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* updating help for makefile * updating template module * cleanups * cont... * cool... * cool... * scoping out updates and upgrades. * 01 Template rename and refresh Rename pyMathTools/pyMathToolsPlotHelpers packages to snake_case (math_tools/math_plot_helpers) and re-parent QuaternionABC onto the new foundation_abc layout per the template conformance spec. * 02 Errors and layering Add the math_tools exception hierarchy (MathToolsError and three domain subtypes) and an AST-based package layering test enforcing math_tools never imports math_plot_helpers/matplotlib, and math_tools.otg (once it exists) never imports numpy. * 03 Governance and readme Add .claude/CLAUDE.md and a real README, correct pyproject dependency names (numpy/scipy were missing), and fix dead MathTypes import paths in the two spherical plotting examples so they import-run cleanly. * updating the github actions * fixes for ci-cd * 04 Precision time interval Add PrecisionTimeInterval: an immutable, hashable, attosecond-exact subclass of PrecisionTimeIntervalABC backed by a single signed total- attosecond int, with full arithmetic/ordering/wire-dict surface per precisionTimeMath.md. * 05 Precision timestamp Add PrecisionTimestamp: an immutable, hashable, epoch-referenced timestamp composing a PrecisionTimeInterval offset plus optional timescale/reference_frame/uncertainty metadata, with Swift-parity can_compare/compare_validated semantics per precisionTimeMath.md. * 06 Position Add Position: a numpy-backed 3D point type subclassing PositionABC with cylindrical/spherical/spherical-iso constructors and inverse accessors, full vector arithmetic, and the shared API idioms (normalize/normalized, isclose, __array__, unhashable). * 07 Quaternion additions Add dot, rotation_matrix_elements (delegating to to_rotation_matrix), rotate_position, __array__, and snake_case aliases for the two existing camelCase methods to Quaternion. Purely additive: legacy tests/test_quaternion.py is untouched. * 08 Spatial pose Add SpatialPose: an SE(3) pose composing Position + Quaternion, subclassing SpatialTransformABC. Constructors (components, homogeneous matrix, Denavit-Hartenberg, identity), composition/transform via *, translated, inverse, relative_pose, interpolate (lerp + slerp), position/angular distance (double-cover safe), and normalize/normalized per spatialMath.md. * 09 Univariate polynomial Add UnivariatePolynomial: an immutable, numpy-backed general polynomial with ascending-degree float64 coefficient storage, derivative/integrate, companion-matrix real_roots (raises PolynomialSolveError on the zero polynomial), and value evaluation via numpy's polyval. * 10 Roots kernel Faithful port of the Swift OTG analytic root kernel (Roots.swift/Utils.swift): solve_cubic, solve_resolvent, solve_quartic_monic, evaluate_polynomial, polynomial_derivative(_monic), shrink_interval, integrate_jerk. Corrects a latent 1/a^4 vs 1/a^3 scaling bug in solve_cubic's halfq term (inert in the Swift source's monic-only call sites, not inert for general coefficients per Compliance 2b), documented in polynomials.md. Re-homes POLYNOMIAL_ZERO_THRESHOLD from polynomial.py into roots.py. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 11 Waveform1D core container Adds the scalar waveform container: attosecond-exact PrecisionTime axis, 22 signal generators, None-on-empty statistics (population variance pinned), attosecond-exact slicing, and the list-vocabulary mutation API. No DSP mixins yet (composed in a later chunk); no arithmetic operators (chunk 12). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 12 Waveform1D operators & comparison Adds the elementwise operator surface: arithmetic (+ - * / // %, forward/ reflected/in-place), bitwise (integer-dtype only), unary, and comparison producers (elements_equal/less_than/greater_than, isclose_elementwise, isclose). Waveform-Waveform ops require equal dt+length (WaveformCompatibilityError otherwise); results carry dt/t0 from the left operand. Fixes a bug where Waveform1D's __array__ let numpy's ufunc machinery bypass Python's operator protocol for numpy-scalar/array operands (e.g. np.float64(2.0) + w silently returned a bare ndarray, discarding dt/t0) by setting __array_ufunc__ = None, with a regression test. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 13 Waveform1D signal generators The 22 generators themselves landed early in chunk 11 (umbrella spec groups them under Constructors). This chunk adds the dedicated compliance-4 test file, and fixes a real gap: sine's frequency parameter had no default, so the spec's own pinned example (Waveform1D.sine(n=1000)) raised TypeError. frequency now defaults to 1.0 Hz on sine only, matching the literal acceptance criterion. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 14 DSP support types + mixin protocol Adds the shared substrate for the upcoming DSP mixin chunks: all 12 support enums + 15 frozen descriptor dataclasses (eq=False on the 5 ndarray-bearing ones), the WaveformProtocol structural contract mixins will depend on, and Waveform1D._with_values (the replace-values factory). WaveformTriggerType (undefined in the Python spec text) is flattened from Swift's associated-value enum into a 4-member discriminator, with the payload moved onto WaveformTrigger's optional fields. