bonesistools 1.2.7__tar.gz → 1.2.8__tar.gz

{bonesistools-1.2.7 → bonesistools-1.2.8}/.gitignore

@@ -112,8 +112,15 @@ benchmarks/results/
 !tests/
 !tests/data/
 !tests/data/*.h5ad
+!tests/golden/
+!tests/golden/**/*.py
+!tests/golden/**/*.md
+!tests/golden/**/*.txt
+!tests/golden/**/*.h5ad
+!tests/golden/**/*.npz
 tests/dbs/data/*.json
 tests/reproducibility/*.json
 !src/bonesistools/sctools/datasets/
+!src/bonesistools/sctools/datasets/*.json
 !src/bonesistools/sctools/datasets/*.h5ad
 scripts/

bonesistools-1.2.8/PKG-INFO

@@ -0,0 +1,246 @@
+Metadata-Version: 2.4
+Name: bonesistools
+Version: 1.2.8
+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>
+License-Expression: CECILL-2.1
+License-File: LICENSE
+Keywords: anndata,atacseq,bioinformatics,bonesis,boolean-networks,gene-regulatory-networks,mudata,rnaseq,single-cell,systems-biology
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Framework :: IPython
+Classifier: Framework :: Matplotlib
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: CEA CNRS Inria Logiciel Libre License, version 2.1 (CeCILL-2.1)
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.7
+Requires-Dist: anndata>=0.8
+Requires-Dist: boolean-py>=4.0
+Requires-Dist: h5py>=3.7
+Requires-Dist: importlib-metadata; python_version < '3.8'
+Requires-Dist: importlib-resources; python_version < '3.9'
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: networkx>=2.1
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3.5
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: scipy>=1.7
+Requires-Dist: typing-extensions>=4.0
+Provides-Extra: all
+Requires-Dist: graphviz>=0.20; extra == 'all'
+Requires-Dist: igraph>=0.10; extra == 'all'
+Requires-Dist: leidenalg>=0.10; extra == 'all'
+Requires-Dist: mpbn>=4.1; extra == 'all'
+Requires-Dist: mudata>=0.3.1; extra == 'all'
+Requires-Dist: multiprocess>=0.70.18; extra == 'all'
+Requires-Dist: numba>=0.60; (python_version >= '3.10') and extra == 'all'
+Requires-Dist: pydot>=3.0.2; extra == 'all'
+Requires-Dist: scikit-misc>=0.5; (python_version >= '3.10') and extra == 'all'
+Requires-Dist: seaborn>=0.11; extra == 'all'
+Requires-Dist: umap-learn>=0.5; extra == 'all'
+Provides-Extra: graphviz
+Requires-Dist: graphviz>=0.20; extra == 'graphviz'
+Provides-Extra: mpbn
+Requires-Dist: mpbn>=4.1; extra == 'mpbn'
+Provides-Extra: mudata
+Requires-Dist: mudata>=0.3.1; extra == 'mudata'
+Provides-Extra: omics
+Requires-Dist: igraph>=0.10; extra == 'omics'
+Requires-Dist: leidenalg>=0.10; extra == 'omics'
+Requires-Dist: numba>=0.60; (python_version >= '3.10') and extra == 'omics'
+Requires-Dist: scikit-misc>=0.5; (python_version >= '3.10') and extra == 'omics'
+Requires-Dist: umap-learn>=0.5; extra == 'omics'
+Description-Content-Type: text/markdown
+
+[![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` provides Python-implemented toolkits for upstream and downstream 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
+
+---
+
+## Single-cell tools
+
+`bt.sct` is inspired by [Scanpy](https://github.com/scverse/scanpy) while providing additional and complementary features for single-cell analyses.
+
+Submodules:
+
+- preprocessing: `bt.sct.pp`
+  - expression transformations, feature selection, filtering and metadata utilities
+
+- tools: `bt.sct.tl`
+  - embeddings, neighborhood graphs, clustering, differential analysis and matrix utilities
+
+- plotting: `bt.sct.pl`
+  - visualization helpers for embeddings, trajectories, distributions and summaries
+
+- datasets: `bt.sct.datasets`
+  - registered single-cell example datasets loaded with `bt.sct.datasets.load(...)`
+
+Example:
+
+```python
+bt.sct.datasets.available()
+bt.sct.datasets.info("pbmc3k")
+adata = bt.sct.datasets.load("pbmc3k")
+adata = bt.sct.datasets.load("nestorowa")
+bt.sct.datasets.clear("pbmc3k")
+```
+
+---
+
+## Boolean modelling utilities
+
+`bt.bpy` provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.
+
+Submodules:
+
+- Boolean algebra: `bt.bpy.ba`
+  - logical objects and transformations for Boolean-state reasoning
+
+- Boolean network: `bt.bpy.bn`
+  - Boolean model representation, conversion, analysis and exchange
+
+- influence graph: `bt.bpy.ig`
+  - signed regulatory graph construction, comparison, analysis and display
+
+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 identifier, synonym and annotation utilities
+
+- OmniPath: `bt.dbs.omnipath`
+  - regulatory interaction datasets
+
+- HCOP: `bt.dbs.hcop`
+  - orthology resources
+
+Example:
+
+```python
+genesyn = bt.dbs.ncbi.genesyn()
+
+grn = bt.dbs.omnipath.collectri(
+    organism="mouse",
+    genesyn=genesyn,
+)
+```
+
+---
+
+## Installation
+
+Install the latest release:
+
+```sh
+pip install bonesistools
+```
+
+Install the omics dependencies:
+
+```sh
+pip install "bonesistools[omics]"
+```
+
+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-1.2.7 → bonesistools-1.2.8}/README.md

