tnfr 6.0.0__py3-none-any.whl → 7.0.0__py3-none-any.whl

tnfr/viz/matplotlib.py

@@ -0,0 +1,246 @@
+"""Matplotlib plots for TNFR telemetry channels."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Iterable, Mapping, MutableMapping, Sequence
+
+import numpy as np
+from matplotlib import pyplot as plt
+from matplotlib.axes import Axes
+from matplotlib.figure import Figure
+
+PathLike = str | Path
+
+
+def _normalise_path(save_path: PathLike | None) -> Path | None:
+    if save_path is None:
+        return None
+    return Path(save_path).expanduser().resolve()
+
+
+def _prepare_metadata(base: Mapping[str, str] | None = None, **entries: float | str) -> MutableMapping[str, str]:
+    metadata: MutableMapping[str, str] = {"engine": "TNFR"}
+    if base is not None:
+        metadata.update(base)
+    for key, value in entries.items():
+        metadata[key] = str(value)
+    return metadata
+
+
+def plot_coherence_matrix(
+    coherence_matrix: np.ndarray,
+    *,
+    channels: Sequence[str] | None = None,
+    save_path: PathLike | None = None,
+    dpi: int = 300,
+    cmap: str = "viridis",
+) -> tuple[Figure, Axes]:
+    """Plot the coherence matrix :math:`C(t)` describing nodal coupling.
+
+    Parameters
+    ----------
+    coherence_matrix:
+        Square matrix reporting pairwise TNFR coherence (0-1). Each entry
+        encodes how two nodes sustain a mutual resonance while the total coherence
+        :math:`C(t)` evolves.
+    channels:
+        Optional channel names aligned with the matrix axes.
+    save_path:
+        Optional filesystem location. When provided the figure is exported with
+        explicit metadata so structural logs can capture how :math:`C(t)` was
+        rendered.
+    dpi:
+        Resolution of the exported artifact in dots per inch.
+    cmap:
+        Matplotlib colormap name used for the coherence heatmap.
+
+    Returns
+    -------
+    (Figure, Axes)
+        The Matplotlib figure and heatmap axis.
+    """
+
+    matrix = np.asarray(coherence_matrix, dtype=float)
+    if matrix.ndim != 2 or matrix.shape[0] != matrix.shape[1]:
+        raise ValueError("coherence_matrix must be a square 2D array")
+
+    fig, ax = plt.subplots(figsize=(6, 5))
+    image = ax.imshow(matrix, cmap=cmap, vmin=0.0, vmax=1.0)
+    ax.set_title("TNFR Coherence Matrix C(t)")
+    ax.set_xlabel("Emission nodes (νf order)")
+    ax.set_ylabel("Reception nodes (νf order)")
+    cbar = fig.colorbar(image, ax=ax, shrink=0.85)
+    cbar.set_label("Structural coherence C(t)")
+
+    size = matrix.shape[0]
+    ticks = np.arange(size)
+    ax.set_xticks(ticks)
+    ax.set_yticks(ticks)
+    if channels is not None and len(channels) == size:
+        ax.set_xticklabels(channels, rotation=45, ha="right")
+        ax.set_yticklabels(channels)
+
+    mean_coherence = float(matrix.mean())
+    metadata = _prepare_metadata(
+        {"tnfr_plot": "coherence_matrix"},
+        c_t_mean=mean_coherence,
+        phase_reference="synchrony-check",
+    )
+
+    resolved_path = _normalise_path(save_path)
+    if resolved_path is not None:
+        fig.savefig(
+            resolved_path,
+            dpi=dpi,
+            bbox_inches="tight",
+            metadata=metadata,
+        )
+
+    return fig, ax
+
+
+def plot_phase_sync(
+    phase_paths: np.ndarray,
+    time_axis: np.ndarray,
+    *,
+    structural_frequency: float,
+    node_labels: Sequence[str] | None = None,
+    save_path: PathLike | None = None,
+    dpi: int = 300,
+) -> tuple[Figure, Axes]:
+    """Plot phase synchrony φ(t) trajectories for TNFR nodes.
+
+    Parameters
+    ----------
+    phase_paths:
+        Array with shape ``(nodes, samples)`` describing the phase of each node
+        in radians. Synchronised paths map how the coupling operator preserves
+        phase locking.
+    time_axis:
+        Monotonic timestamps aligned with the samples describing the evolution of
+        :math:`C(t)`.
+    structural_frequency:
+        Global structural frequency :math:`ν_f` (Hz_str) used as the reference
+        rate for the displayed phases.
+    node_labels:
+        Optional labels describing the emitting nodes. When omitted generic
+        indices are used.
+    save_path:
+        Optional filesystem location to export the figure with TNFR metadata.
+    dpi:
+        Resolution used for exported figures.
