bonesistools 1.2.9__tar.gz → 1.4.0__tar.gz

{bonesistools-1.2.9 → bonesistools-1.4.0}/.gitignore

@@ -32,6 +32,7 @@ venv.bak/
 .coverage.*
 coverage.xml
 htmlcov/
+.cache/
 .pytest_cache/
 .mypy_cache/
 .pyright/
@@ -108,6 +109,7 @@ q.log
 src/bonesistools/databases/omnipath/.cache/
 /data/
 /results/
+/benchmark_results/
 benchmarks/results/
 !tests/
 !tests/data/
@@ -124,3 +126,5 @@ tests/reproducibility/*.json
 !src/bonesistools/sctools/datasets/*.json
 !src/bonesistools/sctools/datasets/*.h5ad
 scripts/
+*.zginml
+!tests/golden/*.zginml

{bonesistools-1.2.9 → bonesistools-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bonesistools
-Version: 1.2.9
+Version: 1.4.0
 Summary: Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework
 Project-URL: Repository, https://github.com/bnediction/bonesistools
 Author: Théo Roncalli
@@ -33,6 +33,7 @@ Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.7
 Requires-Dist: anndata>=0.8
 Requires-Dist: boolean-py>=4.0
+Requires-Dist: clingo>=5.6
 Requires-Dist: h5py>=3.7
 Requires-Dist: importlib-metadata; python_version < '3.8'
 Requires-Dist: importlib-resources; python_version < '3.9'
@@ -44,6 +45,8 @@ Requires-Dist: scikit-learn>=1.0
 Requires-Dist: scipy>=1.7
 Requires-Dist: typing-extensions>=4.0
 Provides-Extra: all
+Requires-Dist: dd<0.6,>=0.5.7; (python_version < '3.11') and extra == 'all'
+Requires-Dist: dd>=0.6; (python_version >= '3.11') and extra == 'all'
 Requires-Dist: graphviz>=0.20; extra == 'all'
 Requires-Dist: igraph>=0.10; extra == 'all'
 Requires-Dist: leidenalg>=0.10; extra == 'all'
@@ -55,10 +58,13 @@ 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: bdd
+Requires-Dist: dd<0.6,>=0.5.7; (python_version < '3.11') and extra == 'bdd'
+Requires-Dist: dd>=0.6; (python_version >= '3.11') and extra == 'bdd'
+Provides-Extra: bn
+Requires-Dist: mpbn>=4.1; extra == 'bn'
 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
@@ -93,70 +99,66 @@ The package provides:
 import bonesistools as bt
 ```
 
-`BoNesisTools` exposes four main namespaces:
+`BoNesisTools` exposes three main namespaces:
 
-- `bt.sct` — single-cell and multimodal annotated data tools
-- `bt.bpy` — Boolean modelling and graph utilities
-- `bt.dbs` — biological database interfaces
+- `bt.omics` — single-cell and multimodal annotated data tools
+- `bt.logic` — Boolean modelling and graph utilities
+- `bt.resources` — 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.
+`bt.omics` is inspired by [Scanpy](https://github.com/scverse/scanpy) while providing additional and complementary features for single-cell analyses.
 
 Submodules:
 
-- preprocessing: `bt.sct.pp`
+- preprocessing: `bt.omics.pp`
   - expression transformations, feature selection, filtering and metadata utilities
 
-- tools: `bt.sct.tl`
-  - embeddings, neighborhood graphs, clustering, differential analysis and matrix utilities
+- tools: `bt.omics.tl`
+  - embeddings, neighborhood graphs, clustering and differential analysis
 
-- plotting: `bt.sct.pl`
-  - visualization helpers for embeddings, trajectories, distributions and summaries
+- input/output: `bt.omics.io`
+  - registered single-cell example datasets, GEO import and matrix export helpers
 
-- datasets: `bt.sct.datasets`
-  - registered single-cell example datasets loaded with `bt.sct.datasets.load(...)`
+- plotting: `bt.omics.pl`
+  - visualization helpers for embeddings, trajectories, distributions and summaries
 
 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")
+bt.omics.io.available()
+bt.omics.io.info("pbmc3k")
+adata = bt.omics.io.load("pbmc3k")
+adata = bt.omics.io.load("nestorowa")
+bt.omics.io.clear("pbmc3k")
 ```
 
