Merge branch 'main' of https://github.com/anders-biostat/Cytovanni

Author: valentinwust

.github/workflows/ci.yaml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: pip install hatchling build twine
+
+      - name: Build
+        run: python -m build
+
+      - name: Check metadata
+        run: twine check dist/*
+
+      - name: Smoke test
+        run: |
+          pip install dist/*.whl --no-deps
+          python -c "from cytovanni.version import __version__; print(__version__)"

.github/workflows/publish.yaml

@@ -0,0 +1,44 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: pip install hatchling build twine
+
+      - name: Build
+        run: python -m build
+
+      - name: Check metadata
+        run: twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

container/container.def

@@ -4,31 +4,12 @@ From: pytorch/pytorch:2.8.0-cuda12.9-cudnn9-devel
 %post
     pip install --no-cache-dir uv
 
-    # install rapids
-    uv pip install --system --pre --extra-index-url=https://pypi.nvidia.com --index-strategy unsafe-best-match \
-    	"cudf-cu12==25.08.*" "dask-cudf-cu12==25.08.*" "cuml-cu12==25.08.*" \
-    	"cugraph-cu12==25.08.*" "nx-cugraph-cu12==25.08.*" "raft-dask-cu12==25.08.*"
-    
     uv pip install --system jupyter ipykernel
-    uv pip install --system "jax[cuda12]"
-    uv pip install --system scvi-tools numpy pandas muon flowkit flowutils readfcs matplotlib seaborn datashader scanpy igraph
-
-    # couldn't get fastplotlib to work
-    #apt update
-    #apt install -y libturbojpeg0-dev libegl1-mesa libgl1-mesa-dri libglx-mesa0 mesa-utils mesa-utils-extra
-    #uv pip install --system "fastplotlib[notebook]" simplejpeg glfw
-    
-    uv pip install --system pykeops geomloss "rapids-singlecell==0.13.2"
-
-    # packages for Arges
-    uv pip install --system mahotas tifffile "cellpose==4.0.4"
-    
-    # packages for documentation
-    uv pip install --system mkdocs mknotebooks mkdocstrings[python] mkdocs-gen-files
+    uv pip install --system numpy pandas flowkit flowutils readfcs matplotlib seaborn scipy scikit-learn anndata statsmodels Pillow
+    uv pip install --system pykeops geomloss
 
     # custom packages
-    uv pip install --system torchgmm
-    # datashader?
+    uv pip install --system datashader colorcet
 
     python -m ipykernel install --user --name=cytovanni-docker --display-name "Python (Cytovanni-docker)"
 

pyproject.toml

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "cytovanni"
+authors = [
+    "Valentin Wüst <valentin.wuest@bioquant.uni-heidelberg.de>",
+    "Simon Anders <simon.anders@bioquant.uni-heidelberg.de>",
+]
+maintainers = ["Valentin Wüst <valentin.wuest@bioquant.uni-heidelberg.de>"]
+dynamic = ["version"]
+description = "Computational Standardization of Flow Cytometry Data"
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.10"
+dependencies = [
+    "numpy",
+    "pandas",
+    "torch",
+    "anndata",
+    "flowkit",
+    "flowio",
+    "flowutils",
+    "matplotlib",
+    "seaborn",
+    "scipy",
+    "scikit-learn",
+    "statsmodels",
+    "tqdm",
+    "Pillow",
+    "python-dateutil",
+]
+
+[project.optional-dependencies]
+geom = ["geomloss", "pykeops"]
+plot = ["datashader", "colorcet"]
+all = ["cytovanni[geom,plot]"]
+
+[project.urls]
+Repository = "https://github.com/anders-biostat/Cytovanni"
+
+[tool.hatch.version]
+path = "src/cytovanni/version.py"