scsplice 2.0.0__tar.gz

scsplice-2.0.0/.github/workflows/docs.yml

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+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: docs
+  cancel-in-progress: false
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    name: Build docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0   # full history required by mike
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install Eigen3
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
+
+      - name: Install package and docs dependencies
+        run: pip install -e ".[docs]"
+
+      - name: Build docs (strict)
+        run: mkdocs build --strict
+
+  deploy:
+    name: Deploy to GitHub Pages
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install Eigen3
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
+
+      - name: Install package and docs dependencies
+        run: pip install -e ".[docs]"
+
+      - name: Configure git identity for mike
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Deploy docs
+        run: mkdocs gh-deploy --force

scsplice-2.0.0/.github/workflows/test.yml

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+name: test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    name: ${{ matrix.os }} / py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Eigen (Linux)
+        if: runner.os == 'Linux'
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
+
+      - name: Install Eigen + libomp (macOS)
+        if: runner.os == 'macOS'
+        run: brew install eigen libomp
+
+      - name: Set OpenMP env (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          LIBOMP_PREFIX="$(brew --prefix libomp)"
+          {
+            echo "OpenMP_ROOT=${LIBOMP_PREFIX}"
+            echo "LDFLAGS=-L${LIBOMP_PREFIX}/lib"
+            echo "CPPFLAGS=-I${LIBOMP_PREFIX}/include"
+          } >> "$GITHUB_ENV"
+
+      - name: Install package + test deps
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[test]"
+
+      - name: Run tests
+        run: pytest -v --maxfail=1

scsplice-2.0.0/.github/workflows/wheels.yml

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+name: wheels
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.21
+        env:
+          # manylinux_2_28 (RHEL/AlmaLinux 8) -> enable EPEL for eigen3-devel.
+          # Stock manylinux2014 does NOT ship EPEL by default and the prior
+          # `yum install eigen3-devel || dnf install eigen3-devel` failed on
+          # both. manylinux_2_28 is selected in pyproject.toml.
+          CIBW_BEFORE_ALL_LINUX: "dnf install -y epel-release && dnf install -y eigen3-devel"
+          # macOS: install eigen only. libomp is intentionally NOT installed
+          # because we disable OpenMP on macOS (SCSPLICE_DISABLE_OPENMP=ON in
+          # pyproject.toml [tool.cibuildwheel.macos]) — libomp discovery
+          # across x86_64/arm64 under cibuildwheel is too fragile and per-row
+          # writes are bit-identical to MT anyway.
+          CIBW_BEFORE_ALL_MACOS: "brew install eigen"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: |
+          python -m pip install --upgrade pip build
+          python -m build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish:
+    # Upload to PyPI on version tags (v1.0.0, etc.)
+    # Requires that the PyPI project has a Trusted Publisher configured
+    # for this GitHub repository (https://docs.pypi.org/trusted-publishers/).
+    # No API tokens are stored in secrets.
+    name: Publish to PyPI
+    needs: [build_wheels, build_sdist]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          pattern: "wheels-*"
+          merge-multiple: true
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

scsplice-2.0.0/.gitignore

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+# Build artifacts
+build/
+dist/
+*.egg-info/
+src/splikit/_version.py
+*.so
+*.dylib
+*.pyd
+*.o
+*.a
+
+# CMake
+CMakeFiles/
+CMakeCache.txt
+CTestTestfile.cmake
+cmake_install.cmake
+_deps/
+.cmake/
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+.python-version
+.venv/
+venv/
+
+# Test / coverage
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+coverage.xml
+.tox/
+
+# Type checkers
+.mypy_cache/
+.pyright/
+.ruff_cache/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Docs
+site/
+docs/_build/
+docs/api/
+.cache/
+
+tests/data/*.large.h5
+
+# Notebooks
+.ipynb_checkpoints/
+
+# AI files
+CLAUDE.md

