snuffled 0.1.0__tar.gz

snuffled-0.1.0/.gitignore

@@ -0,0 +1,33 @@
+# build files
+dist
+*.tar.gz
+*.whl
+
+# no need to track uv.lock for a Python package (where deps are not pinned)
+uv.lock
+
+# Python cache files
+__pycache__
+*.pyc
+
+# Coverage reports
+.coverage
+htmlcov
+
+# Jupyter Notebook checkpoints
+.ipynb_checkpoints
+
+# Virtual environment directories
+venv
+.env
+
+# Pytest cache
+.cache
+
+# OS thumbnail files
+.DS_Store
+Thumbs.db
+
+# IDE files
+.idea
+.vscode

snuffled-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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snuffled-0.1.0/PKG-INFO

@@ -0,0 +1,25 @@
+Metadata-Version: 2.4
+Name: snuffled
+Version: 0.1.0
+Summary: Systematic Numerical Univariate Full Function anaLysis for Establishing Root-finding difficulty
+Project-URL: Source, https://github.com/bertpl/snuffled
+Project-URL: Issues, https://github.com/bertpl/snuffled/issues
+Project-URL: Roadmap, https://github.com/bertpl/snuffled/milestones
+Author-email: Bert Pluymers <bert.pluymers@gmail.com>
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: backports-strenum>=1.3.1
+Requires-Dist: numpy>=1.20
+Provides-Extra: numba
+Requires-Dist: numba>=0.50; extra == 'numba'
+Description-Content-Type: text/markdown
+
+<!--START_SECTION:images-->
+![shields.io-python-versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
+![genbadge-test-count](https://bertpl.github.io/snuffled/version_artifacts/v0.1.0/badge-test-count.svg)
+![genbadge-test-coverage](https://bertpl.github.io/snuffled/version_artifacts/v0.1.0/badge-coverage.svg)
+![snuffled logo](https://bertpl.github.io/snuffled/version_artifacts/v0.1.0/splash.webp)
+<!--END_SECTION:images-->
+
+# SNUFFLED
+**S**ystematic **N**umerical **U**nivariate **F**unction ana**L**ysis for **E**stablishing **D**ifficulty of root-finding.

snuffled-0.1.0/README.md

@@ -0,0 +1,9 @@
+<!--START_SECTION:images-->
+![shields.io-python-versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
+![genbadge-test-count](https://bertpl.github.io/snuffled/version_artifacts/v0.1.0/badge-test-count.svg)
+![genbadge-test-coverage](https://bertpl.github.io/snuffled/version_artifacts/v0.1.0/badge-coverage.svg)
+![snuffled logo](https://bertpl.github.io/snuffled/version_artifacts/v0.1.0/splash.webp)
+<!--END_SECTION:images-->
+
+# SNUFFLED
+**S**ystematic **N**umerical **U**nivariate **F**unction ana**L**ysis for **E**stablishing **D**ifficulty of root-finding.

snuffled-0.1.0/pyproject.toml

@@ -0,0 +1,51 @@
+[project]
+name = "snuffled"
+version = "0.1.0"
+description = "Systematic Numerical Univariate Full Function anaLysis for Establishing Root-finding difficulty"
+readme = "README.md"
+authors = [
+    { name = "Bert Pluymers", email = "bert.pluymers@gmail.com" }
+]
+requires-python = ">=3.10"
+dependencies = [
+    "backports-strenum>=1.3.1",
+    "numpy>=1.20",
+]
+
+[project.urls]
+Source = "https://github.com/bertpl/snuffled"
+Issues = "https://github.com/bertpl/snuffled/issues"
+Roadmap = "https://github.com/bertpl/snuffled/milestones"
+
+
+[project.optional-dependencies]
+numba = [
+    "numba>=0.50",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.sdist]
+packages = ["snuffled"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["snuffled"]
+
+[tool.ruff]
+line-length = 120
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["I"]
+
+[dependency-groups]
+dev = [
+    "genbadge[all]>=1.1.2",
+    "jupyterlab>=4.4.6",
+    "matplotlib>=3.10.5",
+    "notebook>=7.4.5",
+    "pytest>=8.0",
+    "pytest-cov>=6.0",
+]

snuffled-0.1.0/snuffled/__init__.py

@@ -0,0 +1,12 @@
+from ._core import (
+    Diagnostic,
+    FunctionProperty,
+    NamedArray,
+    PropertyExtractionStats,
+    RootProperty,
+    SnuffledDiagnostics,
+    SnuffledFunctionProperties,
+    SnuffledProperties,
+    SnuffledRootProperties,
+    Snuffler,
+)

snuffled-0.1.0/snuffled/_core/__init__.py

@@ -0,0 +1,12 @@
+from .analysis import Snuffler
+from .models import (
+    Diagnostic,
+    FunctionProperty,
+    NamedArray,
+    PropertyExtractionStats,
+    RootProperty,
+    SnuffledDiagnostics,
+    SnuffledFunctionProperties,
+    SnuffledProperties,
+    SnuffledRootProperties,
+)

