linstabpy v1.0.0rc6

The supplement examples ship complete: Martini 0-5, Song 32 deg, and
Savarino, with their parity audits, slim reference fixtures, and the
paper-style figures. Two operator corrections came out of that audit.
On a deformed y-symmetric mesh the metric terms now come from the full
eta operators, so the family second derivatives converge at the axis.
The Floquet shift defaults to the continuum chain rule; the LinStab2D
discrete form stays behind matlab_parity.

Added

• Each Savarino map-walk row records its commit, its Slurm job, and its machine.
• resolvent_analysis returns the factor, SVD, and residual stage clocks.
• The Savarino line campaign times a recycled sweep against a factor at each frequency.
• Song (2023) example complete (examples/song/, θ = 32° only): self-contained
  supplement pipeline from Song FV export through LinStabPy validation figures.
  • prepare_baseflow.py — Plot3D → nodal .npy (601→599 trim, interpolation, nondim).
  • plot_baseflow.py — mesh + mean-flow panels (examples.figure_style LaTeX fonts).
  • configs/run_fd4_n30.yaml — FD4, n = 30, β = 19.2, no operator dissipation (ε = 0).
  • song.py — EVP driver; default config → configs/run_fd4_n30.yaml.
  • report_matched20.py, plot_spectrum_matched20.py, plot_eigenmode_lead.py —
    Hungarian matched-20 spectrum and lead eigenmode vs Song reference.
  • song_plot_utils.py, reference_paths.py; shipped reference under reference/.
  • Shipped validation figures under figures/ (baseflow mesh/fields, matched-20
    spectrum, lead eigenmode; FD4 n = 30, ε = 0).
  • Local-only outputs: inputs/baseflow/, output/fd4_n30/ (gitignored).
  • Validated (FD4 n = 30, ε = 0): 20/20 Song modes within |Δω| ≤ 0.01; lead |Δω| ≈ 0.002.
• Martini (2024) examples 0–5 — presentation + parity closure (examples/martini/):
  audit CLOSED 2026-08-18 (AUDIT_PLAN.md; steps A→E, user sign-off all six cases).
  • Per-case plotters: example_{0..5}_plots.py plus shared
    plot_compare_utils.py, split_martini_fixtures.py,
    run_all_martini_examples_and_plots.py — thesis-style mosaics (LinStab2D |
    linstabpy | peak-normalized % error), spectra, and baseflow panels.
  • Slim MATLAB reference fixtures under examples/martini/LinStab2DResults/
    (compact u+v / u+v+w, complex128); bundled linstab2D_scripts/ and
    regenerate_martini_fixtures.sh for MATLAB → NPZ regen.
  • Bundled baseflow .mat files under examples/martini/baseflows/
    (BL_BF.mat, Step_BF.mat, M09jet.mat, Paraboloid_BF.mat).
  • Shipped presentation PNGs next to each driver (baseflow, spectrum, mode
    mosaics for Ex. 1–5; validation triptych for Ex. 0).
• Savarino (2026) example — reorganized supplement reproduction (examples/savarino/,
  θ = 30.8° SWBLI resolvent validation, Figs. S4–S6):
  • Layout: configs/ (YAMLs + grids), reference/ (author baseflow + packed
    response modes), output/ (run records, figures, local intermediates).
  • Configs (configs/): map_base.yaml, mack_f2_b45.yaml,
    liftup_f1em4_b163.yaml, point.sbatch.template, savarino_map317_points.csv
    (317-pt β–f grid for dense-map campaigns).
  • Shipped reference: Tecplot base flow under reference/baseflow/; packed
    reference/savarino_response_{mack,liftup}.npz (primitive ρ′, u′, v′, w′, T′).
  • Shipped results (output/): savarino_map2_200pt.csv (200-pt gain-map run
    record), savarino_map317pt.csv (317-pt minimal dense subset from PhD
    map_minimal_keep_author200), validation figures under output/figures/
    (mode comparisons + 200-/317-pt gain maps).
  • collect_campaign.py --from-npz — aggregate NPZ + .metrics.json trees into
    the run-record CSV layout (for PhD dense-map campaigns without Slurm logs).
  • gen_campaign.py --grid {author200,dense317} — Slurm/local campaign generator
    for 200- or 317-point grids.
  • Plotters aligned with PhD Savarino2026 style:
    • plot_gain_map.py — tensor/PCHIP interpolation, σ₁² colorbar with ×10⁴
      on top, Mack / lift-up peak markers (plot_resolvent_map_savarino_style.py
      parity); optional --show-points / --baseline-summary for diagnostics.
    • compare_modes.py — Song eigenmode layout, peak-normalised ±1 colourbar,
      ymax 0.06 (Mack) / 0.1 (lift-up) (plot_savarino_modes_linstabpy_template.py
      parity).