scsplice-2.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [2.0.0] - 2026-05-11
+
+### Breaking Changes
+
+- PyPI distribution renamed `splikit-py` → `scsplice`. Install with `pip install scsplice`.
+- Python import alias changes: `import scsplice as scs` (was `import splikit as splk`).
+- `uns["splikit"]` schema key renamed to `uns["scsplice"]`. A one-release compat shim reads the legacy key with a `FutureWarning` and migrates it automatically; will be removed in 3.0.
+- `SPLIKIT_REAL_DATA_DIR` env var renamed to `SCSPLICE_REAL_DATA_DIR`. Old name accepted with `FutureWarning` for one release.
+- C++ extension module renamed `_splikit_cpp` → `_scsplice_cpp`.
+
+### Added
+
+- Compat shim in `scsplice._core._validators` (`get_scsplice_ns` / `setdefault_scsplice_ns`) for graceful migration of v1.0 AnnData objects carrying `uns["splikit"]`.
+- `SCSPLICE_REAL_DATA_DIR` env var support in `tests/conftest.py` with fallback to `SPLIKIT_REAL_DATA_DIR` + `FutureWarning`.
+
+[2.0.0]: https://github.com/Arshammik/scsplice/compare/v1.0.0...v2.0.0
+
+## [1.0.0] - 2026-05-11
+
+### Added
+
+- `splk.io.read_starsolo` — Ingest STARsolo `Solo.out/SJ/` for one or more samples into a single AnnData with M1 (inclusion counts) in `layers["M1"]` and LJV grouping in `var["group_id"]`. Supports spatial data via optional `tissue_positions=` parameter.
+- `splk.io.read_starsolo_gene` — Ingest `Solo.out/Gene/` gene-expression counts into a standard cell × gene AnnData with counts in `X`. Drop-in for `scanpy.pp.normalize_total` and `scvi-tools`. Supports `tissue_positions=` and populates `obsm["spatial"]` for Visium samples.
+- `splk.io.read_starsolo_velocyto` — Ingest `Solo.out/Velocyto/` spliced/unspliced/ambiguous layers into an AnnData compatible with `scvelo`. Handles both modern (split-file) and legacy (stacked `matrix.mtx`) STARsolo wire formats.
+- `scs.tl.make_m2` — Build the exclusion matrix M2 from M1 and LJV grouping via C++ kernel with optional OpenMP parallelism. Output is bit-exact with R splikit.
+- `splk.tl.pseudo_correlation` — Per-event signed pseudo-R² (Cox-Snell or Nagelkerke) against an external predictor matrix via iteratively reweighted least squares (IRLS).
+- `splk.pp.highly_variable_events` — Select highly variable splicing events per library using binomial-deviance scoring.
+- `scsplice.settings` — Global settings object for configurable behavior (verbosity, I/O defaults).
+- MkDocs Material documentation site with tutorials, how-to guides, API reference, and conceptual explanations.
+
+### Known Limitations
+
+- `splk.pl` (plotting) is a v1.1 placeholder. Use `scanpy.pl`, `scvelo.pl`, and `squidpy` for downstream visualization.
+- HVG (highly variable genes) and silhouette metrics are intentionally not ported — compose with `scanpy.pp.highly_variable_genes` and `sklearn.metrics.silhouette_score` instead.
+- GTF annotation and gene-level plotting are out of scope; use `pyranges` for GTF operations.
+- R-equivalence validation suite (cross-language regression tests, R fixtures, tolerance bands) lives on the [`validation` branch](https://github.com/Arshammik/scsplice/tree/validation), not main.
+
+### Internal Notes
+
+This is the inaugural v1.0 PyPI release. The package has been tested for numerical equivalence with R splikit on a fixed reference dataset (M2 bit-exact; HVE deviance rtol=1e-10; pseudo-correlation rtol=1e-7). Production usage at scale is encouraged; please report bugs and feature requests on GitHub.
+
+[1.0.0]: https://github.com/Arshammik/scsplice/releases/tag/v1.0.0

