v1.0.0rc1

.github/codecov.yml

@@ -1,5 +1,5 @@
 ignore:
-  - "scarf/tests/*"
+  - "tests/*"
   - "setup.py"
 
 github_checks: false

.github/workflows/docs.yml

@@ -0,0 +1,51 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - master
+      - development
+    paths:
+      - "docs/**"
+      - "scarf/**"
+      - "pyproject.toml"
+      - "uv.lock"
+      - ".readthedocs.yml"
+      - ".github/workflows/docs.yml"
+  pull_request:
+    branches:
+      - master
+      - development
+    paths:
+      - "docs/**"
+      - "scarf/**"
+      - "pyproject.toml"
+      - "uv.lock"
+      - ".readthedocs.yml"
+      - ".github/workflows/docs.yml"
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    env:
+      HNSWLIB_NO_NATIVE: "1"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install system build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential libfftw3-dev libmetis-dev
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.14"
+      - name: Install documentation dependencies
+        run: uv sync --extra docs --extra test --extra extra
+      - name: Documentation cache tests
+        run: uv run pytest -n 0 tests/test_docs_cache.py
+      - name: Validate committed notebook cache
+        run: uv run python docs/execute_all_vignettes.py --validate
+      - name: Sphinx HTML build (nitpicky, warnings as errors)
+        run: uv run sphinx-build -b html -n -W docs/source docs/build/html
+      - name: Reference coverage (every public symbol documented exactly once)
+        run: uv run python docs/check_reference_coverage.py

.github/workflows/publish.yml

@@ -7,20 +7,18 @@ on:
 jobs:
   build:
     name: Build distribution
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-26.04
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: 3.11.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install --upgrade setuptools wheel build
+        python-version: "3.14"
     - name: Build a binary wheel and a source tarball
-      run: python -m build
+      run: uv build
+    - name: Smoke-test wheel
+      run: uv run --no-project python tests/smoke_wheel.py dist/*.whl
     - name: Store the distribution packages
       uses: actions/upload-artifact@v4
       with:
@@ -31,12 +29,12 @@ jobs:
     name: Publish to PyPI
     needs:
       - build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-26.04
     environment:
       name: pypi
       url: https://pypi.org/p/scarf
     permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
+      id-token: write
     steps:
       - name: Download all the dists
         uses: actions/download-artifact@v4

.github/workflows/pytest.yml

@@ -12,27 +12,78 @@ on:
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-26.04
+    env:
+      HNSWLIB_NO_NATIVE: "1"
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-22.04, windows-2019]
-        python-version: [3.11.9]
+        python-version: ["3.12", "3.13", "3.14"]
+        resolution: [locked]
+        include:
+          - python-version: "3.12"
+            resolution: lowest-direct
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - name: Install system build dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y build-essential libfftw3-dev libmetis-dev
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install dependencies (locked)
+      if: matrix.resolution == 'locked'
+      run: uv sync --group profiling --extra test --extra extra
+    - name: Install dependencies (lowest-direct)
+      if: matrix.resolution == 'lowest-direct'
+      run: uv pip install --resolution lowest-direct -e ".[test,extra]" --group profiling
+    - name: Lint and check formatting
+      if: matrix.resolution == 'locked' && matrix.python-version == '3.12'
+      run: |
+        uv run ruff check scarf profiling tests
+        uv run ruff format --check scarf profiling tests
+    - name: Type check
+      if: matrix.resolution == 'locked' && matrix.python-version == '3.12'
+      run: uv run mypy scarf profiling
+    - name: Download test fixtures
+      run: |
+        if [ "${{ matrix.resolution }}" = "lowest-direct" ]; then
+          uv run --no-sync python -m tests.download_fixtures --with-h5ad
+        else
+          uv run python -m tests.download_fixtures --with-h5ad
+        fi
+    - name: Test with pytest (parallel)
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements_extra.txt
-        pip install pytest pytest-cov topacedo anndata==0.11.4 pcst_fast
-    - name: Test with pytest
+        if [ "${{ matrix.resolution }}" = "lowest-direct" ]; then
+          uv run --no-sync pytest \
+            -n auto \
+            --dist loadfile \
+            --cov=scarf \
+            --cov-report=xml \
+            --cov-report=term
+        else
+          uv run pytest \
+            -n auto \
+            --dist loadfile \
+            --cov=scarf \
+            --cov-report=xml \
+            --cov-report=term
+        fi
+    - name: Compare publication plotting references
+      if: matrix.resolution == 'locked' && matrix.python-version == '3.12'
+      env:
+        MPLBACKEND: Agg
+        SCARF_RUN_VISUAL_REGRESSION: "1"
+      run: uv run pytest -n 0 -m visual tests/test_plotting_showcase.py
+    - name: Build and smoke-test wheel
+      if: matrix.resolution == 'locked' && matrix.python-version == '3.14'
       run: |
-        pytest --cov=.
+        uv build
+        uv run --no-project python tests/smoke_wheel.py dist/*.whl
     - name: Upload coverage to Codecov
+      if: matrix.resolution == 'locked' && matrix.python-version == '3.14'
       uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false

