Release 3.0.0: merge develop → main - #283

Merged

ofloveandhate merged 742 commits into

mainfrom

Jul 7, 2026

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Commits on Jun 29, 2026

docs(tutorial): promote user_homotopy -> HomotopySolver in tutorials

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build(cli): sync the CLI into python/bertini/_bin for editable/dev installs

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build(cli): add a `cli` install component for a CLI-only install

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docs(readme): add a CLI install note covering every build path

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feat(nag): is_nonsolution flag + solutions() filtered getter

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test(nag): make the nonsolution-count assertions seed-robust; rename "junk" -> nonsolutions

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442a2b8
fix(endgames): deterministic, reused c/k probe vector in the Cauchy operating-zone test

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test(start-systems): cross-cutting sanity tests for TotalDegree/MHom homogenization + interop

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tools: add run_with_watchdog.sh (hard timeout + process-group kill for hang-prone solves)

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b27b595
feat(zero-dim): per-path wall-clock timing in solution metadata (path_time_seconds)

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fix(system): System +=/*= handle structured-block systems instead of segfaulting

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4a91d48
docs(precision_models): update solver class-name doctest to the de-templated names

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fix(system): make function() work on structured systems; add slices() (#263)

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docs(adr): update ADR-0040 for is_nonsolution + solutions() getter

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feat(describe): show low-precision coefficients in system describe (#264)

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Merge pull request #49 from ofloveandhate/feature/split_zerodimsolver_homotopysolver
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Merge branch 'develop' into feature/cauchy-probe-sanity-timing
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e7e20e5
Merge remote-tracking branch 'origin/develop' into feature/amp-endgame-numeric-type
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Merge pull request #50 from ofloveandhate/feature/cauchy-probe-sanity-timing
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Merge pull request #51 from ofloveandhate/fix/263-function-on-slice-system
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1beac99
Merge remote-tracking branch 'origin/develop' into feature/amp-endgame-numeric-type
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Merge pull request #52 from ofloveandhate/fix/264-describe-coefficients
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6b833d1
Merge remote-tracking branch 'origin/develop' into feature/amp-endgame-numeric-type
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02c0e6b
bump version to 3.0.0.dev5
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1882d33
fix(docs): moving_slice eval_time_derivative doctest precision mismatch

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Merge pull request #53 from ofloveandhate/fix/moving-slice-doctest-precision
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docs(cpp): add Doxygen doc-lint gate + clean up doc config

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docs(cpp): correct rotted Doxygen comments across the core

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ci: gate the build matrix on the doc lint (fail before any compile)

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chore: add .git-blame-ignore-revs for future formatting passes

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docs(cpp): document the blackbox public API (Phase C)

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docs(cpp): document nag_algorithms event/midpath/trace helpers (Phase C)

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docs(cpp): document the NID algorithm + datatype scaffolding (Phase C)

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docs(cpp): document the classic-output formatters (Phase C)

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docs(cpp): document the zero-dim solver (Phase C)

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docs(cpp): document the nag algorithm config structs + base (Phase C)

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feat(endgames): adaptive numeric type for the AMP Cauchy endgame (double-first)

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feat(endgames): PowerSeries double-first AMP driver; factor migration helpers into AMPEndgame

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test(endgames): prove the PowerSeries double->mpfr migration path

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feat(nag): honest per-solution precision + accuracy in metadata (digit counts)

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docs(tutorial): refresh b1-vs-b2 timing honestly after the adaptive-numeric-type endgame

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docs(cpp): document the function_tree expression-tree core (Phase C)

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3253391

Commits on Jun 30, 2026

fix(start): bound start-system coefficient modulus (replace heavy-tailed RandomRat)

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docs(cpp): document the endgames subsystem (Phase C)

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fix(start): bound RootsOfUnity (binomial) constant modulus too

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docs(cpp): document the trackers subsystem (Phase C)

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refactor(start): rename start systems to TotalDegreeBinomial / TotalDegreeLinearProduct

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refactor(metadata): rename endgame_success -> endgame_success_code (and pre_)

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docs(cpp): document the system subsystem (Phase C)

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docs(cpp): document the detail subsystem (Phase C)

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docs(cpp): document the io subsystem (Phase C)

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docs(cpp): document parallel, pool, and nag_datatypes (Phase C)

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fix(patch): draw patch coefficients with bounded modulus (away from 0 and infinity)

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docs(cpp): document the top-level headers; ratchet reaches 0 (Phase C)

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410b09b
Merge pull request #54 from ofloveandhate/feature/cpp-doc-lint
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a5e08eb
Merge remote-tracking branch 'origin/develop' into feature/amp-endgame-numeric-type
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docs(cpp)+rename: document 55's new entities for the doc-lint; final_solution -> solution

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fix(slice): draw slice coefficients with bounded modulus (away from 0 and infinity)

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docs(adr): ADR-0041 — bounded-modulus random coefficients (start systems, patches, slices)

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feat(random): conjugate-orthonormal random matrices (RandomConjugateOrthonormalMatrix)

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test(docs): un-gate the crossed_paths doc example -- the fast endgame made it quick

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Merge pull request #55 from ofloveandhate/feature/amp-endgame-numeric-type
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2b0a8b6
bump version to 3.0.0.dev6
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3e699a3
fix(mhom): serialize all MHomogeneous members so MPI workers get a valid start system

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docs(scaling): refresh solving_at_scale timing tables on a 16-core M3 Max (#253)

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fix(parse): strip % comments when reading a classic input FILE (Bertini 1 compat)

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test(printing): magnitude-independent terse coefficient bound (fix flaky macOS assertion)

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feat(system): symbolic Jacobian (matrix of expression nodes) + natural-function snapshot at homogenize