 ---
 
 ## Boolean modelling utilities
 
-`bt.bpy` provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.
+`bt.logic` 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 algebra: `bt.logic.ba`
+  - logical objects, configuration sets and transformations for Boolean-state reasoning
 
-- Boolean network: `bt.bpy.bn`
+- Boolean network: `bt.logic.bn`
   - Boolean model representation, conversion, analysis and exchange
 
-- influence graph: `bt.bpy.ig`
+- influence graph: `bt.logic.ig`
   - signed regulatory graph construction, comparison, analysis and display
 
+- input/output: `bt.logic.io`
+  - BNet, GINML, ZGINML, hypercube and influence-graph readers
+
 Example:
 
 ```python
-bn = bt.bpy.bn.BooleanNetwork(
-    {
-        "A": "B & ~C",
-        "B": 1,
-        "C": 0,
-    }
-)
-
+bn = bt.logic.io.read_bnet("model.bnet")
 graph = bn.to_influence_graph()
 
 graph.show()
@@ -166,26 +168,26 @@ graph.show()
 
 ## Biological external resources
 
-`bt.dbs` provides lightweight interfaces and utilities for biological
+`bt.resources` provides lightweight interfaces and utilities for biological
 external resources.
 
 Submodules:
 
-- NCBI: `bt.dbs.ncbi`
+- NCBI: `bt.resources.ncbi`
   - gene identifier, synonym and annotation utilities
 
-- OmniPath: `bt.dbs.omnipath`
+- OmniPath: `bt.resources.omnipath`
   - regulatory interaction datasets
 
-- HCOP: `bt.dbs.hcop`
+- HCOP: `bt.resources.hcop`
   - orthology resources
 
 Example:
 
 ```python
-genesyn = bt.dbs.ncbi.genesyn()
+genesyn = bt.resources.ncbi.genesyn()
 
-grn = bt.dbs.omnipath.collectri(
+grn = bt.resources.omnipath.collectri(
     organism="mouse",
     genesyn=genesyn,
 )

{bonesistools-1.2.9 → bonesistools-1.4.0}/README.md

@@ -22,70 +22,66 @@ The package provides:
 import bonesistools as bt
 ```
 
-`BoNesisTools` exposes four main namespaces:
+`BoNesisTools` exposes three main namespaces:
 
-- `bt.sct` — single-cell and multimodal annotated data tools
-- `bt.bpy` — Boolean modelling and graph utilities
-- `bt.dbs` — biological database interfaces
+- `bt.omics` — single-cell and multimodal annotated data tools
+- `bt.logic` — Boolean modelling and graph utilities
+- `bt.resources` — 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.
+`bt.omics` is inspired by [Scanpy](https://github.com/scverse/scanpy) while providing additional and complementary features for single-cell analyses.
 
 Submodules:
 
-- preprocessing: `bt.sct.pp`
+- preprocessing: `bt.omics.pp`
   - expression transformations, feature selection, filtering and metadata utilities
 
-- tools: `bt.sct.tl`
-  - embeddings, neighborhood graphs, clustering, differential analysis and matrix utilities
+- tools: `bt.omics.tl`
+  - embeddings, neighborhood graphs, clustering and differential analysis
 
-- plotting: `bt.sct.pl`
-  - visualization helpers for embeddings, trajectories, distributions and summaries
+- input/output: `bt.omics.io`
+  - registered single-cell example datasets, GEO import and matrix export helpers
 
-- datasets: `bt.sct.datasets`
-  - registered single-cell example datasets loaded with `bt.sct.datasets.load(...)`
+- plotting: `bt.omics.pl`
+  - visualization helpers for embeddings, trajectories, distributions and summaries
 
 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")
+bt.omics.io.available()
+bt.omics.io.info("pbmc3k")
+adata = bt.omics.io.load("pbmc3k")
+adata = bt.omics.io.load("nestorowa")
+bt.omics.io.clear("pbmc3k")
 ```
 
