Convert to uv (#501)

Author: aarmey

.github/workflows/build.yml

@@ -4,22 +4,19 @@ on: push
 concurrency: gpu
 
 jobs:
-  build:
-    runs-on: self-hosted
-    steps:
-    - uses: actions/checkout@v4
-    - name: Setup rye
-      uses: eifinger/setup-rye@v4
-      with:
-        enable-cache: true
-        version: '0.39.0'
-    - name: Setup environment
-      run: make .venv
-    - name: Build figures
-      run: make all -j 2
-    - name: Upload files
-      uses: actions/upload-artifact@v4
-      with:
-        name: files
-        path: |
-          output/*.svg
+    build:
+        runs-on: self-hosted
+        steps:
+            - uses: actions/checkout@v6
+            - name: Install uv
+              uses: astral-sh/setup-uv@v6
+            - name: Setup environment
+              run: make .venv
+            - name: Build figures
+              run: make all -j 2
+            - name: Upload files
+              uses: actions/upload-artifact@v4
+              with:
+                  name: files
+                  path: |
+                      output/*.svg

.github/workflows/test.yml

@@ -6,28 +6,25 @@ name: Test
 on: push
 
 jobs:
-  build:
-    runs-on: self-hosted
-    steps:
-    - uses: actions/checkout@v4
-    - name: Setup rye
-      uses: eifinger/setup-rye@v4
-      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 RISE
-    - name: Check linting
-      run: rye lint RISE
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        files: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-        fail_ci_if_error: true
+    build:
+        runs-on: self-hosted
+        steps:
+            - uses: actions/checkout@v6
+            - name: Install uv
+              uses: astral-sh/setup-uv@v6
+            - name: Setup environment
+              run: make .venv
+            - name: Test with pytest
+              run: make coverage.xml
+            - name: Check formatting
+              run: rye fmt --check RISE
+            - name: Check linting
+              run: rye lint RISE
+            - name: Upload coverage to Codecov
+              uses: codecov/codecov-action@v4
+              with:
+                  token: ${{ secrets.CODECOV_TOKEN }}
+                  files: ./coverage.xml
+                  flags: unittests
+                  name: codecov-umbrella
+                  fail_ci_if_error: true

RISE/figures/figureS9a_d.py

@@ -11,10 +11,13 @@
 import numpy as np
 import pandas as pd
 import scanorama
+
 # import scvi
 import seaborn as sns
+
 # import torch
 from harmonypy import run_harmony
+from scipy.sparse import csr_array
 
 from RISE.factorization import pf2
 from RISE.figures.common import getSetup, subplotLabel
@@ -123,14 +126,14 @@ def benchmark_algorithm(
 
     elif algorithm == "Harmony":
         # Ensure data.X is a dense array
-        X = data.X.toarray()
+        X = csr_array(data.X).toarray()
 
         # Prepare metadata
         if "pool" not in data.obs:
             raise ValueError(
                 "Data must have 'batch' column in .obs for Harmony integration."
             )
-        meta_data = data.obs[["pool"]]
+        meta_data = pd.DataFrame(data.obs[["pool"]])
 
         start_time = time.time()
         tracemalloc.start()

RISE/tests/test_import.py

@@ -5,15 +5,14 @@
 import numpy as np
 import pytest
 
-from ..imports import (
-    import_thomson,
-)
+from ..imports import import_lupus, import_thomson
 
 
 @pytest.mark.parametrize(
     "import_func",
     [
         import_thomson,
+        import_lupus,
     ],
 )
 def test_imports(import_func):

makefile

@@ -11,19 +11,19 @@ allLupus: $(filter output/figureLupus%, $(allOutput))
 
 output/figure%.svg: RISE/figures/figure%.py
 	@ mkdir -p ./output
-	rye run fbuild $*
+	uv run fbuild $*
 
 test: .venv
-	rye run pytest -s -v -x
+	uv run pytest -s -v -x
 
 .venv: pyproject.toml
-	rye sync
+	uv sync
 
 coverage.xml: .venv
-	rye run pytest --junitxml=junit.xml --cov=RISE --cov-report xml:coverage.xml
+	uv run pytest --junitxml=junit.xml --cov=RISE --cov-report xml:coverage.xml
 
 pyright: .venv
-	rye run pyright RISE
+	uv run pyright RISE
 
 clean:
 	rm -rf output profile profile.svg

pyproject.toml

@@ -8,7 +8,7 @@ requires-python = ">= 3.12"
 
 dependencies = [
     "numpy>=2.2",
-    "scipy>=1.15",
+    "scipy>=1.16",
     "scikit-learn>=1.6",
     "seaborn>=0.13.2",
     "pandas>=2.2.1",
@@ -18,7 +18,7 @@ dependencies = [
     "anndata>=0.10.3",
     "datashader>=0.16",
     "gseapy>=1.1",
-    "scanpy>=1.10",
+    "scanpy>=1.11",
     "pacmap>=0.7.1",
     "tqdm>=4.66.1",
     "tlviz>=0.1.1",
@@ -34,23 +34,21 @@ readme = "README.md"
 fbuild = "RISE.figures.common:genFigure"
 factor = "RISE.imports:factorSave"
 
-
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
-[tool.rye]
-managed = true
-dev-dependencies = [
-    "pytest>=8.0",
-    "pytest-cov>=6.0",
-    "pyright>=1.1.390",
+[dependency-groups]
+dev = [
+    "pytest>=9.0",
+    "pytest-cov>=7.0",
+    "pyright>=1.1.407",
     "scanorama>=1.7.4",
     "harmonypy>=0.0.10",
     "scib>=1.1.5",
+    "ruff>=0.14.7",
 ]
 
-
 [tool.hatch.metadata]
 allow-direct-references = true