| subproject_distr |
2026-09-22 |
retire: only caller of the subproject scheduling framework in simple_qsys_ctrl/simple_qsys_env, removed as dead production code (plan section 9.5) |
- |
| ptcls_ppca_subproject_distr |
2026-09-22 |
retire: as subproject_distr |
- |
| ori |
2026-09-22 |
merge into unit_ori: print-only smoke of the ori API (three THROW_HARDs); wrote a project to disk |
assertions added to simple_ori_tester for ori_from_rotmat, reject, append_ori, delete_entry, get_keys, ori_strlen_trim, ori2chash/chash2ori, ori2json, get/set_ctfvars; get_axis_angle removed from simple_ori (no production caller) |
| ori_test |
2026-09-22 |
merge into unit_ori: same body as ori on the exec route |
as ori |
| oris |
2026-09-22 |
merge into unit_ori: reallocate check plus print-only write/read (read into an empty object checked nothing) |
assertions added to simple_oris_tester for reallocate, write/read round-trip, rnd_oris bounds and Euler limits |
| oris_test |
2026-09-22 |
merge into unit_ori: same body as oris on the exec route |
as oris |
| sym |
2026-09-22 |
merge into unit_ori: sym_tester printed subgroup tables, limits and PASSED/FAILED lines without failing |
new simple_sym_tester (sub-suite symmetry of unit_ori): order and classification, eullims per group, subgroup tables and Lagrange, symops form a group (identity, proper rotations, distinct, closed), apply consistency, rnd_euler limits, rot_to_asym, symrandomize, build_refspiral (size, redundancy, north pole, mirror pairs); sym_tester removed from simple_sym |
| sym_test |
2026-09-22 |
merge into unit_ori: same body as sym on the exec route |
as sym |
| uniform_euler |
2026-09-22 |
delete: printed 2000 random normals for eyeballing; no assertion possible beyond what symmetry/orientation already check (rnd_euler limits, get_normal) |
- |
| uniform_rot |
2026-09-22 |
delete: quaternion-sampling demo using intrinsic rand; exercised no production code |
- |
| angres (standalone) |
2026-09-22 |
modify: the route moved to simple_test_exec test=angres; the standalone program is gone |
simple_test_exec test=angres |
| corrs2weights_test |
2026-09-22 |
merge into unit_numerics: printed corrs2weights(CORRW_CRIT) for twelve values; the only exercise of a production path (motion-correction frame weights) |
simple_stat_tester (sub-suite statistics): weights sum to one, zero for non-positive correlations, monotone, sigmoid threshold, norm_sigm=.false. ratio rule, all-zero case, UNIFORM/RANK/ZSCORE criteria |
| corrs2weights |
2026-09-22 |
merge into unit_numerics: the standalone twin of corrs2weights_test (same body plus UNIFORM_CRIT) |
as corrs2weights_test |
| rank_weights |
2026-09-22 |
merge into unit_numerics: gnuplotted the four rank-weight kernels; their only production caller is conv2rank_weights (wcrit=sum|cen|exp|inv) |
simple_stat_tester: each kernel positive, non-increasing, sums to one, closed-form spot values; conv2rank_weights single/zero/general cases |
| ft_expanded |
2026-09-22 |
merge into unit_numerics: ran test_ftexp_shsrch (already in the gate) and test_ftexp_shsrch2 (not run anywhere) |
both are now sub-suites of unit_numerics (shift search, correlator and shift search, optimiser): a motion-correction optimiser, not an image test (Hans); since 2026-09-25 one sub-suite shift search, simple_ftexp_shsrch_tester |
| order_corr |
2026-09-22 |
delete: printed oris%order() and declared PASSED on the array size |
simple_oris_tester now asserts the corr-descending order |
| phasecorr |
2026-09-22 |
delete: convention demo of a hand-rolled phase correlation on 1000x1000 half-discs with gnuplot windows; touched no production phase-correlation code |
- |
| rotate_ref |
2026-09-22 |
delete: benchmark of two local copies of a rotation routine on random data; the fast copy is the production polarft_calc%rotate_ref_8, which remains untested at unit level |
- |
| eval_polarftcc |
2026-09-22 |
delete: user-supplied volume, timing printout, no assertion; footprint shared with continuous_inplane_cc_grad (which also needs vol1) |
- |
