bonesistools 1.2.0__tar.gz → 1.2.2__tar.gz

bonesistools-1.2.2/.gitignore

@@ -0,0 +1,113 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Build / packaging
+build/
+dist/
+downloads/
+eggs/
+.eggs/
+*.egg-info/
+*.egg
+sdist/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+.installed.cfg
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Test / coverage / type-checker caches
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+.pytest_cache/
+.mypy_cache/
+.pyright/
+.pyre/
+.ruff_cache/
+.tox/
+.nox/
+.hypothesis/
+
+# Jupyter / IPython
+.ipynb_checkpoints/
+ipython_config.py
+
+# Editors / IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Logs / temporary files
+*.log
+/logs/
+/tmp/
+/temp/
+*.tmp
+*.bak
+
+# Generated figures / graph exports
+*.dot
+*.dot.pdf
+*.gv
+*.gv.pdf
+*.png
+*.jpg
+*.jpeg
+
+# Large local single-cell files
+*.h5ad
+*.h5mu
+*.loom
+
+# LaTeX artifacts
+*.aux
+*.bbl
+*.bcf
+*.blg
+*.fdb_latexmk
+*.fls
+*.nav
+*.out
+*.run.xml
+*.snm
+*.synctex.gz
+*.toc
+q.log
+
+# R
+.Rhistory
+.RData
+.Rproj.user/
+
+# Project-specific
+*.md
+!README.md
+!docs/**/*.md
+
+src/bonesistools/databases/omnipath/.cache/
+/data/
+/results/
+!tests/
+!tests/data/
+!tests/data/*.h5ad
+!src/bonesistools/sctools/datasets/
+!src/bonesistools/sctools/datasets/*.h5ad

{bonesistools-1.2.0 → bonesistools-1.2.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: bonesistools
-Version: 1.2.0
-Summary: BoNesisTools is a python package proposing bioinformatics tools for upstream and downstream analysis of BoNesis framework
+Version: 1.2.2
+Summary: Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework
 Project-URL: Repository, https://github.com/bnediction/bonesistools
 Author: Théo Roncalli
 Maintainer-email: Théo Roncalli <theo.roncalli@labri.fr>
@@ -557,7 +557,7 @@ Requires-Dist: networkx>=2.1
 Requires-Dist: numpy>=1.21
 Requires-Dist: pandas>=1.3.5
 Requires-Dist: scipy>=1.7
-Requires-Dist: typing-extensions>=4.0; python_version < '3.8'
+Requires-Dist: typing-extensions>=4.0
 Provides-Extra: all
 Requires-Dist: decoupler>=2.0.0; extra == 'all'
 Requires-Dist: graphviz>=0.20; extra == 'all'
@@ -586,7 +586,16 @@ Description-Content-Type: text/markdown
 
 # BoNesisTools
 
-`BoNesisTools` is a Python package providing bioinformatics utilities for upstream and downstream analyses of the [BoNesis](https://github.com/bnediction/bonesis) framework.
+`BoNesisTools` is a Python package providing utilities for Boolean modelling, regulatory influence graphs and single-cell analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.
+
+The package provides:
+
+- Boolean algebra and partial Boolean abstractions
+- Boolean network manipulation and analysis
+- signed influence graph utilities
+- GRN-informed Boolean predecessor inference
+- single-cell and multimodal analysis helpers
+- biological database interfaces
 
 ## Usage
 
@@ -597,55 +606,140 @@ import bonesistools as bt
 `BoNesisTools` exposes four main namespaces:
 
 - `bt.sct` — single-cell and multimodal annotated data tools
-- `bt.bpy` — Boolean modelling utilities
+- `bt.bpy` — Boolean modelling and graph utilities
 - `bt.dbs` — biological database interfaces
 - `bt.grn` — deprecated alias for `bt.bpy.ig`
 
-`bt.sct` follows a [Scanpy](https://github.com/scverse/scanpy)-like API while providing additional and complementary features for single-cell analyses:
+---
+
+## Single-cell tools
+
+`bt.sct` follows a [Scanpy](https://github.com/scverse/scanpy)-like API while providing additional and complementary features for single-cell analyses.
+
+Submodules:
 
 - preprocessing: `bt.sct.pp`
 - tools: `bt.sct.tl`
 - plotting: `bt.sct.pl`
 - datasets: `bt.sct.datasets`
 
