Upgrade

.github/workflows/test.yml

@@ -8,29 +8,20 @@ on: push
 jobs:
   build:
     runs-on: self-hosted
-    strategy:
-      matrix:
-        python-version:
-          - 3.10.14
-          - 3.11
-          - 3.12
     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: '0.44.0'
-    - name: Pin Python version
-      run: rye pin ${{ matrix.python-version }}
     - name: Setup environment
       run: make .venv
     - name: Test with pytest
       run: make coverage.xml
     - name: Check formatting
-      run: rye fmt --check parafac2
+      run: uv run ruff format --check parafac2
     - name: Check linting
-      run: rye lint parafac2
+      run: uv run ruff check parafac2
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:

.gitignore

@@ -6,36 +6,6 @@ __pycache__/
 # C extensions
 *.so
 
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
 # Unit test / coverage reports
 htmlcov/
 .tox/
@@ -160,6 +130,5 @@ cython_debug/
 #.idea/
 
 .DS_Store
-requirements.lock
-requirements-dev.lock
+uv.lock
 .python-version

makefile

@@ -1,20 +1,20 @@
 .PHONY: clean test pyright
 
 test: .venv
-	rye run pytest -s -v -x --durations=0
+	uv run pytest -s -v -x --durations=0
 
 .venv: pyproject.toml
-	rye sync
+	uv sync --dev
 
 testprofile:
-	rye run python3 -m cProfile -o profile -m pytest -s -x -v
-	rye run gprof2dot -f pstats --node-thres=1.0 profile | dot -Tsvg -o profile.svg
+	uv run python3 -m cProfile -o profile -m pytest -s -x -v
+	uv run gprof2dot -f pstats --node-thres=1.0 profile | dot -Tsvg -o profile.svg
 
 coverage.xml: .venv
-	rye run pytest --junitxml=junit.xml --cov=parafac2 --cov-report xml:coverage.xml
+	uv run pytest --junitxml=junit.xml --cov=parafac2 --cov-report xml:coverage.xml
 
 pyright: .venv
-	rye run pyright parafac2
+	uv run pyright parafac2
 
 clean:
 	rm -rf output profile profile.svg

pyproject.toml

@@ -1,24 +1,24 @@
 [project]
 name = "parafac2"
-version = "0.1.0"
+version = "0.2.0"
 description = "An implementation of PARAFAC2 that handles sparsity for single cell data."
 authors = [{name = "Aaron Meyer", email = "git@asmlab.org" }]
 license = "MIT"
-requires-python = ">= 3.11"
+requires-python = ">= 3.12"
 
 dependencies = [
     "numpy>=2.2",
-    "scipy>=1.15",
+    "scipy>=1.16",
     "tensorly>=0.8.1",
     "tqdm>=4.66",
-    "cupy-cuda12x>=13.4",
-    "anndata>=0.11",
+    "cupy-cuda12x>=13.6",
+    "anndata>=0.12",
 ]
 
-[tool.rye]
-managed = true
-dev-dependencies = [
-    "pytest>=8.3",
+[dependency-groups]
+dev = [
+    "ruff>=0.14.1",
+    "pytest>=8.4",
     "pytest-cov>=6.1",
     "pyright>=1.1.380",
 ]
@@ -48,3 +48,5 @@ select = [
     # type checking
     "TC",
 ]
+
+