| bounds_from_mask3D_test |
2026-09-22 |
merge into unit_image: built a 256^3 cube, wrote cube.mrc, printed the bounds |
simple_image_msk_tester (sub-suite masks): tight bounds of a centred cube against a brute-force scan, crossed bounds for an empty mask, containment of an off-centre voxel |
| bounds_from_mask3D |
2026-09-22 |
merge into unit_image: standalone twin of bounds_from_mask3D_test |
as bounds_from_mask3D_test |
| graphene_mask |
2026-09-22 |
merge into unit_image: printed calc_graphene_mask shell by shell |
masks: exactly the three shells nearest each graphene band are excluded (box 160, 0.358 A) |
| image_bin |
2026-09-22 |
merge into unit_image: printed max_dist, find_ccs, get_nccs, get_imat on 4x4 and 3x3x2 examples |
simple_image_msk_tester (sub-suite binary image): the same examples with their answers (three 8-connected components, labels, sqrt(8) and sqrt(3) distances, full and empty cases) |
| cc_connectivity |
2026-09-22 |
merge into unit_image: the THROW_HARD connectivity contract of find_ccs (standalone only) |
binary image: 26 offsets connect, Chebyshev-2 stays apart, the 1x1xN column regression along z with x/y controls, 8-connectivity in 2D, empty and full volumes |
| mask |
2026-09-22 |
merge into unit_image: disc -> transfer2bimg -> cos_edge -> wrote spherical_mask.mrc |
masks: disc voxel count within 2% of the sphere volume and 1/0 at the radius, transfer2bimg preserves the count, cos_edge is 1 at the surface, 0.5 half way, 0 at the fall-off, monotone |
| otsu_test |
2026-09-22 |
merge into unit_image (first into unit_numerics, moved the same day): thresholded a unimodal Gaussian sample and printed class means (nothing to assert) |
simple_segmentation_tester (sub-suite segmentation of unit_image; moved from statistics the same day): a two-Gaussian mixture is thresholded between the modes, the upper class has the right size within 1%, the mask and binarising overloads agree with the threshold overload |
| otsu |
2026-09-22 |
merge into unit_image: standalone twin of otsu_test |
as otsu_test |
| ptcl_center |
2026-09-22 |
delete: downloaded 1JYX from RCSB, projected it and explored a windowed radial-profile centering heuristic, printing candidate centres; an experiment script |
none; gap recorded: it was the only test naming masscen, roavg, window_center, shift2Dserial, power_spectrum, fproject, get_nyq (image-area basics, for the image review); closed 2026-09-25: simple_image_tester (sub-suite image of unit_image) tests all of them but window_center, which had no caller and is removed |
| peak_thres_fdr |
2026-09-22 |
merge into unit_image: an assertion-bearing exec case for detect_peak_thres_fdr, filed under utils/project by its router only |
simple_segmentation_tester (sub-suite segmentation): the same six checks |
| imgfile |
2026-09-23 |
delete: SPIDER/MRC squares and cubes written, converted both ways and compared by correlation; a strict subset of test_image part 20 (sub-suite image of unit_image) |
test_image part 20; since 2026-09-25 test_file_roundtrip in simple_image_tester, bit-exact |
| inside_write |
2026-09-23 |
merge into unit_project: wrote a project and write_segment_inside('stk') into it, asserting nothing; the six production callers of the in-place segment rewrite had no test |
simple_binoris_tester (sub-suite binoris): the stk segment is rewritten longer in place, the mic/ptcl2D/ptcl3D/projinfo segments read back byte-identical, a missing project file falls back to a full write |
| io |
2026-09-23 |
delete: a 40 GB stack-and-volume read/write throughput benchmark writing SIMPLE_IO_BENCH.txt, no assertion |
the stack_io round trips in stack I/O (unit_core) |
| io_parallel |
2026-09-23 |
delete: as io, with four volumes under an OpenMP team on the standalone route |
as io; rslices/wmrcslices are reached through stack_io%read/write and image%read/write |
| stack_io |
2026-09-23 |
modify: the exec case copied a committed class-average stack and asserted nothing; the standalone was a real test (synthetic stacks, reader/writer round trips, float16 header and chunked round trip) followed by write/read benchmarks |