Changed

• Recycled GMRES restarts. The restart is a Krylov length. It is never the system size.
• certified_rsvd logs every check when one check fails. One seed skips the multi-seed check.
• Floquet shift default is now continuum (LINSTABPY_FLOQUET_SHIFT,
  numerics.floquet_shift): DZ += iα I, D2RZ += iα DR, D2Z += 2iα DZ − α² I,
  the chain rule of (∂z + iα). The LinStab2D algebra (D2RZ += iα I and D2Z
  built from the already-shifted DZ, i.e. −3α² I) stays available as
  matlab_parity; the Martini Ex. 3 YAMLs and examples/sawtooth pin it.
  Plane Poiseuille at Re = 10⁴, α = 1 (Orszag 1971): continuum converges to
  ω = 0.23752649 + 0.00373967i (|Δω| 3.8e-4 → 1.8e-6 for ny 128 → 512);
  matlab_parity stalls at |Δω| ≈ 3.2e-4, a growth rate 8.5 % low, at every
  resolution. Any unpinned Floquet run changes with this default.
• Replaced the legacy Song figure/pack/matrix scripts with the pipeline above;
  see examples/song/README.md for run order.
• song.py creates the output NPZ parent directory before save and reads
  numerics.operator_dissipation from YAML (disabled, ε = 0 for this test).
• song_plot_utils.load_song_leading_mode_npz transposes the shipped reference
  eigenmode NPZ to LinStabPy (ny, nx) layout for plotting.
• .gitignore re-ignores regenerated example outputs (examples/**/figures/,
  examples/**/output/, Song inputs/baseflow/, logs) after the example PNG
  whitelist; Song figures/ and reference NPZ are shipped; raw Plot3D exports
  under inputs/raw/ stay local.
• Song plot scripts require LaTeX via figure_style.check_plot_environment;
  see examples/song/README.md for system packages (texlive-latex-extra, …).
• examples.figure_style: check_plot_environment(require_latex=…) with install
  hint, optional dpi / pad_inches on save(); tests in tests/test_figure_style.py.
• Grouped Song (2023) reference assets under examples/song/reference/:
  baseflow/song_32deg.npz, eigenmode/song_32deg_leading_mode.npz,
  spectrum/eigenvalues.dat, spectrum/omega_i.csv. Added reference_paths.py
  and updated configs, figure scripts, and tests.
• Martini fixture layout and git policy:
  • Shipped NPZ: examples/martini/LinStab2DResults/*.npz only (slim MATLAB
    reference). Root-level example_*.npz from linstabpy drivers are
    gitignored (regenerated locally; several exceed the 60 MiB tracked-file
    guard).
  • Raw MATLAB .mat exports stay outside Git in martini_examples/ (gitignored
    scratch; recreated by regenerate_martini_fixtures.sh).
  • Run logs under examples/martini/_run_logs/ are gitignored.
  • Renamed examples/martini/data/ → baseflows/.
• Martini plot/compare layer (repo mosaics ≤ 0.49% peak-norm vs campaign;
  Ex. 4 cavity audit closed — residual tail is MATLAB eigs convergence, not
  operator/BC):
  • plot_compare_utils.py: used_ind 0-based gridding, matlab_plot_grid_shape,
    compact_resolvent_modes_uvw, peak-normalized mosaic triptychs.
  • example_4_plots.py / split_martini_fixtures.py: slim MATLAB u+v+w compare
    with joint complex scaling; Example 4 YAML pins Pr: 0.7 and
    zero_dmudT: true for LinStab2D parity.
  • compare_martini_examples.py and tests/test_martini_parity_compare.py
    updated for LinStab2DResults/ fixture paths and compact mode layout.
• Moved library validation CLIs from examples/martini/ to tests/tools/
  (assembly_parity.py, assembly_metrics_diff.py, lnse_equivalence_harness.py,
  matlab_source_parity.py, symbolic_compressible_nse.py,
  coefficients_reference_base.py, NSE_DERIVATION.md). See
  tests/tools/README.md for rationale and owner review checklist.
• Removed unused maintainer-only scripts from examples/martini/:
  check_parity_matrices.py, compare_operator_construction.py,
  perf_memory_operator_parity.py, operator_matrix.json, branch_matrix.json,
  martini_c64_max_rel.txt, martini_examples.sbatch.
• Savarino example layout and git policy:
  • Moved point YAMLs, campaign template, and 317-pt grid into configs/; run
    records into output/ (savarino_map2_200pt.csv was at example root).
  • reference_paths.py: GAIN_MAP_CSV, GAIN_MAP_317_CSV, figure paths under
    output/figures/; compare outputs under output/compare/.
  • .gitignore ships only curated Savarino outputs: both map CSVs and
    output/figures/*.png. Gitignored: output/baseflow/*.npy (from
    savarino_to_npy.py), output/compare/**/*.npz (from run_compare_points.py),
    reference/zenodo/. Whitelist repeated after root output/ rule.
  • run_compare_points.py, gen_campaign.py, collect_campaign.py, mode_oracle.py
    updated for configs/ paths.
  • See examples/savarino/README.md for minimal workflow and maintainer scripts
    (verify_norm_convention.py, mode_oracle.py, fetch_zenodo.py,
    pack_reference_modes.py).

