scmito 0.2.0__tar.gz

scmito-0.2.0/.gitignore

@@ -0,0 +1,43 @@
+# Temp files
+*/.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+
+# Distribution / packaging
+/build/
+/dist/
+/*.egg-info/
+**/*.egg-info/
+
+# Tests and coverage
+/.pytest_cache/
+/.cache/
+/data/
+/node_modules/
+
+# docs
+/docs/generated/
+/docs/_build/
+/docs/build/
+
+# IDEs
+/.idea/
+/.vscode/
+.claude/
+
+# Data files from tutorials
+/docs/notebooks/*.fcs
+/docs/notebooks/*.h5ad
+/docs/source/data_test/
+/docs/source/**/*.h5ad
+/docs/source/**/*.fcs
+
+*/__pycache__
+scratch/
+docs/_preview/

scmito-0.2.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.1.5] - 2026-02-03
+- Nat Comm release
+
+## [0.1.4] - 2026-01-01
+- Last bug fixes
+
+## [0.1.3] - 2026-01-29
+### Enhanced
+- **kNN Graph Computations**: Improved k-nearest neighbor graph algorithms
+  - Optimized distance calculations for better performance in large datasets
+  - Enhanced graph construction methods for more accurate neighborhood detection
+  - Improved memory efficiency in graph building operations
+  - Better handling of edge cases in sparse data scenarios
+
+### Technical
+- Refined algorithms for more robust graph-based analyses
+- Enhanced computational efficiency for scalable graph operations
+
+## [0.1.2] - 2025-10-23
+### Enhanced
+- **Performance Optimizations**: Major parallelization improvements using joblib
+  - Parallelized Moran's I computation in `filter_variant_moransI` with batch processing
+  - Parallelized mutation enrichment computation in `MiToTreeAnnotator.get_M` method
+  - Memory-efficient matrix caching to avoid redundant serialization across workers
+  - Configurable core usage and temporary folder management for large datasets
+
+### Added
+- **Multi-allelic Site Filtering**: New quality control functionality
+  - Added `filter_multiallelic_sites` function to remove variants from sites with multiple alleles
+  - Integrated multi-allelic filtering in RedeeM data processing pipeline
+  - Ensures each genomic position has only one variant type for cleaner analyses
+- **Dual Implementation Support**: Both serial and parallel versions available for performance testing
+- **Enhanced RedeeM Support**: Improved data processing for RedeeM scLT system
+
+### Fixed
+- Memory usage optimization in parallel processing by caching matrix variables
+- Proper joblib backend configuration for stable parallel execution
+- Improved progress tracking for long-running computations
+
+### Technical
+- Migrated from multiprocessing to joblib for better memory management
+- Added batch processing patterns for scalable parallel computation
+- Enhanced error handling and progress reporting in parallel workflows
+
+## [0.1.1] - 2025-10-08
+### Enhanced
+- Improved clonal inference algorithm with edge case handling for small phylogenies
+- Added `af_treshold` parameter to `resolve_ambiguous_clones` for better clone merging control
+- Split `infer_clones` and `resolve_ambiguous_clones` methods for better modularity
+- Enhanced grid search optimization with better parameter handling
+- Fixed root node exclusion in `_find_clones` to prevent single-clone edge cases
+
+### Fixed
+- Resolved issue where very small phylogenies would only return root as single clone
+- Improved silhouette score calculation for edge cases with minimal clones
+- Better parameter validation and error handling in clonal inference pipeline
+
+### Refactored
+- Cleaner separation between clone detection and clone resolution phases
+- Improved code organization in `MiToTreeAnnotator` class
+- Better debugging support with modular function structure
+
+## [0.1.0] - 2025-10-06
+### Added
+- Complete documentation overhaul with nbsphinx integration
+- Interactive Jupyter notebook tutorial with full cell outputs and visualizations
+- Comprehensive getting started guide with MiTo workflow examples
+- Hierarchical documentation structure for better navigation
+- ReadTheDocs integration with automated builds
+
+### Improved
+- Streamlined installation guide with clear step-by-step instructions
+- Enhanced plotting library examples and demonstrations
+- Better code organization and documentation structure
+- Cleaner repository structure with proper .gitignore rules
+
+### Fixed
+- nbsphinx configuration for proper notebook rendering
+- Image generation and display in documentation
+- Documentation build process for ReadTheDocs compatibility
+- File size issues with test data exclusion
+
+## [0.0.8] - 2025-09-25
+### Fixed
+- Add mt.io.make_afm behavior
+
+## [0.0.7] - 2025-09-25
+### Fixed
+- Add chrM.fa to assets
+
+## [0.0.6] - 2025-09-17
+### Fixed
+- Fixed asset path detection for conda environments
+- Assets now properly accessible via sys.prefix location
+- Improved _find_assets_path() function to check conda environment directory
+
+## [0.0.4] - 2025-09-12
+### Fixed
+- Fixed asset files inclusion in package distribution (PyPI release)
+- Improved asset path detection for both development and installed environments
+- Assets (dbSNP_MT.txt, REDIdb_MT.txt, formatted_table_wobble.csv, weng2024_mut_spectrum_ref.csv) now properly included in pip installations
+
+## [0.0.3] - 2025-09-11
+### Added
+- Code refactoring and improvements
+- Enhanced functionality and bug fixes
+- Updated documentation
+
+### Fixed
+- Assets (dbSNP_MT.txt, REDIdb_MT.txt, formatted_table_wobble.csv, weng2024_mut_spectrum_ref.csv) now properly included in pip installations
+- Smart asset path finder that works in both development and production environments
+
+## [0.0.2] - 2025-03-25
+### Added
+- Updated docs.
+
+## [0.0.1] - 2025-03-24
+### Added
+- Initial release of the mito package.
+- Packaging via `setup.py` for PyPI distribution.
+- Core functionality for mito analyses.
+- First docs.
+