simple_stack_io_tester (sub-suite stack I/O of unit_core): open/close state, image-written and stack_io-copied stacks pixel by pixel, buffer sizes of 2/3/whole/oversized with a partial last window, forward skipping reads and get_image, float32 and float16 MRC headers (mode, 2014 version stamp, dims, file size), a float16-exact pattern round trip, and a 1025-box float16 stack that crosses the converter's 1 M-element write buffer twice; benchmarks dropped |
| star_export |
2026-09-23 |
delete: timed write_mics_star/write_ptcl2D_star on a test.simple from the working directory |
both are asserted in STAR file (unit_project) |
| starfile_test |
2026-09-23 |
modify: a print-only exercise of the starfile_table wrappers followed by run_all_starproject_tests, which was run from nowhere else |
the wrapper round trip is now assertions in simple_starfile_tester (table names, comment, string, doubles to the %12.6f/%12.6e formatting, absent labels, first/next iteration); run_all_starproject_tests is the sub-suite STAR project of unit_project (its process-wide error stop and thread forcing removed; the OpenMP part restores the thread count it found) |
| starfile |
2026-09-23 |
delete: standalone twin of starfile_test |
as starfile_test |
| binoris |
2026-09-23 |
merge into unit_project: created a project through new_project, then called open/write_header/write_segment/add_segment/update_byte_ranges/is_opened with prints and one assertion (is_opened) |
simple_binoris_tester (sub-suite binoris): header-only files, string and particle segment round trips with header bookkeeping (n_segments, n_records, fromto, record width, first data byte, total bytes = file size, segments_info), partial and sub-range particle reads at absolute indices, legacy 40-value particle records reading with zeros in the new slots, write_segment_inside growing and shrinking a middle segment with its neighbours intact (oris and string-array forms) |
| binoris_io |
2026-09-23 |
merge into unit_project: called binread_oritab/binread_ctfparams_state_eo/binread_nlines/binwrite_oritab on an empty project and printed |
binoris: the .txt and .simple dispatch of all four, the ctf/state/eo merge keeping the keys not in the file, binread_nlines as the segment record count |
| binoris_test |
2026-09-23 |
delete: an empty exec stub (printed a banner) |
as binoris |
| binoris_io_test |
2026-09-23 |
delete: an empty exec stub (printed a banner) |
as binoris_io |
| eigh_test |
2026-09-23 |
merge into unit_numerics: printed svdcmp and eigh of a 5x5 matrix, then eigh of a random 15000x15000 matrix with the result discarded |
simple_linalg_tester (sub-suite linear algebra): eigh largest/smallest against numpy eigenvalues with orthonormal eigenvectors and A v = lambda v, sparse_eigh against eigh, svdcmp reconstruction and singular values, matinv against the reference inverse and a singular flag, jacobi + eigsrt, svdfit/svd_multifit on exact and noisy polynomials, fit_straight_line, fit_lsq_plane/plane_from_points, the vector helpers, gemm_tn; test_eigh removed from simple_linalg |
| eigh |
2026-09-23 |
merge into unit_numerics: standalone twin of eigh_test with a sparse_eigh-vs-eigh check |
as eigh_test |
| kbinterpol_fast |
2026-09-23 |
modify: two assertions on apod_fast, then printed Pearson/mean-diff of the 2D/3D stencils against the outer product over 131k kernels on a 256-box and 10M-evaluation timings |
simple_kbinterpol_tester (sub-suite Kaiser-Bessel kernel): window geometry and beta, apod against the double-precision closed form (I0 series), apod_fast tolerance and its coefficients, apod_fast_value_deriv against central differences, the device forms bit for bit, apod_mat_2d/3d equal to the normalised outer product, the fast stencils within 1e-5, apod_mat_3d_fast_grad against finite differences with the switch margin, instr; no timing |
| maxnloc_test |
2026-09-23 |
merge into unit_numerics: printed the ten largest and smallest of a shuffled 1..1000 next to hpsort's answer |