+
+    Returns
+    -------
+    (Figure, Axes)
+        The Matplotlib figure and axis holding the phase trajectories.
+    """
+
+    phases = np.asarray(phase_paths, dtype=float)
+    times = np.asarray(time_axis, dtype=float)
+    if phases.ndim != 2:
+        raise ValueError("phase_paths must be a 2D array")
+    if times.ndim != 1:
+        raise ValueError("time_axis must be a 1D array")
+    if phases.shape[1] != times.shape[0]:
+        raise ValueError("phase_paths samples must align with time_axis")
+
+    fig, ax = plt.subplots(figsize=(7, 4))
+    labels: Iterable[str]
+    if node_labels is not None and len(node_labels) == phases.shape[0]:
+        labels = node_labels
+    else:
+        labels = (f"node {idx}" for idx in range(phases.shape[0]))
+
+    for path, label in zip(phases, labels):
+        ax.plot(times, path, label=label)
+
+    ax.set_title("TNFR Phase Synchrony φ(t)")
+    ax.set_xlabel("Time (structural cycles)")
+    ax.set_ylabel("Phase (rad)")
+    ax.legend(loc="best")
+
+    metadata = _prepare_metadata(
+        {"tnfr_plot": "phase_sync"},
+        nu_f_hz_str=structural_frequency,
+        phase_span=float(np.ptp(phases)),
+    )
+
+    resolved_path = _normalise_path(save_path)
+    if resolved_path is not None:
+        fig.savefig(
+            resolved_path,
+            dpi=dpi,
+            bbox_inches="tight",
+            metadata=metadata,
+        )
+
+    return fig, ax
+
+
+def plot_spectrum_path(
+    frequencies: np.ndarray,
+    spectrum: np.ndarray,
+    *,
+    label: str = "C(t) spectral density",
+    save_path: PathLike | None = None,
+    dpi: int = 300,
+) -> tuple[Figure, Axes]:
+    """Plot the spectral path of coherence intensity over structural frequency.
+
+    Parameters
+    ----------
+    frequencies:
+        Frequency samples (Hz_str) that describe the spectrum of ΔNFR driven
+        reorganisations.
+    spectrum:
+        Intensity values tracking how coherence redistributes along the
+        structural frequency axis.
+    label:
+        Legend label identifying the traced path of :math:`C(t)`.
+    save_path:
+        Optional filesystem location to persist the figure with TNFR metadata.
+    dpi:
+        Resolution used for exported figures.
+
+    Returns
+    -------
+    (Figure, Axes)
+        The Matplotlib figure and axis holding the spectrum path.
+    """
+
+    freq = np.asarray(frequencies, dtype=float)
+    spec = np.asarray(spectrum, dtype=float)
+    if freq.ndim != 1:
+        raise ValueError("frequencies must be a 1D array")
+    if spec.ndim != 1:
+        raise ValueError("spectrum must be a 1D array")
+    if freq.shape[0] != spec.shape[0]:
+        raise ValueError("frequencies and spectrum must share the same length")
+
+    fig, ax = plt.subplots(figsize=(7, 4))
+    ax.plot(freq, spec, marker="o", label=label)
+    ax.fill_between(freq, spec, alpha=0.2)
+    ax.set_title("TNFR Structural Spectrum")
+    ax.set_xlabel("Structural frequency ν_f (Hz_str)")
+    ax.set_ylabel("Coherence intensity C(t)")
+    ax.legend(loc="best")
+
+    metadata = _prepare_metadata(
+        {"tnfr_plot": "spectrum_path"},
+        nu_f_min=float(freq.min()),
+        nu_f_max=float(freq.max()),
+    )
+
+    resolved_path = _normalise_path(save_path)
+    if resolved_path is not None:
+        fig.savefig(
+            resolved_path,
+            dpi=dpi,
+            bbox_inches="tight",
+            metadata=metadata,
+        )
+
+    return fig, ax
+

{tnfr-6.0.0.dist-info → tnfr-7.0.0.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: tnfr
-Version: 6.0.0
+Version: 7.0.0
 Summary: Modular structural-based dynamics on networks.
