os: ubuntu-latest, python: '3.8', r: 'release'}
-        - {name: '3.7', os: ubuntu-latest, python: '3.7', r: 'oldrel'}
 
     steps:
 
     - name: Get current date
       id: date
-      run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
+      run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -47,7 +47,7 @@ jobs:
         sudo apt-get install -y pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg libhdf5-dev libfribidi-dev libharfbuzz-dev
 
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.config.python }}
 
@@ -113,7 +113,7 @@ jobs:
 
     - name: Upload check results on fail
       if: failure()
-      uses: actions/upload-artifact@master
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ matrix.config.name }}_results
         path: check

pyproject.toml

@@ -0,0 +1,89 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scprep"
+dynamic = ["version"]
+description = "scprep"
+authors = [
+    {name = "Scott Gigante, Daniel Burkhardt and Jay Stanley, Yale University", email = "[email protected]"}
+]
+license = {text = "Yale License"}
+readme = "README.rst"
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.26.0",
+    "scipy>=1.13.0",
+    "scikit-learn>=1.5.0",
+    "decorator>=4.3.0",
+    "pandas>=2.0.0",
+    "packaging",
+]
+keywords = [
+    "big-data",
+    "computational-biology",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Framework :: Jupyter",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "scprep.version.__version__"}
+
+[project.urls]
+Homepage = "https://github.com/KrishnaswamyLab/scprep"
+Repository = "https://github.com/KrishnaswamyLab/scprep"
+Download = "https://github.com/KrishnaswamyLab/scprep/archive/v{version}.tar.gz"
+
+[project.optional-dependencies]
+optional = [
+    "fcsparser<0.2.5",
+    "tables",
+    "h5py",
+    "anndata",
+    "anndata2ri>=1.0.6",
+]
+test = [
+    "nose",
+    "nose2",
+    "coverage",
+    "coveralls",
+    "parameterized",
+    "requests",
+    "packaging",
+    "mock",
+    "h5py",
+    "matplotlib>=3.0",
+    "rpy2>=3.4.3",
+    "black",
+    "fcsparser<0.2.5",
+    "tables",
+    "h5py",
+    "anndata",
+    "anndata2ri>=1.0.6",
+]
+doc = [
+    "sphinx>=2.2,<2.4",
+    "sphinxcontrib-napoleon",
+    "ipykernel",
+    "nbsphinx",
+    "autodocsumm",
+]
+
+[tool.setuptools.packages.find]