simple_srch_sort_loc_tester (sub-suite search, sort, locate): every hpsort form, locate/find at boundaries and exact hits, maxnloc/minnloc (the old check, asserted), min3, peakfinder, reverse/reverse_f, selec for every k, unique, scores2order/dists2order, mask2inds, reorder |
| maxnloc |
2026-09-23 |
merge into unit_numerics: standalone twin of maxnloc_test |
as maxnloc_test |
| neigh |
2026-09-23 |
merge into unit_ori: printed statistics of find_closest_proj, sym_dists, find_angres and nearest_proj_neighbors on a 20000-direction c2 spiral |
simple_sym_tester (symmetry): on a 200-direction spiral for c1/c2/d2, find_closest_proj is the brute-force argmin over symmetry-expanded distances, nearest_proj_neighbors (threshold) is the brute-force set and accumulates, (count) flags exactly nnn of the nearest, sym_dists returns the minimum with a representative realising it, find_angres is of the order of the spacing and smaller for a denser spiral; the c1 forms agree with the oris forms |
| trail_rec_blend |
2026-09-23 |
modify: an assertion-bearing, hermetic exec case (8^3 accumulators) that ran nowhere |
moved as it is into simple_accum_blend_tester (sub-suite trailing-reconstruction blend of unit_image), minus its own report_summary/simple_end |
| class_sample_test |
2026-09-23 |
merge into unit_core: printed three class_sample entries, wrote and read them back and printed class_samples_same |
simple_class_sample_io_tester (sub-suite class sample I/O): a ragged three-class array round-trips field by field, an empty class (no pinds) comes back with pop 0 and zero-sized arrays, a previously allocated array is replaced; print_class_sample, class_samples_same (compared only the integer part) and the private unserialize_class_sample removed from simple_class_sample_io (no production caller) |
| class_sample |
2026-09-23 |
merge into unit_core: standalone twin of class_sample_test |
as class_sample_test |
| clustering |
2026-09-23 |
retire: called test_aff_prop, which is already the affinity propagation sub-suite of unit_numerics |
- (since 2026-09-25 simple_aff_prop_tester) |
| ctf_test |
2026-09-23 |
merge into unit_image: wrote a 256-box CTF image with ctf2img and ft2img and stopped |
simple_ctf_tester (sub-suite CTF): see ctf |
| ctf |
2026-09-23 |
merge into unit_image: the assertion-bearing phase-shift policy test (12 checks) of doc/policies/phase_shift_ctf_policy.md, unassigned |
simple_ctf_tester (sub-suite CTF): the policy checks moved as they are (through eval_canonical + canonical_phshift), plus the 300/200 kV wavelength, the ctfvars conversions, apply_convention, the closed-form CTF at three frequencies and along/across the astigmatism axis, nextrema at three frequencies and at the first three zeros, ctf2img against the closed form, ft2img placement in real/power/sqrt modes and the gen_fplane4rec Hy / |H|y contracts; spafreqsqatnthzero pinned on the first three zeros (the CTF estimator's fitting ranges); ctf%eval (both forms, the six-argument one documented its angle in radians and converted it as degrees) and eval_sign removed (no production caller; eval_canonical is the evaluator) |
| eo_diff |
2026-09-23 |
retire: needed refine3D half-volumes (300^3) in cwd, wrote two volumes, asserted nothing; ran_phases_below_noise_power, its only production call, had no production caller and is removed from simple_image |
- (accepted loss: get_res, subtr) |
| extr_frac |
2026-09-23 |
merge into unit_numerics: printed cos_decay over 100 iterations (the rest commented out); was in CI |
simple_decay_funs_tester (sub-suite decay schedules): cos_decay/inv_cos_decay endpoints, quarter points, monotonicity and mirror symmetry, calc_nsampl_fromto on both branches, inv_nsampl_decay endpoints/midpoint/hold past maxits, calc_update_frac and calc_update_frac_dyn, extremal_decay and extremal_decay2D endpoints, clamps and monotonicity; nsampl_decay removed (no caller), calc_update_frac reduced to what it computed (its half-the-particles and minimum clamps could not change the result) |
| multinomal_test |
2026-09-23 |