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 15 WaveformPosition Adds the position time-series aggregate container: (n,3) float64 storage, on-demand Position materialization, from_components with length/dt validation, vectorized normalize/component_waveforms (never loops over materialized elements), and the full mutation/extend/concatenate verb set. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 16 WaveformQuaternion Adds the quaternion time-series aggregate container, mirroring WaveformPosition's structure: (n,4) float64 storage in w-first order (pinned repo-wide, not Swift's x-first), on-demand Quaternion materialization, w-first component_waveforms/from_components, vectorized are_all_unit/normalize, and the full mutation/extend/concatenate verb set. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 17 WaveformSpatialPose Adds the 6-DOF pose time-series container: parallel (n,3) position + (n,4) w-first quaternion arrays, from_poses/from_waveforms constructors, nested component_waveforms reusing chunks 15/16's per-axis NamedTuples, and the is_valid/sample_count=min(...) semantics for the (deliberately constructible) unequal-array-length edge case. Completes Track C (chunks 11-17). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 18 DspCalcMixin Add CalcMixin (integrate/derivative). Fixed a runtime bug in the planned mixin pattern: nominally subclassing WaveformProtocol shadows Waveform1D's real properties under C3 linearization, so mixins now self-type instead (mypy's documented "mixin classes" idiom). Spec and protocol docs updated accordingly for chunks 19-29. * 19 DspCorrelationMixin Add CorrelationMixin (auto_correlation, cross_correlation, find_max_correlation), backed by scipy.signal.correlate. Lag sign kept as scipy's native convention (spec-permitted divergence from Swift), documented in the module docstring. * 20 DspEnvelopeMixin Add EnvelopeMixin: amplitude_envelope (Hilbert), upper_lower_envelopes (peak/valley interpolation), instantaneous_amplitude (HILBERT/RMS/PEAK). * 21 DspSpectralMixin Add SpectralMixin: fft, power_spectral_density (Welch), spectrogram, mel_spectrogram, spectral_features (centroid/spread/rolloff/flatness). * 22 DspFilteringMixin Add FilteringMixin: low/high/band-pass, dispatcher (incl. band-stop), moving-average, exponential, Savitzky-Golay, Whittaker-Henderson filters, and frequency_response. * 23 DspPeakMixin Add PeakMixin: detect_peaks, detect_valleys, find_most_prominent_peaks, backed by scipy.signal.find_peaks/peak_prominences. * 24 DspPhaseMixin Add PhaseMixin: instantaneous_phase, unwrap_phase, instantaneous_frequency, phase_difference, phase_coherence, phase_synchronization_index, group_delay. * 25 DspResamplingMixin Add ResamplingMixin: decimated, interpolated, resampled, resampled_to_match, polyphase_resampled. Adds WaveformProtocol._with_axis (dt-changing factory sibling to _with_values) since resampling is the first DSP family that changes sample spacing. * 26 DspTimeAlignmentMixin Add TimeAlignmentMixin: aligned, time_lag, synchronize, time_windows, time_segments. Adds WaveformProtocol._with_t0 (t0-changing factory, completing the _with_values/_with_axis/_with_t0 result-factory triangle), since this is the first DSP family whose results carry a different t0 than their source. * 27 DspTriggerMixin Add TriggerMixin: detect_edge_triggers, detect_level_triggers, detect_window_triggers, detect_pattern_triggers, generic detect_triggers dispatcher, with_event_markers. WaveformTrigger gains optional edge/ window_kind fields for the dispatcher; WaveformWithEvents.waveform is now typed WaveformProtocol instead of concrete Waveform1D, which also removes support.py's only import of waveform1d.py (preempts the import cycle flagged in chunk 19). * 28 DspWindowingMixin Add WindowingMixin: generate_window, windowed, window_coherent_gain, window_processing_gain. * 29 DspZeroCrossingMixin Add ZeroCrossingMixin: zero_crossings, zero_crossing_count, zero_crossing_rate, segments_between_zero_crossings. * 30 DspCompose Compose all twelve DSP mixins onto Waveform1D in the spec-pinned base order. Fixes a circular import surfaced by dsp/__init__.py now eagerly re-exporting every mixin (support.py's WaveformProtocol import moved under TYPE_CHECKING). Mixin test files drop their local `class _W(Mixin, Waveform1D)` subclasses in favor of plain Waveform1D. Adds test_compose.py: MRO/concreteness pins plus a live smoke call per mixin family on a real Waveform1D instance. * 31 OtgEnumsAndErrors * 32 OtgInputParameter * 33 OtgProfile * 34 OtgBlockBrakeBound * 35 OtgTrajectoryAndOutput * 36 OtgVelocitySteps * 37 OtgPositionFirstSecondSteps * 38 OtgPositionThirdStep1 * 39 OtgPositionThirdStep2 * 40 OtgCalculatorTarget * 41 OtgDriver Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 42 OtgOracleSuites Corrects otg.md's numeric-truth-table atol from 1e-8 to 1e-6 (semver 0.0.4 -> 0.0.5): the Swift source literals are recorded to only 6 decimal places, so 1e-8 was unsatisfiable by any correct port. Also corrects "32-case" to "31-case" (the Swift array has 31 entries). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 43 PublicSurface Final chunk of the math-tools-port plan: curates the flat `import math_tools as mt` root surface (19 re-exports, no logic), pinned by test_public_surface.py. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * Mark math-tools-port plan complete (all 43 chunks done) Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * 44 OtgStep2UdudDiscriminant Fix j·tf⁴→j·tf³ transcription defect in UDUD-T0246 discriminant (tf_p3→tf_p2) at position_third_order_step2.py:1731,1752,1763; add regression test. Scaffold Track F corrective plan overview. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 45 OtgTrivialProfileLength Trivial branch builds fixed-length 8-element a/v/p arrays and sets pf to current position, per otg.md fidelity requirement 1; add regression tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 46 OtgStep1SqrtGuard Replace 8 bare math.sqrt sites in position_third_order_step1 with the IEEE-754 _ieee754_sqrt (NaN on negative radicand) so out-of-domain candidates are rejected by guards instead of raising; add regression test. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 47 PositionToleranceAndTimestampAccessors Position.is_unit uses rtol=0.0 so only spec atol=1e-12 applies; days_since_epoch/seconds_of_day derive from signed total_attoseconds (floor div/mod) for correct pre-epoch behavior. Add regression tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 48 RootsDegenerateCases solve_cubic uses a scale-relative leading-coefficient degeneracy threshold; shrink_interval guards f==0 before the Newton step to avoid a ZeroDivisionError trap. Update polynomials.md (semver 0.0.4) and add regression tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 49 WaveformSpatialPoseIndexing Route __getitem__/get/pop through a shared _resolve_index helper that bounds against sample_count (not either raw array's length), per waveformCore.md compliance 9; add regression tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 50 AggregateContainerApiIdioms Add __array__ and isclose to the three aggregate waveform containers, restore WaveformSpatialPose.from_components, and fix Waveform1D.__array__ copy=False contract (C-7). Update waveformCore.md (semver 0.0.3) and add tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 51 WaveformGeneratorPhaseConventions chirp/heaviside/sigmoid derive total duration from an endpoint-inclusive (n-1)*dt span via _span_seconds (0.0 at n<=1), fixing off-by-one phase conventions. Update waveformCore.md (semver 0.0.4) and add tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 52 SubpackagePublicSurface Give math_tools.spherical and math_plot_helpers curated __all__ re-exports; update README/examples to import at subpackage level; pin the surface with tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 53 WindowConventionReconciliation Reconcile window symmetric/periodic conventions: add periodic param to windowing helpers (default symmetric), share DEFAULT_KAISER_BETA across windowing/spectral. Document per-family rule in waveformDsp.md (semver 0.0.8) and add tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 54 TestClosureTracksBC Close 11 Track B/C test-coverage gaps (hashability, double-cover isclose, operator surface, generator analytics, bulk smoke, indexing); set Quaternion.__hash__ = None explicitly (the one permitted src edit). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 55 TestClosureDsp Close 23 DSP test-coverage gaps with value-level known-answer/analytic assertions across all DSP mixin families; tests only, no src changes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 56 TestClosureOtgOracles Close 8 OTG oracle-coverage gaps: add a reproducible 450-case multi-DOF corpus that exercises Step2 (0->900 invocations), plus continuity, retarget, invariant, and the missing testBugFix_NegativeTimeInterval_Case3 cases. Correct chunk 42's stale 'all 4 testBugFix' claim. Tests/data only. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * 57 DocsAndConventionSweep Reconcile docs against post-fix repo: fix dead CI/workflow refs, stale OTG tolerance (1e-6) and case-count claims, install/keyword drift; wire examples/ into the gate (lint+typecheck clean); delete hints.py dead __main__; add governance tests. Bump templateConformance (0.0.3) and overview (0.1.1). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * Mark math-tools-port plan complete (Track F, all 57 chunks done) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * clean room installs requirements.txt before the package pyproject declares dependency NAMES ONLY per the BKM; requirements.txt carries the pins and git pointers. testInEnvInstallFromSetup ran `pip install ".[dev]"` alone, so pip resolved the bare name pyFoundationTools against PyPI and failed with "No matching distribution found". Every other install path here already installs -r requirements.txt first. make testInEnv now green: 1550 passed. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * rename clean-room sub-steps so they stop implying tests Back-port of the py-cookiecut rename. testInEnv green end-to-end after the rename (1550 passed in the clean room). Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * cont.... * bump ver --------- Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
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