snuffled-0.1.0/snuffled/_core/analysis/__init__.py

@@ -0,0 +1,2 @@
+from ._function_sampler import FunctionSampler
+from .snuffler import Snuffler

snuffled-0.1.0/snuffled/_core/analysis/_function_sampler.py

@@ -0,0 +1,257 @@
+import math
+from collections.abc import Callable
+from functools import cache
+
+import numpy as np
+
+from snuffled._core.models.root_analysis import Root
+from snuffled._core.utils.constants import EPS, SEED_OFFSET_FUNCTION_SAMPLER
+from snuffled._core.utils.math import smooth_sign_array
+from snuffled._core.utils.root_finding import find_odd_root
+from snuffled._core.utils.sampling import multi_scale_samples, sample_integers
+
+
+class FunctionSampler:
+    """
+    Class holding (cached) data related to a specific function, shared across different analyses.
+    All the following classes make use of this class to access the data they need for their analyses:
+      - FunctionAnalyser
+      - RootAnalyser
+      - DiagnosticAnalyser
+    """
+
+    # -------------------------------------------------------------------------
+    #  Constructor
+    # -------------------------------------------------------------------------
+    def __init__(
+        self,
+        fun: Callable[[float], float],
+        x_min: float,
+        x_max: float,
+        dx: float,
+        seed: int,
+        n_fun_samples: int = 1_000,
+        n_roots: int = 100,
+        rel_tol_scale: float = 10.0,
+    ):
+        # --- randomization -------------------------------
+        self._seed = seed + SEED_OFFSET_FUNCTION_SAMPLER
+
+        # --- function properties -------------------------
+        self._fun = fun
+        self.x_min = x_min
+        self.x_max = x_max
+
+        # --- settings ------------------------------------
+        self.dx = dx
+        self.n_fun_samples = n_fun_samples
+        self.n_roots = n_roots
+        self.rel_tol = EPS * rel_tol_scale
+
+        # --- cache ---------------------------------------
+        self._fun_cache: dict[float, float] = dict()
+
+    # -------------------------------------------------------------------------
+    #  Low-level generic functionality
+    # -------------------------------------------------------------------------
+    def f(self, x: float | list[float]) -> float | list[float]:
+        # simple cached version of fun(x), without size limit (and simpler than lru_cache, so less overhead)
+        if isinstance(x, list):
+            # --- get MULTIPLE f(x) values ------
+            fx_values = []
+            for single_x in x:
+                if not (self.x_min <= single_x <= self.x_max):
+                    raise ValueError(f"x={single_x} is out of bounds [{self.x_min}, {self.x_max}]")
+                elif single_x not in self._fun_cache:
+                    self._fun_cache[single_x] = fx = self._fun(single_x)
+                else:
+                    fx = self._fun_cache[single_x]
+                fx_values.append(fx)
+            return fx_values
+        else:
+            # --- get SINGLE f(x) values --------
+            if x in self._fun_cache:
+                return self._fun_cache[x]
+            elif self.x_min <= x <= self.x_max:
+                fx = self._fun(x)
+                self._fun_cache[x] = fx
+                return fx
+            else:
+                raise ValueError(f"x={x} is out of bounds [{self.x_min}, {self.x_max}]")
+
+    @cache
+    def x_values(self) -> np.ndarray:
+        """
+        Returns an array of x-values in [x_min, x_max] that we use to sample the function and infer its properties.
+        This is based on the multi_scale_samples function and does not include any other cached x-values resulting
+        from other calls to .f(.)
+        """
+        return multi_scale_samples(
+            x_min=self.x_min,
+            x_max=self.x_max,
+            dx_min=self.dx,
+            n=self.n_fun_samples,
+            seed=self._seed,
+        )
+
+    @cache
+    def fx_values(self) -> np.ndarray:
+        """f(x) values corresponding to the x_values()."""
+        return np.array(self.f(list(self.x_values())), dtype=np.float64)
+
+    def function_cache(self) -> list[tuple[float, float]]:
+        """
+        Returns contents of the function cache as a list of (x, f(x))-tuples.
+        Note this might return more information than .x_values() and .fx_values(), since those methods
+        only return information related to the initial multiscale sampling.
+        """
+        return list(self._fun_cache.items())
+
+    def function_cache_size(self) -> int:
+        """Return number of values in function cache."""
+        return len(self._fun_cache)
+
+    @cache
+    def fx_diff_values(self) -> np.ndarray:
+        return np.diff(self.fx_values())
+
+    @cache
+    def fx_quantile(self, q: float, absolute: bool) -> float:
+        """
+        Returns the requested quantile f(x).
+            absolute==False    --> quantile of f(x)
+            absolute==True     --> quantile of abs(f(x))
+        """
+        if absolute:
+            return float(np.quantile(abs(self.fx_values()), q))
+        else:
+            return float(np.quantile(self.fx_values(), q))
+
+    @cache
+    def robust_estimated_fx_max(self) -> float:
+        """
+        Robust, approximate estimate of max(f(x)), without being susceptible to single-sample outliers, which might