retire: printed sampled frequencies of a 7-way multinomial; test_multinomal is already the multinomial random draw sub-suite of unit_numerics; was in CI |
- |
| pca_all |
2026-09-23 |
merge into unit_numerics: printed PPCA, SVD PCA and (standalone) exact/Nystroem/RBF kPCA feature vectors and pre-images of a 3x4 matrix |
simple_pca_tester (sub-suite PCA): pca_svd on the D >= N and D < N branches against numpy (exact reconstruction at full rank, the rank-1 and rank-2 approximations, feature energies = squared singular values, the first feature vector up to sign); ppca on a rank-2-plus-noise 5x16 fixture against the Tipping-Bishop maximum-likelihood solution (retained eigenvalues, sigma^2 = mean of the discarded ones, signal eigenvalues, the reconstruction sum_k (1 - sigma^2/lambda_k) u_k u_k^T x, latent means, reconstruct_external, calc_bic (now the PPCA marginal-likelihood BIC; the residual form let the rank scan climb with the iteration cap), suggest_rank picks 2 with ordered BICs and sigma^2); kpca_svd on a two-cluster 4x12 fixture against a double-precision emulation of the same pipeline: exact/cosine and exact/RBF kernel eigenvalues, features and converged pre-images (the cosine rule now with non-negative weights), Nystroem with every point a landmark (eigenvalues, features and RBF pre-images equal to the exact ones after the scaling fix, the power-weighted cosine pre-image), a 6-landmark Nystroem run (ordered spectrum, pre-images inside the data's bounding box and on their own cluster's side) and suggest_kpca_nystrom_neigs |
| pca_imgvar |
2026-09-23 |
merge into unit_numerics: printed PPCA feature vectors of a 25x25 pairwise-difference matrix built from two 5x5 images |
as pca_all |
| sp_project |
2026-09-23 |
merge into unit_project: the assertion-bearing standalone (phase-shift record policy, write/read of 87 mics and 5646 particles, non-mutating read from another cwd, simple_path not persisted, three partial binwrite_oritab documents merged, write_segment2txt and print_segment_json called without checks); the exec case was its older subset |
simple_sp_project_tester (sub-suite project records): the phase-shift checks moved as they are (add_single_movie/add_stk/add_stktab, get_micparams/get_ctfparams, text and binary serialisation), the round trip at 7 mics / 300 particles, the read probe, the merge, and print_segment_json parsed back from a diverted logfhandle (data window and indices_pre/post, ascending and descending sorts, histogram and plot blocks, a particle segment); write_segment2txt removed (no production caller); print_segment_json sized indices_post from the caller's window instead of the remapped one for a descending sort, printed every ptcl2D record as it went and dereferenced the absent sort_key for the histogram/plot blocks, all fixed |
| lbfgsb |
2026-09-23 |
merge into unit_numerics: printed the L-BFGS-B minimum of a 1D quadratic |
simple_opt_tester (sub-suite optimisers): opt_spec bookkeeping (defaults, limits, hooks, re-specify), L-BFGS-B on the quadratic (free and bound-constrained, convergence flag, evaluation counters), on the direction-finding problem and on Rosenbrock, differential evolution and the restarted simplex on a 2D quadratic (preset and random starts); bfgs2, bforce, stde optimisers, simple_opt_helpers, the line searches of simple_opt_subs and the opt parameter removed (no production caller; production uses lbfgsb, de and simplex) |
| lbfgsb_cosine |
2026-09-23 |
merge into unit_numerics: printed the L-BFGS-B minimum of the angle to a fixed direction from ten restarts |
as lbfgsb (the smooth 1 - cos form; acos has an infinite derivative at the optimum) |
| lplims |
2026-09-23 |
merge into unit_numerics: printed mskdiam2lplimits over mask diameters 300..90; was in CI |
simple_lpstages_tester (sub-suite low-pass stages): the three clamp regimes |
| lpstages_test |
2026-09-23 |
merge into unit_numerics: called lpstages with a flat FRC and printed |