.gitignore

@@ -3,19 +3,60 @@
 __pycache__
 build
 dist
+*.egg-info
 scarf.egg-info
 scarf_toolkit.egg-info
+.venv
+.venv*/
+.ruff_cache
 dask-worker-space
+# zarr ":memory:" URL materialized as a local directory by older tests
+:memory:
+:memory:/
 *.ipynb_checkpoints
 *.ipynb
+!docs/.jupyter_cache/executed/**/base.ipynb
+docs/.jupyter_cache/_parallel/
+docs/.jupyter_cache.backup/
+docs/.jupyter_cache.candidate-*/
+docs/.jupyter_cache.lock
+docs/.jupyter_cache.resume/
+docs/.jupyter_cache.work-*/
+docs/.ipython/
 docs/source/vignettes/README.md
 docs/source/vignettes/scarf_datasets
 docs/source/vignettes/dev
 docs/source/vignettes/*.txt
 docs/source/vignettes/*.mtx
+docs/build/
+docs/_build/
 docs/jupyter_execute
+# Downloaded/converted notebook datasets (path depends on CWD during execute)
+docs/source/scarf_datasets/
+docs/source/tutorials/scarf_datasets/
+docs/**/scarf_datasets/
+*.zarr/
+**/*.zarr/
 .coverage
+coverage.xml
+htmlcov/
 .pytest_cache
 interrogate_badge.svg
-scarf/tests/datasets/*
-test_data
+tests/datasets/*
+!tests/datasets/markers_all_clusters.csv
+tests/.env
+tests/.env.*
+benchmarks/.env
+benchmarks/.env.*
+!benchmarks/.env.example
+profiling/.env
+profiling/.env.*
+!profiling/.env.example
+profiling/config.toml
+# Generated / local-only run configs (machine grids). Keep LEARNINGS.md + examples.
+profiling/layouts/
+test_data
+# Generated plotting showcase outputs. Curated references live in tests/visual.
+/artifacts/
+/plotting_showcase/
+tests/visual/showcase/*.json

.readthedocs.yml

@@ -1,19 +1,22 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
+  jobs:
+    pre_build:
+      - uv run python docs/execute_all_vignettes.py --validate
 
 python:
   install:
-    - requirements: requirements.txt
-    - requirements: requirements_extra.txt
-    - requirements: docs/source/requirements.txt
-    - method: pip
-      path: .
+    - method: uv
+      command: sync
+      extras:
+        - docs
+        - extra
 
 sphinx:
   configuration: docs/source/conf.py
   builder: html
-  fail_on_warning: false
+  fail_on_warning: true

Dockerfile

@@ -1,28 +1,19 @@
-FROM ubuntu:22.04
+FROM ubuntu:26.04
 
 RUN apt update -y && apt autoremove -y && apt clean -y && apt autoclean -y && apt upgrade -y
-RUN apt install -y wget build-essential git nano
+RUN apt install -y wget build-essential git nano curl libfftw3-dev libmetis-dev libtbb-dev
 
-# The following is done to make sure that tzdata package doesnt prompt for timezone during installation
 ARG TZ="Europe/Stockholm"
 RUN DEBIAN_FRONTEND="noninteractive" TZ=$TZ apt-get -y install tzdata
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone &
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
-#Installing dependencies for sgtsne
-RUN apt install -y libmetis-dev libtbb-dev libfftw3-dev lib32gcc-7-dev libflann-dev libcilkrts5
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
-# Installing lastest Miniconda3
-RUN wget -O miniconda_inst "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" && \
-	bash miniconda_inst -b && \
-	rm miniconda_inst
+WORKDIR /workspace
+COPY . /workspace
 
-# Exporting PATH and also saving it in bashrc for next session
-# /workspace/bin is so that sgtsne can be found
-RUN echo "export PATH=$PATH:/root/miniconda3/bin:/workspace/bin" >> /root/.bashrc
-ENV PATH=$PATH:/root/miniconda3/bin:/workspace/bin
+RUN uv python install 3.14 && uv sync --extra extra
+ENV PATH="/workspace/.venv/bin:$PATH"
 
-# Installing numpy and pybind11 beforehand because sometimes they don't install so well from requirements.txt
-RUN pip install --upgrade pip
-RUN pip install --no-cache-dir -U numpy pybind11
-
-RUN pip install scarf
+RUN echo "export PATH=/workspace/.venv/bin:/workspace/bin:$PATH" >> /root/.bashrc
+ENV PATH=/workspace/.venv/bin:/workspace/bin:$PATH

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) [2021], [Dhapola P, Karlsson G]
+Copyright (c) 2026, Nygen Analytics AB
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -7,11 +7,11 @@ exclude .readthedocs.yml
 exclude Dockerfile
 prune scarf_toolkit.egg-info
 prune docs
-prune scarf/tests
+prune tests
+prune profiling
+prune scripts
 prune .circleci
 prune .github
-include requirements.txt
-include requirements_extra.txt
 include VERSION
-include pypi_README.rst
+include README.md
 graft bin