@@ -27,7 +27,6 @@ import bonesistools as bt
 - `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`
 
 ---
 
@@ -38,21 +37,26 @@ import bonesistools as bt
 Submodules:
 
 - preprocessing: `bt.sct.pp`
-  - gene name harmonization
-  - metadata transfer utilities
-  - lightweight preprocessing helpers
+  - expression transformations, feature selection, filtering and metadata utilities
 
 - tools: `bt.sct.tl`
-  - K-nearest-neighbor and shared-neighbor graph utilities
-  - marker and log-fold-change analysis
-  - regression and matrix conversion utilities
+  - embeddings, neighborhood graphs, clustering, differential analysis and matrix utilities
 
 - plotting: `bt.sct.pl`
-  - embedding, density, composition and graph visualizations
-  - distribution utilities
+  - visualization helpers for embeddings, trajectories, distributions and summaries
 
 - datasets: `bt.sct.datasets`
-  - packaged reference datasets
+  - registered single-cell example datasets loaded with `bt.sct.datasets.load(...)`
+
+Example:
+
+```python
+bt.sct.datasets.available()
+bt.sct.datasets.info("pbmc3k")
+adata = bt.sct.datasets.load("pbmc3k")
+adata = bt.sct.datasets.load("nestorowa")
+bt.sct.datasets.clear("pbmc3k")
+```
 
 ---
 
@@ -63,19 +67,13 @@ Submodules:
 Submodules:
 
 - Boolean algebra: `bt.bpy.ba`
-  - partial Boolean abstractions and hypercube representations
-  - Boolean differential and predecessor inference utilities
+  - logical objects and transformations for Boolean-state reasoning
 
 - Boolean network: `bt.bpy.bn`
-  - Boolean network manipulation and analysis
-  - fixed-point computation
-  - `.bnet` import/export
+  - Boolean model representation, conversion, analysis and exchange
 
 - 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
+  - signed regulatory graph construction, comparison, analysis and display
 
 Example:
 
@@ -103,15 +101,13 @@ external resources.
 Submodules:
 
 - NCBI: `bt.dbs.ncbi`
-  - gene synonym harmonization
-  - gene annotation utilities
+  - gene identifier, synonym and annotation utilities
 
 - OmniPath: `bt.dbs.omnipath`
-  - DoRothEA transcription factor interactions
-  - CollecTRI regulatory interaction networks
+  - regulatory interaction datasets
 
 - HCOP: `bt.dbs.hcop`
-  - orthology mappings
+  - orthology resources
 
 Example:
 

{bonesistools-1.2.7 → bonesistools-1.2.8}/pyproject.toml

@@ -5,8 +5,8 @@ build-backend = "hatchling.build"
 [project]
 name = "bonesistools"
 description = "Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework"
-version = "1.2.7"
-license = {file = "LICENSE"}
+version = "1.2.8"
+license = "CECILL-2.1"
 credits = ["BNeDiction", "PEPR Santé Numérique 2030"]
 authors = [
     { name = "Théo Roncalli" },
@@ -67,6 +67,9 @@ keywords = [
     "bonesis",
 ]
 
+[project.license-files]
+paths = ["LICENSE"]
+
 [project.optional-dependencies]
 all = [
     "graphviz>=0.20",
@@ -75,6 +78,7 @@ all = [
     "pydot>=3.0.2",
     "igraph>=0.10",
     "leidenalg>=0.10",
+    "numba>=0.60; python_version >= '3.10'",
     "seaborn>=0.11",
     "scikit-misc>=0.5; python_version >= '3.10'",
     "umap-learn>=0.5",
@@ -86,6 +90,7 @@ mpbn = [ "mpbn>=4.1" ]
 omics = [
     "igraph>=0.10",
     "leidenalg>=0.10",
+    "numba>=0.60; python_version >= '3.10'",
     "scikit-misc>=0.5; python_version >= '3.10'",
     "umap-learn>=0.5",
 ]
@@ -93,11 +98,11 @@ omics = [
 [tool.hatch.build.targets.sdist]
 ignore-vcs = true
 include = [
-    "*.py",
-    "src/bonesistools/py.typed",
-    "src/bonesistools/databases/hcop/data/*.tsv.gz",
-    "src/bonesistools/databases/ncbi/data/gi/*.tsv.gz",
-    "src/bonesistools/sctools/datasets/*.h5ad",
+    "/LICENSE",
+    "/README.md",
+    "/pyproject.toml",
+    "/src/bonesistools",
+    "/tests",
 ]
 