simple_lpstages_tester: lpstages with one stage, from a falling FRC (limits, thresholds, crop boxes, sampling, shift limits), particle vs class-average thresholds, the linear fallback of a flat FRC, lpstages_fast (floor, force_lpstart), lpstages_setlims (incl. the no-crop case), the Butterworth kernel in all four forms against its closed form; verbose added to lpstages_fast/setlims (default unchanged) |
| lpstages |
2026-09-23 |
merge into unit_numerics: unassigned standalone with five THROW_HARD checks on lpstages/lpstages_fast/lpstages_setlims |
as lpstages_test (all five checks are among the assertions) |
| opt_lp |
2026-09-23 |
retire: a manual experiment (downloads 1JYX from RCSB, converts, reprojects, prints Butterworth-band residuals), no assertion; create_hist_vector stays (otsu uses it) |
- (accepted loss by name: apply_filter and avg_sdev, both exercised elsewhere) |
| ui_hash_test |
2026-09-23 |
merge into unit_ui: called test_ui_hash, a print-only PASS/FAIL routine embedded in the production module simple_ui_hash; the routine is deleted with it, as are the unused set_ui_param/get_ui_param accessors and the unused string-key set / char-key get overloads |
simple_ui_hash_tester (sub-suite UI hash): set by char key and get by string key with pointer identity, reference semantics, absent key and wrong dynamic type as typed misses, overwrite retargeting, key trimming, found optional |
| reproject |
2026-09-23 |
merge into simulate_particles: same 6VXX volume and the same three checks (stack, box/smpd, orientation count) on the reproject commander |
simulate_particles (workflow): reproject stage with nspace=100 |
| mini_stream (standalone route) |
2026-09-23 |
delete: byte-identical body to the commander route |
simple_test_exec test=mini_stream (manual) |
| continuous_3D_pcg_reconstruction |
2026-09-23 |
modify: child-process driver with a fixture self-test, the gauran/add_gauran contracts and a half-set PCG-vs-gridding study writing twelve MRC volumes per run |
simple_gauran_tester (unit_reconstruction, observation noise) and simple_pcg_halfset_tester (lib_reconstruction, PCG half-set) |
| rec3D_backend |
2026-09-23 |
merge into unit_reconstruction: defaults, backend resolution and two factory branches, error stop on failure; was in CI |
simple_rec3D_strategy_tester (rec3D backend): defaults, resolution incl. case and blanks, wiring, six factory branches |
| continuous_inplane_cc_grad |
2026-09-23 |
merge into unit_pftc_align2D3D: needed vol1; cc evaluator grid identity, FD gradient, penalty |
simple_pftc_inplane_tester (continuous in-plane) |
| continuous_inplane_hybrid_grad |
2026-09-23 |
merge into unit_pftc_align2D3D: needed vol1; hybrid evaluator |
as continuous_inplane_cc_grad |
| continuous_inplane_rotation2D_stage1_validation |
2026-09-23 |
merge into unit_pftc_align2D3D: needed vol1; three fixtures x three cases of parity, gradient, stress and recovery, aliasing printed only |
as continuous_inplane_cc_grad (fixtures reduced to truth 37 deg with shift, 359.375 deg hard-edge full band, 0 deg) |
| continuous_inplane_rotation2D_route_identity |
2026-09-23 |
merge into unit_pftc_align2D3D: needed vol1; route identities, seed parity, strategy2D route flags, hybrid rejection via child process |
as continuous_inplane_cc_grad; the rejection is not asserted |
| continuous_inplane_refine3D |
2026-09-23 |
merge into unit_pftc_align2D3D: child-process driver over seven cases; two needed a finished project |
simple_strategy3D_inplane_tester (refine3D in-plane state) and continuous in-plane (synthetic recovery) |
| continuous_inplane_rotation2D |
2026-09-23 |
delete: shell driver over the family with GNU find, a vanished upstream test and two abinitio2D runs |
- |
| continuous_inplane_rotation2D_metadata |
2026-09-23 |
delete: post-run e3/inpl scan of a user project |
resolve_inplane_e3 test in refine3D in-plane state; workflow-level check is Phase 5 |
| pose_cont_refinement |
2026-09-23 |
merge into unit_cart_align3D: numerics and solver of the Cartesian pose refiner, error stop assertions |
simple_cartesian_pose_refiner_tester (pose refiner) |
| pose_cont_refine3D_adapter |