scsplice-2.0.0/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.18)
+
+project(scsplice_cpp LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif()
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+set(CMAKE_VISIBILITY_INLINES_HIDDEN ON)
+
+# Optional build switch: skip OpenMP entirely (useful on macOS where libomp
+# discovery from cibuildwheel is fragile — see wheels.yml).
+option(SCSPLICE_DISABLE_OPENMP "Disable OpenMP even when CMake can find it" OFF)
+
+# Find Python (Development.Module is the right component for pybind11_add_module)
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+
+# Make `cmake -S . -B build` work outside scikit-build-core by pointing
+# pybind11's CMake config at the build-environment site-packages install.
+# scikit-build-core sets pybind11_DIR itself, so a non-empty hint here is
+# only used when invoking CMake directly.
+if(NOT DEFINED pybind11_DIR OR pybind11_DIR STREQUAL "")
+    execute_process(
+        COMMAND ${Python_EXECUTABLE} -c "import pybind11; print(pybind11.get_cmake_dir())"
+        OUTPUT_VARIABLE _pybind11_cmake_dir
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        RESULT_VARIABLE _pybind11_lookup_result
+    )
+    if(_pybind11_lookup_result EQUAL 0 AND _pybind11_cmake_dir)
+        set(pybind11_DIR "${_pybind11_cmake_dir}" CACHE PATH "pybind11 CMake config dir")
+        message(STATUS "Discovered pybind11_DIR from Python: ${pybind11_DIR}")
+    endif()
+endif()
+
+# pybind11 from the Python site-packages of the build environment (scikit-build-core
+# installs it at build time via [build-system].requires)
+find_package(pybind11 CONFIG REQUIRED)
+
+# Eigen3 (header-only); fail loudly if not found
+find_package(Eigen3 NO_MODULE REQUIRED)
+
+# OpenMP (optional); kernels degrade gracefully when absent.
+if(NOT SCSPLICE_DISABLE_OPENMP)
+    find_package(OpenMP)
+endif()
+
+add_subdirectory(src/_scsplice_cpp)

scsplice-2.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Arsham Mikaeili Namini and the Computational and Statistical Genomics Laboratory, McGill University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

scsplice-2.0.0/NOTICE

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+NOTICE
+
+This software contains code ported from the R package splikit
+(https://github.com/csglab/splikit), maintained by the Computational
+and Statistical Genomics Laboratory, McGill University.
+
+Ported components (from splikit/src/):
+  - make_m2_cpp.cpp   → src/_scsplice_cpp/make_m2.cpp
+  - calcDeviances.cpp → src/_scsplice_cpp/deviance.cpp
+  - cpp_pseudoR2.cpp  → src/_scsplice_cpp/pseudo_r2.cpp
+
+The R splikit package is licensed under the MIT License.
+For details, see https://github.com/csglab/splikit/blob/main/LICENSE.
+
+Original R splikit authors:
+  CSG Laboratory (Computational and Statistical Genomics)
+  Department of Human Genetics
+  McGill University