scmito-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 acox1
+
+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.

scmito-0.2.0/PKG-INFO

@@ -0,0 +1,178 @@
+Metadata-Version: 2.4
+Name: scmito
+Version: 0.2.0
+Summary: Mitochondrial lineage tracing and single-cell multi-omics in Python
+Project-URL: Homepage, https://github.com/andrecossa5/MiTo
+Project-URL: Documentation, https://scmito.readthedocs.io/en/latest/index.html
+Project-URL: Repository, https://github.com/andrecossa5/MiTo
+Project-URL: Issues, https://github.com/andrecossa5/MiTo/issues
+Author-email: Andrea Cossa <andrea.cossa05@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2023 acox1
+        
+        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.
+License-File: LICENSE
+Keywords: lineage-tracing,mitochondrial-DNA,phylogenetics,scLT,single-cell
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: ac-plotting-ut>=0.2.1
+Requires-Dist: anndata>=0.10
+Requires-Dist: bbmix>=0.1
+Requires-Dist: biopython>=1.80
+Requires-Dist: cassiopeia-mt>=2.1.3
+Requires-Dist: circlify>=0.15
+Requires-Dist: gseapy>=1.1
+Requires-Dist: igraph>=0.10
+Requires-Dist: joblib>=1.3
+Requires-Dist: leidenalg>=0.10
+Requires-Dist: lightgbm>=4.0
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: mquad>=0.1.8
+Requires-Dist: networkx>=3.1
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.2
+Requires-Dist: scanpy>=1.10
+Requires-Dist: scikit-learn>=1.4
+Requires-Dist: scipy>=1.11
+Requires-Dist: seaborn>=0.13
+Requires-Dist: shap>=0.44
+Requires-Dist: statsmodels>=0.14
+Requires-Dist: tqdm>=4.60
+Requires-Dist: umap-learn>=0.5
+Provides-Extra: docs
+Requires-Dist: furo; extra == 'docs'
+Requires-Dist: ipykernel; extra == 'docs'
+Requires-Dist: nbsphinx; extra == 'docs'
+Requires-Dist: sphinx-copybutton; extra == 'docs'
+Requires-Dist: sphinx-design; extra == 'docs'
+Requires-Dist: sphinx>=7; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: pytest-cov>=4.0; extra == 'test'
+Requires-Dist: pytest>=7.0; extra == 'test'
+Description-Content-Type: text/markdown
+
+<div align="center">
+  <img src="image/MiTo_logo_transparent.png" alt="MiTo" width="260">
+</div>
+
+# MiTo (Mitochondrial single-cell lineage tracing Toolkit)
+
+**Mitochondrial single-cell multi-omics in Python.**
+
+[![PyPI](https://img.shields.io/pypi/v/scmito.svg)](https://pypi.org/project/scmito/)
+[![Python](https://img.shields.io/pypi/pyversions/scmito.svg)](https://pypi.org/project/scmito/)
+[![Tests](https://github.com/andrecossa5/MiTo/actions/workflows/test.yml/badge.svg)](https://github.com/andrecossa5/MiTo/actions/workflows/test.yml)