 ---
 
 ## Boolean modelling utilities
 
-`bt.bpy` provides utilities for Boolean modelling, logical abstractions and signed regulatory graphs.
+`bt.logic` 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 algebra: `bt.logic.ba`
+  - logical objects, configuration sets and transformations for Boolean-state reasoning
 
-- Boolean network: `bt.bpy.bn`
+- Boolean network: `bt.logic.bn`
   - Boolean model representation, conversion, analysis and exchange
 
-- influence graph: `bt.bpy.ig`
+- influence graph: `bt.logic.ig`
   - signed regulatory graph construction, comparison, analysis and display
 
+- input/output: `bt.logic.io`
+  - BNet, GINML, ZGINML, hypercube and influence-graph readers
+
 Example:
 
 ```python
-bn = bt.bpy.bn.BooleanNetwork(
-    {
-        "A": "B & ~C",
-        "B": 1,
-        "C": 0,
-    }
-)
-
+bn = bt.logic.io.read_bnet("model.bnet")
 graph = bn.to_influence_graph()
 
 graph.show()
@@ -95,26 +91,26 @@ graph.show()
 
 ## Biological external resources
 
-`bt.dbs` provides lightweight interfaces and utilities for biological
+`bt.resources` provides lightweight interfaces and utilities for biological
 external resources.
 
 Submodules:
 
-- NCBI: `bt.dbs.ncbi`
+- NCBI: `bt.resources.ncbi`
   - gene identifier, synonym and annotation utilities
 
-- OmniPath: `bt.dbs.omnipath`
+- OmniPath: `bt.resources.omnipath`
   - regulatory interaction datasets
 
-- HCOP: `bt.dbs.hcop`
+- HCOP: `bt.resources.hcop`
   - orthology resources
 
 Example:
 
 ```python
-genesyn = bt.dbs.ncbi.genesyn()
+genesyn = bt.resources.ncbi.genesyn()
 
-grn = bt.dbs.omnipath.collectri(
+grn = bt.resources.omnipath.collectri(
     organism="mouse",
     genesyn=genesyn,
 )

{bonesistools-1.2.9 → bonesistools-1.4.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "bonesistools"
 description = "Bioinformatics toolkit for upstream and downstream analyses around the BoNesis framework"
-version = "1.2.9"
+version = "1.4.0"
 license = "CECILL-2.1"
 credits = ["BNeDiction", "PEPR Santé Numérique 2030"]
 authors = [
@@ -53,6 +53,7 @@ dependencies = [
     "h5py>=3.7",
     "anndata>=0.8",
     "boolean.py>=4.0",
+    "clingo>=5.6",
 ]
 keywords = [
     "bioinformatics",
@@ -72,6 +73,8 @@ paths = ["LICENSE"]
 
 [project.optional-dependencies]
 all = [
+    "dd>=0.5.7,<0.6; python_version < '3.11'",
+    "dd>=0.6; python_version >= '3.11'",
     "graphviz>=0.20",
     "mudata>=0.3.1",
     "multiprocess>=0.70.18",
@@ -84,9 +87,15 @@ all = [
     "umap-learn>=0.5",
     "mpbn>=4.1",
 ]
+bdd = [
+    "dd>=0.5.7,<0.6; python_version < '3.11'",
+    "dd>=0.6; python_version >= '3.11'",
+]
 graphviz = [ "graphviz>=0.20" ]
 mudata = [ "mudata>=0.3.1" ]
-mpbn = [ "mpbn>=4.1" ]
+bn = [
+    "mpbn>=4.1",
+]
 omics = [
     "igraph>=0.10",
     "leidenalg>=0.10",
@@ -108,9 +117,11 @@ include = [
 [tool.hatch.build.targets.wheel]
 packages = [ "src/bonesistools" ]
 artifacts = [
-    "src/bonesistools/databases/hcop/data/*.tsv.gz",
-    "src/bonesistools/databases/ncbi/data/gi/*.tsv.gz",
-    "src/bonesistools/sctools/datasets/*.json",
+    "src/bonesistools/py.typed",
+    "src/bonesistools/**/*.pyi",
+    "src/bonesistools/resources/hcop/data/*.tsv.gz",
+    "src/bonesistools/resources/ncbi/data/gi/*.tsv.gz",
+    "src/bonesistools/omics/input_output/*.json",
 ]
 
