scloop 0.1.9__tar.gz

scloop-0.1.9/LICENSE

@@ -0,0 +1,203 @@
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scloop-0.1.9/MANIFEST.in

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+include src/scloop/utils/linear_algebra_gf2/libm4ri.a
+recursive-include src/scloop/utils/linear_algebra_gf2/include *.h
+include src/scloop/utils/linear_algebra_gf2/*.pyx
+include src/scloop/utils/distance_metrics/*.pyx
+include src/scloop/data/*.pyx
+include src/scloop/data/*.cpp
+include src/scloop/data/*.h

scloop-0.1.9/PKG-INFO

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+Metadata-Version: 2.4
+Name: scloop
+Version: 0.1.9
+Summary: single-cell loop analysis
+Author-email: "Zhiyuan(Stan) Yu" <zyyu@umich.edu>, Idse Heemskerk <idse.heemskerk@gmail.com>
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cython>=3.0.12
+Requires-Dist: glasbey==0.3
+Requires-Dist: igraph>=0.11
+Requires-Dist: loguru==0.7.3
+Requires-Dist: numba>=0.62.1
+Requires-Dist: numpy<2
+Requires-Dist: pandas
+Requires-Dist: pip>=25.2
+Requires-Dist: pydantic>=2.11.4
+Requires-Dist: pytest>=8.4
+Requires-Dist: rich==14.2
+Requires-Dist: scanpy[leiden]>=1.11.2
+Requires-Dist: scikit-misc>=0.5.2
+Requires-Dist: statsmodels==0.14.4
+Requires-Dist: tensorflow>=2.18.1
+Requires-Dist: torch
+Requires-Dist: torchdyn>=1.0.6
+Requires-Dist: torchvision
+Requires-Dist: tqdm-joblib>=0.0.5
+Requires-Dist: umap-learn>=0.5.7
+Dynamic: license-file
+
+# scloop - single-cell loop analysis
+
+[![Test Import](https://github.com/stanfish06/scLoop/actions/workflows/test-import.yml/badge.svg)](https://github.com/stanfish06/scLoop/actions/workflows/test-import.yml)
+[![Test Build](https://github.com/stanfish06/scLoop/actions/workflows/test-build.yml/badge.svg)](https://github.com/stanfish06/scLoop/actions/workflows/test-build.yml)
+
+**Note: this package is still under development.**
+
+scLoop is a library to identify statistically significant loops in single-cell RNA-seq data.
+
+<img src="examples/loop.png" alt="persistent homology" width="300"/>
+
+## Basic Usage
+```python
+import scloop as scl
+scl.pp.prepare_adata(adata, downsample=True, n_downsample=500)
+scl.tl.find_loops(adata)
+```
+
+## Build Instructions
+```bash
+make build
+```
+
+or
+
+```bash
+make rebuild
+```
+
+## Virtual Envrionemnt
+```bash
+make sync
+```
+
+or
+
+```bash
+make full-sync
+```
+
+to prevent partial compilation of some modules
+
+## Installation
+**Note: this package is still under development. The current build will likely not work.**
+```bash
+pip install scloop
+```
+
+## Project Structure
+```
+src/scloop/
+├── analyzing
+│   └── __init__.py
+├── benchmarking
+│   └── __init__.py
+├── computing
+│   ├── homology.py
+│   └── __init__.py
+├── data
+│   ├── analysis_containers.py
+│   ├── containers.py
+│   ├── __init__.py
+│   ├── loop_reconstruction.py
+│   ├── metadata.py
+│   ├── ripser.cpp
+│   ├── ripser.hpp
+│   ├── ripser_lib.cpp
+│   ├── ripser_lib.pyx
+│   ├── types.py
+│   └── utils.py
+├── __init__.py
+├── matching
+│   ├── data_modules.py
+│   ├── __init__.py
+│   ├── mlp.py
+│   └── nf.py
+├── plotting
+│   ├── _homology.py
+│   └── __init__.py
+├── preprocessing
+│   ├── delve
+│   │   ├── delve.py
+│   │   ├── __init__.py
+│   │   └── kh.py
+│   ├── downsample.py
+│   ├── __init__.py
+│   └── prepare.py
+├── py.typed
+├── tools
+│   ├── _cross_match.py
+│   ├── __init__.py
+│   └── _loops.py
+└── utils
+    ├── distance_metrics
+    │   ├── discrete-frechet-distance
+    │   ├── frechet.cpp
+    │   ├── frechet.pyx
+    │   └── __init__.py
+    ├── __init__.py
+    └── linear_algebra_gf2
+        ├── gf2_toolkit_lib.pyx
+        ├── __init__.py
+        ├── m4ri_lib.c
+        └── m4ri_lib.pyx
+```