+[![Documentation](https://readthedocs.org/projects/scmito/badge/?version=latest)](https://scmito.readthedocs.io/en/latest/index.html)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**MiTo** infer clonal ancestries in single-cell data from natural mtDNA variation. 
+
+The framework provides the infrastructure to convert MAESTER, scmtATAC-seq and RedeeM pre-processing outputs
+into Allele Frequency Matrices (i.e., [AnnData](https://anndata.readthedocs.io/) objects), filter informative mtDNA variants, genotype individual cells, and
+infer mitochondrial phylogenies and clones for dowstream multi-omic analysis.
+
+## Installation
+
+```bash
+pip install scmito
+```
+
+Requires Python 3.11+.
+
+```python
+import mito as mt
+print(mt.__version__)
+```
+
+## Quick start
+
+```python
+import scanpy as sc
+import mito as mt
+
+# Allele Frequency Matrix (cell x site AnnData with AD / DP layers)
+afm = sc.read('afm_unfiltered.h5ad')
+
+# Cell and variant filters, distances in mtDNA mutation space
+afm = mt.pp.filter_cells(afm, cell_filter='filter2')
+afm = mt.pp.filter_afm(afm, filtering='MiTo')
+
+# Phylogeny and clonal inference
+tree = mt.tl.build_tree(afm, precomputed=True, solver='UPMGA')
+annotator = mt.tl.MiToTreeAnnotator(tree)
+annotator.clonal_inference()
+
+# Visualization
+mt.pl.plot_tree(tree, features=['MiTo clone'])
+```
+
+See [getting-started tutorial](https://scmito.readthedocs.io/en/latest/getting_started_tutorial.html) for 
+the full vignette.
+
+## API
+
+MiTo follows the `scverse` layout, composing with `scanpy` and `anndata`:
+
+| Module | Purpose |
+| --- | --- |
+| `io` | Build AFMs from pre-processing outputs, read/write Newick tree objects |
+| `pp` | Cell and variant filtering, genotying, distances, kNN graphs, embeddings |
+| `tl` | Tree building, clonal inference, clustering, fate bias |
+| `pl` | Trees, heatmaps, embeddings, coverage and variant-spectrum plots |
+| `ut` | Metrics, helpers |
+
+**Supported platforms:** scRNA-seq (MAESTER), scmtATAC-seq and 10x MultiOme (RedeeM).
+
+Full reference: [MiTo docs](https://scmito.readthedocs.io/en/latest/index.html).
+
+## Development
+
+```bash
+git clone https://github.com/andrecossa5/MiTo.git
+cd MiTo
+pip install -e ".[test]"
+pytest
+```
+
+## Citation
+
+If MiTo is useful in your work, please cite:
+
+> Cossa, A. Dalmasso A. et al. *MiTo: mitochondrial lineage tracing and single-cell multi-omics.*
+> Nat Comm (2026). [https://doi.org/10.1038/s41467-026-71607-5](https://www.nature.com/articles/s41467-026-71607-5)
+
+MiTo builds on the [Cassiopeia](https://github.com/YosefLab/Cassiopeia) package for phylogeny reconstruction and data infrastructure. Please, cite it as well.
+
+## Releases
+
+See [CHANGELOG.md](CHANGELOG.md).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