 [project.urls]
@@ -128,7 +139,7 @@ select = ["E", "F", "I"]
 typing-modules = ["bonesistools._compat"]
 
 [tool.ruff.lint.per-file-ignores]
-"src/bonesistools/sctools/datasets/datasets.json" = ["E501"]
+"src/bonesistools/omics/input_output/datasets.json" = ["E501"]
 
 [tool.pyright]
 typeCheckingMode = "standard"

bonesistools-1.4.0/src/bonesistools/__init__.py

@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+
+"""
+BoNesisTools provides bioinformatics utilities for upstream and downstream
+analyses of the BoNesis framework.
+
+Packages
+--------
+omics
+    Single-cell and multimodal annotated data tools.
+logic
+    Boolean modelling utilities.
+resources
+    Biological database and prior-knowledge resources.
+
+Credits: BNeDiction; PEPR Santé Numérique 2030.
+"""
+
+from __future__ import annotations
+
+import sys as _sys
+from types import ModuleType as _ModuleType
+from typing import Dict as _Dict
+from typing import List as _List
+from typing import Tuple as _Tuple
+
+from . import logic, omics, resources
+from ._metadata import package_version as _package_version
+from ._warnings import _warn_deprecated
+
+__credits__ = "BNeDiction; PEPR Santé Numérique 2030"
+__version__ = _package_version()
+
+__all__ = [
+    "__version__",
+    "omics",
+    "logic",
+    "resources",
+]
+
+_DEPRECATED_ALIASES: _Dict[str, _Tuple[str, _ModuleType]] = {
+    "sct": ("omics", omics),
+    "bpy": ("logic", logic),
+    "dbs": ("resources", resources),
+}
+
+_sys.modules.update(
+    {
+        f"{__name__}.{alias}": module
+        for alias, (_, module) in _DEPRECATED_ALIASES.items()
+    }
+)
+_sys.modules[f"{__name__}.sctools"] = omics
+_sys.modules[f"{__name__}.boolpy"] = logic
+_sys.modules[f"{__name__}.databases"] = resources
+
+_sys.modules.update(
+    {
+        f"{__name__}.omics.{alias}": getattr(omics, alias)
+        for alias in ["pp", "tl", "io", "pl"]
+    }
+)
+_sys.modules[f"{__name__}.omics.datasets"] = getattr(omics, "_datasets")
+_sys.modules.update(
+    {
+        f"{__name__}.sctools.{alias}": getattr(omics, alias)
+        for alias in ["pp", "tl", "io", "pl"]
+    }
+)
+_sys.modules[f"{__name__}.sctools.datasets"] = getattr(omics, "_datasets")
+_sys.modules.update(
+    {
+        f"{__name__}.sct.{alias}": getattr(omics, alias)
+        for alias in ["pp", "tl", "io", "pl"]
+    }
+)
+_sys.modules[f"{__name__}.sct.datasets"] = getattr(omics, "_datasets")
+
+_sys.modules.update(
+    {
+        f"{__name__}.logic.{alias}": getattr(logic, alias)
+        for alias in ["ba", "bn", "ig", "io"]
+    }
+)
+_sys.modules.update(
+    {
+        f"{__name__}.boolpy.{alias}": getattr(logic, alias)
+        for alias in ["ba", "bn", "ig", "io"]
+    }
+)
+
+_sys.modules.update(
+    {
+        f"{__name__}.resources.{alias}": getattr(resources, alias)
+        for alias in ["hcop", "ncbi", "omnipath"]
+    }
+)
+_sys.modules.update(
+    {
+        f"{__name__}.dbs.{alias}": getattr(resources, alias)
+        for alias in ["hcop", "ncbi", "omnipath"]
+    }
+)
+_sys.modules.update(
+    {
+        f"{__name__}.databases.{alias}": getattr(resources, alias)
+        for alias in ["hcop", "ncbi", "omnipath"]
+    }
+)
+_sys.modules.update(
+    {
+        f"{__name__}.bpy.{alias}": getattr(logic, alias)
+        for alias in ["ba", "bn", "ig", "io"]
+    }
+)
+
+
+def __getattr__(name: str) -> object:
+    if name in _DEPRECATED_ALIASES:
+        replacement, module = _DEPRECATED_ALIASES[name]
+        _warn_deprecated(
+            f"`bt.{name}`",
+            replacement=f"`bt.{replacement}`",
+            stacklevel=2,
+        )
+        return module
+
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __dir__() -> _List[str]:
+    return sorted(name for name in (set(globals()) | set(__all__)) if name[0] != "_")