2026-09-23 |
modify: adapter contracts and the opt-in 1JYX experiment in one program |
simple_pose_cont_refine3D_adapter_tester (pose adapter, fast) and simple_pose_cont_1jyx_tester (pose 1JYX recovery, lib_cart_align3D) |
| cartesian_fourier |
2026-09-23 |
merge into unit_cart_align3D: self-re-executing driver over the KB derivative and neutral-extraction cases |
simple_cartesian_fourier_tester (Cartesian Fourier) |
| flex_pca (standalone) |
2026-09-23 |
merge into unit_heterogeneity: driver over six THROW_HARD self-tests embedded in production modules |
simple_flex_pca_tester (flex PCA) |
| flex_pcg (standalone) |
2026-09-23 |
modify: driver over the white-box operator self-test, three ignored debug runs |
simple_flex_pcg_tester (flex PCG operator, fast and nightly) |
| flex_gpu (standalone) |
2026-09-23 |
keep, rerouted: the same five routines behind simple_test_exec test=flex_gpu |
platform entry flex_gpu (USE_FLEX_CUDA) |
| gui_assembler (standalone) |
2026-09-23 |
delete: duplicate driver of a gate sub-suite |
GUI assembler (unit_ui) |
| gui_metadata (standalone) |
2026-09-23 |
delete: duplicate driver of a gate sub-suite |
GUI metadata (unit_ui) |
| project_merge (standalone) |
2026-09-23 |
delete: duplicate driver of a gate sub-suite |
project merge (unit_project) |
| rnd_shuffle |
2026-09-23 |
merge into unit_numerics: seven assertions, /dev/urandom seed |
simple_rnd_tester (random draws) |
| phshift_star |
2026-09-23 |
merge into unit_project: four assertions on the RELION phase-shift contract |
test_relion_phase_shift in STAR project |
| ui_visibility |
2026-09-23 |
merge into unit_ui: about 170 assertions in a program body |
simple_ui_visibility_tester (UI visibility) |
| phshift_policy |
2026-09-23 |
merge into unit_ui: error-stop checks of five UI contracts |
test_phshift_contract in UI visibility |
| discrete_stack_io |
2026-09-23 |
merge into unit_core: THROW_HARD checks |
stack I/O (simple_stack_io_tester) |
| sigma2_state |
2026-09-23 |
merge into unit_pftc_align2D3D: error-stop checks |
simple_sigma2_state_tester (sigma2 state) |
| eul_prob_tab2D_io |
2026-09-23 |
merge into unit_pftc_align2D3D: THROW_HARD checks |
simple_eul_prob_tab2D_tester (2D probability table I/O) |
| projdir_accumulator |
2026-09-23 |
merge into unit_reconstruction: five assertions |
simple_classaverager_tester (class-average accumulator) |
| cavg_quality_relations |
2026-09-23 |
merge into unit_numerics: driver over a self-test embedded in production |
simple_cavg_quality_relations_tester (cavg quality relations) |
| nu_envmask |
2026-09-23 |
delete: synthetic NU evidence-envelope checks; nu_filt3D exercises the filter |
simple_exec prg=nu_filt3D |
| nu_filter |
2026-09-23 |
delete: user-data driver, no assertions |
simple_exec prg=nu_filt3D |
| phase_rand_fsc |
2026-09-23 |
delete: correction-rule check of phase_rand_fsc |
simple_exec prg=fsc |
| diff_map_graphs |
2026-09-23 |
merge into unit_numerics: stop checks that exited 0 |
simple_diff_map_graphs_tester (diffusion-map graphs) |
| create_gain |
2026-09-23 |
delete: movie-driven runner, no assertions |
test_normalized_inverse_average_intensity in motion gain |
| search_gain_flips |
2026-09-23 |
delete: movie-driven runner, no assertions |
motion gain (analyser batch updates) |
| atomfit |
2026-09-23 |
delete: needed a PDB fixture, no assertions; atoms%fit_bfactors (no caller) deleted with it |
- |
| stream_initial_analysis |
2026-09-23 |
delete: commander smoke on a missing folder |
- |
| openacc |
2026-09-23 |
delete: exec body commented out; standalone saxpy timing, no assertions; OpenACC unused in src |
- |
| openmp |
2026-09-23 |
delete: OpenMP-runtime race demonstration, no assertions (was in CI) |
- |
| simd |
2026-09-23 |
delete: simd timing, no assertions (was in CI) |
- |
| qsys_ctrl |
2026-09-23 |
merge into unit_parallel: flag checks |
simple_qsys_ctrl_tester (qsys control) |
| qsys_env |
2026-09-23 |
merge into unit_parallel: THROW_HARD checks |
simple_qsys_env_tester (qsys environment) |
| socket_client |
2026-09-23 |