scloop-0.1.9/README.md

@@ -0,0 +1,105 @@
+# scloop - single-cell loop analysis
+
+[![Test Import](https://github.com/stanfish06/scLoop/actions/workflows/test-import.yml/badge.svg)](https://github.com/stanfish06/scLoop/actions/workflows/test-import.yml)
+[![Test Build](https://github.com/stanfish06/scLoop/actions/workflows/test-build.yml/badge.svg)](https://github.com/stanfish06/scLoop/actions/workflows/test-build.yml)
+
+**Note: this package is still under development.**
+
+scLoop is a library to identify statistically significant loops in single-cell RNA-seq data.
+
+<img src="examples/loop.png" alt="persistent homology" width="300"/>
+
+## Basic Usage
+```python
+import scloop as scl
+scl.pp.prepare_adata(adata, downsample=True, n_downsample=500)
+scl.tl.find_loops(adata)
+```
+
+## Build Instructions
+```bash
+make build
+```
+
+or
+
+```bash
+make rebuild
+```
+
+## Virtual Envrionemnt
+```bash
+make sync
+```
+
+or
+
+```bash
+make full-sync
+```
+
+to prevent partial compilation of some modules
+
+## Installation
+**Note: this package is still under development. The current build will likely not work.**
+```bash
+pip install scloop
+```
+
+## Project Structure
+```
+src/scloop/
+├── analyzing
+│   └── __init__.py
+├── benchmarking
+│   └── __init__.py
+├── computing
+│   ├── homology.py
+│   └── __init__.py
+├── data
+│   ├── analysis_containers.py
+│   ├── containers.py
+│   ├── __init__.py
+│   ├── loop_reconstruction.py
+│   ├── metadata.py
+│   ├── ripser.cpp
+│   ├── ripser.hpp
+│   ├── ripser_lib.cpp
+│   ├── ripser_lib.pyx
+│   ├── types.py
+│   └── utils.py
+├── __init__.py
+├── matching
+│   ├── data_modules.py
+│   ├── __init__.py
+│   ├── mlp.py
+│   └── nf.py
+├── plotting
+│   ├── _homology.py
+│   └── __init__.py
+├── preprocessing
+│   ├── delve
+│   │   ├── delve.py
+│   │   ├── __init__.py
+│   │   └── kh.py
+│   ├── downsample.py
+│   ├── __init__.py
+│   └── prepare.py
+├── py.typed
+├── tools
+│   ├── _cross_match.py
+│   ├── __init__.py
+│   └── _loops.py
+└── utils
+    ├── distance_metrics
+    │   ├── discrete-frechet-distance
+    │   ├── frechet.cpp
+    │   ├── frechet.pyx
+    │   └── __init__.py
+    ├── __init__.py
+    └── linear_algebra_gf2
+        ├── gf2_toolkit_lib.pyx
+        ├── __init__.py
+        ├── m4ri_lib.c
+        └── m4ri_lib.pyx
+```

scloop-0.1.9/pyproject.toml

@@ -0,0 +1,118 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+# [tool.setuptools]
+# package-dir = { "" = "src" }
+# ext-modules = [
+#   { name = "scloop.data.ripser_lib", sources = [
+#     "./src/scloop/data/ripser_lib.pyx",
+#     "./src/scloop/data/ripser.cpp",
+#   ], language = "c++", optional = false },
+#   { name = "scloop.utils.linear_algebra_gf2.m4ri_lib", sources = [
+#     "./src/scloop/utils/linear_algebra_gf2/m4ri_lib.pyx",
+#   ], language = "c", optional = false, libraries = ["m4ri"], extra-objects = [
+#     "./src/scloop/utils/linear_algebra_gf2/libm4ri.a",
+#   ], include-dirs = [
+#     "./src/scloop/utils/linear_algebra_gf2/include",
+#   ] },
+# ]
+requires = [ "cython>=3.0.12", "setuptools>=74.1" ]
+
+[project]
+name = "scloop"
+version = "0.1.9"
+description = "single-cell loop analysis"
+readme = "README.md"
+authors = [
+  { name = "Zhiyuan(Stan) Yu", email = "zyyu@umich.edu" },
+  { name = "Idse Heemskerk", email = "idse.heemskerk@gmail.com" },
+]
+requires-python = ">=3.12"
+# tensorflow hasn't supported 3.13 yet
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+  "cython>=3.0.12",
+  "glasbey==0.3",
+  "igraph>=0.11",
+  "loguru==0.7.3",
+  "numba>=0.62.1",
+  "numpy<2",
+  "pandas",
+  "pip>=25.2",
+  "pydantic>=2.11.4",
+  "pytest>=8.4",
+  "rich==14.2",
+  "scanpy[leiden]>=1.11.2",
+  "scikit-misc>=0.5.2",
+  "statsmodels==0.14.4",
+  "tensorflow>=2.18.1",
+  "torch",
+  "torchdyn>=1.0.6",
+  "torchvision",
+  "tqdm-joblib>=0.0.5",
+  "umap-learn>=0.5.7",
+]
+
+[dependency-groups]
+dev = [
+  "pyright==1.1.406",
+  "ty>=0.0.1a34",
+]
+
+[tool.uv]
+package = true
+
+[tool.uv.extra-build-dependencies]
+scloop = [ "Cython" ]
+
+[tool.uv.sources]
+torch = [
+  { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
+]
+
+torchvision = [
+  { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
+]
+
+[[tool.uv.index]]
+name = "pytorch-cu128"
+url = "https://download.pytorch.org/whl/cu128"
+explicit = true
+
+[tool.ruff]
+format.indent-style = "space"
+format.quote-style = "double"
+lint.extend-select = [ "I" ]
+lint.fixable = [ "ALL" ]
+
+[tool.pyproject-fmt]
+column_width = 120
+indent = 2
+keep_full_version = false
+max_supported_python = "3.12"
+
+# use 1.1.406 pyright or a version after 1.1.407 (does not work well with pydantic dataclass)
+
+[tool.pyright]
+include = [ "src" ]
+exclude = [
+  "**/__pycache__",
+  "examples",
+  "**/*.pyx",
+  "**/*.pxd",
+]
+
+reportMissingImports = "error"
+reportMissingTypeStubs = false
+
+pythonVersion = "3.12"
+pythonPlatform = "Linux"
+
+executionEnvironments = [
+  { root = "src" },
+]
+
+venvPath = "/home/stanfish/Git/scloop"
+venv = ".venv"