Fixed

• Mesh.deform on a y-symmetric mesh with a non-separable map: the dJ/Q
  metric terms of the symm/asymm family operators are now differentiated with
  the full Dy/D2y (the coordinate map has no η parity), as LinStab2D
  DeformMesh.m does. Before, the family stencils were applied to the
  coordinates themselves and D2y_asymm/D2y_symm did not converge at the axis
  rows (relative error growing like 1/h under refinement: 7.7 → 61 for
  n = 16 → 128 on a polynomial map; 3.5 → 29 on the Z² map). After: 2.2e-4 → 3.9e-7
  (order 3, asymm) and 2.1e-3 → 3.1e-5 (order 2, symm). Only y_symmetry=True
  meshes on the full-2D deform path are affected (Martini Ex. 5 paraboloid;
  the SWBLI cases are untouched). Regression: test_deform_full_2d_family_metric_terms_use_full_operators.
• The walk probe uses the last response, not a ones vector.
• A walk GMRES has a four-iteration cap. A dead walk raises and factors this omega.
• append_row refuses a row that does not match the header.

Removed

• Dropped song_fig{1,2,3}_*.py, pack_run.py, run_song_2023_*.py, song.sh,
  song_32deg_spectrum_quoted.csv, and the old song_32deg*.yaml / sbatch configs
  from examples/song/.
• Dropped committed LinStabPy outputs from the old flat examples/song/ layout
  (song_32deg_modes.npz, song_32deg_spectrum.csv, song_matlab_timing.json,
  root-level song_fig*.png). Large EVP dumps and raw Plot3D inputs stay local;
  curated reference NPZ and validation PNGs now live under reference/ and
  figures/ respectively.
• Dropped the 31.6 deg Song example from examples/song/: baseflow
  (song_316deg.npz, song_316deg_leading_mode.npz), reference spectrum
  (song_316_eigenvalues.dat), configs (song_316deg.yaml, song_316deg.sbatch),
  and comparison helpers (compare_evp_to_song316.py, parse_song316_eigenvalues.py).
  The shipped example is 32 deg only; 31.6 deg validation stays in the PhD case tree.
• Dropped committed linstabpy driver NPZ from examples/martini/ root
  (example_*.npz, legacy *_values.npz / *_modes.npz / *_logs.npz splits).
  Regenerate locally via ./run_all_examples.sh or per-case drivers; parity
  against MATLAB uses LinStab2DResults/ only.
• Dropped old debug/support PNGs from examples/martini/ (per-case
  *_support_components*.png, legacy single-panel example_*_{blasius,jet,...}.png
  layouts superseded by mosaic figures).
• Dropped savarino_corner_probe_uv.yaml and savarino_corner_probe_wonly.yaml
  (side experiments; not part of the S4–S6 reproduction path).
• Dropped example-root Savarino YAMLs and Slurm template (now under configs/):
  savarino_point_f2_b45.yaml, savarino_point.sbatch.template; renamed
  compare_liftup_f1em4_b163.yaml → liftup_f1em4_b163.yaml.
• Dropped committed PNGs from examples/savarino/reference/ (figures now under
  output/figures/).