-`bt.bpy` provides utilities for Boolean modelling:
+---
+
+## Boolean modelling utilities
+
+`bt.bpy` provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.
+
+Submodules:
+
+- Boolean algebra: `bt.bpy.ba`
+  - partial Boolean abstractions and hypercube representations
+  - Boolean differential and predecessor inference utilities
+
+- Boolean network: `bt.bpy.bn`
+  - Boolean network manipulation and analysis
+  - fixed-point computation
+  - `.bnet` import/export
+
+- influence graph: `bt.bpy.ig`
+  - signed regulatory influence graphs
+  - feedback circuit and SCC analysis
+  - signed interaction scoring from bounded walks
+  - graph compression and visualization utilities
+
+Example:
+
+```python
+bn = bt.bpy.bn.BooleanNetwork(
+    {
+        "A": "B & ~C",
+        "B": 1,
+        "C": 0,
+    }
+)
+
+graph = bn.to_influence_graph()
+
+graph.show()
+```
+
+---
+
+## Biological external resources
 
-- Boolean algebra and partial Boolean abstractions: `bt.bpy.ba`
-- Boolean network utilities: `bt.bpy.bn`
-- interaction and influence graph utilities: `bt.bpy.ig`
+`bt.dbs` provides lightweight interfaces and utilities for biological
+external resources.
+
+Submodules:
+
+- NCBI: `bt.dbs.ncbi`
+  - gene synonym harmonization
+  - gene annotation utilities
+
+- OmniPath: `bt.dbs.omnipath`
+  - DoRothEA transcription factor interactions
+  - CollecTRI regulatory interaction networks
+
+Example:
+
+```python
+genesyn = bt.dbs.ncbi.GeneSynonyms()
+
+grn = bt.dbs.omnipath.load_collectri_grn(
+    organism="mouse",
+    genesyn=genesyn,
+)
+```
+
+---
 
 ## Installation
 
 Install the latest release:
+
 ```sh
 pip install bonesistools
 ```
 
-Install the single-cell tools dependencies:
+Install the single-cell dependencies:
+
 ```sh
 pip install "bonesistools[sctools]"
 ```
 
-Install with all extra dependencies:
+Install all optional dependencies:
+
 ```sh
 pip install "bonesistools[all]"
 ```
 
 Install the development version:
+
 ```sh
 git clone https://github.com/bnediction/bonesistools.git
 cd bonesistools
 pip install -e ".[all]"
 ```
+
 or directly:
+
 ```sh
 pip install git+https://github.com/bnediction/bonesistools.git
 ```
 
+---
+
 ## Bugs
 
-Please report any bugs or ask questions [here](https://github.com/bnediction/bonesistools/issues).
+Please report bugs or ask questions here:
+
+https://github.com/bnediction/bonesistools/issues
+
+---
 
 ## License
 
 This package is distributed under the [CeCILL v2.1](http://www.cecill.info/index.en.html) free software license (GNU GPL compatible).
+
+This package also includes third-party data resources derived from the
+NCBI Gene database (`gene_info`). NCBI places no restrictions on the
+use or redistribution of these data: https://www.ncbi.nlm.nih.gov/home/about/policies/

