Move package management over to uv (#24)

* Moved over

* Done

Author: aarmey

.github/workflows/build.yml

@@ -7,11 +7,10 @@ jobs:
     runs-on: self-hosted
     steps:
     - uses: actions/checkout@v4
-    - name: Setup rye
-      uses: eifinger/setup-rye@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
         enable-cache: true
-        version: '0.39.0'
     - name: Setup environment
       run: make .venv
     - name: Build figures

.github/workflows/test.yml

@@ -10,16 +10,15 @@ jobs:
     runs-on: self-hosted
     steps:
     - uses: actions/checkout@v4
-    - name: Setup rye
-      uses: eifinger/setup-rye@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
         enable-cache: true
-        version: '0.39.0'
     - name: Setup environment
       run: make .venv
     - name: Test with pytest
       run: make coverage.xml
     - name: Check formatting
-      run: rye fmt --check
+      run: uv run ruff format --check
     - name: Check linting
-      run: rye lint
+      run: uv run ruff check

makefile

@@ -9,24 +9,24 @@ all: $(allOutput)
 
 output/figure%.svg: pf2barcode/figures/figure%.py .venv
 	@ mkdir -p ./output
-	rye run fbuild $*
+	uv run fbuild $*
 
 .venv: pyproject.toml
-	rye sync
+	uv sync --all-extras
 
 test: .venv
-	rye run pytest -s -x -v pf2barcode/tests/test_import.py
+	uv run pytest -s -x -v pf2barcode/tests/test_import.py
 
 clean:
 	rm -rf output profile profile.svg
 	rm -rf factor_cache
 
 pyright: .venv
-	rye run pyright pf2barcode
+	uv run pyright pf2barcode
 
 coverage.xml: .venv
-	rye run pytest --cov=pf2barcode --cov-report xml:coverage.xml
+	uv run pytest --cov=pf2barcode --cov-report xml:coverage.xml
 
 testprofile: .venv
-	rye run python3 -m cProfile -o profile -m pytest -s -v -x
+	uv run python3 -m cProfile -o profile -m pytest -s -v -x
 	gprof2dot -f pstats --node-thres=5.0 profile | dot -Tsvg -o profile.svg

pf2barcode/geneontology.py

@@ -2,7 +2,7 @@
 import pandas as pd
 
 
-def geneOntology(X, var_names) -> pd.DataFrame:
+def geneOntology(X, var_names: list[str]) -> pd.DataFrame:
     """Plots top Gene Ontology terms for molecular function,
     biological process, cellular component. Uses factors as
     input for function"""

pyproject.toml

@@ -1,33 +1,33 @@
 [project]
 name = "pf2barcode"
 version = "0.1.0"
+readme = "README.md"
 description = "Single cell analysis across conditions using PARAFAC2."
 authors = [
     { name = "Aaron Meyer", email = "git@asmlab.org" }
 ]
 license = { text = "MIT" }
-requires-python = ">=3.12,<3.13"
+requires-python = ">=3.13.1,<3.14"
 dependencies = [
     "numpy>=2.2",
-    "scipy==1.15.3",
+    "scipy>=1.16",
     "scikit-learn>=1.7",
     "seaborn>=0.13",
     "pandas>=2.3",
     "gseapy>=1.1",
-    "scanpy>=1.11.2",
+    "scanpy>=1.11",
     "ipykernel>=6.29",
-    "anndata>=0.11.4",
+    "anndata>=0.12",
 ]
 
-[tool.rye]
-managed = true
-dev-dependencies = [
+[dependency-groups]
+dev = [
+    "pyright>=1.1.406",
     "pytest>=8.2.0",
-    "pytest-cov>=5.0",
+    "pytest-cov>=6.0",
+    "ruff>=0.14.1",
 ]
 
-readme = "README.md"
-
 [project.scripts]
 fbuild = "pf2barcode.figures.common:genFigure"