+        arise in certain corner cases.
+
+        NOTE: this value is not guaranteed to be equal or larger than abs(f(x)), but should provide a reasonable
+              estimate under most regular circumstances.
+        """
+        q = 1 - (1 / math.sqrt(self.n_fun_samples))
+        return (1 / q) * self.fx_quantile(q, absolute=True)
+
+    # -------------------------------------------------------------------------
+    #  Specialized - Tolerances
+    # -------------------------------------------------------------------------
+    @cache
+    def tol_array_local(self) -> np.ndarray:
+        """
+        Return (n_fun_samples, )-sized array with absolute tolerance values > 0, representing the LOCAL tolerance wrt
+        numerical rounding errors on a LOCAL per-sample basis, i.e. computed based on the magnitude of each f(x) sample.
+        """
+        return self.rel_tol * abs(self.fx_values())
+
+    @cache
+    def tol_array_global(self) -> np.ndarray:
+        """
+        Return (n_fun_samples, )-sized array with absolute tolerance values > 0, representing the GLOBAL tolerance wrt
+        numerical rounding errors on a GLOBAL basis, i.e. computed based on the overall (~maximum) magnitude of f(x).
+        This is a constant matrix.
+        """
+        return np.full(self.n_fun_samples, self.rel_tol * self.robust_estimated_fx_max())
+
+    @cache
+    def fx_diff_smooth_sign(self) -> np.ndarray:
+        """
+        Returns an array with elements in [-1,+1] representing a more nuanced np.sign(np.diff(fx_values())).
+
+        Local and global tolerances are used to determine the threshold around which differences transition
+        (smoothly) from 0 to 1 or 0 to -1.
+
+        See also smooth_sign().
+        """
+
+        # determine inner_tol, outer_tol
+        tol_global = self.tol_array_global()
+        tol_local = self.tol_array_local()
+
+        inner_tol = np.minimum(tol_local, tol_global)  # make sure inner_tol[i] is the smallest of both tolerances
+        outer_tol = np.maximum(tol_local, tol_global)  # make sure outer_tol[i] is the largest of both tolerances
+
+        # reduce to size n-1 from size n  (take sum)
+        inner_tol = inner_tol[1:] + inner_tol[:-1]  # take sum of both tolerances
+        outer_tol = outer_tol[1:] + outer_tol[:-1]  # take sum of both tolerances
+
+        # compute smooth_sign
+        return smooth_sign_array(
+            x=self.fx_diff_values(),
+            inner_tol=inner_tol,
+            outer_tol=outer_tol,
+        )
+
+    # -------------------------------------------------------------------------
+    #  Specialized - Roots
+    # -------------------------------------------------------------------------
+    @cache
+    def candidate_root_intervals(self) -> tuple[list[tuple[float, float]], list[tuple[float, float]]]:
+        """
+        Return a list of 'root intervals' and 'non-root intervals', with the root intervals serving as candidates
+        (but potentially too many) for root finding.
+        :return: (root_intervals, non_root_intervals)-tuple
+                    root_intervals      : list of (x_left, x_right)-tuples   WITH    sign flip
+                    non_root_intervals  : list of (x_left, x_right)-tuples   WITHOUT sign flip
+        """
+
+        # multi-scale samples as (x, fx)-tuples
+        samples = list(zip(self.x_values(), self.fx_values()))
+
+        # remove 0-valued samples, we are looking for strict sign flips
+        samples = [(x, fx) for i, (x, fx) in enumerate(samples) if (fx != 0.0)]
+
+        # split in root- and non-root-intervals
+        root_intervals = []
+        non_root_intervals = []
+        for (x_left, fx_left), (x_right, fx_right) in zip(samples[:-1], samples[1:]):
+            if np.sign(fx_left) != np.sign(fx_right):
+                # sign flip
+                root_intervals.append((x_left, x_right))
+            else:
+                # no sign flip
+                non_root_intervals.append((x_left, x_right))
+
+        # we're done
+        return root_intervals, non_root_intervals
+
+    @cache
+    def roots(self) -> list[Root]:
+        """
+        Returns at most 'n_roots' root intervals [root_min, root_max] obtained using find_root_and_width().
+        We start from the candidate_root_intervals and - if needed - sample 'n_roots' intervals randomly
+        to if there are too many candidate intervals.
+        :return: list of Root objects, with deriv_sign != 0.
+        """
+
+        # get intervals
+        cand_intervals, _ = self.candidate_root_intervals()
+
+        # sample if needed
+        if len(cand_intervals) > self.n_roots:
+            cand_intervals = [
+                cand_intervals[i]
+                for i in sample_integers(
+                    i_min=0,
+                    i_max=len(cand_intervals),
+                    n=self.n_roots,
+                    seed=self._seed,
+                )
+            ]
+
+        # compute roots & return
+        return [
+            find_odd_root(
+                fun=self.f,
+                x_min=x_min,
+                x_max=x_max,
+                dx_min=(EPS * EPS) * (self.x_max - self.x_min),
+            )
+            for x_min, x_max in cand_intervals
+        ]