scloop-0.1.9/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

scloop-0.1.9/setup.py

@@ -0,0 +1,35 @@
+import os
+
+from Cython.Build import cythonize
+from setuptools import Extension, setup
+
+project_root = os.path.dirname(os.path.abspath(__file__))
+m4ri_dir = os.path.join(project_root, "src/scloop/utils/linear_algebra_gf2")
+
+extensions = [
+    Extension(
+        "scloop.data.ripser_lib",
+        sources=["./src/scloop/data/ripser_lib.pyx", "./src/scloop/data/ripser.cpp"],
+        language="c++",
+        include_dirs=["./src/scloop/data"],
+    ),
+    Extension(
+        "scloop.utils.linear_algebra_gf2.m4ri_lib",
+        sources=["./src/scloop/utils/linear_algebra_gf2/m4ri_lib.pyx"],
+        include_dirs=[os.path.join(m4ri_dir, "include")],
+        extra_objects=[os.path.join(m4ri_dir, "libm4ri.a")],
+        extra_compile_args=["-fopenmp"],
+        extra_link_args=["-fopenmp"],
+    ),
+    Extension(
+        "scloop.utils.distance_metrics.frechet",
+        sources=[
+            "./src/scloop/utils/distance_metrics/frechet.pyx",
+            "./src/scloop/utils/distance_metrics/discrete-frechet-distance/Frechet.cpp",
+        ],
+        include_dirs=["./src/scloop/utils/distance_metrics/discrete-frechet-distance"],
+        language="c++",
+    ),
+]
+
+setup(ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}))

scloop-0.1.9/src/scloop/__init__.py

@@ -0,0 +1,27 @@
+import warnings
+
+from loguru import logger
+
+warnings.filterwarnings("ignore", category=FutureWarning, module="scanpy")
+warnings.filterwarnings("ignore", category=FutureWarning, module="anndata")
+warnings.filterwarnings("ignore", category=SyntaxWarning, module="colorspacious")
+
+try:
+    from . import plotting as pl
+except ImportError as e:
+    logger.warning(f"Could not import plotting modules: {e}")
+    pl = None
+
+try:
+    from . import preprocessing as pp
+except ImportError as e:
+    logger.warning(f"Could not import preprocessing modules: {e}")
+    pp = None
+
+try:
+    from . import tools as tl
+except ImportError as e:
+    logger.warning(f"Could not import tools modules: {e}")
+    tl = None
+
+__all__ = [pkg for pkg in ["pl", "pp", "tl"] if globals().get(pkg) is not None]

scloop-0.1.9/src/scloop/benchmarking/__init__.py

@@ -0,0 +1 @@
+#

scloop-0.1.9/src/scloop/computing/__init__.py

@@ -0,0 +1,8 @@
+"""Lightweight compute helpers used by the public API layer."""
+# Copyright 2025 Zhiyuan Yu (Heemskerk's lab, University of Michigan)
+
+from .homology import (
+    compute_boundary_matrix_data,
+    compute_persistence_diagram_and_cocycles,
+    compute_sparse_pairwise_distance,
+)