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feat(python): bind the symbolic Jacobian -> bertini.jacobian + System.jacobian

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test(jacobian): cover every block type (linear-forms, slice, products-of-linears, randomization, blend)

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feat(random): bertini.random_matrix (orthonormal / bounded-modulus / units, complex or real)

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feat(criticality): nullvector critical-points recipe -- test, tutorial, example

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fix(system): snapshot pre-homogenization functions BEFORE resizing homogenizing_variables_

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342cffa
docs(criticality): explain critical points as branch points (where the fiber count jumps)

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Commits on Jul 1, 2026

docs(criticality): fix the projection-direction arrow (project ALONG the fibers, not along π)

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cfa7c32
docs(criticality): fix two section-underline lengths (sphinx warnings)

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fix(slp): stop over-reading the instruction tape by one word in Eval

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prototype(slp-cse): power-fold x*x -> x^2 at operator*= (binary/adjacent only)

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feat(slp-cse): flatten + sort + power-fold products in CanonicalizeNaryOperands

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feat(slp-cse): instruction-level value-numbering in the SLP compiler

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fix(slp-cse): don't splice divisor sub-products when flattening (avoid x/y/z)

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fix(function_tree): correct group-degree of an integer power of a sum

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Merge pull request #56 from ofloveandhate/fix/parallel_serialization
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Merge pull request #58 from ofloveandhate/fix/slp-eval-tape-overread
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Merge remote-tracking branch 'origin/develop' into feature/symbolic-jacobian
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docs(cpp): document NodeMatrix rows/cols members + note the doc-lint gate in CLAUDE.md

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test(slp-cse): env-var A/B toggles + isolated SLP benchmark

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docs(criticality): make the tutorial honest -- full reducible curve, all critical points

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Merge remote-tracking branch 'origin/develop' into feature/slp-cse-fold-and-value-numbering
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Merge pull request #59 from ofloveandhate/feature/symbolic-jacobian
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Merge pull request #60 from ofloveandhate/feature/slp-cse-fold-and-value-numbering
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docs(tutorials): one folder per tutorial (index.rst) with owned assets

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chore(examples): delete dead/redundant example scripts

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docs(tutorials): complete runnable script at the bottom of 5 tutorials

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docs(tutorials): complete runnable script at the bottom of 5 more tutorials

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docs(tutorials): complete runnable script at the bottom of 6 more tutorials

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docs(tutorials): complete runnable script at the bottom of the 3 plot tutorials

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tools: refresh_doc_artifacts.py -- one entry point, timings/plots split

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docs(solving_at_scale): numbers as data, not prose

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build(version): single-source VERSION file + full version in C++/CLI

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35c5438
updated year
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docs(detailed): auto-generate the API reference with autosummary :recursive:

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Merge pull request #61 from ofloveandhate/feature/version-single-source-file
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b716285
feat(parsing,system): Unicode identifiers + collision-safe path variables

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476b4f5
fix(python): stop leaking os/sys/info into the bertini.* namespace

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feat(function_tree): validate variable names are well-formed identifiers

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feat(naming): allow emoji in variable names, including multi-code-point sequences

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docs(refresh): timing-freshness release gate + critical_points plot regenerator

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Merge pull request #63 from ofloveandhate/feature/docs_structure
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Merge pull request #62 from ofloveandhate/feature/unicode-identifiers-and-collision-safe-pathvars
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Bump version to 3.0.0.dev7
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2917e81

Commits on Jul 2, 2026

Commits on Jul 3, 2026

Commits on Jul 4, 2026

fix(random): draw composition order is a contract — the x86/arm architecture split, found and fixed

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docs(adr): bring 0043/0046/0047 current — ask composition, JSON config archive, the shipped casual surface

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perf(linalg): reciprocal-multiply pivot scaling + extend LU parity to N=100 & pivoting

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fix(records): one shared OutputDirectory per directory per process

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feat(records): records_dir(path) is the one-line ambient switch for bare solvers

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rename: 'hydrate' -> 'recall' across API and prose

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fix(records): record_to binding uses the process-shared OutputDirectory

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ci(diag): gdb backtrace for the container CLI SIGSEGV before wheel pytest

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Commits on Jul 5, 2026

Commits on Jul 6, 2026

Commits on Jul 7, 2026

ci(publish): don't skip the whole release when the timing gate is skipped

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ci(publish): don't skip the release when the timing gate is skipped (#267)
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ci(publish): fix downstream skip + prerelease misclassification

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ci(test): install matplotlib in every test env (close the matplotlib skips)

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ci(deps): add prebuilt manylinux Boost+eigenpy image (producer)

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ci(deps): expand image to the complete Linux build+test env

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ci(deps): install scipy for the eigenpy build in the image

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docs(conf): show the package version (not a commit hash) on the front, furo-correct footer

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docs(tools): add versioned-docs assembler (tools/assemble_versioned_docs.py)

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ci(docs): deploy versioned docs to a persistent docs-store branch

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ci(docs): install sympy + networkx for the Sphinx autosummary import walk

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ci(deps): macOS prebuilt Boost+eigenpy tarball producer

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ci(macos): consume prebuilt deps tarballs + mpi4py for 0 skips

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ci(windows): persist ccache across runs for the wheel build (experiment)

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ci(deps): parallelize the image build (per-CPython matrix + assemble)

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ci: single-source Boost/Eigen/eigenpy versions; bumps trigger the image

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ci: add workflow_dispatch `os` input to target specific OS(es)

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ci(linux): build wheels against the prebuilt GHCR deps image

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ci: skip the macOS wheel-test job when the matrix has no macOS

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e8202eb
bump version to 3.0.0rc1

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