 Author: fmg
 License: MIT
 Project-URL: Homepage, https://pypi.org/project/tnfr/
 Project-URL: Repository, https://github.com/fermga/TNFR-Python-Engine
-Project-URL: GPT, https://chatgpt.com/g/g-67abc78885a88191b2d67f94fd60dc97-tnfr-teoria-de-la-naturaleza-fractal-resonante
+Project-URL: GPT, https://chatgpt.com/g/g-67abc78885a88191b2d67f94fd60dc97-tnfr-resonant-fractal-nature-theory
 Keywords: TNFR,complex systems,fractals,resonance,networks,structural dynamics,structural analysis
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
@@ -28,23 +28,47 @@ Requires-Dist: cachetools>=5
 Requires-Dist: typing-extensions>=4.4; python_version < "3.10"
 Provides-Extra: numpy
 Requires-Dist: numpy>=1.24; extra == "numpy"
+Provides-Extra: jax
+Requires-Dist: jax>=0.4; extra == "jax"
+Provides-Extra: torch
+Requires-Dist: torch>=2.1; extra == "torch"
 Provides-Extra: yaml
 Requires-Dist: pyyaml>=6.0; extra == "yaml"
 Provides-Extra: orjson
 Requires-Dist: orjson>=3; extra == "orjson"
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.7; extra == "viz"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.2; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.25; extra == "docs"
+Requires-Dist: myst-parser>=2.0; extra == "docs"
+Requires-Dist: nbsphinx>=0.9; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.3; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid>=0.9; extra == "docs"
+Requires-Dist: ipykernel>=6; extra == "docs"
+Requires-Dist: nbconvert>=7.16; extra == "docs"
+Requires-Dist: pypandoc-binary>=1.14; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pytest>=7; extra == "test"
 Requires-Dist: pytest-benchmark>=4; extra == "test"
 Requires-Dist: pydocstyle>=6; extra == "test"
 Requires-Dist: coverage>=7; extra == "test"
+Requires-Dist: hypothesis>=6; extra == "test"
+Requires-Dist: hypothesis-networkx>=0.3; extra == "test"
 Requires-Dist: flake8>=5; extra == "test"
 Requires-Dist: flake8-pyproject>=1.2; extra == "test"
 Requires-Dist: vulture>=2; extra == "test"
+Requires-Dist: matplotlib>=3.7; extra == "test"
 Provides-Extra: typecheck
 Requires-Dist: mypy>=1.8; extra == "typecheck"
 Requires-Dist: networkx-stubs>=0.0.1; extra == "typecheck"
 Requires-Dist: types-cachetools>=6.0.0.0; extra == "typecheck"
 Requires-Dist: numpy>=1.24; extra == "typecheck"
+Provides-Extra: release
+Requires-Dist: python-semantic-release<11,>=10.4; extra == "release"
+Requires-Dist: setuptools-scm<9,>=8; extra == "release"
+Requires-Dist: build>=1; extra == "release"
+Requires-Dist: towncrier>=23; extra == "release"
 Dynamic: license-file
 
 # TNFR Python Engine
@@ -72,31 +96,51 @@ Install from PyPI (Python ≥ 3.9):
 pip install tnfr
 ```
 
-Then follow the [quickstart guide](docs/getting-started/quickstart.md) for Python and CLI
+Then follow the [quickstart guide](docs/source/getting-started/quickstart.md) for Python and CLI
 walkthroughs plus optional dependency caching helpers.
 
+## CLI profiling helpers
+
+Generate Sense Index and ΔNFR profiling artefacts directly from the CLI with the
+``profile-pipeline`` subcommand. The helper reproduces the performance benchmark that
+captures vectorised and fallback execution traces for the full pipeline:
+
+```bash
+tnfr profile-pipeline \
+  --nodes 120 --edge-probability 0.28 --loops 3 \
+  --si-chunk-sizes auto 48 --dnfr-chunk-sizes auto \
+  --si-workers auto --dnfr-workers auto \
+  --output-dir profiles/pipeline
+```
+
+The command writes ``.pstats`` and JSON summaries for each configuration/mode pair, making
+it easy to inspect hot paths with :mod:`pstats`, Snakeviz, or downstream tooling.
+
 ## Documentation map
 
-- [Documentation index](docs/index.md) — navigation hub for API chapters and examples.
-- [API overview](docs/api/overview.md) — package map, invariants, and structural data flow.
-- [Structural operators](docs/api/operators.md) — canonical grammar, key concepts, and typical
+- [Documentation index](docs/source/home.md) — navigation hub for API chapters and examples.
+- [API overview](docs/source/api/overview.md) — package map, invariants, and structural data flow.
+- [Structural operators](docs/source/api/operators.md) — canonical grammar, key concepts, and typical
   workflows.
-- [Telemetry & utilities](docs/api/telemetry.md) — coherence metrics, trace capture, locking,
+- [Telemetry & utilities](docs/source/api/telemetry.md) — coherence metrics, trace capture, locking,
   and helper facades.
-- [Examples](docs/examples/README.md) — runnable scenarios, CLI artefacts, and token legend.
+- [Examples](docs/source/examples/README.md) — runnable scenarios, CLI artefacts, and token legend.
 
 ## Documentation build workflow
 
-Netlify publishes the documentation with [MkDocs](https://www.mkdocs.org/) so the generated
-site preserves the canonical TNFR structure. The same steps can be executed locally:
+Netlify now renders the documentation with [Sphinx](https://www.sphinx-doc.org/) so MyST Markdown,
+doctests, and notebooks share a single pipeline. Reproduce the hosted site locally as follows:
 
 1. Create and activate a virtual environment (e.g. `python -m venv .venv && source .venv/bin/activate`).
-2. Install the documentation toolchain: `python -m pip install -r docs/requirements.txt`.