scsplice-2.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: scsplice
+Version: 2.0.0
+Summary: Single-cell alternative-splicing analysis on AnnData (Python port of R splikit)
+Keywords: single-cell,splicing,scverse,anndata,scrna-seq
+Author-Email: Arsham Mikaeili Namini <arsham.mikaeilinamini@mail.mcgill.ca>
+License: MIT License
+         
+         Copyright (c) 2026 Arsham Mikaeili Namini and the Computational and Statistical Genomics Laboratory, McGill University
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy
+         of this software and associated documentation files (the "Software"), to deal
+         in the Software without restriction, including without limitation the rights
+         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+         copies of the Software, and to permit persons to whom the Software is
+         furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all
+         copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+         
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: C++
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Project-URL: Documentation, https://arshammik.github.io/scsplice/
+Project-URL: Homepage, https://github.com/Arshammik/scsplice
+Project-URL: Issues, https://github.com/Arshammik/scsplice/issues
+Project-URL: Changelog, https://github.com/Arshammik/scsplice/blob/main/CHANGELOG.md
+Project-URL: Source, https://github.com/Arshammik/scsplice
+Requires-Python: >=3.10
+Requires-Dist: anndata>=0.10
+Requires-Dist: numpy>=2.0
+Requires-Dist: scipy>=1.13
+Requires-Dist: pandas>=2.2
+Requires-Dist: h5py>=3.10
+Provides-Extra: test
+Requires-Dist: pytest>=8.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-xdist; extra == "test"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.6; extra == "docs"
+Requires-Dist: mkdocs-material>=9.5; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.26; extra == "docs"
+Requires-Dist: mkdocs-jupyter>=0.25; extra == "docs"
+Requires-Dist: pymdown-extensions>=10.7; extra == "docs"
+Requires-Dist: mike>=2.1; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: scsplice[docs,test]; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Description-Content-Type: text/markdown
+
+# scsplice
+
+Single-cell alternative-splicing analysis for the [scverse](https://scverse.org) ecosystem.
+
+`scsplice` is the Python port of the R package [splikit](https://github.com/csglab/splikit). It analyses splice-junction count data in single-cell RNA-seq, treating each event as a pair of inclusion (`M1`) and exclusion (`M2`) counts derived from local junction variants (LJVs). The package is AnnData-native — junctions live on the `var` axis, M1 and M2 sit in `layers`, and downstream analysis composes naturally with `scanpy`.
+
+## Status
+
+v1.0. v1.0 scope is intentionally narrow:
+
+- `scs.io.read_starsolo` — ingest STARsolo `Solo.out/SJ/` for one or more samples.
+- `scs.tl.make_m2` — build the exclusion matrix from M1 + LJV grouping.
+- `scs.pp.highly_variable_events` — per-library binomial-deviance HVE selection.
+- `scs.tl.pseudo_correlation` — beta-binomial Cox-Snell / Nagelkerke pseudo-R² against an external matrix.
+
+HVG, plotting, and silhouette utilities from the R package are intentionally omitted — `scanpy`, `pyranges`, and `sklearn` already cover those.
+
+## Installation
+
+`scsplice` ships a C++ extension built via `scikit-build-core` + `pybind11`.
+Eigen3 (header-only) is required at install time; OpenMP is optional but
+strongly recommended for multi-threaded kernels.
+
+### From PyPI (once v2.0 is published)
+
+```bash
+pip install scsplice
+```
+
+### From source
+
+```bash
+git clone https://github.com/Arshammik/scsplice
+cd scsplice
+pip install .
+```
+
+System dependencies before running `pip install`:
+
+**Ubuntu / Debian**
+
+```bash
+sudo apt install libeigen3-dev libomp-dev
+```
+
+**macOS** (Homebrew)
+
+```bash
+brew install eigen libomp
+# tell CMake where Apple Clang's OpenMP lives
+export OpenMP_ROOT="$(brew --prefix libomp)"
+export LDFLAGS="-L${OpenMP_ROOT}/lib"
+export CPPFLAGS="-I${OpenMP_ROOT}/include"
+```
+
+**HPC cluster (Compute Canada / Sharcnet pattern)**
+
+```bash
+module load eigen/3.4.0
+# any modern GCC with OpenMP (gcc/12+) on the system module path
+```
+
+### Editable install (development)
+
+```bash
+pip install -e ".[dev]"
+```
+
+This installs the package, all test dependencies, the docs toolchain
+(`mkdocs-material`, `mkdocstrings[python]`, `mkdocs-jupyter`), and `ruff` /
+`pre-commit`. C++ edits require re-running `pip install -e .`; pure-Python
+edits take effect immediately.
+
+## Quick start
+
+```python
+import scsplice as scs
+import scanpy as sc
+
+# (1) Ingest STARsolo splice-junction counts (M1) and LJV grouping
+adata = scs.io.read_starsolo(
+    sj_dirs=["sample1/Solo.out/SJ", "sample2/Solo.out/SJ"],
+    sample_ids=["s1", "s2"],
+)
+
+# (2) Build exclusion matrix (M2) from inclusion counts + junction grouping
+scs.tl.make_m2(adata, n_threads=8)
+
+# (3) Identify highly variable events per library using binomial deviance
+scs.pp.highly_variable_events(adata, min_row_sum=50, n_threads=8)
+
+# Optional: compose with scanpy on the splicing embedding
+# (PCA / neighbors / leiden over logit(M1 / (M1 + M2)))
+```
+
+## Numerical equivalence
+
+`scsplice` reproduces R `splikit` results to a documented tolerance on a
+fixed reference dataset (M2 bit-exact; HVE deviance `rtol=1e-10`;
+pseudo-correlation `rtol=1e-7`). The cross-language regression suite,
+R reference fixtures, and end-to-end M1/M2 validation pipeline live on the
+[`validation` branch](https://github.com/Arshammik/scsplice/tree/validation).
+
+## Documentation
+
+Full documentation is available at https://arshammik.github.io/scsplice/.
+
+Topics include:
+- [Getting Started](https://arshammik.github.io/scsplice/getting-started/) — installation and first workflow
+- [Tutorials](https://arshammik.github.io/scsplice/tutorials/) — step-by-step notebooks
+- [How-to Guides](https://arshammik.github.io/scsplice/how-to-guides/) — recipes for common tasks
+- [Reference](https://arshammik.github.io/scsplice/reference/) — complete API documentation
+- [Explanation](https://arshammik.github.io/scsplice/explanation/) — conceptual background and design
+
+## License
+
+MIT.