scmito-0.2.0/README.md

@@ -0,0 +1,99 @@
+<div align="center">
+  <img src="image/MiTo_logo_transparent.png" alt="MiTo" width="260">
+</div>
+
+# MiTo (Mitochondrial single-cell lineage tracing Toolkit)
+
+**Mitochondrial single-cell multi-omics in Python.**
+
+[![PyPI](https://img.shields.io/pypi/v/scmito.svg)](https://pypi.org/project/scmito/)
+[![Python](https://img.shields.io/pypi/pyversions/scmito.svg)](https://pypi.org/project/scmito/)
+[![Tests](https://github.com/andrecossa5/MiTo/actions/workflows/test.yml/badge.svg)](https://github.com/andrecossa5/MiTo/actions/workflows/test.yml)
+[![Documentation](https://readthedocs.org/projects/scmito/badge/?version=latest)](https://scmito.readthedocs.io/en/latest/index.html)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**MiTo** infer clonal ancestries in single-cell data from natural mtDNA variation. 
+
+The framework provides the infrastructure to convert MAESTER, scmtATAC-seq and RedeeM pre-processing outputs
+into Allele Frequency Matrices (i.e., [AnnData](https://anndata.readthedocs.io/) objects), filter informative mtDNA variants, genotype individual cells, and
+infer mitochondrial phylogenies and clones for dowstream multi-omic analysis.
+
+## Installation
+
+```bash
+pip install scmito
+```
+
+Requires Python 3.11+.
+
+```python
+import mito as mt
+print(mt.__version__)
+```
+
+## Quick start
+
+```python
+import scanpy as sc
+import mito as mt
+
+# Allele Frequency Matrix (cell x site AnnData with AD / DP layers)
+afm = sc.read('afm_unfiltered.h5ad')
+
+# Cell and variant filters, distances in mtDNA mutation space
+afm = mt.pp.filter_cells(afm, cell_filter='filter2')
+afm = mt.pp.filter_afm(afm, filtering='MiTo')
+
+# Phylogeny and clonal inference
+tree = mt.tl.build_tree(afm, precomputed=True, solver='UPMGA')
+annotator = mt.tl.MiToTreeAnnotator(tree)
+annotator.clonal_inference()
+
+# Visualization
+mt.pl.plot_tree(tree, features=['MiTo clone'])
+```
+
+See [getting-started tutorial](https://scmito.readthedocs.io/en/latest/getting_started_tutorial.html) for 
+the full vignette.
+
+## API
+
+MiTo follows the `scverse` layout, composing with `scanpy` and `anndata`:
+
+| Module | Purpose |
+| --- | --- |
+| `io` | Build AFMs from pre-processing outputs, read/write Newick tree objects |
+| `pp` | Cell and variant filtering, genotying, distances, kNN graphs, embeddings |
+| `tl` | Tree building, clonal inference, clustering, fate bias |
+| `pl` | Trees, heatmaps, embeddings, coverage and variant-spectrum plots |
+| `ut` | Metrics, helpers |
+
+**Supported platforms:** scRNA-seq (MAESTER), scmtATAC-seq and 10x MultiOme (RedeeM).
+
+Full reference: [MiTo docs](https://scmito.readthedocs.io/en/latest/index.html).
+
+## Development
+
+```bash
+git clone https://github.com/andrecossa5/MiTo.git
+cd MiTo
+pip install -e ".[test]"
+pytest
+```
+
+## Citation
+
+If MiTo is useful in your work, please cite:
+
+> Cossa, A. Dalmasso A. et al. *MiTo: mitochondrial lineage tracing and single-cell multi-omics.*
+> Nat Comm (2026). [https://doi.org/10.1038/s41467-026-71607-5](https://www.nature.com/articles/s41467-026-71607-5)
+
+MiTo builds on the [Cassiopeia](https://github.com/YosefLab/Cassiopeia) package for phylogeny reconstruction and data infrastructure. Please, cite it as well.
+
+## Releases
+
+See [CHANGELOG.md](CHANGELOG.md).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