bonesistools-1.2.2/README.md

@@ -0,0 +1,164 @@
+[![tests](https://github.com/bnediction/bonesistools/actions/workflows/tests.yml/badge.svg)](https://github.com/bnediction/bonesistools/actions/workflows/tests.yml)
+[![PyPI](https://img.shields.io/pypi/v/bonesistools.svg)](https://pypi.org/project/bonesistools)
+[![python](https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fbnediction%2Fbonesistools%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&query=%24.project.requires-python&style=flat&label=python)](https://www.python.org/)
+[![license](https://img.shields.io/pypi/l/bonesistools.svg)](https://github.com/bnediction/bonesistools/blob/main/LICENSE)
+
+# BoNesisTools
+
+`BoNesisTools` is a Python package providing utilities for Boolean modelling, regulatory influence graphs and single-cell analyses around the [BoNesis](https://github.com/bnediction/bonesis) ecosystem.
+
+The package provides:
+
+- Boolean algebra and partial Boolean abstractions
+- Boolean network manipulation and analysis
+- signed influence graph utilities
+- GRN-informed Boolean predecessor inference
+- single-cell and multimodal analysis helpers
+- biological database interfaces
+
+## Usage
+
+```python
+import bonesistools as bt
+```
+
+`BoNesisTools` exposes four main namespaces:
+
+- `bt.sct` — single-cell and multimodal annotated data tools
+- `bt.bpy` — Boolean modelling and graph utilities
+- `bt.dbs` — biological database interfaces
+- `bt.grn` — deprecated alias for `bt.bpy.ig`
+
+---
+
+## Single-cell tools
+
+`bt.sct` follows a [Scanpy](https://github.com/scverse/scanpy)-like API while providing additional and complementary features for single-cell analyses.
+
+Submodules:
+
+- preprocessing: `bt.sct.pp`
+- tools: `bt.sct.tl`
+- plotting: `bt.sct.pl`
+- datasets: `bt.sct.datasets`
+
+---
+
+## Boolean modelling utilities
+
+`bt.bpy` provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.
+
+Submodules:
+
+- Boolean algebra: `bt.bpy.ba`
+  - partial Boolean abstractions and hypercube representations
+  - Boolean differential and predecessor inference utilities
+
+- Boolean network: `bt.bpy.bn`
+  - Boolean network manipulation and analysis
+  - fixed-point computation
+  - `.bnet` import/export
+
+- influence graph: `bt.bpy.ig`
+  - signed regulatory influence graphs
+  - feedback circuit and SCC analysis
+  - signed interaction scoring from bounded walks
+  - graph compression and visualization utilities
+
+Example:
+
+```python
+bn = bt.bpy.bn.BooleanNetwork(
+    {
+        "A": "B & ~C",
+        "B": 1,
+        "C": 0,
+    }
+)
+
+graph = bn.to_influence_graph()
+
+graph.show()
+```
+
+---
+
+## Biological external resources
+
+`bt.dbs` provides lightweight interfaces and utilities for biological
+external resources.
+
+Submodules:
+
+- NCBI: `bt.dbs.ncbi`
+  - gene synonym harmonization
+  - gene annotation utilities
+
+- OmniPath: `bt.dbs.omnipath`
+  - DoRothEA transcription factor interactions
+  - CollecTRI regulatory interaction networks
+
+Example:
+
+```python
+genesyn = bt.dbs.ncbi.GeneSynonyms()
+
+grn = bt.dbs.omnipath.load_collectri_grn(
+    organism="mouse",
+    genesyn=genesyn,
+)
+```
+
+---
+
+## Installation
+
+Install the latest release:
+
+```sh
+pip install bonesistools
+```
+
+Install the single-cell dependencies:
+
+```sh
+pip install "bonesistools[sctools]"
+```
+
+Install all optional dependencies:
+
+```sh
+pip install "bonesistools[all]"
+```
+
+Install the development version:
+
+```sh
+git clone https://github.com/bnediction/bonesistools.git
+cd bonesistools
+pip install -e ".[all]"
+```
+
+or directly:
+
+```sh
+pip install git+https://github.com/bnediction/bonesistools.git
+```
+
+---
+
+## Bugs
+
+Please report bugs or ask questions here:
+
+https://github.com/bnediction/bonesistools/issues
+
+---
+
+## License
+
+This package is distributed under the [CeCILL v2.1](http://www.cecill.info/index.en.html) free software license (GNU GPL compatible).
+
+This package also includes third-party data resources derived from the
+NCBI Gene database (`gene_info`). NCBI places no restrictions on the
+use or redistribution of these data: https://www.ncbi.nlm.nih.gov/home/about/policies/

{bonesistools-1.2.0 → bonesistools-1.2.2}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bonesistools"
-description = "BoNesisTools is a python package proposing bioinformatics tools for upstream and downstream analysis of BoNesis framework"
-version = "1.2.0"
+description = "Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework"
+version = "1.2.2"
 license = {file = "LICENSE"}
 credits = ["BNeDiction", "PEPR Santé Numérique 2030"]
 authors = [
@@ -42,7 +42,7 @@ classifiers = [
 requires-python = ">=3.7"
 dependencies = [
     "importlib_resources; python_version < '3.9'",
-    "typing-extensions>=4.0; python_version < '3.8'",
+    "typing-extensions>=4.0",
     "numpy>=1.21",
     "pandas>=1.3.5",
     "scipy>=1.7",
@@ -86,6 +86,7 @@ sctools = [ "scikit-learn>=1.0" ]
 ignore-vcs = true
 include = [
     "*.py",
+    "src/bonesistools/py.typed",
     "src/bonesistools/databases/ncbi/data/gi/*.tsv",
     "src/bonesistools/sctools/datasets/*.h5ad",
 ]
@@ -99,6 +100,15 @@ Repository = "https://github.com/bnediction/bonesistools"
 [tool.black]
 target-version = ["py37"]
 
+[tool.ruff]
+target-version = "py37"
+line-length = 88
+extend-exclude = ["ensemble"]
+
+[tool.ruff.lint]
+select = ["E", "F", "I"]
+typing-modules = ["bonesistools._compat"]
+
 [tool.pytest.ini_options]
 filterwarnings = [
     "ignore:The NumPy module was reloaded:UserWarning",

{bonesistools-1.2.0 → bonesistools-1.2.2}/src/bonesistools/__init__.py

@@ -18,14 +18,23 @@ grn
 Credits: BNeDiction; PEPR Santé Numérique 2030.
 """
 
+from __future__ import annotations
+
 import importlib as _importlib
 import sys as _sys
 import warnings as _warnings
+from types import ModuleType as _ModuleType
+from typing import TYPE_CHECKING as _TYPE_CHECKING
 
 from . import boolpy as bpy
 from . import databases as dbs
 from . import sctools as sct
 