delete: socket role program, no assertions; the socket modules it drove had no production caller |
IPC TCP socket (unit_ipc) tests the live transport |
| socket_comm_distr |
2026-09-23 |
delete: socket role program, no assertions; the socket modules it drove had no production caller |
IPC TCP socket (unit_ipc) tests the live transport |
| socket_io |
2026-09-23 |
delete: socket role program, no assertions; the socket modules it drove had no production caller |
IPC TCP socket (unit_ipc) tests the live transport |
| socket_server |
2026-09-23 |
delete: socket role program, no assertions; the socket modules it drove had no production caller |
IPC TCP socket (unit_ipc) tests the live transport |
| detect_atoms |
2026-09-23 |
merge into lib_single: a prefix of atoms_stats |
nanoparticle atoms (lib_single) |
| simulate_nanoparticle |
2026-09-23 |
merge into lib_single: a prefix of atoms_stats |
nanoparticle atoms (lib_single) |
| detect_calpha |
2026-09-23 |
merge into unit_single: exec case moved to a tester |
simple_calpha_finder_tester (C-alpha finder) |
| abinitio2D_stream |
2026-09-24 |
delete: one abinitio2D iteration with a command line that is not the stream chunk's, no separation check; abinitio2D runs nightly in simulated_workflow |
simulated_workflow_6vxx, simulated_workflow_1jxy |
| assign_optics |
2026-09-24 |
merge into lib_stream: exec case moved to a tester |
optics assignment (lib_stream, simple_stream_tester) |
| gen_pickrefs |
2026-09-24 |
merge into lib_stream: exec case moved to a tester |
picking references (lib_stream) |
| pick_extract |
2026-09-24 |
merge into lib_stream: exec case moved to a tester |
pick and extract (lib_stream) |
| sieve_cavgs |
2026-09-24 |
merge into unit_project: exec case moved to the ptcl_sieve tester |
particle sieve (unit_project), test_collect_and_reject_hard_gates |
| master |
2026-09-24 |
merge into forked_process: it tested the GUI heartbeat, not the master |
stream heartbeat (forked_process platform entry, simple_gui_assembler_tester) |
| ansi_colors (both routes) |
2026-09-24 |
merge into unit_core: printed coloured words |
string (unit_core), test_ansi_format_str |
| stringmatch (both routes) |
2026-09-24 |
merge into unit_core: printed a parsed list |
string (unit_core), test_list_of_ints2arr |
| cmdline (both routes) |
2026-09-24 |
merge into unit_core: mostly duplicated command line |
command line (unit_core), test_read_line_typed_values |
| serialize (both routes) |
2026-09-24 |
merge into unit_image: displayed images, checked nothing |
image serialisation (unit_image) |
| cavg_registration (both routes) |
2026-09-24 |
merge into unit_pftc_align2D3D: self-test moved out of the production module |
class-average registration (unit_pftc_align2D3D) |
| pdb2mrc (both routes) |
2026-09-24 |
merge into lib_single |
pdb2mrc (lib_single) |
| cif2mrc |
2026-09-24 |
delete: a run of the production program on a download, no check |
- |
| cif2pdb |
2026-09-24 |
delete: as cif2mrc |
- |
| install (both routes) |
2026-09-24 |
delete: ran the vanished simple_test_units |
simple_test_exec test=units, the fast gate |
| nice (both routes) |
2026-09-24 |
delete: posted to a nonexistent server, no check |
- |
| coarrays (standalone route) |
2026-09-24 |
delete: a two-image sync check; the exec case runs the coarray path end to end |
coarrays platform entry, simple_test_exec test=coarrays |
| openmp_offload (standalone program) |
2026-09-24 |
moved: library module behind simple_test_exec |
simple_test_exec test=openmp_offload (platform) |
| gencorrs_fft |
2026-09-24 |
merge into unit_pftc_align2D3D: the lib_fft suite was never built |
polar correlation (unit_pftc_align2D3D, simple_polarft_corr_tester) |
| angres (exec route) |
2026-09-24 |
retire: a program measures what the test printed |
simple_exec prg=measure_projspace_angres; the ladder is a comment above find_angres |
| msk_routines |
2026-09-24 |
merge into unit_image: lib_masks was never built; an explicit team of three replaces the environment's |
masks (unit_image), test_masks_parallel_equals_serial |