scmito-0.2.0/pyproject.toml

@@ -0,0 +1,141 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "scmito"
+dynamic = ["version"]
+description = "Mitochondrial lineage tracing and single-cell multi-omics in Python"
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.11"
+authors = [{ name = "Andrea Cossa", email = "andrea.cossa05@gmail.com" }]
+keywords = [
+    "single-cell",
+    "lineage-tracing",
+    "mitochondrial-DNA",
+    "phylogenetics",
+    "scLT",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+
+    # core scientific stack
+    "numpy>=1.26",
+    "scipy>=1.11",
+    "pandas>=2.2",
+    "statsmodels>=0.14",
+    "scikit-learn>=1.4",
+    "joblib>=1.3",
+    "tqdm>=4.60",
+
+    # scverse
+    "anndata>=0.10",
+    "scanpy>=1.10",
+
+    # plotting
+    "matplotlib>=3.8",
+    "seaborn>=0.13",
+    "ac-plotting-ut>=0.2.1",
+    "circlify>=0.15",
+
+    # graphs and embeddings
+    "networkx>=3.1",
+    "igraph>=0.10",
+    "leidenalg>=0.10",
+    "umap-learn>=0.5",
+    # phylogenetics
+    "cassiopeia-mt>=2.1.3",
+    "biopython>=1.80",
+
+    # variant calling / modelling
+    "mquad>=0.1.8",
+    "bbmix>=0.1",
+    "lightgbm>=4.0",
+    "shap>=0.44",
+    
+    # Others
+    "gseapy>=1.1"
+
+]
+
+[project.optional-dependencies]
+test = ["pytest>=7.0", "pytest-cov>=4.0"]
+docs = [
+    "sphinx>=7",
+    "furo",
+    "nbsphinx",
+    "sphinx-copybutton",
+    "sphinx-design",
+    "ipykernel",
+]
+
+[project.urls]
+Homepage = "https://github.com/andrecossa5/MiTo"
+Documentation = "https://scmito.readthedocs.io/en/latest/index.html"
+Repository = "https://github.com/andrecossa5/MiTo"
+Issues = "https://github.com/andrecossa5/MiTo/issues"
+
+[tool.hatch.version]
+path = "src/mito/__init__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/mito"]
+
+[tool.hatch.build.targets.sdist]
+include = ["src/mito", "tests", "README.md", "LICENSE", "CHANGELOG.md"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-v"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+extend-include = ["*.ipynb"]
+format.docstring-code-format = true
+lint.select = [
+    "B",      # flake8-bugbear
+    "BLE",    # flake8-blind-except
+    "C4",     # flake8-comprehensions
+    "E",      # pycodestyle errors
+    "F",      # pyflakes
+    "I",      # isort
+    "RUF100", # unused noqa directives
+    "TID",    # flake8-tidy-imports
+    "UP",     # pyupgrade
+    "W",      # pycodestyle warnings
+]
+lint.ignore = [
+    "B008", # function calls in argument defaults -- fine when the result is immutable
+    "E501", # long lines: long comments are accepted, the formatter handles code
+    "E731", # lambda assignment is convenient
+    "E741", # allow I, O, l as names -- I is the identity matrix
+]
+lint.per-file-ignores."*/__init__.py" = ["F401"]
+lint.per-file-ignores."docs/*" = ["I"]
+lint.per-file-ignores."tests/*" = ["D"]
+lint.pydocstyle.convention = "numpy"
+
+[tool.codespell]
+skip = ".git,*.ipynb,*.csv,*.txt,*.fa,*.gz,docs/_build"
+# NB: "treshold"/"tresh" and "indeces" appear in public parameter names
+# (e.g. MiToTreeAnnotator.clonal_inference(similarity_tresholds=...)), so they are
+# ignored rather than corrected: fixing them would be a breaking API change.
+ignore-words-list = "coo,nd,ist,hist,mut,muts,ND,SNS,treshold,tresholds,tresh,indeces,simmetric"
+
+[tool.coverage.run]
+source = ["mito"]
+omit = ["*/tests/*"]

scmito-0.2.0/src/mito/__init__.py

@@ -0,0 +1,5 @@
+__version__ = "0.2.0"
+
+from . import io, pl, pp, tl, ut
+
+__all__ = ["pl", "pp", "tl", "io", "ut"]