+if _TYPE_CHECKING:
+    from . import grntools as grn
+
+del annotations
+
 __credits__ = "BNeDiction; PEPR Santé Numérique 2030"
 
 __all__ = [
@@ -47,15 +56,21 @@ _sys.modules.update(
 )
 
 _sys.modules.update(
-    {f"{__name__}.bpy.{alias}": getattr(bpy, alias) for alias in ["ba", "bn", "ig"]}
+    {
+        f"{__name__}.bpy.{alias}": getattr(bpy, alias)
+        for alias in ["ba", "bn", "ig", "pl"]
+    }
 )
 
 
-def __getattr__(name):
+def __getattr__(name: str) -> _ModuleType:
     if name == "grn":
-        _warnings.warn(
+        message = (
             "`bt.grn` is deprecated and will be removed in a future release; "
-            "use `bt.bpy.ig` instead.",
+            "use `bt.bpy.ig` instead."
+        )
+        _warnings.warn(
+            message,
             FutureWarning,
             stacklevel=2,
         )
@@ -68,5 +83,5 @@ def __getattr__(name):
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
 
 
-def __dir__():
+def __dir__() -> list[str]:
     return sorted(set(globals()) | set(__all__))

bonesistools-1.2.2/src/bonesistools/_compat.py

@@ -0,0 +1,15 @@
+#!/usr/bin/env python
+
+"""
+Compatibility imports shared across the package.
+"""
+
+try:
+    from typing import Literal, get_args
+except ImportError:
+    from typing_extensions import Literal, get_args
+
+__all__ = [
+    "Literal",
+    "get_args",
+]

{bonesistools-1.2.0 → bonesistools-1.2.2}/src/bonesistools/boolpy/__init__.py

@@ -3,8 +3,8 @@
 """
 Utilities for Boolean modelling.
 
-The `bpy` package provides tools for Boolean algebra, Boolean networks
-and interaction/influence graphs.
+The `bpy` package provides tools for Boolean algebra, Boolean networks,
+influence graphs and plotting.
 
 Sub-packages
 ------------
@@ -13,48 +13,65 @@ ba
 bn
     Boolean networks and logical modelling utilities.
 ig
-    Interaction and influence graph utilities.
+    Influence graph utilities.
+pl
+    Plotting utilities.
 """
 
-import warnings as _warnings
+from __future__ import annotations
+
 import sys as _sys
+import warnings as _warnings
+from types import ModuleType as _ModuleType
+from typing import cast as _cast
 
 from . import boolean_algebra as ba
 from . import boolean_network as bn
-from . import interaction_graph as ig
+from . import influence_graph as ig
+from . import plotting as pl
+
+del annotations
 
 _sys.modules.update(
-    {f"{__name__}.{alias}": globals()[alias] for alias in ["ba", "bn", "ig"]}
+    {f"{__name__}.{alias}": globals()[alias] for alias in ["ba", "bn", "ig", "pl"]}
 )
 
-_DEPRECATED = {
+_MODULES: dict[str, _ModuleType] = {
+    "ba": ba,
+    "bn": bn,
+    "ig": ig,
+    "pl": pl,
+}
+
+_DEPRECATED: dict[str, tuple[str, str]] = {
     "PartialBoolean": ("ba", "PartialBoolean"),
     "BooleanNetworkEnsemble": ("bn", "BooleanNetworkEnsemble"),
-    "Hypercube": ("bn", "Hypercube"),
-    "HypercubeCollection": ("bn", "HypercubeCollection"),
+    "Hypercube": ("ba", "Hypercube"),
+    "HypercubeCollection": ("ba", "HypercubeCollection"),
     "bn_to_pydot": ("bn", "bn_to_pydot"),
 }
 
+__all__ = [
+    "ba",
+    "bn",
+    "ig",
+    "pl",
+]
+
 
-def __getattr__(name):
+def __getattr__(name: str) -> object:
     if name in _DEPRECATED:
         module_alias, attr = _DEPRECATED[name]
         _warnings.warn(
-            f"`bt.bpy.{name}` is deprecated; use `bt.bpy.{module_alias}.{attr}` instead.",
+            f"`bt.bpy.{name}` is deprecated; use "
+            f"`bt.bpy.{module_alias}.{attr}` instead.",
             DeprecationWarning,
             stacklevel=2,
         )
-        return getattr(globals()[module_alias], attr)
+        return _cast(object, getattr(_MODULES[module_alias], attr))
 
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
 
 
-__all__ = [
-    "ba",
-    "bn",
-    "ig",
-]
-
-
-def __dir__():
+def __dir__() -> list[str]:
     return sorted(set(globals()) | set(__all__))