 [tool.hatch.build.targets.wheel]
@@ -105,6 +110,7 @@ packages = [ "src/bonesistools" ]
 artifacts = [
     "src/bonesistools/databases/hcop/data/*.tsv.gz",
     "src/bonesistools/databases/ncbi/data/gi/*.tsv.gz",
+    "src/bonesistools/sctools/datasets/*.json",
 ]
 
 [project.urls]
@@ -116,16 +122,26 @@ 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]
-norecursedirs = [
-    "tests/reproducibility",
-]
-filterwarnings = [
-    "ignore:The NumPy module was reloaded:UserWarning",
+[tool.ruff.lint.per-file-ignores]
+"src/bonesistools/sctools/datasets/datasets.json" = ["E501"]
+
+[tool.pyright]
+typeCheckingMode = "standard"
+include = ["src/bonesistools"]
+exclude = [
+    "**/__pycache__",
+    "**/.*",
+    "**/node_modules",
+    ".git",
+    ".pytest_cache",
+    "build",
+    "dist",
+    "tests",
 ]
+extraPaths = ["src"]
+pythonVersion = "3.13"

{bonesistools-1.2.7 → bonesistools-1.2.8}/src/bonesistools/__init__.py

@@ -12,28 +12,19 @@ bpy
     Boolean modelling utilities.
 dbs
     Biological database interfaces.
-grn
-    Deprecated alias for `bpy.ig`.
 
 Credits: BNeDiction; PEPR Santé Numérique 2030.
 """
 
 from __future__ import annotations
 
-import importlib as _importlib
 import sys as _sys
-from types import ModuleType as _ModuleType
-from typing import TYPE_CHECKING as _TYPE_CHECKING
 from typing import List as _List
 
 from . import boolpy as bpy
 from . import databases as dbs
 from . import sctools as sct
 from ._metadata import package_version as _package_version
-from ._warnings import _warn_deprecated
-
-if _TYPE_CHECKING:
-    from . import grntools as grn
 
 del annotations
 
@@ -45,7 +36,6 @@ __all__ = [
     "sct",
     "bpy",
     "dbs",
-    "grn",
 ]
 
 _sys.modules.update(
@@ -67,21 +57,5 @@ _sys.modules.update(
 )
 
 
-def __getattr__(name: str) -> _ModuleType:
-    if name == "grn":
-        _warn_deprecated(
-            "`bt.grn`",
-            replacement="`bt.bpy.ig`",
-            stacklevel=2,
-        )
-
-        grn = _importlib.import_module(".grntools", __name__)
-        _sys.modules[f"{__name__}.grn"] = grn
-
-        return grn
-
-    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
-
-
 def __dir__() -> _List[str]:
     return sorted(set(globals()) | set(__all__))

{bonesistools-1.2.7 → bonesistools-1.2.8}/src/bonesistools/boolpy/boolean_algebra/__init__.py

@@ -10,9 +10,18 @@ differential and predecessor inference utilities.
 
 from typing import List as _List
 
-from ._algebra import BooleanPredecessorInference, PartialBooleanDifferential
+from ._algebra import (
+    BooleanPredecessorInference,
+)
 from ._boolean import PartialBoolean
 from ._hypercube import Hypercube, HypercubeCollection
+from ._kleene import (
+    KleeneValue,
+    KleeneValueLike,
+    diff,
+    join,
+    meet,
+)
 from ._parser import read_hypercube, read_hypercubes
 from ._representation import rule_to_string
 from ._structure import dnf_to_structure, expressions_equivalent
@@ -26,15 +35,19 @@ from ._typing import (
     is_boolean_rule_like,
     is_configuration_like,
     is_hypercube_like,
+    is_kleene_value_like,
     is_partial_boolean_like,
 )
 
 __all__ = [
     "BooleanPredecessorInference",
-    "PartialBooleanDifferential",
     "PartialBoolean",
+    "KleeneValue",
     "Hypercube",
     "HypercubeCollection",
+    "diff",
+    "meet",
+    "join",
     "expressions_equivalent",
     "dnf_to_structure",
     "rule_to_string",
@@ -42,12 +55,14 @@ __all__ = [
     "read_hypercubes",
     "BooleanRule",
     "ConfigurationLike",
+    "KleeneValueLike",
     "PartialBooleanLike",
     "HypercubeLike",
     "is_boolean_expression_available",
     "is_boolean_expression_like",
     "is_boolean_rule_like",
     "is_configuration_like",
+    "is_kleene_value_like",
     "is_partial_boolean_like",
     "is_hypercube_like",
 ]