bonesistools-1.4.0/src/bonesistools/__init__.pyi

@@ -0,0 +1,12 @@
+from . import logic as logic
+from . import omics as omics
+from . import resources as resources
+
+__version__: str
+
+__all__ = [
+    "__version__",
+    "omics",
+    "logic",
+    "resources",
+]

{bonesistools-1.2.9/src/bonesistools/boolpy → bonesistools-1.4.0/src/bonesistools/logic}/__init__.py

@@ -3,8 +3,8 @@
 """
 Utilities for Boolean modelling.
 
-The `bpy` package provides tools for Boolean algebra, Boolean networks,
-influence graphs and plotting.
+The `logic` package provides tools for Boolean algebra, Boolean networks,
+and influence graphs.
 
 Sub-packages
 ------------
@@ -14,8 +14,8 @@ bn
     Boolean networks and logical modelling utilities.
 ig
     Influence graph utilities.
-pl
-    Plotting utilities.
+io
+    Input/output helpers.
 """
 
 from __future__ import annotations
@@ -31,19 +31,25 @@ from .._warnings import _warn_deprecated
 from . import boolean_algebra as ba
 from . import boolean_network as bn
 from . import influence_graph as ig
-from . import plotting as pl
+from . import input_output as io
 
-del annotations
+for _name in [
+    "boolean_algebra",
+    "boolean_network",
+    "influence_graph",
+    "input_output",
+]:
+    globals().pop(_name, None)
 
 _sys.modules.update(
-    {f"{__name__}.{alias}": globals()[alias] for alias in ["ba", "bn", "ig", "pl"]}
+    {f"{__name__}.{alias}": globals()[alias] for alias in ["ba", "bn", "ig", "io"]}
 )
 
 _MODULES: _Dict[str, _ModuleType] = {
     "ba": ba,
     "bn": bn,
     "ig": ig,
-    "pl": pl,
+    "io": io,
 }
 
 _DEPRECATED: _Dict[str, _Tuple[str, str]] = {
@@ -58,7 +64,7 @@ __all__ = [
     "ba",
     "bn",
     "ig",
-    "pl",
+    "io",
 ]
 
 
@@ -66,8 +72,8 @@ def __getattr__(name: str) -> object:
     if name in _DEPRECATED:
         module_alias, attr = _DEPRECATED[name]
         _warn_deprecated(
-            f"`bt.bpy.{name}`",
-            replacement=f"`bt.bpy.{module_alias}.{attr}`",
+            f"`bt.logic.{name}`",
+            replacement=f"`bt.logic.{module_alias}.{attr}`",
             stacklevel=2,
         )
         return _cast(object, getattr(_MODULES[module_alias], attr))
@@ -76,4 +82,4 @@ def __getattr__(name: str) -> object:
 
 
 def __dir__() -> _List[str]:
-    return sorted(set(globals()) | set(__all__))
+    return sorted(name for name in set(globals()) | set(__all__) if name[0] != "_")

bonesistools-1.4.0/src/bonesistools/logic/__init__.pyi

@@ -0,0 +1,11 @@
+from . import boolean_algebra as ba
+from . import boolean_network as bn
+from . import influence_graph as ig
+from . import input_output as io
+
+__all__ = [
+    "ba",
+    "bn",
+    "ig",
+    "io",
+]