-3. Preview changes live with `mkdocs serve` or reproduce the Netlify pipeline with
-   `mkdocs build`, which writes the static site to the `site/` directory.
+2. Install the documentation toolchain and project extras:
+   `python -m pip install -r docs/requirements.txt && python -m pip install -e .[docs]`.
+3. Execute the doctest suite with `sphinx-build -b doctest docs/source docs/_build/doctest` to ensure
+   structural snippets remain coherent.
+4. Generate the HTML site with `make docs`, which wraps `sphinx-build -b html docs/source docs/_build/html`.
 
-The Netlify build (`netlify.toml`) runs `python -m pip install -r docs/requirements.txt && mkdocs build`
-and publishes the resulting `site/` directory, ensuring the hosted documentation matches local builds.
+The Netlify build (`netlify.toml`) runs `python -m pip install -r docs/requirements.txt && make docs`
+and publishes the resulting `docs/_build/html` directory, keeping the hosted documentation aligned with
+local verification runs.
 
 ## Local development
 
@@ -122,11 +166,11 @@ integration.
 
 ## Migration notes
 
-- **Si dispersion keys:** Replace any remaining ``dSi_ddisp_fase`` entries in graph payloads
-  or configuration files with the English ``dSi_dphase_disp`` key before upgrading. The
-  runtime now raises :class:`ValueError` listing any unexpected sensitivity keys, and
+- **Si dispersion keys:** Ensure graph payloads and configuration files use the canonical
+  ``dSi_dphase_disp`` attribute for Si dispersion sensitivity before upgrading. The runtime now
+  raises :class:`ValueError` listing any unexpected sensitivity keys, and
   :func:`tnfr.metrics.sense_index.compute_Si_node` rejects unknown keyword arguments.
-- Refer to the [release notes](docs/releases.md#1100-si-dispersion-legacy-keys-removed) for
+- Refer to the [release notes](docs/source/releases.md#1100-si-dispersion-legacy-keys-removed) for
   a migration snippet that rewrites stored graphs in place prior to running the new version.
 
 ## Licensing

tnfr-7.0.0.dist-info/RECORD

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{tnfr-6.0.0.dist-info → tnfr-7.0.0.dist-info}/licenses/LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2025 TNFR - Teoría de la naturaleza fractral resonante
+Copyright (c) 2025 TNFR – Resonant Fractal Nature Theory
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

tnfr/constants_glyphs.py

@@ -1,16 +0,0 @@
-"""Backward compatibility shim for glyph constants."""
-
-from __future__ import annotations
-
-import warnings
-
-from .config.constants import *  # noqa: F401,F403 - re-export legacy API
-from .config.constants import __all__ as _CONFIG_ALL
-
-warnings.warn(
-    "'tnfr.constants_glyphs' is deprecated; use 'tnfr.config.constants' instead",
-    DeprecationWarning,
-    stacklevel=2,
-)
-
-__all__ = _CONFIG_ALL

tnfr/constants_glyphs.pyi

@@ -1,12 +0,0 @@
-from typing import Any
-
-__all__: Any
-
-def __getattr__(name: str) -> Any: ...
-
-ANGLE_MAP: Any
-DISRUPTORS: Any
-STABILIZERS: Any
-GLYPHS_CANONICAL: Any
-GLYPHS_CANONICAL_SET: Any
-GLYPH_GROUPS: Any

tnfr/grammar.py

@@ -1,25 +0,0 @@
-"""Backwards compatibility layer for grammar helpers.
-
-The canonical implementations now live in :mod:`tnfr.validation`.  This
-module only re-exports them to avoid breaking external callers until the
-new import paths are fully adopted.
-"""
-
-from .validation.compatibility import CANON_COMPAT, CANON_FALLBACK
-from .validation.grammar import (
-    GrammarContext,
-    apply_glyph_with_grammar,
-    enforce_canonical_grammar,
-    on_applied_glyph,
-    _gram_state,
-)
-
-__all__ = [
-    "GrammarContext",
-    "CANON_COMPAT",
-    "CANON_FALLBACK",
-    "enforce_canonical_grammar",
-    "on_applied_glyph",
-    "apply_glyph_with_grammar",
-    "_gram_state",
-]

tnfr/grammar.pyi

@@ -1,13 +0,0 @@
-from typing import Any
-
-__all__: Any
-
-def __getattr__(name: str) -> Any: ...
-
-CANON_COMPAT: Any
-CANON_FALLBACK: Any
-GrammarContext: Any
-_gram_state: Any
-apply_glyph_with_grammar: Any
-enforce_canonical_grammar: Any
-on_applied_glyph: Any